First committing

AFM_thumbs/Channel.py

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+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import re
+
+from AFM_thumbs.Variables import globvar_ThumbPara
+from AFM_thumbs.Variables import globvar_AFMdata
+from AFM_thumbs.Variables import ID_list
+from AFM_thumbs.Variables import globvar_color_dict
+from AFM_thumbs.Variables import globvar_spaces
+
+
+
+def rename_channel(name):
+
+    if re.search(ID_list[0],name):
+        globvar_AFMdata.channel.append("Topography")
+
+    elif re.search(ID_list[4],name):
+        if re.search(ID_list[5],name):
+            globvar_AFMdata.channel.append("filtered df")
+        else:
+            globvar_AFMdata.channel.append("df")
+
+    elif re.search(ID_list[1],name):
+        globvar_AFMdata.channel.append("Amplitude")
+
+    elif re.search(ID_list[6],name):
+        globvar_AFMdata.channel.append("Dissipation")
+
+    elif re.search(ID_list[2],name):
+        if re.search(ID_list[3],name):
+            globvar_AFMdata.channel.append("Kelvin Error")
+        else:
+            globvar_AFMdata.channel.append("Kelvin")
+
+    elif re.search(ID_list[8],name):
+        globvar_AFMdata.channel.append("Ext 1")
+
+    elif re.search(ID_list[9],name):
+        globvar_AFMdata.channel.append("Ext 2")
+
+    elif re.search(ID_list[7],name):
+        globvar_AFMdata.channel.append("Excitation")
+
+    elif re.search(ID_list[10],name):
+        globvar_AFMdata.channel.append("Phase")
+    else:
+        found = False
+        for chan in globvar_ThumbPara.channel_names:
+            if not chan == "":
+                if re.search(chan,name):
+                    found = True
+
+        globvar_AFMdata.channel.append(name)
+
+        if not found:
+            print(globvar_spaces + "    Channel not found: " + name)
+            return False
+
+    return True
+
+
+def proceed_with(image_nr,direction):
+
+    if globvar_AFMdata.channel[image_nr] == "Topography":
+        if direction == "forward" and globvar_ThumbPara.thumbs[0]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.thumbs[1]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "df":
+        if not globvar_AFMdata.channel[image_nr] == "filtered":
+            if direction == "forward" and globvar_ThumbPara.thumbs[2]:
+                return True
+            elif direction == "backward" and globvar_ThumbPara.thumbs[3]:
+                return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Dissipation":
+        if direction == "forward" and globvar_ThumbPara.thumbs[4]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.thumbs[5]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Amplitude":
+        if direction == "forward" and globvar_ThumbPara.thumbs[6]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.thumbs[7]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin":
+        if not globvar_AFMdata.channel[image_nr] == "Error":
+            if direction == "forward" and globvar_ThumbPara.thumbs[8]:
+                return True
+            elif direction == "backward" and globvar_ThumbPara.thumbs[9]:
+                return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
+        if direction == "forward" and globvar_ThumbPara.thumbs[10]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.thumbs[11]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 1":
+        if direction == "forward" and globvar_ThumbPara.thumbs[12]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.thumbs[13]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 2":
+        if direction == "forward" and globvar_ThumbPara.thumbs[14]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.thumbs[15]:
+            return True
+
+    else:
+        for i, chan in enumerate(globvar_ThumbPara.channel_names):
+            if not chan == "":
+                if re.search(chan,globvar_AFMdata.channel[image_nr]):
+                    if direction == "forward" and \
+                        globvar_ThumbPara.thumbs[2*i+16]:
+                        return True
+                    elif direction == "backward" and \
+                        globvar_ThumbPara.thumbs[2*i+17]:
+                        return True
+
+        return False
+
+
+def line_fit(image_nr,direction):
+
+    if globvar_AFMdata.channel[image_nr] == "Topography":
+        if direction == "forward" and globvar_ThumbPara.line_fit[0]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.line_fit[1]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "df":
+        if direction == "forward" and globvar_ThumbPara.line_fit[2]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.line_fit[3]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Dissipation":
+        if direction == "forward" and globvar_ThumbPara.line_fit[4]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.line_fit[5]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Amplitude":
+        if direction == "forward" and globvar_ThumbPara.line_fit[6]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.line_fit[7]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin":
+        if direction == "forward" and globvar_ThumbPara.line_fit[8]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.line_fit[9]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
+        if direction == "forward" and globvar_ThumbPara.line_fit[10]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.line_fit[11]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 1":
+        if direction == "forward" and globvar_ThumbPara.line_fit[12]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.line_fit[13]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 2":
+        if direction == "forward" and globvar_ThumbPara.line_fit[14]:
+            return True
+        elif direction == "backward" and globvar_ThumbPara.line_fit[15]:
+            return True
+
+    else:
+        for i, chan in enumerate(globvar_ThumbPara.channel_names):
+            if not chan == "":
+                if re.search(chan,globvar_AFMdata.channel[image_nr]):
+                    if direction == "forward" and \
+                        globvar_ThumbPara.line_fit[2*i+16]:
+                        return True
+                    elif direction == "backward" and \
+                        globvar_ThumbPara.line_fit[2*i+17]:
+                        return True
+
+        return False
+
+
+def plane_fit(image_nr,direction):
+
+    if globvar_AFMdata.channel[image_nr] == "Topography":
+        if direction == "forward" and globvar_ThumbPara.plane_fit[0]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.plane_fit[1]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "df":
+        if direction == "forward" and globvar_ThumbPara.plane_fit[2]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.plane_fit[3]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Dissipation":
+        if direction == "forward" and globvar_ThumbPara.plane_fit[4]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.plane_fit[5]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Amplitude":
+        if direction == "forward" and globvar_ThumbPara.plane_fit[6]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.plane_fit[7]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin":
+        if direction == "forward" and globvar_ThumbPara.plane_fit[8]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.plane_fit[9]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
+        if direction == "forward" and globvar_ThumbPara.plane_fit[10]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.plane_fit[11]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 1":
+        if direction == "forward" and globvar_ThumbPara.plane_fit[12]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.plane_fit[13]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 2":
+        if direction == "forward" and globvar_ThumbPara.plane_fit[14]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.plane_fit[15]:
+            return True
+
+    else:
+        for i, chan in enumerate(globvar_ThumbPara.channel_names):
+            if not chan == "":
+                if re.search(chan,globvar_AFMdata.channel[image_nr]):
+                    if direction == "forward" and \
+                        globvar_ThumbPara.plane_fit[2*i+16]:
+                        return True
+                    elif direction == "backward" and \
+                        globvar_ThumbPara.plane_fit[2*i+17]:
+                        return True
+
+        return False
+
+
+def invert(image_nr,direction):
+
+    if not (direction == "forward" or direction == "backward"):
+        if image_nr%2 == 0:
+            direction = "forward"
+        elif image_nr%2 != 0:
+            direction = "backward"
+
+    if globvar_AFMdata.channel[image_nr] == "Topography":
+        if direction == "forward" and globvar_ThumbPara.invert[0]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.invert[1]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "df":
+        if direction == "forward" and globvar_ThumbPara.invert[2]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.invert[3]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Dissipation":
+        if direction == "forward" and globvar_ThumbPara.invert[4]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.invert[5]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Amplitude":
+        if direction == "forward" and globvar_ThumbPara.invert[6]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.invert[7]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin":
+        if direction == "forward" and globvar_ThumbPara.invert[8]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.invert[9]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
+        if direction == "forward" and globvar_ThumbPara.invert[10]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.invert[11]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 1":
+        if direction == "forward" and globvar_ThumbPara.invert[12]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.invert[13]:
+            return True
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 2":
+        if direction == "forward" and globvar_ThumbPara.invert[14]:
+            return True
+        if direction == "backward" and globvar_ThumbPara.invert[15]:
+            return True
+
+    else:
+        for i, chan in enumerate(globvar_ThumbPara.channel_names):
+            if not chan == "":
+                if re.search(chan,globvar_AFMdata.channel[image_nr]):
+                    if direction == "forward" and \
+                        globvar_ThumbPara.invert[2*i+16]:
+                        return True
+                    elif direction == "backward" and \
+                        globvar_ThumbPara.invert[2*i+17]:
+                        return True
+
+        return False
+
+
+def define_color(color):
+
+    if color in globvar_color_dict:
+        return globvar_color_dict[color]
+
+    else:
+        return globvar_color_dict["Grey"]
+
+
+def select_color(image_nr,direction):
+
+    if not (direction == "forward" or direction == "backward"):
+        if image_nr%2 == 0:
+            direction = "forward"
+        elif image_nr%2 != 0:
+            direction = "backward"
+
+    if globvar_AFMdata.channel[image_nr] == "Topography":
+        if direction == "forward":
+            return globvar_ThumbPara.colors[0]
+        if direction == "backward":
+            return globvar_ThumbPara.colors[1]
+
+    elif globvar_AFMdata.channel[image_nr] == "df":
+        if direction == "forward":
+            return globvar_ThumbPara.colors[2]
+        if direction == "backward":
+            return globvar_ThumbPara.colors[3]
+
+    elif globvar_AFMdata.channel[image_nr] == "Dissipation":
+        if direction == "forward":
+            return globvar_ThumbPara.colors[4]
+        if direction == "backward":
+            return globvar_ThumbPara.colors[5]
+
+    elif globvar_AFMdata.channel[image_nr] == "Amplitude":
+        if direction == "forward":
+            return globvar_ThumbPara.colors[6]
+        if direction == "backward":
+            return globvar_ThumbPara.colors[7]
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin":
+        if direction == "forward":
+            return globvar_ThumbPara.colors[8]
+        if direction == "backward":
+            return globvar_ThumbPara.colors[9]
+
+    elif globvar_AFMdata.channel[image_nr] == "Kelvin Error":
+        if direction == "forward":
+            return globvar_ThumbPara.colors[10]
+        if direction == "backward":
+            return globvar_ThumbPara.colors[11]
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 1":
+        if direction == "forward":
+            return globvar_ThumbPara.colors[12]
+        if direction == "backward":
+            return globvar_ThumbPara.colors[13]
+
+    elif globvar_AFMdata.channel[image_nr] == "Ext 2":
+        if direction == "forward":
+            return globvar_ThumbPara.colors[14]
+        if direction == "backward":
+            return globvar_ThumbPara.colors[15]
+
+    else:
+        for i, chan in enumerate(globvar_ThumbPara.channel_names):
+            if not chan == "":
+                if re.search(chan,globvar_AFMdata.channel[image_nr]):
+                    if direction == "forward":
+                        return globvar_ThumbPara.colors[2*i+16]
+                    elif direction == "backward":
+                        return globvar_ThumbPara.colors[2*i+17]
+
+        return False

AFM_thumbs/Colour.py

@@ -0,0 +1,145 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import sys
+import os
+import numpy as np
+
+# The following is a bit confusing but needed for crontab and ssh under Linux:
+# Matplotlib needs an X-Server, which does not exist when doing, e.g., ssh.
+# In the following we ask if the DISPLAY variable of the Linux system is set. 
+# If this is not the case then we tell Python to do something special for 
+# matplotlib (use of 'Agg')
+#
+# From: "http://stackoverflow.com/questions/4931376/
+# generating-matplotlib-graphs-without-a-running-x-server"
+# Other solution: matplotlib API, see "http://www.dalkescientific.com/writings/
+# diary/archive/2005/04/23/matplotlib_without_gui.html"
+if sys.platform == "linux2":
+    environ = os.environ
+    if "DISPLAY" not in environ:
+        import matplotlib as mpl
+        mpl.use('Agg')
+        # This is a one time message, which is not included in thumbs.py
+        # Otherwise it is reproduced 2 times.
+        print("\n\n**** ATTENTION!\n" + 
+              "**** No X-Server is detected under Linux. It seems that\n" +
+              "**** AFM_thumbs is executed via ssh or crontab ... no problem.\n\n")
+import matplotlib.pyplot as plt
+from matplotlib.colors import LinearSegmentedColormap
+
+from AFM_thumbs.Variables import Color_list
+from AFM_thumbs.Variables import globvar_color_options
+
+def plot_color_gradients():
+    
+    # Get the lenght of the colour list
+    nrows = len(Color_list)
+    # Gradients
+    gradient = np.linspace(0, 1, 256)
+    gradient = np.vstack((gradient, gradient))
+    
+    fig, axes = plt.subplots(nrows=nrows)
+    fig.subplots_adjust(top=0.95, bottom=0.01, left=0.2, right=0.99)
+    axes[0].set_title("Color maps", fontsize=14)
+
+    # Go through all colours.
+    for ax, colour, colourname in zip(axes, Color_list, globvar_color_options):
+         
+        # What kind of color scale do we have?
+        # Is it a pre-definied color from matplotlib, then it must be a string.                   
+        if type(colour) is str:
+            colormap = colour
+        # If it is not a string, then it must be a color definied by ourselves,
+        # so go to here and transform this linear segment into a colormap.
+        else:
+            colormap = LinearSegmentedColormap("Colormap",colour)         
+  
+        # Prepare the plot
+        ax.imshow(gradient, aspect='auto', cmap=plt.get_cmap(colormap))
+        pos = list(ax.get_position().bounds)
+        x_text = pos[0] - 0.01
+        y_text = pos[1] + pos[3]/2.
+        fig.text(x_text, y_text, colourname, 
+                 va='center', ha='right', fontsize=10)
+
+    # Turn off *all* ticks & spines, not just the ones with colormaps.
+    for ax in axes:
+        ax.set_axis_off()
+
+    # Show the plot.
+    plt.show()
+
+
+# This definition was taken from
+# http://stackoverflow.com/questions/3279560/invert-colormap-in-matplotlib
+# User Mattijn
+def reverse_colourmap(ctype, cmap, name = 'my_cmap_r'):
+    """
+    In: 
+    cmap, name 
+    Out:
+    my_cmap_r
+
+    Explanation:
+    t[0] goes from 0 to 1
+    row i:   x  y0  y1 -> t[0] t[1] t[2]
+                   /
+                  /
+    row i+1: x  y0  y1 -> t[n] t[1] t[2]
+
+    so the inverse should do the same:
+    row i+1: x  y1  y0 -> 1-t[0] t[2] t[1]
+                   /
+                  /
+    row i:   x  y1  y0 -> 1-t[n] t[2] t[1]
+    """            
+    
+    if ctype == "LinearSegmentedColormap":
+
+        reverse = []
+        k = []   
+
+        for key in cmap._segmentdata:    
+            k.append(key)
+            channel = cmap._segmentdata[key]
+            data = []
+
+            for t in channel:                    
+                data.append((1-t[0],t[2],t[1]))            
+            reverse.append(sorted(data))    
+
+        LinearL = dict(zip(k,reverse))
+        my_cmap_r = LinearSegmentedColormap(name, LinearL) 
+        
+    elif ctype == "ListedColormap":
+
+        if cmap[-2:] == "_r":
+            my_cmap_r = cmap[:-2]
+        else:
+            my_cmap_r = cmap + "_r"
+            
+    return my_cmap_r

AFM_thumbs/Command_line.py

@@ -0,0 +1,308 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import os
+import matplotlib
+from optparse import OptionParser
+
+from AFM_thumbs.Variables  import RHK_special
+from AFM_thumbs.Variables  import globvar_fonts
+from AFM_thumbs.Variables  import globvar_bad_fonts
+from AFM_thumbs.Variables  import globvar_ThumbPara
+from AFM_thumbs.Variables  import globvar_AFMdir
+from AFM_thumbs.Variables  import globvar_thumb_size_x
+from AFM_thumbs.Variables  import globvar_thumb_size_y
+from AFM_thumbs.Variables  import globvar_spaces
+from AFM_thumbs.Initialize import initialize_check_config
+from AFM_thumbs.Channel    import define_color
+
+
+def command_line():
+
+    print("\n\n")
+
+    parser = OptionParser(usage="usage: %prog [options]", version="%prog 1.6")
+
+    parser.add_option("-d", "--directory",
+                      action="store",
+                      type="string",
+                      dest="directory",
+                      help="the working directory, from which all other " \
+                           "sub-directories are eventually considered " \
+                           "(see config file of AFM_thumb).")
+
+    parser.add_option("-c", "--configfile",
+                      action="store",
+                      type="string",
+                      dest="configfile",
+                      help="the file path of the config file." \
+                           " - This option only acts if the " \
+                           "-d option is choosen.")
+
+    parser.add_option("-p", "--pdf",
+                      action="store",
+                      dest="pdf",
+                      help="the path of the directory, in which the " \
+                           "PDF files shall be stored into." \
+                           " - This option only acts if the " \
+                           "-d option is choosen.")
+
+
+    (options, args) = parser.parse_args()
+
+    # If the working directory (-d option) is set => command line, no GUI
+    if options.directory is not None:
+
+        # Does the working directory exist? If not => exit!
+        if not os.path.isdir(options.directory):
+            print("Usage: AFM_thumbs.py [options]\n\n" \
+                  "AFM_thumbs.py: error: working directory does not exist!")
+            exit(-1)
+
+        # ............. Start without GUI
+        config_file = initialize_check_config(options.configfile)
+        read_configfile(config_file)
+
+        # Does a special pdf path exist?
+        if options.pdf is not None:
+            if os.path.isdir(options.pdf):
+                globvar_AFMdir.pdf_path = options.pdf
+            # Strange, the directory does not exist! Error and exit.
+            else:
+                print("Usage: AFM_thumbs.py [options]\n\n" \
+                      "AFM_thumbs.py: error: The pdf directory " +
+                      "'" + options.pdf + "' does not exist !")
+                exit(-1)
+
+        return (False, options.directory, config_file)
+
+    # If no options are set and there is nothing in args: start the GUI
+    elif options.directory == None and \
+         options.pdf == None and \
+         options.configfile == None and \
+         args == []:
+        return (True, None, None)
+
+    # -p option but where is the -d option?
+    elif options.pdf is not None:
+        print("Usage: AFM_thumbs.py [options]\n\n" \
+              "AFM_thumbs.py: error: working directory ?")
+        exit(-1)
+
+    # -c option but where is the -d option?
+    elif options.configfile is not None:
+        print("Usage: AFM_thumbs.py [options]\n\n" \
+              "AFM_thumbs.py: error: working directory ?")
+        exit(-1)
+
+    # All other: exit.
+    else:
+        print("Usage: AFM_thumbs.py [options]\n\n" \
+              "AFM_thumbs.py: error: options ?")
+        exit(-1)
+
+
+def read_configfile(filepath_config):
+
+    # From here on, the parameters from the config file are stored into
+    # the variables.
+    # filepath_config = os.path.join(globvar_configfile_path,
+    #                                globvar_configfile)
+
+    config_file_p = open(filepath_config, "r")
+
+    # This has to be modified ...
+    for line in config_file_p:
+        if "PDF Path:" in line:
+            globvar_AFMdir.pdf_path = ""
+            break
+
+    # Go to parameters.
+    for line in config_file_p:
+        if "Parameters" in line:
+            break
+
+    # The whole config file is read
+    for line in config_file_p:
+
+        if "Channelname " in line:
+            break
+
+        if "Rows" in line:
+            globvar_ThumbPara.row = int(line[25:-1])
+        if "Columns" in line:
+            globvar_ThumbPara.col = int(line[25:-1])
+        if "Rms" in line:
+            globvar_ThumbPara.rms = line[25:-1]
+        if "Image resolution" in line:
+            globvar_ThumbPara.res = line[25:-1]
+        if "Jpeg quality" in line:
+            globvar_ThumbPara.jpeg = line[25:-1]
+        if "X text position" in line:
+            globvar_ThumbPara.text_x = line[25:-1]
+        if "Y text position" in line:
+            globvar_ThumbPara.text_y = line[25:-1]
+        if "Text size" in line:
+            globvar_ThumbPara.text_size = line[25:-1]
+        if "Dx of text" in line:
+            globvar_ThumbPara.text_block = line[25:-1]
+        if "Font" in line:
+            font_list = get_fonts()
+            if line[25:-1] in font_list:
+                globvar_ThumbPara.font = line[25:-1]
+            else:
+                # If the font is not available then take the first of the
+                # list of available preferred fonts.
+                globvar_ThumbPara.font = font_list[0]
+        if "Deleting thumbs before" in line:
+            globvar_ThumbPara.thumbs_before = bool(int(line[25:-1]))
+        if "Deleting thumbs after" in line:
+            globvar_ThumbPara.thumbs_after = bool(int(line[25:-1]))
+        if "Spektral Options" in line:
+            globvar_ThumbPara.spektra = bool(int(line[25:-1]))
+        if "Peek Options" in line:
+            globvar_ThumbPara.peek = bool(int(line[25:-1]))
+        if "Format Options" in line:
+            globvar_ThumbPara.png = bool(int(line[25:-1]))
+        if "Date" in line:
+            globvar_ThumbPara.date = bool(int(line[25:-1]))
+        if "Size in nm" in line:
+            globvar_ThumbPara.sizenm = bool(int(line[25:-1]))
+        if "Size in px" in line:
+            globvar_ThumbPara.sizepx = bool(int(line[25:-1]))
+        if "Offset" in line:
+            globvar_ThumbPara.offset = bool(int(line[25:-1]))
+        if "Voltage" in line:
+            globvar_ThumbPara.voltage = bool(int(line[25:-1]))
+        if "Feedback" in line:
+            globvar_ThumbPara.feedback = bool(int(line[25:-1]))
+        if "Gain" in line:
+            globvar_ThumbPara.gain = bool(int(line[25:-1]))
+        if "Speed" in line:
+            globvar_ThumbPara.speed = bool(int(line[25:-1]))
+        if "Amplitude" in line:
+            globvar_ThumbPara.ampl = bool(int(line[25:-1]))
+        if "Angle" in line:
+            globvar_ThumbPara.angle = bool(int(line[25:-1]))
+        if "Extra directories" in line:
+            globvar_ThumbPara.extra_direct = bool(int(line[25:-1]))
+        if "Subdirs" in line:
+            globvar_ThumbPara.subdirs = bool(int(line[25:-1]))
+        if "File extension" in line:
+            globvar_ThumbPara.extension = line[25:-1]
+        if "Master directory" in line:
+            globvar_ThumbPara.masterdir = line[25:-1]
+        if "Filename" in line:
+            globvar_ThumbPara.filename = line[25:-1]
+        if "Replace pdfs" in line:
+            globvar_ThumbPara.pdfs = bool(int(line[25:-1]))
+        if "RHK Special Options" in line:
+            RHK_special.true = bool(int(line[25:-1]))
+
+    # Read now the channels:
+    config_file_p.seek(0, 0)
+    for line in config_file_p:
+        if "Tooltips" in line:
+            break
+    for line in config_file_p:
+        if "Channelname " in line:
+            globvar_ThumbPara.channel_names.append(line[25:-1])
+
+    # Read now the thumb bools:
+    config_file_p.seek(0, 0)
+    for line in config_file_p:
+        if "Tooltips" in line:
+            break
+    for line in config_file_p:
+        if "Thumb " in line:
+            globvar_ThumbPara.thumbs.append(bool(int(line[25:-1])))
+
+    # Read now the line_fit bools:
+    config_file_p.seek(0, 0)
+    for line in config_file_p:
+        if "Tooltips" in line:
+            break
+    for line in config_file_p:
+        if "LineFit " in line:
+            globvar_ThumbPara.line_fit.append(bool(int(line[25:-1])))
+
+    # Read now the plane_fit bools:
+    config_file_p.seek(0, 0)
+    for line in config_file_p:
+        if "Tooltips" in line:
+            break
+    for line in config_file_p:
+        if "PlaneFit " in line:
+            globvar_ThumbPara.plane_fit.append(bool(int(line[25:-1])))
+
+    # Read now the inverted bools:
+    config_file_p.seek(0, 0)
+    for line in config_file_p:
+        if "Tooltips" in line:
+            break
+    for line in config_file_p:
+        if "Inverted " in line:
+            globvar_ThumbPara.invert.append(bool(int(line[25:-1])))
+
+    # Read now the colors:
+    config_file_p.seek(0, 0)
+    for line in config_file_p:
+        if "Tooltips" in line:
+            break
+    for line in config_file_p:
+        if "Color " in line:
+            globvar_ThumbPara.colors.append(define_color(line[25:-1]))
+
+    globvar_ThumbPara.geometry_x.append(globvar_thumb_size_x * \
+                                                float(globvar_ThumbPara.res))
+    globvar_ThumbPara.geometry_y.append(globvar_thumb_size_y * \
+                                                float(globvar_ThumbPara.res))
+
+    config_file_p.close()
+
+
+# This definition clarifies, which fonts are available on the system and which
+# of the preferred fonts in 'globvar_fonts' is in the list of available_fonts.
+# Return the list of available preferred fonts.
+# In the variable 'globvar_bad_fonts' one finds the bad fonts (e.g., NotoColorEmoji),
+# which are excluded here!
+def get_fonts():
+
+    font_list = []
+
+    all_fonts_with_path = matplotlib.font_manager.get_fontconfig_fonts()
+    all_fonts = []
+    for fname in all_fonts_with_path:
+        if str(os.path.basename(fname)) in globvar_bad_fonts:
+            continue
+        tmp = matplotlib.font_manager.FontProperties(fname=fname).get_name()
+        all_fonts.append(tmp)
+
+    for font in globvar_fonts:
+        if font in all_fonts:
+            font_list.append(font)
+
+    return font_list

AFM_thumbs/Config_AFM_thumbs.conf

@@ -0,0 +1,166 @@
+#
+#
+#   This is the config file of the 'Advanced SCALA contact sheets' tool
+#
+#   Don't make any changes
+#
+
+
+Last directory: /media/cle/Daten/Data/X -- 2022/Programming/Python_AFM_thumbs/AFM_thumbs/Aktuelle_version_python3/TESTS
+PDF Path:
+
+
+Parameters
+==========
+Rows                   : 6
+Columns                : 4
+Rms                    : 2.5
+Image resolution       : 100
+Jpeg quality           : 40
+X text position        : 0
+Y text position        : 0
+Text size              : 13
+Dx of text             : 0
+Font                   : Arial
+Date                   : 1
+Size in nm             : 1
+Size in px             : 1
+Offset                 : 1
+Voltage                : 1
+Feedback               : 1
+Gain                   : 1
+Speed                  : 1
+Amplitude              : 1
+Angle                  : 1
+Deleting thumbs before : 0
+Deleting thumbs after  : 0
+Extra directories      : 0
+Replace pdfs           : 0
+Subdirs                : 1
+Spektral Options       : 1
+Format Options         : 1
+Peek Options           : 0
+Minimum on zero Options: 0
+Master directory       : 
+Filename               : 
+Color                  : ReiGreen
+File extension         : 
+Direction              : 0
+Linefit                : 0
+Planefit               : 3
+AddChannel             : 17
+ChannelNumber          : 3
+Tooltips               : 0
+Channelname 1          : FN
+Channelname 2          : FL
+Channelname 3          : I
+Thumb 1                : 1
+Thumb 2                : 1
+Thumb 3                : 1
+Thumb 4                : 1
+Thumb 5                : 1
+Thumb 6                : 1
+Thumb 7                : 1
+Thumb 8                : 1
+Thumb 9                : 1
+Thumb 10               : 1
+Thumb 11               : 1
+Thumb 12               : 1
+Thumb 13               : 1
+Thumb 14               : 1
+Thumb 15               : 1
+Thumb 16               : 1
+Thumb 17               : 1
+Thumb 18               : 1
+Thumb 19               : 1
+Thumb 20               : 1
+Thumb 21               : 1
+Thumb 22               : 1
+LineFit 1              : 1
+LineFit 2              : 1
+LineFit 3              : 1
+LineFit 4              : 1
+LineFit 5              : 1
+LineFit 6              : 1
+LineFit 7              : 1
+LineFit 8              : 1
+LineFit 9              : 1
+LineFit 10             : 1
+LineFit 11             : 1
+LineFit 12             : 1
+LineFit 13             : 1
+LineFit 14             : 1
+LineFit 15             : 1
+LineFit 16             : 1
+LineFit 17             : 1
+LineFit 18             : 1
+LineFit 19             : 1
+LineFit 20             : 1
+LineFit 21             : 1
+LineFit 22             : 1
+PlaneFit 1             : 0
+PlaneFit 2             : 0
+PlaneFit 3             : 0
+PlaneFit 4             : 0
+PlaneFit 5             : 0
+PlaneFit 6             : 0
+PlaneFit 7             : 0
+PlaneFit 8             : 0
+PlaneFit 9             : 0
+PlaneFit 10            : 0
+PlaneFit 11            : 0
+PlaneFit 12            : 0
+PlaneFit 13            : 0
+PlaneFit 14            : 0
+PlaneFit 15            : 0
+PlaneFit 16            : 0
+PlaneFit 17            : 0
+PlaneFit 18            : 0
+PlaneFit 19            : 0
+PlaneFit 20            : 0
+PlaneFit 21            : 0
+PlaneFit 22            : 0
+Inverted 1             : 0
+Inverted 2             : 0
+Inverted 3             : 1
+Inverted 4             : 1
+Inverted 5             : 0
+Inverted 6             : 0
+Inverted 7             : 0
+Inverted 8             : 0
+Inverted 9             : 0
+Inverted 10            : 0
+Inverted 11            : 0
+Inverted 12            : 0
+Inverted 13            : 1
+Inverted 14            : 1
+Inverted 15            : 0
+Inverted 16            : 0
+Inverted 17            : 0
+Inverted 18            : 0
+Inverted 19            : 0
+Inverted 20            : 0
+Inverted 21            : 0
+Inverted 22            : 0
+Color 1                : AFMhot
+Color 2                : AFMhot
+Color 3                : Grey
+Color 4                : Grey
+Color 5                : Yellow
+Color 6                : Yellow
+Color 7                : Grey
+Color 8                : Grey
+Color 9                : ReiGreen
+Color 10               : ReiGreen
+Color 11               : Red
+Color 12               : Red
+Color 13               : Blue2
+Color 14               : Blue2
+Color 15               : ReiGreen
+Color 16               : ReiGreen
+Color 17               : Blue2
+Color 18               : Blue2
+Color 19               : Blue
+Color 20               : Blue
+Color 21               : Ocean
+Color 22               : Ocean

AFM_thumbs/Config_AFM_thumbs.conf~

@@ -0,0 +1,166 @@
+#
+#
+#   This is the config file of the 'Advanced SCALA contact sheets' tool
+#   
+#   Don't make any changes
+#
+
+
+Last directory: /media/cle/Daten/Data/X -- 2012/rawdata/sample_Brice/NaCl_C60_01june2012p2
+PDF Path: 
+
+
+Parameters
+==========
+Rows                   : 6
+Columns                : 4
+Rms                    : 1.3
+Image resolution       : 100
+Jpeg quality           : 40
+X text position        : 0
+Y text position        : 0
+Text size              : 13
+Dx of text             : 0
+Font                   : FreeSans
+Date                   : 1
+Size in nm             : 1
+Size in px             : 1
+Offset                 : 1
+Voltage                : 1
+Feedback               : 1
+Gain                   : 1
+Speed                  : 1
+Amplitude              : 1
+Angle                  : 1
+Deleting thumbs before : 0
+Deleting thumbs after  : 0
+Extra directories      : 0
+Replace pdfs           : 1
+Subdirs                : 1
+Spektral Options       : 1
+Format Options         : 0
+Peek Options           : 0
+Minimum on zero Options: 0
+Master directory       : 
+Filename               : 
+Color                  : ReiGreen
+File extension         : _noline
+Direction              : 0
+Linefit                : 3
+Planefit               : 3
+AddChannel             : 17
+ChannelNumber          : 3
+Tooltips               : 0
+Channelname 1          : FN
+Channelname 2          : FL
+Channelname 3          : I
+Thumb 1                : 1
+Thumb 2                : 1
+Thumb 3                : 1
+Thumb 4                : 1
+Thumb 5                : 1
+Thumb 6                : 1
+Thumb 7                : 1
+Thumb 8                : 1
+Thumb 9                : 1
+Thumb 10               : 1
+Thumb 11               : 1
+Thumb 12               : 1
+Thumb 13               : 1
+Thumb 14               : 1
+Thumb 15               : 1
+Thumb 16               : 1
+Thumb 17               : 1
+Thumb 18               : 1
+Thumb 19               : 1
+Thumb 20               : 1
+Thumb 21               : 1
+Thumb 22               : 1
+LineFit 1              : 0
+LineFit 2              : 0
+LineFit 3              : 0
+LineFit 4              : 0
+LineFit 5              : 0
+LineFit 6              : 0
+LineFit 7              : 0
+LineFit 8              : 0
+LineFit 9              : 0
+LineFit 10             : 0
+LineFit 11             : 0
+LineFit 12             : 0
+LineFit 13             : 0
+LineFit 14             : 0
+LineFit 15             : 0
+LineFit 16             : 0
+LineFit 17             : 0
+LineFit 18             : 0
+LineFit 19             : 0
+LineFit 20             : 0
+LineFit 21             : 0
+LineFit 22             : 0
+PlaneFit 1             : 0
+PlaneFit 2             : 0
+PlaneFit 3             : 0
+PlaneFit 4             : 0
+PlaneFit 5             : 0
+PlaneFit 6             : 0
+PlaneFit 7             : 0
+PlaneFit 8             : 0
+PlaneFit 9             : 0
+PlaneFit 10            : 0
+PlaneFit 11            : 0
+PlaneFit 12            : 0
+PlaneFit 13            : 0
+PlaneFit 14            : 0
+PlaneFit 15            : 0
+PlaneFit 16            : 0
+PlaneFit 17            : 0
+PlaneFit 18            : 0
+PlaneFit 19            : 0
+PlaneFit 20            : 0
+PlaneFit 21            : 0
+PlaneFit 22            : 0
+Inverted 1             : 1
+Inverted 2             : 1
+Inverted 3             : 1
+Inverted 4             : 1
+Inverted 5             : 1
+Inverted 6             : 1
+Inverted 7             : 1
+Inverted 8             : 1
+Inverted 9             : 1
+Inverted 10            : 1
+Inverted 11            : 1
+Inverted 12            : 1
+Inverted 13            : 1
+Inverted 14            : 1
+Inverted 15            : 1
+Inverted 16            : 1
+Inverted 17            : 1
+Inverted 18            : 1
+Inverted 19            : 1
+Inverted 20            : 1
+Inverted 21            : 1
+Inverted 22            : 1
+Color 1                : BluePurple
+Color 2                : PurpleBlue
+Color 3                : Grey
+Color 4                : Grey
+Color 5                : PupleRed
+Color 6                : RedPurple
+Color 7                : Grey
+Color 8                : Grey
+Color 9                : OrangeRed
+Color 10               : PurpleBlueGreen
+Color 11               : Red
+Color 12               : Red
+Color 13               : Gnuplot
+Color 14               : Gnuplot2
+Color 15               : ReiGreen
+Color 16               : ReiGreen
+Color 17               : Blue2
+Color 18               : Blue2
+Color 19               : Blue
+Color 20               : Blue
+Color 21               : Ocean
+Color 22               : Ocean

AFM_thumbs/Config_default.conf

@@ -0,0 +1,177 @@
+#
+#
+#	This is the config file of the 'Advanced SCALA contact sheets' tool
+#	
+#	Don't make any changes
+#
+
+
+Last directory: /media/cle/Daten/Data/X -- 2021/rawdata/NANONIS
+PDF Path: 
+
+
+Parameters
+==========
+Rows                   : 6
+Columns                : 4
+Rms                    : 1.3
+Image resolution       : 100
+Jpeg quality           : 40
+X text position        : 0
+Y text position        : 0
+Text size              : 13
+Dx of text             : 0
+Font                   : FreeSans
+Date                   : 1
+Size in nm             : 1
+Size in px             : 1
+Offset                 : 1
+Voltage                : 1
+Feedback               : 1
+Gain                   : 1
+Speed                  : 1
+Amplitude              : 1
+Angle                  : 1
+Deleting thumbs before : 0
+Deleting thumbs after  : 0
+Extra directories      : 0
+Replace pdfs           : 0
+Subdirs                : 1
+Spektral Options       : 1
+Format Options         : 0
+Peek Options           : 0
+Minimum on zero Options: 0
+Master directory       : 
+Filename               : 
+Color                  : ReiGreen
+File extension         : 
+Direction              : 0
+Linefit                : 3
+Planefit               : 3
+AddChannel             : 20
+ChannelNumber          : 4
+Tooltips               : 0
+Channelname 1          : FN
+Channelname 2          : FL
+Channelname 3          : I
+Channelname 4          : Phase
+Thumb 1                : 1
+Thumb 2                : 1
+Thumb 3                : 1
+Thumb 4                : 1
+Thumb 5                : 1
+Thumb 6                : 1
+Thumb 7                : 1
+Thumb 8                : 1
+Thumb 9                : 1
+Thumb 10               : 1
+Thumb 11               : 1
+Thumb 12               : 1
+Thumb 13               : 1
+Thumb 14               : 1
+Thumb 15               : 1
+Thumb 16               : 1
+Thumb 17               : 1
+Thumb 18               : 1
+Thumb 19               : 1
+Thumb 20               : 1
+Thumb 21               : 1
+Thumb 22               : 1
+Thumb 23               : 1
+Thumb 24               : 1
+LineFit 1              : 1
+LineFit 2              : 1
+LineFit 3              : 1
+LineFit 4              : 1
+LineFit 5              : 1
+LineFit 6              : 1
+LineFit 7              : 1
+LineFit 8              : 1
+LineFit 9              : 1
+LineFit 10             : 1
+LineFit 11             : 1
+LineFit 12             : 1
+LineFit 13             : 1
+LineFit 14             : 1
+LineFit 15             : 1
+LineFit 16             : 1
+LineFit 17             : 1
+LineFit 18             : 1
+LineFit 19             : 1
+LineFit 20             : 1
+LineFit 21             : 1
+LineFit 22             : 1
+LineFit 23             : 1
+LineFit 24             : 1
+PlaneFit 1             : 0
+PlaneFit 2             : 0
+PlaneFit 3             : 0
+PlaneFit 4             : 0
+PlaneFit 5             : 0
+PlaneFit 6             : 0
+PlaneFit 7             : 0
+PlaneFit 8             : 0
+PlaneFit 9             : 0
+PlaneFit 10            : 0
+PlaneFit 11            : 0
+PlaneFit 12            : 0
+PlaneFit 13            : 0
+PlaneFit 14            : 0
+PlaneFit 15            : 0
+PlaneFit 16            : 0
+PlaneFit 17            : 0
+PlaneFit 18            : 0
+PlaneFit 19            : 0
+PlaneFit 20            : 0
+PlaneFit 21            : 0
+PlaneFit 22            : 0
+PlaneFit 23            : 0
+PlaneFit 24            : 0
+Inverted 1             : 0
+Inverted 2             : 0
+Inverted 3             : 1
+Inverted 4             : 1
+Inverted 5             : 0
+Inverted 6             : 0
+Inverted 7             : 0
+Inverted 8             : 0
+Inverted 9             : 0
+Inverted 10            : 0
+Inverted 11            : 0
+Inverted 12            : 0
+Inverted 13            : 1
+Inverted 14            : 1
+Inverted 15            : 0
+Inverted 16            : 0
+Inverted 17            : 0
+Inverted 18            : 0
+Inverted 19            : 0
+Inverted 20            : 0
+Inverted 21            : 0
+Inverted 22            : 0
+Inverted 23            : 0
+Inverted 24            : 0
+Color 1                : Gist_heat
+Color 2                : Gist_heat
+Color 3                : Grey
+Color 4                : Grey
+Color 5                : AFMhot
+Color 6                : AFMhot
+Color 7                : Grey
+Color 8                : Grey
+Color 9                : Grey
+Color 10               : Grey
+Color 11               : Red
+Color 12               : Red
+Color 13               : Blue2
+Color 14               : Blue2
+Color 15               : ReiGreen
+Color 16               : ReiGreen
+Color 17               : Blue2
+Color 18               : Blue2
+Color 19               : Blue
+Color 20               : Blue
+Color 21               : Ocean
+Color 22               : Ocean
+Color 23               : Grey
+Color 24               : Grey

AFM_thumbs/Config_default.conf~

@@ -0,0 +1,166 @@
+#
+#
+#	This is the config file of the 'Advanced SCALA contact sheets' tool
+#	
+#	Don't make any changes
+#
+
+
+Last directory: /media/cle/Daten/Data/X -- 2016/rawdata/sample_Pd-HOPG/Ceria_10ML_Pd_annealed_Ethylene_2016-01-03
+PDF Path: /media/cle/Daten/Data/X -- 2016/rawdata/sample_Pd-HOPG/Ficken
+
+
+Parameters
+==========
+Rows                   : 6
+Columns                : 4
+Rms                    : 1.3
+Image resolution       : 100
+Jpeg quality           : 40
+X text position        : 0
+Y text position        : 0
+Text size              : 13
+Dx of text             : 0
+Font                   : Arial
+Date                   : 1
+Size in nm             : 1
+Size in px             : 1
+Offset                 : 1
+Voltage                : 1
+Feedback               : 1
+Gain                   : 1
+Speed                  : 1
+Amplitude              : 1
+Angle                  : 1
+Deleting thumbs before : 0
+Deleting thumbs after  : 0
+Extra directories      : 0
+Replace pdfs           : 1
+Subdirs                : 0
+Spektral Options       : 1
+Format Options         : 0
+Peek Options           : 0
+Minimum on zero Options: 0
+Master directory       : 
+Filename               : 
+Color                  : ReiGreen
+File extension         : _noline
+Direction              : 0
+Linefit                : 3
+Planefit               : 3
+AddChannel             : 17
+ChannelNumber          : 3
+Tooltips               : 0
+Channelname 1          : FN
+Channelname 2          : FL
+Channelname 3          : I
+Thumb 1                : 1
+Thumb 2                : 1
+Thumb 3                : 1
+Thumb 4                : 1
+Thumb 5                : 1
+Thumb 6                : 1
+Thumb 7                : 1
+Thumb 8                : 1
+Thumb 9                : 1
+Thumb 10               : 1
+Thumb 11               : 1
+Thumb 12               : 1
+Thumb 13               : 1
+Thumb 14               : 1
+Thumb 15               : 1
+Thumb 16               : 1
+Thumb 17               : 1
+Thumb 18               : 1
+Thumb 19               : 1
+Thumb 20               : 1
+Thumb 21               : 1
+Thumb 22               : 1
+LineFit 1              : 0
+LineFit 2              : 0
+LineFit 3              : 0
+LineFit 4              : 0
+LineFit 5              : 0
+LineFit 6              : 0
+LineFit 7              : 0
+LineFit 8              : 0
+LineFit 9              : 0
+LineFit 10             : 0
+LineFit 11             : 0
+LineFit 12             : 0
+LineFit 13             : 0
+LineFit 14             : 0
+LineFit 15             : 0
+LineFit 16             : 0
+LineFit 17             : 0
+LineFit 18             : 0
+LineFit 19             : 0
+LineFit 20             : 0
+LineFit 21             : 0
+LineFit 22             : 0
+PlaneFit 1             : 1
+PlaneFit 2             : 1
+PlaneFit 3             : 0
+PlaneFit 4             : 0
+PlaneFit 5             : 0
+PlaneFit 6             : 0
+PlaneFit 7             : 0
+PlaneFit 8             : 0
+PlaneFit 9             : 0
+PlaneFit 10            : 0
+PlaneFit 11            : 0
+PlaneFit 12            : 0
+PlaneFit 13            : 1
+PlaneFit 14            : 1
+PlaneFit 15            : 0
+PlaneFit 16            : 0
+PlaneFit 17            : 0
+PlaneFit 18            : 0
+PlaneFit 19            : 0
+PlaneFit 20            : 0
+PlaneFit 21            : 0
+PlaneFit 22            : 0
+Inverted 1             : 0
+Inverted 2             : 0
+Inverted 3             : 1
+Inverted 4             : 1
+Inverted 5             : 0
+Inverted 6             : 0
+Inverted 7             : 0
+Inverted 8             : 0
+Inverted 9             : 0
+Inverted 10            : 0
+Inverted 11            : 0
+Inverted 12            : 0
+Inverted 13            : 1
+Inverted 14            : 1
+Inverted 15            : 0
+Inverted 16            : 0
+Inverted 17            : 0
+Inverted 18            : 0
+Inverted 19            : 0
+Inverted 20            : 0
+Inverted 21            : 0
+Inverted 22            : 0
+Color 1                : Gist_heat
+Color 2                : Gist_heat
+Color 3                : Grey
+Color 4                : Grey
+Color 5                : AFMhot
+Color 6                : AFMhot
+Color 7                : Grey
+Color 8                : Grey
+Color 9                : Grey
+Color 10               : Grey
+Color 11               : Red
+Color 12               : Red
+Color 13               : Blue2
+Color 14               : Blue2
+Color 15               : ReiGreen
+Color 16               : ReiGreen
+Color 17               : Blue2
+Color 18               : Blue2
+Color 19               : Blue
+Color 20               : Blue
+Color 21               : Ocean
+Color 22               : Ocean

AFM_thumbs/Initialize.py

@@ -0,0 +1,223 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import os
+import shutil
+
+from AFM_thumbs.Variables import globvar_AFMdata
+from AFM_thumbs.Variables import globvar_AFMdir
+from AFM_thumbs.Variables import globvar_ThumbPara
+from AFM_thumbs.Variables import globvar_spaces
+from AFM_thumbs.Variables import globvar_configfile_path
+from AFM_thumbs.Variables import globvar_configfile
+from AFM_thumbs.Variables import globvar_python_directory
+from AFM_thumbs.Variables import globvar_default_config
+from AFM_thumbs.Variables import RHK_PositionCounter
+
+
+def initialize_position_counter():
+    RHK_PositionCounter.position = 0
+
+
+def initialize_AFM_data():
+    globvar_AFMdata.date = ""
+    globvar_AFMdata.x_size = ""
+    globvar_AFMdata.y_size = ""
+    globvar_AFMdata.x_pixel = ""
+    globvar_AFMdata.y_pixel = ""
+    globvar_AFMdata.x_off = ""
+    globvar_AFMdata.y_off = ""
+    globvar_AFMdata.voltage = ""
+    globvar_AFMdata.measurement_type = ""
+    globvar_AFMdata.feedback = ""
+    globvar_AFMdata.gain = ""
+    globvar_AFMdata.gain_prop  = ""
+    globvar_AFMdata.gain_int  = ""
+    globvar_AFMdata.gain_xy = ""
+    globvar_AFMdata.gain_signal = ""
+    globvar_AFMdata.gain_z = ""
+    globvar_AFMdata.speed = ""
+    globvar_AFMdata.res_freq = ""
+    globvar_AFMdata.amplitude = ""
+    globvar_AFMdata.angle = ""
+    globvar_AFMdata.scan_updown = ""
+    globvar_AFMdata.sweep_f0 = ""
+    globvar_AFMdata.sweep_phase = ""
+    globvar_AFMdata.sweep_A_exec = ""
+    globvar_AFMdata.sweep_Q = ""
+    globvar_AFMdata.NONE = ""
+    globvar_AFMdata.datfile[:] = []
+    globvar_AFMdata.channel[:] = []
+    globvar_AFMdata.unit[:] = []
+    globvar_AFMdata.z_average = 0.0
+    globvar_AFMdata.z_factor[:] = []
+    globvar_AFMdata.z_offset[:] = []
+    globvar_AFMdata.z_calibration[:] = []
+    globvar_AFMdata.z_amplitude[:] = []
+    globvar_AFMdata.z_min[:] = []
+    globvar_AFMdata.z_max[:] = []
+    globvar_AFMdata.scandir[:] = []
+    globvar_AFMdata.spec_x_unit[:] = []
+    globvar_AFMdata.spec_x_label[:] = []
+    globvar_AFMdata.spec_y_unit[:] = []
+    globvar_AFMdata.spec_y_label[:] = []
+    globvar_AFMdata.spec_y_factor[:] = []
+    globvar_AFMdata.spec_points[:] = []
+    globvar_AFMdata.spec_feedback[:] = []
+    globvar_AFMdata.spec_acquisition[:] = []
+    globvar_AFMdata.spec_delay[:] = []
+    globvar_AFMdata.spec_time[:] = []
+    globvar_AFMdata.spec_position[:] = []
+    globvar_AFMdata.spec_files[:] = []
+
+
+def initialize_dir():
+    # If the user chooses 'Cancel' -> exit
+    if not globvar_AFMdir.working_directory:
+        return False
+
+    # The pdfs shall not be replaced if 0
+    if globvar_ThumbPara.pdfs == 0:
+        # There is no special path for the pdfs ...
+        if globvar_AFMdir.pdf_path == "":
+            # The name of the pdf that may exist
+            file_pdf = os.path.abspath(globvar_AFMdir.working_directory) + \
+                       globvar_ThumbPara.extension+".pdf"
+
+        # ... there is a special path for the pdfs!
+        else:
+            # The name of the pdf that may exist
+            file_pdf = os.path.basename(globvar_AFMdir.working_directory)  + \
+                       globvar_ThumbPara.extension + \
+                       ".pdf"
+            file_pdf = os.path.join(globvar_AFMdir.pdf_path, file_pdf)
+
+
+        # If the pdf does exist, then simply do nothing => return False!
+        if os.path.isfile(file_pdf):
+            print(globvar_spaces + "The pdf file\n" +
+                  globvar_spaces +
+                  "'" + file_pdf + "'\n" +
+                  globvar_spaces +
+                  "does already exist !\n")
+            return False
+
+
+    # Name of directory
+    globvar_AFMdir.data_directory_name = \
+                            os.path.basename(globvar_AFMdir.working_directory)
+
+    # Thumbnail directory will be created in the working directory
+    globvar_AFMdir.thumbnail_directory = \
+                                os.path.join(globvar_AFMdir.working_directory,
+                                "thumbnails" + globvar_ThumbPara.extension)
+
+    # If some thumbnails are already existing but shall be deleted, then do ...
+    if globvar_ThumbPara.thumbs_before == True:
+        if os.path.isdir(globvar_AFMdir.thumbnail_directory):
+            delete_string = globvar_AFMdir.thumbnail_directory
+            shutil.rmtree(delete_string)
+#==============================================================================
+#         delete_string = "rm -rf \""+globvar_AFMdir.thumbnail_directory+"\""
+#         os.system(delete_string)
+#==============================================================================
+
+
+    # Name of superior directory
+    superior_directory = os.path.dirname(globvar_AFMdir.working_directory)
+
+    # Name of directory even above
+    if (len(superior_directory)-superior_directory.rfind(os.pathsep))>0:
+       superior_2_times_directory = os.path.dirname(superior_directory)
+
+    if globvar_ThumbPara.extra_direct == True:
+
+        # Create, if it doesn't exist, a directory 'WSxM' and 'Gwyddion', which
+        # are on the same level as 'sample'.
+        # This is for future work, where treated WSxM and Gwyddion files can
+        # hutil be stored in these directories and ...
+        directory_WSxM = os.path.join(superior_2_times_directory,"WSxM")
+        if not os.path.isdir(directory_WSxM):
+            os.mkdir(directory_WSxM)
+
+        directory_Gwyddion = os.path.join(superior_2_times_directory,
+                                          "Gwyddion")
+        if not os.path.isdir(directory_Gwyddion):
+            os.mkdir(directory_Gwyddion)
+
+        # ... in the respective sub directories
+        directory_WSxM_data = os.path.join(directory_WSxM,
+                                           globvar_AFMdir.data_directory_name)
+        if not os.path.isdir(directory_WSxM_data):
+            os.mkdir(directory_WSxM_data)
+
+        directory_Gwyddion_data = os.path.join(directory_Gwyddion,
+                                           globvar_AFMdir.data_directory_name)
+        if not os.path.isdir(directory_Gwyddion_data):
+            os.mkdir(directory_Gwyddion_data)
+
+    # Thumbnail directory in working directory
+    if not os.path.isdir(globvar_AFMdir.thumbnail_directory):
+        os.mkdir(globvar_AFMdir.thumbnail_directory)
+
+    return True
+
+
+# Determine the config file.
+def initialize_check_config(file_config):
+
+    if file_config == None:
+        file_config = os.path.join(globvar_configfile_path,globvar_configfile)
+
+    path_rel_default_config = os.path.join(globvar_python_directory,
+                                           globvar_default_config)
+
+    if not os.path.isfile(file_config):
+        print(globvar_spaces + "Attention: The config file\n" +
+              globvar_spaces + file_config + "\n" + globvar_spaces +
+              "does not exist!\n" + globvar_spaces +
+              "The default config file '" +
+              path_rel_default_config +
+              "' " +
+              "is now used!\n" + globvar_spaces +
+              "If you have your own config file, put in the correct " +
+              "file name and path\n" + globvar_spaces +
+              "in 'AFM_thumbs/Variables.py' => " +
+              "'globvar_configfile' and 'globvar_configfile_path'\n")
+
+        filepath_program = os.path.realpath(__file__)
+        path_program = os.path.dirname(filepath_program)
+        file_config = os.path.join(path_program,globvar_default_config)
+
+        if not os.path.isfile(file_config):
+            print(globvar_spaces +
+                  "Attention, MAJOR ERROR !!! The default config file\n" +
+                  globvar_spaces + file_config + "\n" + globvar_spaces +
+                  "does not exist! Re-install the whole program.\n" +
+                  globvar_spaces + "Exit!\n")
+            exit(-1)
+
+    return file_config

AFM_thumbs/Linalg.py

@@ -0,0 +1,251 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import scipy
+from scipy import linalg
+import numpy as np
+from AFM_thumbs.Variables import globvar_spaces
+from AFM_thumbs.Variables import globvar_LINALG
+from AFM_thumbs.Variables import globvar_AFMdata
+from AFM_thumbs.Variables import globvar_ThumbPara
+
+
+def linalg_plane_fit(size_x, size_y, data):
+
+    size_x_float = float(size_x)
+    size_y_float = float(size_y)
+
+    if size_x == 512 and size_y == 512:
+
+        M     = globvar_LINALG.plane_M512
+        x_vec = globvar_LINALG.plane_x_vec512
+        y_vec = globvar_LINALG.plane_y_vec512
+
+    elif size_x == 1024 and size_y == 1024:
+
+        M     = globvar_LINALG.plane_M1024
+        x_vec = globvar_LINALG.plane_x_vec1024
+        y_vec = globvar_LINALG.plane_y_vec1024
+
+    else:
+
+        x_vec = np.arange(size_x_float)
+        y_vec = np.arange(size_y_float)
+
+        x   = x_vec.sum() * size_x_float
+        y   = y_vec.sum() * size_y_float
+        xx  = (x_vec * x_vec).sum() * size_x_float
+        yy  = (y_vec * y_vec).sum() * size_y_float
+        xy  = (y_vec * (x / size_x_float)).sum()
+
+        M = scipy.mat([[xx,xy,x],
+                       [xy,yy,y],
+                       [x,y,size_x_float*size_y_float]])
+
+    z  = data.sum()
+    xz = (data * x_vec).sum()
+    yz = (data * y_vec.reshape(size_y,1)).sum()
+    B  = scipy.mat([[xz], [yz], [z]])
+
+    c,resid,rank,sigma = linalg.lstsq(M,B)
+
+    array_one = np.array([[1 for i in range(size_x)] for j in range(size_y)])
+
+    plane_const = array_one * c[2][0]
+    plane_x     = array_one * x_vec                   * c[0][0]
+    plane_y     = array_one * y_vec.reshape(size_y,1) * c[1][0]
+    plane       = plane_const + plane_x + plane_y
+
+    # The plane substraction
+    data = data - plane
+
+    # Put zero onto lowest value
+    # min_value = min(data)
+    # data = data - float(min_value)
+
+    return data
+
+
+def linalg_line_fit(size_x, size_y, data):
+
+    size_x_float = float(size_x)
+    size_y_float = float(size_y)
+
+    if size_x == 512 and size_y == 512:
+
+        M     = globvar_LINALG.line_M512
+        x_vec = globvar_LINALG.line_x_vec512
+
+    elif size_x == 1024 and size_y == 1024:
+
+        M     = globvar_LINALG.line_M1024
+        x_vec = globvar_LINALG.line_x_vec1024
+
+    else:
+
+        x_vec = np.arange(size_x_float)
+        x   = x_vec.sum()
+        xx  = (x_vec * x_vec).sum()
+        M   = scipy.mat([[xx,x],
+                         [x,size_x_float]])
+
+    plane = []
+    for line in data:
+
+        y  = sum(line)
+        xy = sum(line*x_vec)
+
+        B  = scipy.mat([[xy],[y]])
+        c,resid,rank,sigma = linalg.lstsq(M,B)
+
+        plane.append([i * c[0][0] + c[1][0] for i in range(size_x)])
+
+    # The plane substraction
+    data = data - plane
+
+    # Put zero onto lowest value
+    # min_value = min(data)
+    # data = data - float(min_value)
+
+    return data
+
+
+def initialize_linalg():
+
+    # Plane
+    x_vec = np.arange(512)
+    y_vec = np.arange(512)
+    x   = x_vec.sum() * 512.0
+    y   = y_vec.sum() * 512.0
+    xx  = (x_vec * x_vec).sum() * 512.0
+    yy  = (y_vec * y_vec).sum() * 512.0
+    xy  = (y_vec * (x / 512.0)).sum()
+
+    globvar_LINALG.plane_M512 = scipy.mat([[xx,xy,x],
+                                   [xy,yy,y],
+                                   [x,y,512.0*512.0]])
+    globvar_LINALG.plane_x_vec512 = x_vec
+    globvar_LINALG.plane_y_vec512 = y_vec
+
+    x_vec = np.arange(1024)
+    y_vec = np.arange(1024)
+    x   = x_vec.sum() * 1024.0
+    y   = y_vec.sum() * 1024.0
+    xx  = (x_vec * x_vec).sum() * 1024.0
+    yy  = (y_vec * y_vec).sum() * 1024.0
+    xy  = (y_vec * (x / 1024.0)).sum()
+
+    globvar_LINALG.plane_M1024 = scipy.mat([[xx,xy,x],
+                              [xy,yy,y],
+                              [x,y,1024.0*1024.0]])
+    globvar_LINALG.plane_x_vec1024 = x_vec
+    globvar_LINALG.plane_y_vec1024 = y_vec
+
+    # Line
+    x_vec = np.arange(512)
+    x   = x_vec.sum()
+    xx  = (x_vec * x_vec).sum()
+    globvar_LINALG.line_M512 = scipy.mat([[xx,x],
+                                  [x,512.0]])
+    globvar_LINALG.line_x_vec512 = x_vec
+
+    x_vec = np.arange(1024)
+    x   = x_vec.sum()
+    xx  = (x_vec * x_vec).sum()
+    globvar_LINALG.line_M1024 = scipy.mat([[xx,x],
+                                   [x,1024.0]])
+    globvar_LINALG.line_x_vec1024 = x_vec
+
+
+def check_image_properties(data, data_file):
+
+    size_x = int(globvar_AFMdata.x_pixel)
+    size_y = int(globvar_AFMdata.y_pixel)
+    size   = size_x * size_y
+
+    old_y_size  = ""
+    old_y_pixel = ""
+
+    # Part 1
+    # ======
+    #
+    # We first put all NaNs onto the mean value! This is important for, e.g.,
+    # Nanonis files.
+    if np.isnan(data.min()) or np.isnan(data.max()):
+
+        list_nans = np.where(np.isnan(data))[0]
+        data_clean = np.delete(data, list_nans)
+        data_mean = np.mean(data_clean)
+
+        for nan in list_nans:
+            data[nan] = data_mean
+
+    # Part 2
+    # ======
+    #
+    # Check now the lenght of the array, and send the true size, if the image
+    # is not complete (important for Omicron SCALA images that were stored
+    # before the complete image was finished).
+    if len(data) != size:
+       size_diff = len(data) - size
+       print
+       print(globvar_spaces + "Attention, error in data file!")
+       print(globvar_spaces + "Length of data is not equal to size_x * size_y")
+       print(globvar_spaces + "Size x,y   : "+str(size_x) + "x" + \
+                               str(size_y) + ", " + str(size_x*size_y))
+       print(globvar_spaces + "Data       : "+str(len(data)))
+       print(globvar_spaces + "Data-Size  : "+str(size_diff))
+       print(globvar_spaces + "File       : " + data_file)
+
+       # This is for ONE line:
+       if abs(size_diff) < size_x:
+          data    = data[ : -(size_x + size_diff) ]
+          size_y -= 1
+          print(globvar_spaces + "Error has been fixed by removing one"
+                               + " line from the data.")
+       # This is for several lines.
+       elif abs(size_diff) > size_x:
+          remove_lines = int(size_diff / size_x)
+          remove_data  = size_diff % size_x
+          size_y      -= abs(remove_lines)
+          if remove_data != 0:
+              data         = data[ : -remove_data ]
+          print(globvar_spaces + "Error has been fixed by removing "
+                + str(abs(remove_lines)) + " lines from the data.")
+
+       old_y_size  = globvar_AFMdata.y_size
+       old_y_pixel = globvar_AFMdata.y_pixel
+       globvar_AFMdata.y_pixel = str(size_y)
+       globvar_AFMdata.y_size  = str(float(globvar_AFMdata.x_size) * \
+                                 (float(size_y)/float(size_x)))
+       # Two digits after the .dot. .
+       globvar_AFMdata.y_size  = globvar_AFMdata.y_size[: \
+                                             globvar_AFMdata.y_size.find(".")+2]
+
+    return data, old_y_size, old_y_pixel
+
+
+

AFM_thumbs/Nanotec_DULCINEA.py

@@ -0,0 +1,452 @@
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import os
+import numpy as np
+
+from AFM_thumbs.Variables import globvar_AFMdata
+from AFM_thumbs.Variables import globvar_AFMdir
+from AFM_thumbs.Variables import globvar_ThumbPara
+from AFM_thumbs.Variables import Nanotec_DULCINEA_suffix
+from AFM_thumbs.Variables import Nanotec_DULCINEA_forward
+from AFM_thumbs.Variables import Nanotec_DULCINEA_backward
+from AFM_thumbs.Variables import Nanotec_DULCINEA_must_exist
+from AFM_thumbs.Linalg import linalg_plane_fit
+from AFM_thumbs.Linalg import linalg_line_fit
+from AFM_thumbs.Linalg import check_image_properties
+from AFM_thumbs.Thumbs import create_thumb_images
+from AFM_thumbs.Initialize import initialize_AFM_data
+
+from AFM_thumbs.Channel import proceed_with
+from AFM_thumbs.Channel import line_fit
+from AFM_thumbs.Channel import plane_fit
+from AFM_thumbs.Channel import rename_channel
+
+def is_Nanotec_DULCINEA_file(directory, files):
+
+    list_directories_par = []
+
+    # A directroy is only interesting if there is at least
+    # one par and tf0 file.
+    FLAG = False
+    for filename in files:
+        file_name = os.path.join(directory, filename)
+        if FLAG == True:
+            if os.path.isdir(directory):
+                list_directories_par.append(directory)
+                break
+        if file_name[-6:] == Nanotec_DULCINEA_must_exist:
+            FLAG = True
+
+    return list_directories_par
+
+
+def prepare_Nanotec_DULCINEA_images(AFMfile):
+
+    file_basis = AFMfile[:-5]
+
+    read_Nanotec_DULCINEA_data(file_basis + Nanotec_DULCINEA_suffix[0])
+
+    for (image_nr, data_file) in enumerate(globvar_AFMdata.datfile):
+
+        if proceed_with(image_nr,globvar_AFMdata.scandir[image_nr]):
+
+            # Now, we determine only the file name without path.
+            # The way to do it is a bit complicated but does not depend
+            # on the system.
+
+            # Cut everything til the first appereabce of "." from the left ...
+            position = data_file.find(".")
+            # and note the suffix.
+            data_file_only_suffix = data_file[position+1:]
+            # Cat the basis of the file name and the suffix
+            data_file_name = file_basis + data_file_only_suffix
+
+            # If the file doesn't exist continue. But this would be strange, so
+            # output an error message.
+            if not os.path.isfile(data_file):
+                print(globvar_spaces + "The AFM data file ...\n<" + \
+                                     + ">\n... does not exist (?).\n\n")
+                print
+                continue
+
+            # If the thumb image exists continue with next one ... .
+            # (Don't calculate a second time.)
+            if globvar_ThumbPara.png:
+                image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                          data_file_name) + ".png"
+            else:
+                image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                          data_file_name) + ".jpeg"
+
+            if os.path.isfile(image_path):
+                continue
+            datafile = open(data_file, 'rb')
+            data = datafile.read()
+            datafile.close()
+
+            # Read the position of the binary data.
+            pos = data.find(b"[Header end]") + 12
+            # data[pos:pos+12].decode("utf-8")
+            data = data[pos:-2]
+
+            size_x = int(globvar_AFMdata.x_pixel)
+            size_y = int(globvar_AFMdata.y_pixel)
+
+            # Reopen the file
+            datafile = open(data_file, 'rb')
+            # Move to position in file
+            datafile.seek(pos,0)
+            # Straight to numpy data (no buffering)
+            data = np.fromfile(datafile,dtype = np.int16,count = size_x*size_y)
+            datafile.close()
+
+            # old_y_size and old_y_pixel are needed to temporarily store
+            # the original size in y (nm and pixel). This is then used
+            # at the end to put back the original values for
+            # globvar_AFMdata.y_size and globvar_AFMdata.y_pixel, for the
+            # text in the thumbs.
+            data, old_y_size, old_y_pixel = check_image_properties(data, data_file)
+            # If there is some corrupt image the y value, which has been
+            # changed in check_image_properties, needs to be updated.
+            size_y = int(globvar_AFMdata.y_pixel)
+
+            # First, transform the integers into floats. This is needed for all
+            # mathematical operations.
+            data = data.astype(float)
+            # Average value
+            average = np.average(data)
+            # Put the lowest point onto ZERO.
+            data = data - data.min()
+
+            # Scale the image with the values found in the file.
+            z_diff_unit = float(globvar_AFMdata.z_amplitude[image_nr])
+            z_diff      = float(data.max()) - float(data.min())
+            factor = z_diff_unit / z_diff
+            data = data * factor
+            # Calibrate the average value and write it into the
+            # globvar_AFMdata structure.
+            globvar_AFMdata.z_average = average * factor
+
+            # Make now a 2D array.
+            data.shape = np.array([size_y, size_x])
+
+            # Mirror the data along x and y
+            data = np.fliplr(data)
+            data = np.flipud(data)
+
+            # Line fit
+            if line_fit(image_nr,globvar_AFMdata.scandir[image_nr]):
+                 data = linalg_line_fit(size_x, size_y, data)
+
+            # Plane fit
+            if plane_fit(image_nr,globvar_AFMdata.scandir[image_nr]):
+                 data = linalg_plane_fit(size_x, size_y, data)
+
+            create_thumb_images(data,image_nr,data_file_name,data_file_name)
+
+            if old_y_size != "" and old_y_pixel != "":
+                globvar_AFMdata.y_size  = old_y_size
+                globvar_AFMdata.y_pixel = old_y_pixel
+
+        else:
+            continue
+
+    return True
+
+
+def read_Nanotec_DULCINEA_data(AFM_file):
+
+    initialize_AFM_data()
+
+    #  Go through the directory and find all files of ONE measurement.
+    AFMfiles = filter(lambda x: x.startswith(AFM_file[:-5]),
+                      os.listdir(globvar_AFMdir.working_directory))
+    AFMfiles = sorted(AFMfiles)
+
+    # For all those files, do ...
+    for AFMfile in AFMfiles:
+
+        AFMfile_split = AFMfile.split(".")
+
+        # Check the AFM file:
+        if AFMfile_split[-2] == "b" or AFMfile_split[-2] == "f":
+            # So, there is a ".f." or ".b.". If now the last suffix is NOT
+            # in the list of known 'channels', continue with the loop. In other
+            # words an unknown channel has been found, which is not supported.
+            if AFMfile[-5:] not in Nanotec_DULCINEA_suffix:
+                continue
+        # No second suffix ".f." or ".b." could be found. For some channels have
+        # something like ".b.2nd.Auxfeed". So, check the 3rd suffix:
+        else:
+            if AFMfile_split[-3] == "b" or AFMfile_split[-3] == "f":
+                # Reconstruct all the 3 suffix
+                AFMfile_2suffix = "." +                     \
+                                  AFMfile_split[-3] + "." + \
+                                  AFMfile_split[-2] + "." + \
+                                  AFMfile_split[-1]
+                # As above, an unknown channel has been found, which is not
+                # supported.
+                if AFMfile_2suffix not in Nanotec_DULCINEA_suffix:
+                    continue
+
+            # Strange, not found. It seems to be a completely different file!
+            else:
+                continue
+
+        # ... open the file and ...
+        file_path = os.path.join(globvar_AFMdir.working_directory,AFMfile)
+        file_p = open(file_path, "rb")
+
+        globvar_AFMdata.datfile.append(file_path)
+
+        if Nanotec_DULCINEA_backward in AFMfile:
+            globvar_AFMdata.scandir.append("backward")
+        if Nanotec_DULCINEA_forward in AFMfile:
+            globvar_AFMdata.scandir.append("forward")
+
+        # ... find the data for the lists from above.
+        for line in file_p:
+
+            line = line.decode("utf-8")
+
+            if "[Head Settings]" in line:
+                break
+
+            if "Acquisition channel:" in line:
+                position1 = str.find(line, ":")+2
+                rename_channel(line[position1:])
+
+            if "Acquisition primary channel:" in line:
+                position1 = str.find(line, ":")+2
+                globvar_AFMdata.NONE = None
+
+            if "Conversion Factor 00:" in line:
+                globvar_AFMdata.unit.append(line.rsplit(" ")[-1].rstrip())
+                globvar_AFMdata.z_factor.append(line.rsplit(" ")[-2].rstrip())
+
+            if "Z Calibration:" in line:
+                list_split = line.split(" ")
+                globvar_AFMdata.z_calibration.append(list_split[-2])
+
+            if "Maximum: " in line:
+                list_split = line.split(" ")
+                globvar_AFMdata.z_max.append(list_split[-1])
+
+            if "Minimum: " in line:
+                list_split = line.split(" ")
+                globvar_AFMdata.z_min.append(list_split[-1])
+
+            if "Z Amplitude: " in line:
+                list_split = line.split(" ")
+                globvar_AFMdata.z_amplitude.append(list_split[-2])
+
+        file_p.close()
+
+    file_path = os.path.join(globvar_AFMdir.working_directory,AFM_file)
+    file_p = open(file_path, "rb")
+
+    for line in file_p:
+
+        line = line.decode("utf-8")
+
+        if "[Head Settings]" in line:
+            break
+
+        if "Angle: " in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.angle = line[position1:].rstrip()
+
+        if "Set Point: " in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.feedback = line[position1:].rstrip()
+
+        if "Signal Gain:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.gain_signal = line[position1:].rstrip()
+
+        if "Topography Bias:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.voltage = line[position1:].rstrip()
+
+        if "X Amplitude:" in line:
+            position1 = str.find(line, ":")+2
+            position2 = str.find(line, "nm")-1
+            globvar_AFMdata.x_size = line[position1:position2]
+
+        if "X Offset:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.x_off = line[position1:].rstrip()
+
+        if "X-Frequency:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.speed = line[position1:].rstrip()
+
+        if "XY Gain:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.gain_xy = line[position1:].rstrip()
+
+        if "Y Amplitude:" in line:
+            position1 = str.find(line, ":")+2
+            position2 = str.find(line, "nm")-1
+            globvar_AFMdata.y_size = line[position1:position2]
+
+        if "Y Offset:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.y_off = line[position1:].rstrip()
+
+        if "Z Gain:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.gain_z = line[position1:].rstrip()
+
+        if "Z Offset:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Integral:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.gain_int = line[position1:].rstrip()
+
+        if "Proportional:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.gain_prop = line[position1:].rstrip()
+
+        if "Tilt X:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Tilt Y:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Acquisition time:" in line:
+            position1 = str.find(line, ":")+2
+            position2 = str.rfind(line, ":")
+            globvar_AFMdata.date = line[position1:position2].rstrip()
+
+        if "Conversion Factor 01:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Conversion Offset 00:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Conversion Offset 01:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Force constant:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Head type:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Image Data Type:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Number of columns:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.x_pixel = line[position1:].rstrip()
+
+        if "Number of rows:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.y_pixel = line[position1:].rstrip()
+
+        if "X scanning direction:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Y scanning direction:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Head Name:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "X Calibration:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Y Calibration:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Acquired with version:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "CH 12:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "CH 13:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "CH 14:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Comments:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "DSP voltage range:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Dulcinea serial number:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Sampling frequency:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Saved with version:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Version:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Z Scale Factor:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+        if "Z Scale Offset:" in line:
+            position1 = str.find(line, ":")+2
+            globvar_AFMdata.NONE = None
+
+    # Close the Omicron par file ...
+    file_p.close()
+
+    return True

AFM_thumbs/Omicron_SCALA.py

@@ -0,0 +1,417 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import sys
+import os
+import numpy as np
+
+from AFM_thumbs.Variables import globvar_AFMdata
+from AFM_thumbs.Variables import globvar_AFMdir
+from AFM_thumbs.Variables import globvar_ThumbPara
+from AFM_thumbs.Variables import globvar_thumb_size_x
+from AFM_thumbs.Variables import globvar_thumb_size_y
+from AFM_thumbs.Variables import Omicron_SCALA_forward
+from AFM_thumbs.Variables import Omicron_SCALA_backward
+from AFM_thumbs.Linalg import linalg_plane_fit
+from AFM_thumbs.Linalg import linalg_line_fit
+from AFM_thumbs.Linalg import check_image_properties
+from AFM_thumbs.Thumbs import create_thumb_images
+from AFM_thumbs.Thumbs import create_thumb_spectra
+from AFM_thumbs.Initialize import initialize_AFM_data
+
+from AFM_thumbs.Channel import proceed_with
+from AFM_thumbs.Channel import line_fit
+from AFM_thumbs.Channel import plane_fit
+from AFM_thumbs.Channel import rename_channel
+
+def is_omicron_SCALA_file(directory, files):
+
+    list_directories_par = []
+
+    # A directroy is only interesting if there is at least
+    # one par and tf0 file.
+    FLAG_par = False
+    FLAG_tf0 = False
+    for filename in files:
+        file_name = os.path.join(directory, filename)
+        if FLAG_par == True and FLAG_tf0 == True:
+            if os.path.isdir(directory):
+                list_directories_par.append(directory)
+                break
+        if file_name[-4:] == ".par":
+            FLAG_par = True
+        if file_name[-4:] == ".tf0":
+            FLAG_tf0 = True
+
+    return list_directories_par
+
+
+def read_Omicron_SCALA_data(par_file):
+
+    initialize_AFM_data()
+
+    par_file_path = os.path.join(globvar_AFMdir.working_directory,par_file)
+    par_file_p = open(par_file_path, "r")
+
+    # The spectroscopy parameters are read ................................. .
+    for line in par_file_p:
+        if "; Spectroscopic Channels." in line:
+            break
+
+    for line in par_file_p:
+
+        if ";Parameter" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.spec_x_label.append(split_list[0])
+            if split_list[0] == "Z":
+                globvar_AFMdata.spec_x_unit.append("nm")
+            elif split_list[0] == "V":
+                globvar_AFMdata.spec_x_unit.append("V")
+            elif split_list[0] == "U":
+                globvar_AFMdata.spec_x_unit.append("V")
+            elif split_list[0] == "Macro":
+                globvar_AFMdata.spec_x_unit.append("a.u.")
+            else:
+                globvar_AFMdata.spec_x_unit.append("a.u.")
+        if ";Display name" in line:
+            pos = line.find(";")
+            line = line[34:pos]
+            line = line.replace(" ", "")
+            globvar_AFMdata.spec_y_label.append(line)
+        if ";Physical unit" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.spec_y_unit.append(split_list[0])
+        if ";Maximum value in physical unit" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.spec_y_factor.append(float(split_list[0]))
+        if ";Number of spectroscopy points" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.spec_points.append(split_list[0])
+        if ";Feedback On/Off" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.spec_feedback.append(split_list[0])
+        if ";Acquisition time per spectroscopy point" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.spec_acquisition.append(split_list[0])
+        if ";Delay time per spectroscopy point" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.spec_delay.append(split_list[0])
+        # Added on 2017-07-28
+        if ";Filename" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.spec_files.append(split_list[0])
+
+    # Go to the beginning of the file.
+    par_file_p.seek(0, 0)
+
+    # The image parameters are read ................................. .
+    for line in par_file_p:
+
+        # Jump over the spectroscopy part
+        if "; Spectroscopic Channels." in line:
+            for line in par_file_p:
+                if "; Measurement parameters." in line:
+                    break
+
+        if "Date" in line:
+            position1 = str.find(line, ":")
+            globvar_AFMdata.date = line[position1+2:-7]+", "+line[-7:-1]
+        if "Field X Size" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+2
+            globvar_AFMdata.x_size = line[position1:position2]
+        if "Field Y Size" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+2
+            globvar_AFMdata.y_size = line[position1:position2]
+        if "Image Size in X" in line:
+            position1 = str.find(line, ":")
+            globvar_AFMdata.x_pixel = line[position1+2:-1]
+        if "Image Size in Y" in line:
+            position1 = str.find(line, ":")
+            globvar_AFMdata.y_pixel = line[position1+2:-1]
+        if "X Offset" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+2
+            globvar_AFMdata.x_off = line[position1:position2]
+        if "Y Offset" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+2
+            globvar_AFMdata.y_off = line[position1:position2]
+        if "Measured Gap Voltage" not in line:
+            if "Gap Voltage" in line:
+                position1 = str.find(line, ":")+2
+                # Change 2017-06-25
+                # From '+2' to + '4' => two digits more for Ugap
+                position2 = -(len(line)-str.rfind(line, "."))+4
+                globvar_AFMdata.voltage = line[position1:position2]
+        if "Feedback Set" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+4
+            globvar_AFMdata.feedback = line[position1:position2]
+        if "Loop Gain" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+2
+            globvar_AFMdata.gain = line[position1:position2]
+        if "Scan Speed" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+2
+            globvar_AFMdata.speed = line[position1:position2]
+        if "Amplitude" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+2
+            globvar_AFMdata.amplitude = line[position1:position2]
+        if "Scan Angle" in line:
+            position1 = str.find(line, ":")+2
+            position2 = -(len(line)-str.rfind(line, "."))+2
+            globvar_AFMdata.angle = line[position1:position2]
+        if "Topographic Channel             :" in line:
+            position1 = str.find(line[34:], " ") + 34
+            if line[position1+1] is not " ":
+                position1 = position1 + 2
+            # 'rename_channel': see in Channel.py
+            rename_channel(line[34:position1])
+        if ";Physical unit" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.unit.append(split_list[0])
+        if ";Filename" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.datfile.append(split_list[0])
+            if Omicron_SCALA_backward in split_list[0]:
+                globvar_AFMdata.scandir.append("backward")
+            if Omicron_SCALA_forward in split_list[0]:
+                globvar_AFMdata.scandir.append("forward")
+        if "Maximum value in physical unit" in line:
+            split_list = line.rsplit()
+            globvar_AFMdata.z_factor.append(float(split_list[0]))
+
+    # We calculate now the total time of the spectroscopy in ms.
+    for tau, delay, points in zip(globvar_AFMdata.spec_acquisition,
+                                  globvar_AFMdata.spec_delay,
+                                  globvar_AFMdata.spec_points):
+        time = float(points) * ( float(tau) + float(delay) ) * 1000.0
+        globvar_AFMdata.spec_time.append("%.1f" % time)
+
+    # Close the Omicron par file ...
+    par_file_p.close()
+
+    return True
+
+
+def prepare_Omicron_SCALA_images(par_file):
+
+    # Loop over all channels. The channels are stored in the list
+    # 'globvar_AFMdata.datfile', which contains the file names (without path)
+    # as values.
+    for (image_nr, data_file) in enumerate(globvar_AFMdata.datfile):
+
+        # The definition 'proceed_with' is very important! It is 'connected'
+        # with the GUI of AFM_thumbs where one can choose if a channel in a
+        # specific scanning direction shall be represented in a pdf file or not.
+        if proceed_with(image_nr,globvar_AFMdata.scandir[image_nr]):
+
+            # Path to the image
+            data_file_name = data_file
+            data_file = os.path.join(globvar_AFMdir.working_directory,
+                                     data_file)
+
+            # Very strange 'if' but anyway ... if yes then simply continue.
+            if not os.path.isfile(data_file):
+                continue
+
+            # Image file name
+            image_name = data_file_name[:-4]
+            if image_name[2] == "_":
+                image_name = image_name[0:1]+"00"+image_name[1:]
+            if image_name[3] == "_":
+                image_name = image_name[0:1]+"0"+image_name[1:]
+            image_name = image_name + "_" + str(image_nr)
+
+            if globvar_ThumbPara.png:
+               image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                         image_name) + ".png"
+            else:
+                image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                          image_name) + ".jpeg"
+
+            # If the thumb image exists continue with next one ... .
+            # (Don't calculate a second time.)
+            if os.path.isfile(image_path):
+                continue
+
+            data = np.fromfile(file=data_file,dtype=np.int16)
+
+            size_x = int(globvar_AFMdata.x_pixel)
+            size_y = int(globvar_AFMdata.y_pixel)
+
+            # Data is cut by the definition check_image_properties.
+            #
+            # Note
+            # ====
+            # old_y_size and old_y_pixel are needed to temporarily store
+            # the original size in y (nm and pixel). This is then used
+            # at the end to put back the original values for
+            # globvar_AFMdata.y_size and globvar_AFMdata.y_pixel, for the
+            # text in the thumbs.
+            data, old_y_size, old_y_pixel = check_image_properties(data, data_file)
+            # If there is some corrupt image the y value, which has been
+            # changed in 'check_image_properties', needs to be updated.
+            size_y = int(globvar_AFMdata.y_pixel)
+
+            data = data.byteswap()
+            data = (globvar_AFMdata.z_factor[image_nr] * data) / 32767.0
+            globvar_AFMdata.z_average = np.average(data)
+
+            if globvar_ThumbPara.minimum_on_zero:
+                data = data - float(min(data))
+            data.shape = np.array([size_y, size_x])
+
+            # Mirror the data along y
+            data = np.flipud(data)
+
+            # Line fit
+            if line_fit(image_nr,globvar_AFMdata.scandir[image_nr]):
+                 data = linalg_line_fit(size_x, size_y, data)
+
+            # Plane fit
+            if plane_fit(image_nr,globvar_AFMdata.scandir[image_nr]):
+                 data = linalg_plane_fit(size_x, size_y, data)
+
+            create_thumb_images(data, image_nr, image_name, data_file_name)
+
+            if old_y_size != "" and old_y_pixel != "":
+                globvar_AFMdata.y_size  = old_y_size
+                globvar_AFMdata.y_pixel = old_y_pixel
+
+        else:
+            continue
+
+    return True
+
+
+def prepare_Omicron_SCALA_spectra_curves(par_file):
+
+    """
+    print(par_file)
+    print(globvar_AFMdata.spec_files,
+          globvar_AFMdata.spec_x_unit,
+          globvar_AFMdata.spec_x_label,
+          globvar_AFMdata.spec_y_unit,
+          globvar_AFMdata.spec_y_label,
+          globvar_AFMdata.spec_y_factor,
+          globvar_AFMdata.spec_points,
+          globvar_AFMdata.spec_feedback,
+          globvar_AFMdata.spec_acquisition,
+          globvar_AFMdata.spec_delay)
+    """
+
+    i = 0
+
+    for data_file in globvar_AFMdata.spec_files:
+
+        data_file_name = data_file
+        data_file = os.path.join(globvar_AFMdir.working_directory,data_file)
+
+        # If the file does not exist continue loop
+        if not os.path.isfile(data_file):
+            continue
+
+        # If the file is 0Byte large (empty) continue loop (Do not consider
+        # the file)
+        if os.stat(data_file)[6] == 0:
+            continue
+
+        Channel = int(data_file[-1:])
+
+        # Image name - Cut the suffix.
+        image_name = data_file_name[:-4]
+
+        # Put in some zeros after the 'm'.
+        if image_name[2] == "_":
+            image_name = image_name[0:1]+"00"+image_name[1:]
+        if image_name[3] == "_":
+            image_name = image_name[0:1]+"0"+image_name[1:]
+        # Suffix. New since 2017-07-28.
+        image_name = image_name + "_s0" + str(Channel)
+
+        if globvar_ThumbPara.png:
+            image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                         image_name) + ".png"
+        else:
+            image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                          image_name) + ".jpeg"
+
+        if os.path.isfile(image_path):
+            continue
+
+        data_file_p = open(data_file, "r")
+
+        for line in data_file_p:
+            if "END COORD" in line:
+                break
+
+        for line in data_file_p:
+            if "BEGIN" in line:
+                break
+
+        x_data_list = []
+        y_data_list = []
+
+        for line in data_file_p:
+
+            if "BEGIN" in line:
+                continue
+
+            x_data = []
+            y_data = []
+            for line in data_file_p:
+
+                if "END" in line:
+                    break
+
+                split_list = line.rsplit()
+
+                x_data.append(split_list[0])
+                y_data.append(globvar_AFMdata.spec_y_factor[i]
+                              * (float(split_list[1])/32767.0 ))
+
+            if x_data != [] and y_data != []:
+                x_data_list.append(x_data)
+                y_data_list.append(y_data)
+
+
+        # Close the Omicron file
+        data_file_p.close()
+
+        create_thumb_spectra(x_data_list,
+                             y_data_list,
+                             i,
+                             image_name,
+                             image_path,
+                             globvar_AFMdata.spec_y_label[i])
+        i += 1
+
+    return True

AFM_thumbs/PDF.py

@@ -0,0 +1,267 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import os
+import shutil
+import re
+
+from AFM_thumbs.Variables import globvar_AFMdata
+from AFM_thumbs.Variables import globvar_AFMdir
+from AFM_thumbs.Variables import globvar_ThumbPara
+from AFM_thumbs.Variables import globvar_spaces
+
+
+# This is the definiton which produces the pdf. We will make use of
+# graphicsmagic's 'gm montage' to realize the montage of thumbnail images in a
+# x/y pattern into png/jpeg sheets. After, imagemagick's 'convert' will be used
+# to create pdfs from the pngs/jpegs. Last, it is pdftk that puts together all
+# pdfs.
+#
+# May be, all this can be changed such that we either have only graphicsmagic
+# or imagemagick. Can we avoid also pdftk? Let's see in future.
+def prepare_PDFs():
+
+    # Decide over the image ending
+    if globvar_ThumbPara.png:
+        end = '.png'
+    else:
+        end = '.jpeg'
+
+    # Get the list of images in the thumbnail directory.
+    image_file_list = filter(lambda x: x.endswith(end),
+                             os.listdir(globvar_AFMdir.thumbnail_directory))
+    image_file_list = list(image_file_list)
+
+    if image_file_list == []:
+        print(globvar_spaces + "There are no images in the directory\n" +
+              globvar_spaces + globvar_AFMdir.thumbnail_directory + " !\n" +
+              globvar_spaces + "We leave this out ... .\n")
+        return False
+
+    # The list is well ordered thanks to the 001, 002, etc. order (see
+    # definitions in Omicron_SCALA.py, Nanotec_DULCINEA.py and RHK.py)
+    image_file_list.sort()
+
+    # Initialize the string for gm montage
+    # p: font size of the title, scale with number of images in one row
+    para_mon_p = globvar_ThumbPara.col * 8
+    str_tile = str(globvar_ThumbPara.col) + "x" + str(globvar_ThumbPara.row)
+
+    geo_x = max(globvar_ThumbPara.geometry_x)
+    geo_y = max(globvar_ThumbPara.geometry_y)
+
+    # First part of the string for graphicsmagick with standard parameters for
+    # all pdfs.
+    para_gm_mon_1 = ("gm montage -geometry " + str(geo_x) + "x" + str(geo_y) +
+                     " -pointsize " + str(para_mon_p) +
+                     " -title \"" + globvar_AFMdir.working_directory + "\"" +
+                     " -tile " + str_tile + " " )
+
+    # Initialization of the string for gm and convert
+    m_str = ""
+    r     = 0        # counter - total number of images on one page
+    q     = 0        # counter - number of pages
+    FLAG_first_spec_image = False
+
+    # This "for loop" takes up to 'globvar_ThumbPara.col*globvar_ThumbPara.row'
+    # images for one page. The code is done such that first single pdf pages
+    # are created in the thumbnail directory. The reason is that graphicsmagic
+    # is asking for too much RAM otherwise. After all, pdftk puts together
+    # all pdf pages (see below).
+    #
+    # This was strongly improved on 2017-07-28.
+    for image_file in image_file_list:
+
+        if r < globvar_ThumbPara.col*globvar_ThumbPara.row:
+
+            # If a spectroscopy image appears then ...
+            if "_s" in image_file:
+            #if image_file[9:10] == "s":
+
+                # For the first spectroscopy image:
+                if "_s00" in image_file:
+                #if image_file[9:11] == "s0":
+
+                    # Note that there is some spectroscopy data.
+                    FLAG_first_spec_image = True
+
+                    # Number of free slots in a row.
+                    if r % globvar_ThumbPara.col == 0:
+                        free_slots_in_row = 0
+                    else:
+                        free_slots_in_row = globvar_ThumbPara.col - (r % globvar_ThumbPara.col)
+
+    				# If there is still some place in the row, fill it
+    				# with dummies.
+                    if free_slots_in_row != 0:
+                        for i in range (free_slots_in_row):
+                            m_str = m_str + " \"" + \
+                                    os.path.join(globvar_AFMdir.thumbnail_directory,
+                                                 "dummy_image.png\"")
+                            r += 1
+            # ... if it is an image then ...
+            else:
+                # Uuups, the last image was obviously a spectroscopy image, now
+                # it is an SPM image. If so, new row:
+                if FLAG_first_spec_image == True:
+
+                    # Number of free slots in a row.
+                    if r % globvar_ThumbPara.col == 0:
+                        free_slots_in_row = 0
+                    else:
+                        free_slots_in_row = globvar_ThumbPara.col - (r % globvar_ThumbPara.col)
+
+    				# If there is still some place in the row, fill it
+    				# with dummies.
+                    if free_slots_in_row != 0:
+                        for i in range (free_slots_in_row):
+                            m_str = m_str + " \"" + \
+                                    os.path.join(globvar_AFMdir.thumbnail_directory,
+                                                 "dummy_image.png\"")
+                            r += 1
+
+                    FLAG_first_spec_image = False
+
+            # Put image and ...
+            m_str = m_str + " \"" + \
+                    os.path.join(globvar_AFMdir.thumbnail_directory,
+                                 image_file) + "\""
+            # ... image counter one up
+            r += 1
+
+        # globvar_ThumbPara.col*globvar_ThumbPara.row images are
+        # collected, or, end of image_file_list. So then do:
+        else:
+            # Create only one page first!
+            # Reason for this: If about 20 pages shall be created the pages
+            # cannot be stored within one pdf because Graphicsmagick is
+            # asking for too much RAM!!! So, page after page ...
+
+            # Number of pages
+            q += 1
+
+            # Graphicsmagic - montage
+            last_part = "_%.02d" + end + "\""
+            image_string = (para_gm_mon_1 + m_str + " \"" + \
+                            os.path.join(globvar_AFMdir.thumbnail_directory,
+                                         globvar_AFMdir.data_directory_name) + \
+                            last_part % q)
+
+            os.system(image_string)
+
+            # Imagemagic - pdf
+            middle_part = "_%.02d" + end + "\" \""
+            pdf_string  = ("convert -density 300 -compress JPEG -quality " + \
+                           str(globvar_ThumbPara.jpeg) + " \"" + \
+                           os.path.join(globvar_AFMdir.thumbnail_directory,
+                                        globvar_AFMdir.data_directory_name) + \
+                           middle_part%q + \
+                           os.path.join(globvar_AFMdir.thumbnail_directory,
+                                        globvar_AFMdir.data_directory_name) + \
+                           "_%.03d.pdf\" "%q )
+
+            os.system(pdf_string)
+
+            # Initialize and put in the first image
+            r = 1
+            m_str = "\""+os.path.join(globvar_AFMdir.thumbnail_directory,
+                                      image_file) + "\""
+
+            # If the image is a 'first' spectroscopy image then ...
+            if "_s00" in image_file:
+            # if image_file[9:11] == "s00":
+                # Note that there is some spectroscopy data.
+                FLAG_first_spec_image = True
+
+
+    # if there are remaining pages (r > 1) put them on one page
+    if r > 1:
+
+        q += 1
+
+        last_part = "_%.02d" + end + "\""
+        image_string = (para_gm_mon_1+m_str + " \"" + \
+                        os.path.join(globvar_AFMdir.thumbnail_directory,
+                                     globvar_AFMdir.data_directory_name) + \
+                        last_part % q )
+        os.system(image_string)
+
+        middle_part = "_%.02d" + end + "\" \""
+        pdf_string  = ("convert -density 300 -compress JPEG -quality " + \
+                       str(globvar_ThumbPara.jpeg) + " \"" + \
+                       os.path.join(globvar_AFMdir.thumbnail_directory,
+                                    globvar_AFMdir.data_directory_name) + \
+                       middle_part%q + \
+                       os.path.join(globvar_AFMdir.thumbnail_directory,
+                                    globvar_AFMdir.data_directory_name) + \
+                       "_%.03d.pdf\" "%q )
+        os.system(pdf_string)
+
+
+
+    #
+    #
+    # Prepare the command string for pdftk for connecting all pdf pages.
+    #
+    #
+
+    # This following 'directory thing' was done for pdftk under Windows XP.
+    # First, we save the directory of AFM_thumbs and ...
+    AFM_thumbs_directory = os.getcwd()
+    # ... then, we go inside the thumbnail directory, and later we put the
+    # system path back onto 'AFM_thumbs_directory' (see below).
+    os.chdir(globvar_AFMdir.thumbnail_directory)
+
+    # Apply pdftk for putting together the pdfs.
+    if globvar_AFMdir.pdf_path == "":
+        pdf_string = ("pdftk *.pdf cat output \"" + \
+                      globvar_AFMdir.working_directory + \
+                      globvar_ThumbPara.extension + ".pdf\"" )
+    else:
+        pdf_string = ("pdftk *.pdf cat output \"" + \
+                      os.path.join(globvar_AFMdir.pdf_path,
+                                   globvar_AFMdir.data_directory_name) + \
+                      globvar_ThumbPara.extension+".pdf\"" )
+    # Execute pdftk
+    os.system(pdf_string)
+
+    # Now, we go back into the directory of AFM_thumbs
+    os.chdir(AFM_thumbs_directory)
+
+    # If true, delete all thumbnails and pdfs and finally the thumbnail
+    # directory
+    if globvar_ThumbPara.thumbs_after:
+        delete_string = globvar_AFMdir.thumbnail_directory
+        shutil.rmtree(delete_string)
+    else:
+        file_list = os.listdir(globvar_AFMdir.thumbnail_directory)
+        for f in file_list:
+            if f.endswith(".pdf"):
+                os.remove(os.path.join(globvar_AFMdir.thumbnail_directory,f))
+            elif f.endswith(end):
+                if re.search(globvar_AFMdir.data_directory_name,f):
+                    os.remove(os.path.join(globvar_AFMdir.thumbnail_directory,f))
+

AFM_thumbs/RHK.py

@@ -0,0 +1,674 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import sys
+import os
+import struct
+import numpy
+import math
+import re
+
+from AFM_thumbs.Variables import globvar_AFMdata
+from AFM_thumbs.Variables import globvar_AFMdir
+from AFM_thumbs.Variables import globvar_ThumbPara
+from AFM_thumbs.Variables import globvar_spaces
+from AFM_thumbs.Variables import RHK_must_exist
+from AFM_thumbs.Variables import RHK_PositionCounter
+from AFM_thumbs.Variables import globvar_thumb_size_x
+from AFM_thumbs.Variables import globvar_thumb_size_y
+from AFM_thumbs.Linalg import check_image_properties
+from AFM_thumbs.Thumbs import create_thumb_images
+from AFM_thumbs.Thumbs import create_thumb_spectra
+from AFM_thumbs.Thumbs import spectra_text
+from AFM_thumbs.Linalg import linalg_plane_fit
+from AFM_thumbs.Linalg import linalg_line_fit
+from AFM_thumbs.Initialize import initialize_AFM_data
+
+from AFM_thumbs.Channel import proceed_with
+from AFM_thumbs.Channel import line_fit
+from AFM_thumbs.Channel import plane_fit
+from AFM_thumbs.Channel import rename_channel
+
+# Method to determine whether there are RHK files.
+def is_RHK_file(directory, files):
+
+    list_directories_sm4 = []
+
+    # A directroy is only interesting if there is at least
+    # one SM4 file.
+    FLAG = False
+    for filename in files:
+        file_name = os.path.join(directory, filename)
+        if file_name[-4:] in RHK_must_exist:
+            FLAG = True
+        if FLAG == True:
+            if os.path.isdir(directory):
+                list_directories_sm4.append(directory)
+                break
+
+    return list_directories_sm4
+
+# This method reads out the scan information.
+# RHK technology stores all measurement data in one file with no order!
+# Because of this the plane- and linefitting settings doesn't matter in the
+# current version of this method
+def read_RHK_data(SM4_file):
+
+    # _______________________________________________________ Direction check
+
+    initialize_AFM_data()
+
+    sm4_file_path = os.path.join(globvar_AFMdir.working_directory,SM4_file)
+
+    with open(sm4_file_path, "rb") as sm4_datafile: # open file
+
+        sm4_file = sm4_datafile.read()
+
+    globvar_AFMdata.datfile.append(sm4_file_path)
+
+    # ___________________________________________ Reading of the File Header
+
+    # Version Check
+    current_position = 38
+    version = sm4_file[0:current_position]
+    if not version[2:-2:2] == "STiMage 005.004 1":
+        version_error = "This method was written on base of SM4 Version " \
+                        "\'STiMage 005.004 1\'. The results of any other " \
+                        "version can differ from the expected one. The current " \
+                        "file version: "
+        print(globvar_spaces + version_error + version.decode("utf-8"))
+        print
+
+    # File Header information
+    total_page_count = struct.unpack('i', sm4_file[current_position: \
+                                    current_position+4])[0]
+    current_position += 4
+    object_list_count = struct.unpack('i', sm4_file[current_position: \
+                                    current_position+4])[0]
+    current_position += 4
+
+    # Check the Ocject Field size
+    if not struct.unpack('i', sm4_file[current_position: \
+    current_position+4])[0] == 12:
+        obJect_field_error = "Wrong size of object field. " \
+                             "This may cause a problem."
+        print(globvar_spaces + obJect_field_error)
+        print
+
+    current_position += 12
+
+    # Create Array for the Object List Items
+    objects = numpy.zeros((object_list_count, 3))
+
+    for i in range(object_list_count):
+        objects[i,0] = struct.unpack('i', sm4_file[current_position: \
+                                    current_position+4])[0] # tape
+        current_position += 4
+        objects[i,1] = struct.unpack('i', sm4_file[current_position: \
+                                    current_position+4])[0] # offset
+        current_position += 4
+        objects[i,2] = struct.unpack('i', sm4_file[current_position: \
+                                    current_position+4])[0] # size
+        current_position += 4
+
+    # _________________________________________ Content of PAGE INDEX HEADER
+
+    # Page Count Check
+    page_count = struct.unpack('i', sm4_file[current_position: \
+                                current_position+4])[0]
+
+    current_position += 4
+    if not page_count == total_page_count:
+        page_count_error = "The total number of pages is not the same as " \
+        "the number of pages. Some data may be left out or doubled."
+        print(globvar_spaces + page_count_error)
+        print
+
+    page_object_list_count  = struct.unpack('i', sm4_file[current_position: \
+                                            current_position+4])[0]
+    current_position += 4
+
+    current_position += 8
+
+    # Page Index Object
+    index_array = numpy.zeros((page_object_list_count, 3))
+
+    for i in range(page_object_list_count):
+        index_array[i,0] = struct.unpack('i', sm4_file[current_position: \
+                                        current_position+4])[0];
+        current_position += 4
+        # beginning of the Page index Array
+        index_array[i,1] = struct.unpack('i', sm4_file[current_position: \
+                                        current_position+4])[0];
+        current_position += 4
+        index_array[i,2] = struct.unpack('i', sm4_file[current_position: \
+                                        current_position+4])[0];
+        current_position += 4
+
+    # Page ID Offset
+    pageindex_page_id_offset = 16 # Page ID hat Laenge 16
+
+    # for-loop over all channels
+    for channel in range(page_count):
+
+        # Determining the startpoint
+        if channel is 0:
+            next_page_index_array_offset = 0
+            current_position = int(index_array[0,1]) + pageindex_page_id_offset
+        else:
+            current_position = int(next_page_index_array_offset) \
+                                    + pageindex_page_id_offset
+
+        # Page Index Array
+        current_position += 4
+
+        # Page Type
+        page_data_type = struct.unpack('i', sm4_file \
+                                    [current_position:current_position+4])[0]
+        current_position += 4
+
+        pageindex_object_list_count = struct.unpack('i', sm4_file \
+                                    [current_position:current_position+4])[0]
+        current_position += 4
+        current_position += 4
+
+        # Create an array for the Object List Items
+        array_objects = numpy.zeros((pageindex_object_list_count, 3))
+
+        for i in range(pageindex_object_list_count):
+            array_objects[i,0] = struct.unpack('i', sm4_file[current_position \
+                                            :current_position+4])[0] # tape
+            current_position += 4
+            array_objects[i,1] = struct.unpack('i', sm4_file[current_position \
+                                            :current_position+4])[0] # offset
+            current_position += 4
+            array_objects[i,2] = struct.unpack('i', sm4_file[current_position \
+                                            :current_position+4])[0]  # size
+            current_position += 4
+
+        # Request of the current position for the start of the next loop
+        next_page_index_array_offset = current_position
+
+        # Page header
+        current_position = int(array_objects[0,1])+4
+        page_type = str(struct.unpack('i', sm4_file[current_position: \
+                                            current_position+4])[0])
+
+        # Pixel
+        current_position = int(array_objects[0,1])+24
+        globvar_AFMdata.x_pixel = str(struct.unpack('i',
+                            sm4_file[current_position:current_position+4])[0])
+        current_position += 4
+        globvar_AFMdata.y_pixel = str(struct.unpack('i',
+                            sm4_file[current_position:current_position+4])[0])
+        current_position += 4
+
+        # Scan direction
+        current_position = int(array_objects[0,1])+36
+        scan_direction = struct.unpack('i',
+                            sm4_file[current_position:current_position+4])[0];
+        current_position += 4
+
+        if scan_direction == 0:
+            globvar_AFMdata.scandir.append("right")
+        elif scan_direction == 1:
+            globvar_AFMdata.scandir.append("left")
+        elif scan_direction == 2:
+            globvar_AFMdata.scandir.append("up")
+        elif scan_direction == 3:
+            globvar_AFMdata.scandir.append("down")
+
+        current_position += 4
+        data_size = struct.unpack('i', sm4_file[current_position: \
+                                current_position+4])[0]
+        current_position += 4
+
+        # Maximum z-Values
+        globvar_AFMdata.z_min.append(struct.unpack('=l',
+                            sm4_file[current_position:current_position+4])[0])
+        current_position += 4
+        globvar_AFMdata.z_max.append(struct.unpack('=l',
+                            sm4_file[current_position:current_position+4])[0])
+        current_position += 4
+
+        # Sizes
+        globvar_AFMdata.x_size = struct.unpack('f', sm4_file[current_position:\
+                                                    current_position+4])[0]
+        current_position += 4
+
+        globvar_AFMdata.y_size = struct.unpack('f', sm4_file[current_position:\
+                                                    current_position+4])[0]
+        current_position += 4
+
+        globvar_AFMdata.z_factor.append(struct.unpack('f',
+                            sm4_file[current_position:current_position+4])[0])
+        current_position += 4
+
+        # Offsets
+        current_position += 4
+        globvar_AFMdata.x_off = struct.unpack('f', sm4_file[current_position: \
+                                                    current_position+4])[0]
+        current_position += 4
+        globvar_AFMdata.y_off = struct.unpack('f', sm4_file[current_position: \
+                                                    current_position+4])[0]
+        current_position += 4
+
+        # Speed
+        current_position += 4
+
+        globvar_AFMdata.speed = struct.unpack('f', sm4_file[current_position: \
+                                current_position+4])[0] * \
+                                int(globvar_AFMdata.x_pixel) * 1000
+        current_position += 4
+
+        # Voltage
+        globvar_AFMdata.voltage = "{0:.1f}".format(struct.unpack('f',
+                                    sm4_file[current_position: \
+                                    current_position+4])[0])
+        current_position += 4
+
+        # Angle
+
+        current_position += 4
+        globvar_AFMdata.angle = "{0:.1f}".format(struct.unpack('f', sm4_file[ \
+                                    current_position:current_position+4])[0])
+        current_position += 4
+
+        # Page Header Object List
+        current_position += 12
+        page_header_object_list_count = struct.unpack('i', sm4_file \
+                                    [current_position:current_position+4])[0]
+        current_position += 4
+
+        # Go to the page header object list.
+        current_position = int(array_objects[0,1]) + int(array_objects[0,2])
+
+        array_header_objects = numpy.zeros((page_header_object_list_count, 3))
+
+        for i in range(page_header_object_list_count):
+            array_header_objects[i,0] = struct.unpack('i', \
+                            sm4_file[current_position:current_position+4])[0]
+            current_position += 4
+            array_header_objects[i,1] = struct.unpack('i', \
+                            sm4_file[current_position:current_position+4])[0]
+            current_position += 4
+            array_header_objects[i,2] = struct.unpack('i', \
+                            sm4_file[current_position:current_position+4])[0]
+            current_position += 4
+
+        # Go to the text string to get the title.
+        current_position = int(array_header_objects[0,1])
+        str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                    current_position+2])[0]
+        current_position += 2
+        channel_name = sm4_file[current_position:current_position+str_length:2]
+        current_position += str_length
+
+        # __________________________________________________ Check the title
+
+        # Substitut all whitespaces with underscore.
+        channel_name = str(re.sub('\s', '_', channel_name.decode("utf-8")))
+
+        # Search all special characters and change the title.
+        if re.search('\W', channel_name):
+            channel_name_index = re.search('\W', channel_name).start()
+            channel_name = channel_name[:channel_name_index]
+
+        # If there are underscores at the end of the title, eliminate them.
+        Space = True
+        while Space:
+            if channel_name[-1] == "_":
+                channel_name = channel_name[:-1]
+            else:
+                Space = False
+
+        # Replace all underscores with a simple whitespace
+        channel_name = re.sub('_', ' ', channel_name)
+
+        # Add the channel name.
+        rename_channel(channel_name)
+
+        # Skip next 4 strings.
+        for i in range(4):
+            str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                        current_position+2])[0]
+            current_position += 2
+            current_position += str_length
+
+        # date
+        str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                    current_position+2])[0]
+        current_position += 2
+        globvar_AFMdata.date = sm4_file[current_position: \
+                                current_position+str_length:2].decode("utf-8")
+        current_position += str_length
+
+        # time
+        str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                          current_position+2])[0]
+        current_position += 2
+
+        globvar_AFMdata.date += ", " + sm4_file[current_position: \
+                                       current_position+str_length:2].decode("utf-8")
+        current_position += str_length
+
+        # Units
+        str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                     current_position+2])[0]
+        current_position += 2
+        globvar_AFMdata.spec_x_unit.append(sm4_file[current_position: \
+                                           current_position+str_length:2].decode("utf-8"))
+
+        # Clemens Barth, 2016-01-15 ........................
+        #
+        # There is a problem with the unit for y! The following code
+        # needs to be revized.
+
+        current_position += str_length
+        str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                     current_position+2])[0]
+        current_position += 2
+        globvar_AFMdata.spec_y_unit.append(sm4_file[current_position: \
+                                           current_position+str_length:2].decode("utf-8"))
+
+        #print(globvar_AFMdata.spec_x_unit, globvar_AFMdata.spec_y_unit)
+
+        # ...................... until here
+
+        current_position += str_length
+        str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                                    current_position+2])[0]
+        current_position += 2
+        globvar_AFMdata.unit.append(sm4_file[current_position: \
+                                    current_position+str_length:2].decode("utf-8"))
+        current_position += str_length
+
+        # Topography scale is in nm.
+        if globvar_AFMdata.channel[-1].find("Topography") != -1 and \
+            globvar_AFMdata.unit[-1].find("m") != -1:
+            globvar_AFMdata.z_factor[-1] = float(globvar_AFMdata.z_factor[-1] \
+                                                *math.pow(10,9))
+            globvar_AFMdata.unit[-1] = "nm"
+
+        # Labels
+        str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                                    current_position+2])[0]
+        current_position += 2
+        globvar_AFMdata.spec_x_label.append(sm4_file[current_position: \
+                                            current_position+str_length:2].decode("utf-8"))
+        current_position += str_length
+        str_length = 2*struct.unpack('h', sm4_file[current_position: \
+                                                    current_position+2])[0]
+        current_position += 2
+        globvar_AFMdata.spec_y_label.append(sm4_file[current_position: \
+                                            current_position+str_length:2].decode("utf-8"))
+        current_position += str_length
+
+        # _____________________________________________________ Prepare image
+
+        if channel%2 == 0:
+            direction = "forward"
+        elif channel%2 != 0:
+            direction = "backward"
+
+        if int(page_data_type) != 0:
+            prepare_RHK_spektra(sm4_file_path, SM4_file,
+                            channel,
+                            int(array_objects[1,1]))
+
+        elif int(page_type) in [16,38,39]:
+            if globvar_ThumbPara.spektra == 1:
+                prepare_RHK_spektra(sm4_file_path,
+                                SM4_file, channel,
+                                int(array_objects[1,1]))
+
+        else:
+            if proceed_with(channel,direction):
+                prepare_RHK_images(sm4_file_path, SM4_file,
+                                channel,
+                                int(array_objects[1,1]))
+
+            else:
+                 continue
+
+    return True
+
+
+# This methods reads out the measurement data and prepares it for the image.
+def prepare_RHK_images(file_path, file_name, image_nr, data_off):
+
+    # If the thumb image exists continue with the next one ... .
+    # (Don't calculate a second time.)
+    if image_nr%2 == 0:
+        direction = "forward"
+    elif image_nr%2 != 0:
+        direction = "backward"
+
+    picture_file_name = globvar_AFMdata.channel[-1].replace(" ","_") + "_" + \
+                        direction + "_" + file_name
+
+    # Add the specific number of the channel.
+    # Fill empty space with zeros.
+    if int(RHK_PositionCounter.position / 10) == 0:
+        picture_file_name = "000" + str(RHK_PositionCounter.position) + \
+                            "_" + picture_file_name
+        RHK_PositionCounter.add()
+
+    elif int(RHK_PositionCounter.position / 10) < 10:
+        picture_file_name = "00" + str(RHK_PositionCounter.position) + \
+                            "_" + picture_file_name
+        RHK_PositionCounter.add()
+
+    elif int(RHK_PositionCounter.position / 10) < 100:
+        picture_file_name = "0" + str(RHK_PositionCounter.position) + \
+                            "_" + picture_file_name
+        RHK_PositionCounter.add()
+
+    else:
+        picture_file_name = str(RHK_PositionCounter.position) + \
+                            "_" + picture_file_name
+        RHK_PositionCounter.add()
+
+    if globvar_ThumbPara.png:
+        image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                  picture_file_name) + ".png"
+    else:
+        image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                  picture_file_name) + ".jpeg"
+
+    if os.path.isfile(image_path):
+        return
+
+    # Format Information
+    size_x = int(globvar_AFMdata.x_pixel)
+    size_y = int(globvar_AFMdata.y_pixel)
+
+    globvar_AFMdata.speed = "{0:.1f}".format(globvar_AFMdata.speed)
+
+    globvar_AFMdata.x_size = int(globvar_AFMdata.x_pixel) * \
+                            float(globvar_AFMdata.x_size)*math.pow(10,9)
+    globvar_AFMdata.y_size = int(globvar_AFMdata.y_pixel) * \
+                            float(globvar_AFMdata.y_size)*math.pow(10,9)
+
+    mirror_x = False
+    mirror_y = False
+
+    if globvar_AFMdata.x_size < 0:
+        mirror_x = True
+    if globvar_AFMdata.y_size < 0:
+        mirror_y = True
+
+    globvar_AFMdata.x_size = "{0:.1f}".format(abs(globvar_AFMdata.x_size))
+    globvar_AFMdata.y_size = "{0:.1f}".format(abs(globvar_AFMdata.y_size))
+
+    globvar_AFMdata.x_off = "{0:.1f}".format(float(globvar_AFMdata.x_off) * \
+                                                                math.pow(10,9))
+    globvar_AFMdata.y_off = "{0:.1f}".format(float(globvar_AFMdata.y_off) * \
+                                                                math.pow(10,9))
+
+    # Read the position of the binary data.
+    with open(file_path, "rb") as sm4_file: # open file
+
+        # Go to position in the file.
+        sm4_file.seek(data_off,0)
+
+        # Go straight to numpy data (no buffering).
+        data = numpy.fromfile(sm4_file, dtype = numpy.int32,
+                              count = size_x*size_y)
+
+    # Check if the image really has the expected size.
+    # 'size_x*size_y'.
+    # old_y_size and old_y_pixel are needed to temporarily store
+    # the original size in y (nm and pixel). This is then used
+    # at the end to put back the original values for
+    # globvar_AFMdata.y_size and globvar_AFMdata.y_pixel, for the
+    # text in the thumbs.
+    data, old_y_size, old_y_pixel = check_image_properties(data,
+                                                 globvar_AFMdata.datfile[-1])
+
+    # If there is some corrupt image the y value, which has been
+    # changed in check_image_properties, needs to be updated.
+    size_y = int(globvar_AFMdata.y_pixel)
+
+    # First, transform the integers into floats. This is needed for all
+    # mathematical operations.
+    data = data.astype(float)
+
+    # Average value
+    average = numpy.average(data)
+
+    data = data * globvar_AFMdata.z_factor[-1]
+    # Calibrate the avergae value and write it into the globvar_AFMdata
+    # structure.
+    globvar_AFMdata.z_average = average * globvar_AFMdata.z_factor[-1]
+
+    # Make now a 2D array.
+    data.shape = numpy.array([size_y, size_x])
+
+    # Mirror the data
+    if mirror_x:
+        data = numpy.fliplr(data)
+    if not mirror_y:
+        data = numpy.flipud(data)
+
+    # Fitting
+    if line_fit(image_nr,direction):
+        data = linalg_line_fit(size_x, size_y, data)
+
+    if plane_fit(image_nr,direction):
+        data = linalg_plane_fit(size_x, size_y, data)
+
+    create_thumb_images(data, image_nr, picture_file_name, file_name)
+
+    if old_y_size != "" and old_y_pixel != "":
+        globvar_AFMdata.y_size  = old_y_size
+        globvar_AFMdata.y_pixel = old_y_pixel
+
+    return True
+
+
+def prepare_RHK_spektra(file_path, file_name, image_nr, data_off):
+
+    picture_file_name = globvar_AFMdata.channel[-1].replace(" ","_") + "_" + \
+                        file_name
+
+    # Add the specific number of the channel.
+    # Fill empty space with zeros.
+    if int(RHK_PositionCounter.position / 10) == 0:
+        picture_file_name = "000" + str(RHK_PositionCounter.position) + \
+                            "_" + picture_file_name
+        RHK_PositionCounter.add()
+
+    elif int(RHK_PositionCounter.position / 10) < 10:
+        picture_file_name = "00" + str(RHK_PositionCounter.position) + \
+                            "_" + picture_file_name
+        RHK_PositionCounter.add()
+
+    elif int(RHK_PositionCounter.position / 10) < 100:
+        picture_file_name = "0" + str(RHK_PositionCounter.position) + \
+                            "_" + picture_file_name
+        RHK_PositionCounter.add()
+
+    else:
+        picture_file_name = str(RHK_PositionCounter.position) + \
+                            "_" + picture_file_name
+        RHK_PositionCounter.add()
+
+    if globvar_ThumbPara.png:
+        image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                  picture_file_name) + ".png"
+    else:
+        image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                  picture_file_name) + ".jpeg"
+
+    if os.path.isfile(image_path):
+        return
+
+    # Format Text
+    globvar_AFMdata.spec_points = [0]
+    globvar_AFMdata.spec_points[0] = globvar_AFMdata.x_pixel
+
+    globvar_AFMdata.spec_acquisition.append(
+                    "{0:.6f}".format(globvar_AFMdata.speed / math.pow(10,6)))
+    globvar_AFMdata.spec_delay = [""]
+    globvar_AFMdata.spec_feedback = [""]
+
+    # Read the position of the binary data.
+    size_x = int(globvar_AFMdata.x_pixel)
+    size_y = int(globvar_AFMdata.y_pixel)
+
+    x_data_list = []
+    y_data_list = []
+
+    x_data = [(x*abs(float(globvar_AFMdata.x_size))) + \
+                        float(globvar_AFMdata.x_off) for x in range(size_x)]
+
+    with open(file_path, "rb") as sm4_file: # open file
+
+        # Go to position in the file.
+        sm4_file.seek(data_off,0)
+
+        # Go straight to numpy data (no buffering).
+        for i in range(size_y):
+
+            x_data_list.append(x_data)
+
+            y_data = numpy.fromfile(sm4_file, dtype = numpy.int32,
+                                   count = size_x)
+
+            y_data = y_data.astype(float)
+            y_data =  y_data*globvar_AFMdata.z_factor[-1]
+            y_data += globvar_AFMdata.y_off
+            y_data_list.append(y_data)
+
+        create_thumb_spectra(x_data_list,
+                             y_data_list,
+                             0,
+                             picture_file_name,
+                             image_path,
+                             globvar_AFMdata.channel[-1])
+
+    return True

AFM_thumbs/SPECS_Nanonis.py

@@ -0,0 +1,947 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import sys
+import os
+import numpy as np
+
+from AFM_thumbs.Variables  import globvar_AFMdata
+from AFM_thumbs.Variables  import globvar_AFMdir
+from AFM_thumbs.Variables  import globvar_ThumbPara
+from AFM_thumbs.Variables  import globvar_thumb_size_x
+from AFM_thumbs.Variables  import globvar_thumb_size_y
+from AFM_thumbs.Variables  import SPECS_Nanonis_images_must_exist
+from AFM_thumbs.Variables  import SPECS_Nanonis_spectroscopy_must_exist
+from AFM_thumbs.Linalg     import linalg_plane_fit
+from AFM_thumbs.Linalg     import linalg_line_fit
+from AFM_thumbs.Linalg     import check_image_properties
+from AFM_thumbs.Thumbs     import create_thumb_images
+from AFM_thumbs.Thumbs     import create_thumb_spectra
+from AFM_thumbs.Initialize import initialize_AFM_data
+
+from AFM_thumbs.Channel    import proceed_with
+from AFM_thumbs.Channel    import line_fit
+from AFM_thumbs.Channel    import plane_fit
+from AFM_thumbs.Channel    import rename_channel
+
+
+# _________________________________________________________________ Definitions
+
+def is_SPECS_Nanonis_file(directory, files):
+
+    list_directories = []
+
+    # A directroy is listed if there is at least one Nanonis file.
+    for filename in files:
+        file_name = os.path.join(directory, filename)
+
+        if os.path.splitext(filename)[1] == SPECS_Nanonis_images_must_exist:
+            if os.path.isdir(directory):
+                list_directories.append(directory)
+                break
+
+        if os.path.splitext(filename)[1] == SPECS_Nanonis_spectroscopy_must_exist:
+            if os.path.isdir(directory):
+                list_directories.append(directory)
+                break
+
+
+    return list_directories
+
+
+# This is the definition, which stores diverse parameters from the header of
+# an .sxm into the parameter class of AFM_thumbs.
+def read_SPECS_Nanonis_image_data(nanonis_file):
+
+    # # Print the entire header.
+    # nanonis_file_path = os.path.join(globvar_AFMdir.working_directory, nanonis_file)
+    # nanonis_file_p = open(nanonis_file_path, "rb")
+    # line = ""
+    # while line!=b':SCANIT_END:':
+    #     line = nanonis_file_p.readline().rstrip()
+    #     print(line)
+    # nanonis_file_p.close()
+
+    initialize_AFM_data()
+
+    # Open the Nanonis file.
+    nanonis_file_path = os.path.join(globvar_AFMdir.working_directory,
+                                     nanonis_file)
+    nanonis_file_p = open(nanonis_file_path, "rb")
+
+    # Read until the end of the header and convert all into string.
+    line_ = ""
+    list_line = []
+    while line_!=b':SCANIT_END:':
+        line_ = nanonis_file_p.readline().rstrip()
+        list_line.append(line_.decode("utf-8"))
+
+    # Offset position of the data inside the sxm file. It is said that these
+    # are normally 4 bytes after the identifier ':SCANIT_END:'. However,
+    # the following seems to be the 'correct way'.
+    while nanonis_file_p.read(1)!=b'\x1a':
+        pass
+    assert nanonis_file_p.read(1)==b'\x04'
+
+    # Note the offset and ...
+    data_offset = nanonis_file_p.tell()
+    # ... close the Nanonis file ...
+    nanonis_file_p.close()
+
+    # Read now the header in 'list_line'.
+    for i in range(len(list_line)):
+
+        if ":REC_DATE:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().strip()
+            globvar_AFMdata.date = line
+        if ":REC_TIME:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().strip()
+            globvar_AFMdata.date += ", " + line
+        if ":SCAN_FILE:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().strip()
+            globvar_AFMdata.datfile = [line]
+        if ":SCAN_RANGE:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().split(' ')
+            line = [x for x in line if x]
+            # The unit of x and y in nm.
+            x_size = float(line[0]) / 1e-9
+            y_size = float(line[1]) / 1e-9
+            globvar_AFMdata.x_size = "%.1f" % x_size
+            globvar_AFMdata.y_size = "%.1f" % y_size
+        if ":SCAN_PIXELS:" in list_line[i]:
+            line = list_line[i+1].rstrip().split(' ')
+            line = [x for x in line if x]
+            globvar_AFMdata.x_pixel = line[0]
+            globvar_AFMdata.y_pixel = line[1]
+        if ":SCAN_OFFSET:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().split(' ')
+            line = [x for x in line if x]
+            # The unit of x and y in nm.
+            x_off = float(line[0]) / 1e-9
+            y_off = float(line[1]) / 1e-9
+            globvar_AFMdata.x_off = "%.1f" % x_off
+            globvar_AFMdata.y_off = "%.1f" % y_off
+        if ":SCAN_ANGLE:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().strip()
+            globvar_AFMdata.angle = str(float(line))
+        if ":SCAN_DIR:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().strip()
+            globvar_AFMdata.scan_updown = line
+        if ":SCAN_TIME:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().split(' ')
+            line = [x for x in line if x]
+            globvar_AFMdata.speed = float(line[0])
+            #   :ACQ_TIME:
+            #          255.6
+            #   :SCAN_TIME:
+            #          4.992E-1             4.992E-1
+        if ":BIAS:" in list_line[i]:
+            i += 1
+            line = list_line[i].rstrip().strip()
+            globvar_AFMdata.voltage = str(float(line))
+        if ":Z-CONTROLLER:" in list_line[i]:
+            #   :Z-CONTROLLER:
+            #   Name           on   Setpoint     P-gain       I-gain         T-const
+            #   log Current    1    2.000E-10 A  2.937E-11 m  3.865E-7 m/s   7.599E-5 s
+            i += 2
+            line = list_line[i].rstrip()
+            line = line.split("	")
+            line = [x for x in line if x]
+            globvar_AFMdata.measurement_type = line[0]
+            # The unit of the feedback is needed further below
+            globvar_AFMdata.feedback = line[2]
+            # Remove the units of the gain
+            globvar_AFMdata.gain_prop = line[3].split(' ')[0]
+            globvar_AFMdata.gain_int = line[4].split(' ')[0]
+            #globvar_AFMdata.gain = line[5]
+        if ":DATA_INFO:" in list_line[i]:
+            #      :DATA_INFO:
+            #      	Channel  Name               Unit	Direction	Calibration   Offset
+            #       14       Z                  m       both        1.400E-7      0.000E+0
+            #       0C       Current            A       both        3.000E-10     2.218E-12
+            #       16       OC_D1_Phase        deg     both        1.800E+1      0.000E+0
+            #       17       OC_D1_Amplitude    m       both        1.000E-9      0.000E+0
+            #       18       OC_M1_Freq._Shift  Hz      both        7.812E+3      0.000E+0
+            #       19       OC_M1_Excitation   V       both        1.000E-2      0.000E+0
+
+            #       The channels with the following  names are not supported.
+            #
+            #       Bias
+            #       Laser_power_mon.
+            #       Laser_Setpoint
+            #       Output_3
+            #       Output_4
+            #       X
+            #       Y
+            #       Output_8
+            channels_not_supported = ["Bias",
+                                      "Laser_power_mon.",
+                                      "Laser_Setpoint",
+                                      "Output_3",
+                                      "Output_4",
+                                      "X",
+                                      "Y",
+                                      "Output_8"]
+
+            i += 1
+            line = list_line[i]
+            while True:
+                i += 1
+                line = list_line[i].rstrip()
+                if line == '':
+                    break
+                line = line.split("	")
+                line = [x for x in line if x]
+
+                # Channel name
+                channel_name = line[1]
+                # Just continue if a channel with a specific name is not
+                # supported.
+                if channel_name in channels_not_supported:
+                    continue
+
+                # Assign the correct channel names
+                if channel_name == "Current":
+                    channel_name = "I"
+                if channel_name == "OC_D1_Phase":
+                    channel_name = "Phase"
+                if channel_name == "OC_D1_Amplitude":
+                    channel_name = "Amplitude"
+                if channel_name == "OC_M1_Freq._Shift":
+                    channel_name = "df"
+                if channel_name == "OC_M1_Excitation":
+                    channel_name = "Dissipation"
+                if channel_name == "KPFM":
+                    channel_name = "Kelvin"
+                if channel_name == "KPFM_err":
+                    channel_name = "KELVIN_ERR"
+
+                globvar_AFMdata.scandir.append("forward")
+                globvar_AFMdata.scandir.append("backward")
+                # Put in 2x for forward and backward scanning direction.
+                rename_channel(channel_name)
+                rename_channel(channel_name)
+                globvar_AFMdata.unit.append(line[2])
+                globvar_AFMdata.unit.append(line[2])
+                globvar_AFMdata.z_calibration.append(line[4])
+                globvar_AFMdata.z_calibration.append(line[4])
+                globvar_AFMdata.z_offset.append(line[5])
+                globvar_AFMdata.z_offset.append(line[5])
+
+        # AFM part
+        if ":Oscillation Control>Center Frequency (Hz):" in list_line[i]:
+            if "Frequency" in globvar_AFMdata.measurement_type:
+                i += 1
+                line = list_line[i].rstrip().strip()
+                globvar_AFMdata.res_freq = line
+        if ":Oscillation Control>FrequencyShift (Hz):" in list_line[i]:
+            if "Frequency" in globvar_AFMdata.measurement_type:
+                i += 1
+                line = list_line[i].rstrip().strip()
+        if ":Oscillation Control>Amplitude Setpoint (m):" in list_line[i]:
+            if "Frequency" in globvar_AFMdata.measurement_type:
+                i += 1
+                line = list_line[i].rstrip().strip()
+                # Amplitude in nm!
+                amplitude = "%.1f" % (float(line) * 1e9)
+        if ":Oscillation Control>Input Calibration (m/V):" in list_line[i]:
+            if "Frequency" in globvar_AFMdata.measurement_type:
+                i += 1
+                line = list_line[i].rstrip().strip()
+                # S_A in nm/V!
+                S_A = "%.1f" % (float(line) * 1e9)
+
+
+    # The amplitude info is a combination of the amplitude in nm AND the
+    # S_A calibration factor in nm/V.
+    if "Frequency" in globvar_AFMdata.measurement_type:
+        globvar_AFMdata.amplitude = amplitude + ", S_A: " + S_A
+
+    # Preparation of some variables
+    # =============================
+    # 1. We need to prepare the feedback variable. It can be the current
+    # (I, here in nA), force (here in nN) or df (here in Hz).
+    feedback = globvar_AFMdata.feedback.split(' ')
+    # For current and force
+    if feedback[-1] == 'A' or feedback[-1] == 'F':
+        globvar_AFMdata.feedback = str(float(feedback[0]) * 1e9)
+    # Everything in Hz etc.
+    else:
+        globvar_AFMdata.feedback = str(float(feedback[0]))
+
+    # 2. The scan speed. Currently it is the time per line, however, we
+    # translate it into nm/s. Later, it is translated into frequency (Hz).
+    speed = float(globvar_AFMdata.x_size) / globvar_AFMdata.speed
+    globvar_AFMdata.speed = "%.2f" % speed
+
+    # Return the offset, which is used in the definition
+    # 'prepare_Nanonis_images'.
+    return data_offset
+
+
+# This is the definition, which prepares the image data of all channels. The
+# data is then directly send to the definition, which prepares the thumbnails.
+def prepare_SPECS_Nanonis_images(nanonis_file, data_offset):
+
+    # Open the Nanonis file. Inside this file, all images can be found. So,
+    # the file remains open during the entire loading of the images.
+    nanonis_file_path = os.path.join(globvar_AFMdir.working_directory,
+                                     nanonis_file)
+    nanonis_file_p = open(nanonis_file_path, "rb")
+
+    # Go through all channels and create the thumbnails.
+    for image_nr, channel in enumerate(globvar_AFMdata.channel):
+
+        # The definition 'proceed_with' is 'connected' with the GUI of
+        # AFM_thumbs where one can choose if a channel of a specific
+        # scanning direction shall be represented in a pdf file or not.
+        if proceed_with(image_nr,globvar_AFMdata.scandir[image_nr]):
+
+            # Prepare the file path.
+            pos = globvar_AFMdata.datfile[0].rfind('\\')
+            data_file_name = globvar_AFMdata.datfile[0][pos+1:]
+
+            # The name of the thumbnail image, in a correct order.
+            image_name = data_file_name[:-4]
+            if image_name[2] == "_":
+                image_name = image_name[0:1]+"00"+image_name[1:]
+            if image_name[3] == "_":
+                image_name = image_name[0:1]+"0"+image_name[1:]
+            image_name = image_name + "_" + str(image_nr)
+
+            # This is a code that is related to the option in the GUI, if the
+            # thumbs shall be saved as pngs or jpegs.
+            if globvar_ThumbPara.png:
+               image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                         image_name) + ".png"
+            else:
+                image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                          image_name) + ".jpeg"
+
+            # If a thumb image exists continue with the next one (don't
+            # calculate a second time).
+            if os.path.isfile(image_path):
+                continue
+
+            # x/y size of the image, taken from the parameter class.
+            size_x = int(globvar_AFMdata.x_pixel)
+            size_y = int(globvar_AFMdata.y_pixel)
+
+            # Put the file pointer onto the correct position. One has to
+            # multipy by a factor of 4 because ... .
+            nanonis_file_p.seek(data_offset + image_nr*size_x*size_y*4)
+
+            # Read the data block. It is 'big endian float 32' type of data.
+            # A block (an image) has the image size of 'size_x*size_y'.
+            data = np.fromfile(nanonis_file_p,
+                               dtype = '>f4',
+                               count = size_x*size_y)
+            # 'big endian float 32'   : '>f4'
+            # 'little endian float 32': '<f4'
+            # 'big endian float 64'   : '>f8'
+            # 'little endian float 64': '<f8'
+
+            # old_y_size and old_y_pixel are needed to temporarily store
+            # the original size in y (nm and pixel). This is then used
+            # at the end to put back the original values for
+            # globvar_AFMdata.y_size and globvar_AFMdata.y_pixel, for the
+            # text in the thumbs.
+            # The 'nanonis_file_path' is used for an eventual error message.
+            data, old_y_size, old_y_pixel = check_image_properties(data,
+                                                             nanonis_file_path)
+            # If there is some corrupt image the y value, which has been
+            # changed in check_image_properties, needs to be updated.
+            size_y = int(globvar_AFMdata.y_pixel)
+
+            # Average value
+            average = np.average(data)
+            # Put the lowest point onto ZERO.
+            data = data - data.min()
+
+            # Scale the image with the values found in the header.
+            # A bit strange: in 'globvar_AFMdata.z_calibration[image_nr]'
+            # the factor does not seem to be the correct one for z values. To
+            # be clarified in future.
+            data = data * 1e9
+            # Calibrate the average value.
+            globvar_AFMdata.z_average = average * 1e9
+
+            # Make now a 2D array.
+            data.shape = np.array([size_y, size_x])
+
+            # Mirror the data along the y-axis for backward images
+            if globvar_AFMdata.scandir[image_nr] == "backward":
+                # Left-right flip
+                data = np.fliplr(data)
+
+            # Mirror the data along the x-axisy for down scanning.
+            if globvar_AFMdata.scan_updown == "down":
+                # Up-down flip
+                data = np.flipud(data)
+
+            # Line fit
+            if line_fit(image_nr,globvar_AFMdata.scandir[image_nr]):
+                 data = linalg_line_fit(size_x, size_y, data)
+
+            # Plane fit
+            if plane_fit(image_nr,globvar_AFMdata.scandir[image_nr]):
+                 data = linalg_plane_fit(size_x, size_y, data)
+
+            create_thumb_images(data, image_nr, image_name, data_file_name)
+
+            if old_y_size != "" and old_y_pixel != "":
+                globvar_AFMdata.y_size  = old_y_size
+                globvar_AFMdata.y_pixel = old_y_pixel
+
+        else:
+            continue
+
+    # Close the Nanonis file ...
+    nanonis_file_p.close()
+
+
+# This is the definition, which stores diverse parameters from the header of
+# a spectrum/sweep file into the parameter class of AFM_thumbs.
+def read_SPECS_Nanonis_spectra_data(nanonis_file):
+
+    # If the file is 0 Byte large (empty) continue loop (Do not consider
+    # the file)
+    if os.stat(nanonis_file)[6] == 0:
+        return [], []
+
+    # Initialization of FLAGs
+    # =======================
+    # Regular z spectroscopy
+    FLAG_Z_SPEC = False
+    # Regular bias sweep spectroscopy
+    FLAG_U_SWEEP = False
+    # Regular bias spectroscopy
+    FLAG_U_SPEC = False
+    # Frequency sweep
+    FLAG_f0_SPEC = False
+    # NP charging spectroscopy
+    FLAG_NPC    = False
+    # Focre curve alignement (FCA) spectroscopy
+    FLAG_FCA    = False
+
+    # Open the file
+    data_file_p = open(nanonis_file, "r")
+    # Determine the type of spectroscopy.
+    for line in data_file_p:
+
+        # End of header, get out.
+        if "[DATA]" in line:
+            break
+        if "Experiment	Z spectroscopy	" in line:
+            FLAG_Z_SPEC = True
+        if "Experiment	bias sweep	" in line:
+            FLAG_U_SWEEP = True
+        if "Experiment	bias spectroscopy" in line:
+            FLAG_U_SPEC = True
+        if "Q	" in line:
+            FLAG_f0_SPEC = True
+        if "#     Calibrate Amplitude" in line:
+            FLAG_FCA = True
+        if "#     Charge Nanoparticles" in line:
+            FLAG_NPC = True
+
+    # Close the file.
+    data_file_p.close()
+
+
+    # Open the file again.
+    data_file_p = open(nanonis_file, "r")
+
+    # Parse the entire file.
+    FLAG_real_dat_file = False
+    spec_position = ""
+    for line in data_file_p:
+
+        # End of header
+        if "[DATA]" in line:
+            FLAG_real_dat_file = True
+            break
+
+        # For all: x, y, z, z_offset position, date
+        # =========================================
+        if "X (m)	" in line[:7]:
+            line = line.rstrip().split('	')
+            spec_pos_x = "Pos: %.1f" % (float(line[-1]) * 1e9)
+        if "Y (m)	" in line[:7]:
+            line = line.rstrip().split('	')
+            spec_pos_y = "%.1f" % (float(line[-1]) * 1e9)
+        if "Z (m)	" in line[:7]:
+            line = line.rstrip().split('	')
+            spec_pos_z = "%.1f" % (float(line[-1]) * 1e9)
+        if "Z offset (m)	" in line:
+            line = line.rstrip().split('	')
+            spec_pos_z_off = "%.1f" % (float(line[-1]) * 1e9)
+        if "Saved Date" in line:
+            date = line[10:].rstrip().strip()
+            date = date.split()
+            date = date[0] + ", " + date[1]
+
+
+        # Distance spectroscopy
+        # =====================
+        if FLAG_Z_SPEC:
+            if "Z offset (m)	" in line:
+                line = line.rstrip().split('	')
+                spec_z_off = "%.1f" % (float(line[-1]) * 1e9)
+            if "Z sweep distance (m)	" in line:
+                line = line.rstrip().split('	')
+                spec_z_dist = "%.1f" % (float(line[-1]) * 1e9)
+            if "Integration time (s)	" in line:
+                line = line.rstrip().split('	')
+                spec_z_t_integr = "%.1f" % (float(line[-1]) * 1000.0)
+            if "Settling time (s)	" in line:
+                line = line.rstrip().split('	')
+                spec_z_t_settl = "%.1f" % (float(line[-1]) * 1000.0)
+            if "Filter type	" in line:
+                line = line.rstrip().split('	')
+                spec_z_filter = line[-1]
+
+        # Bias spectroscopy
+        # =================
+        if FLAG_U_SPEC:
+            if "Integration time (s)	" in line:
+                line = line.rstrip().split('	')
+                spec_U_t_integr = "%.1f" % (float(line[-1]) * 1000.0)
+            if "Settling time (s)	" in line:
+                line = line.rstrip().split('	')
+                spec_U_t_settl = "%.1f" % (float(line[-1]) * 1000.0)
+            if "Filter type	" in line:
+                line = line.rstrip().split('	')
+                spec_U_filter = line[-1]
+
+        # Bias sweep
+        # ==========
+        if FLAG_U_SWEEP:
+            if "Number of steps	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_points = line[-1]
+            if "Initial Bias (V)	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_ini = "%.2f" % float(line[-1])
+            if "Lower limit (V)	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_lower_limit = "%.2f" % float(line[-1])
+            if "Upper limit (V)	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_upper_limit = "%.2f" % float(line[-1])
+            if "Step size (V)	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_step = "%.2f" % float(line[-1])
+            if "Measurement period (s)	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_t_integr = "%.1f" % (float(line[-1]) * 1000.0)
+            if "Settling time (s)	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_t_settl = "%.1f" % (float(line[-1]) * 1000.0)
+            if "Z-Controller off	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_controller = line[-1]
+            if "Reset Bias	" in line:
+                line = line.rstrip().split('	')
+                sweep_U_reset = line[-1]
+
+
+        # Normal f0 sweep
+        # ===============
+        if FLAG_f0_SPEC:
+            if "Number of points	" in line:
+                line = line.rstrip().split('	')
+                sweep_points_curve = line[-1]
+            if "f_res (Hz)	" in line:
+                line = line.rstrip().split('	')
+                sweep_f0 = "%.2f" % (float(line[-1]) / 1000.0)
+            if "Q	" in line:
+                line = line.rstrip().split('	')
+                sweep_Q = line[-1]
+            if "Phase (deg)	" in line:
+                line = line.rstrip().split('	')
+                sweep_phase = "%.1f" % float(line[-1])
+            if "Amp/Exc (nm/mV)	" in line:
+                line = line.rstrip().split('	')
+                sweep_A_exi_cal= "%.2f" % float(line[-1])
+            if "Oscillation Control>Input Calibration (m/V)	" in line:
+                line = line.rstrip().split('	')
+                sweep_A_cali = "%.2f" % (float(line[-1]) * 1e9)
+            if "Oscillation Control>Excitation (V)	" in line:
+                line = line.rstrip().split('	')
+                sweep_A_exi = "%.2f" % (float(line[-1]) * 1000.0)
+
+        # NPC (NP charging)
+        # =================
+        if FLAG_NPC:
+            if "Add_dz_start (m)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_add_dz_start = "%.2f" % (float(line[-1]) * 1e9)
+            if "No_points	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_n_points = str(int(line[-1]) * 2)
+            if "DV_to_CPD (V)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_dv_to_cpd = "%.2f" % (float(line[-1]))
+            if "CPD_measured (V)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_cpd_measured = "%.2f" % (float(line[-1]))
+            if "Delay_for_CPD (ms)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_cpd_delay = "%.1f" % (float(line[-1]))
+            if "Bias_voltage_range (V)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_bias_range = "%.2f" % (float(line[-1]))
+            if "Z_averaging_time (s)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_z_average_t = "%.2f" % (float(line[-1]) * 1000.0)
+            if "Z_offset (m)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_z_off = "%.2f" % (float(line[-1]) * 1e9)
+            if "Integration_time (s)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_t_integr = "%.2f" % (float(line[-1]) * 1000.0)
+            if "Settling_time (s)	" in line or "Settling time (s)	" in line:
+                line = line.rstrip().split('	')
+                spec_NPC_t_settl = "%.2f" % (float(line[-1]) * 1000.0)
+
+
+        # FCA (force curve alignement method)
+        # ===================================
+        if FLAG_FCA:
+            if "No_points_curve	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_points_curve = line[-1]
+            if "Oscillation Control>Center Frequency (Hz)	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_f0 = "%.2f" % (float(line[-1]) / 1000.0)
+            if "Z_offset (m)	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_z_off = "%.1f" % (float(line[-1]) * 1e9)
+            if "Spring_constant (Hz)	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_k = "%.2f" % (float(line[-1]))
+            if "No_amplitude_values	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_A_no = line[-1]
+            if "Amplitude_start (V)	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_A_start = "%.2f" % (float(line[-1]))
+            if "Amplitude_change (V)	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_A_change = "%.2f" % (float(line[-1]))
+            if "Sweep_distance (m)	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_sweep_dist = "%.2f" % (float(line[-1]) * 1e9)
+            if "Time_acq_point (ms)	" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_acquisition = "%.2f" % (float(line[-1]) / 1000.0)
+            if "Time_passed_loop" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_t_loop = "%.2f" % (float(line[-1]))
+            if "Time_passed_tot" in line:
+                line = line.rstrip().split('	')
+                spec_FCA_t_tot = "%.2f" % (float(line[-1]))
+
+    # It is not a Nanonis data file because the identifier '[DATA]' could not
+    # be found!
+    if not FLAG_real_dat_file:
+        return [], []
+
+    list_data = []
+    for i, line in enumerate(data_file_p):
+
+        # Do not consider empty lines.
+        if line[:-2] == "":
+            continue
+
+        # Do not consider FCA specific identifiers.
+        if "loop_" in line.lower():
+            continue
+
+        line = line.rstrip().strip().split('	')
+
+        if i == 0:
+            for channel in line[1:]:
+                # We basically use always the same x values
+                unit = line[0].split(' ')[-1][1:-1]
+                globvar_AFMdata.spec_x_label.append(line[0][:-(len(unit)+2)])
+                globvar_AFMdata.spec_x_unit.append(unit)
+                # The y values
+                unit = channel.split(' ')[-1][1:-1]
+                globvar_AFMdata.spec_y_label.append(channel[:-(len(unit)+2)])
+                globvar_AFMdata.spec_y_unit.append(unit)
+            continue
+
+        list_data.append(line)
+
+    # Close the file.
+    data_file_p.close()
+
+    list_X = []
+    list_Y = []
+    for i in range(len(list_data[0])-1):
+        list_x = []
+        list_y = []
+        for line in list_data:
+            list_x.append(float(line[0]))
+            list_y.append(float(line[i+1]))
+        list_X.append(list_x)
+        list_Y.append(list_y)
+
+    nr_channels = len(list_data[0])-1
+    nr_points   = len(list_X[0])
+
+    # Preparation of text string for the thumbs
+    # =========================================
+
+    # Attention!
+    # ----------
+    # We have to adapt to the 'old' way of SCALA doing... . However, we ceate
+    # our specific 'globvar_AFMdata.spec_other' variable, which contains all
+    # parameters. Preparing the text string already here is much more easy ... .
+
+    globvar_AFMdata.spec_other = ""
+
+    if 'date' in locals():
+        globvar_AFMdata.spec_other += "-- " + date + " -- "
+
+    # First the x, y, z position
+    spec_position = ""
+    if 'spec_pos_x' in locals():
+        spec_position +=        spec_pos_x     + "|"
+    if 'spec_pos_y' in locals():
+        spec_position +=        spec_pos_y     + "|"
+    if 'spec_pos_z' in locals():
+        spec_position +=        spec_pos_z
+    else:
+        if globvar_AFMdata.spec_position != "":
+            spec_position = spec_position[:-1]
+    if 'spec_pos_z_off' in locals():
+        spec_position += "(" + spec_pos_z_off + ")"
+
+    globvar_AFMdata.spec_position = [spec_position] * nr_channels
+
+    # Text for z spectroscopy
+    if FLAG_Z_SPEC:
+        globvar_AFMdata.spec_other += "Points: "            + str(nr_points)   + "nm, "
+        if 'spec_z_off' in locals():
+            globvar_AFMdata.spec_other += "Z off: "         + spec_z_off       + "nm, "
+        if 'spec_z_dist' in locals():
+            globvar_AFMdata.spec_other += "Z dist. range: " + spec_z_dist      + "nm, "
+        if 'spec_z_filter' in locals():
+            globvar_AFMdata.spec_other += "Filter: "        + spec_z_filter    + ", "
+        if 'spec_z_t_integr' in locals():
+            globvar_AFMdata.spec_other += "t (integr): "    + spec_z_t_integr  + "ms, "
+        if 'spec_z_t_settl' in locals():
+            globvar_AFMdata.spec_other += "t (settl): "     + spec_z_t_settl   + "ms, "
+        if 'spec_z_t_integr' in locals() and 'spec_z_t_settl':
+            spec_z_t_total = "%.2f" % ((float(spec_z_t_integr) +
+                                        float(spec_z_t_settl)) *
+                                        float(nr_points) / 1000.0)
+            globvar_AFMdata.spec_other += "t (tot): "       + spec_z_t_total + "s, "
+
+    # Text for U spectroscopy
+    if FLAG_U_SPEC:
+        globvar_AFMdata.spec_other += "Points: "          + str(nr_points)   + "nm, "
+        if 'spec_U_filter' in locals():
+            globvar_AFMdata.spec_other += "Filter: "      + spec_U_filter    + ", "
+        if 'spec_U_t_integr' in locals():
+            globvar_AFMdata.spec_other += "t (integr): "  + spec_U_t_integr  + "ms, "
+        if 'spec_U_t_settl' in locals():
+            globvar_AFMdata.spec_other += "t (settl): "   + spec_U_t_settl   + "ms, "
+        if 'spec_U_t_integr' in locals() and 'spec_U_t_settl' in locals():
+            spec_t_total = "%.2f" % ((float(spec_U_t_integr) +
+                                      float(spec_U_t_settl)) *
+                                      float(nr_points) / 1000.0)
+            globvar_AFMdata.spec_other += "t (tot): "     + spec_t_total     + "s, "
+
+    # Text for U sweep
+    if FLAG_U_SWEEP:
+        if 'sweep_U_points' in locals():
+            globvar_AFMdata.spec_other += "Points: "      + sweep_U_points      + ", "
+        if 'sweep_U_ini' in locals():
+            globvar_AFMdata.spec_other += "U_ini: "       + sweep_U_ini         + "V, "
+        if 'sweep_U_lower_limit' in locals():
+            globvar_AFMdata.spec_other += "U_low: "       + sweep_U_lower_limit + "V, "
+        if 'sweep_U_upper_limit' in locals():
+            globvar_AFMdata.spec_other += "U_up: "        + sweep_U_upper_limit + "V, "
+        if 'sweep_U_step' in locals():
+            globvar_AFMdata.spec_other += "U_step: "      + sweep_U_step        + "V, "
+        if 'sweep_U_controller' in locals():
+            globvar_AFMdata.spec_other += "Controller: "  + sweep_U_controller  + ", "
+        if 'sweep_U_reset' in locals():
+            globvar_AFMdata.spec_other += "Reset: "       + sweep_U_reset       + ", "
+        if 'sweep_U_t_integr' in locals():
+            globvar_AFMdata.spec_other += "t (integr): "  + sweep_U_t_integr    + "ms, "
+        if 'sweep_U_t_settl' in locals():
+            globvar_AFMdata.spec_other += "t (settl): "   + sweep_U_t_settl     + "ms, "
+        if 'sweep_U_t_integr' in locals() and 'sweep_U_t_settl' in locals() and 'sweep_U_points' in locals():
+            sweep_t_total = "%.2f" % ((float(sweep_U_t_integr) +
+                                       float(sweep_U_t_settl)) *
+                                       float(sweep_U_points) / 1000.0)
+            globvar_AFMdata.spec_other += "t (tot): "     + sweep_t_total      + "s, "
+
+    # Text for f0 sweep
+    if FLAG_f0_SPEC:
+        if 'sweep_points_curve' in locals():
+            globvar_AFMdata.spec_other += "Points: "     + sweep_points_curve + ", "
+        if 'sweep_f0' in locals():
+            globvar_AFMdata.spec_other += "f0: "         + sweep_f0           + "Hz, "
+        if 'sweep_Q' in locals():
+            globvar_AFMdata.spec_other += "Q: "          + sweep_Q            + ", "
+        if 'sweep_phase' in locals():
+            globvar_AFMdata.spec_other += "Phi: "        + sweep_phase        + "V, "
+        if 'sweep_A_exi_cal' in locals():
+            globvar_AFMdata.spec_other += "A_exi_cal: "  + sweep_A_exi_cal    + "nm/mV, "
+        if 'sweep_A_cali' in locals():
+            globvar_AFMdata.spec_other += "A_cali: "     + sweep_A_cali       + "nm/V, "
+        if 'sweep_A_exi' in locals():
+            globvar_AFMdata.spec_other += "A_exi: "      + sweep_A_exi        + "mV"
+
+    # Text for the NPC method
+    if FLAG_NPC:
+        if 'spec_NPC_n_points' in locals():
+            globvar_AFMdata.spec_other += "Points: "      + spec_NPC_n_points     + ", "
+        if 'spec_NPC_add_dz_start' in locals():
+            globvar_AFMdata.spec_other += "Add_z_start: " + spec_NPC_add_dz_start + "nm, "
+        if 'spec_NPC_dv_to_cpd' in locals():
+            globvar_AFMdata.spec_other += "CPD-dV: "      + spec_NPC_dv_to_cpd    + "V, "
+        if 'spec_NPC_cpd_measured' in locals():
+            globvar_AFMdata.spec_other += "CPD: "         + spec_NPC_cpd_measured + "V, "
+        if 'spec_NPC_cpd_delay' in locals():
+            globvar_AFMdata.spec_other += "t (CPD): "     + spec_NPC_cpd_delay    + "ms, "
+        if 'spec_NPC_bias_range' in locals():
+            globvar_AFMdata.spec_other += "V range: "     + spec_NPC_bias_range   + "V, "
+        if 'spec_NPC_z_average_t' in locals():
+            globvar_AFMdata.spec_other += "Z average t: " + spec_NPC_z_average_t  + "ms, "
+        if 'spec_NPC_z_off' in locals():
+            globvar_AFMdata.spec_other += "Z off: "       + spec_NPC_z_off        + "nm, "
+        if 'spec_NPC_t_integr' in locals():
+            globvar_AFMdata.spec_other += "t (integr): "  + spec_NPC_t_integr     + "ms, "
+        if 'spec_NPC_t_settl' in locals():
+            globvar_AFMdata.spec_other += "t (settl): "   + spec_NPC_t_settl      + "ms, "
+        if 'spec_NPC_t_integr' in locals() and 'spec_NPC_n_points' in locals() and 'spec_NPC_t_settl' in locals():
+            spec_NPC_t_total = "%.2f" % ((float(spec_NPC_t_integr) +
+                                          float(spec_NPC_t_settl)) *
+                                          float(spec_NPC_n_points) / 1000.0)
+            globvar_AFMdata.spec_other += "t (tot): "     + spec_NPC_t_total      + "s, "
+
+    # Text for the FCA method
+    if FLAG_FCA:
+        if 'spec_FCA_points_curve' in locals():
+            globvar_AFMdata.spec_other += "Points/curve: "  + spec_FCA_points_curve + ", "
+        if 'spec_FCA_k' in locals():
+            globvar_AFMdata.spec_other += "k: "             + spec_FCA_k            + "N/m, "
+        if 'spec_FCA_f0' in locals():
+            globvar_AFMdata.spec_other += "f0: "            + spec_FCA_f0           + "Hz, "
+        if 'spec_FCA_A_no' in locals():
+            globvar_AFMdata.spec_other += "No. Ampls: "     + spec_FCA_A_no         + ", "
+        if 'spec_FCA_A_start' in locals():
+            globvar_AFMdata.spec_other += "A_start: "       + spec_FCA_A_start      + "V, "
+        if 'spec_FCA_A_change' in locals():
+            globvar_AFMdata.spec_other += "A_change: "      + spec_FCA_A_change     + "V, "
+        if 'spec_FCA_z_off' in locals():
+            globvar_AFMdata.spec_other += "Z_offset: "      + spec_FCA_z_off        + "nm, "
+        if 'spec_FCA_sweep_dist' in locals():
+            globvar_AFMdata.spec_other += "Dist: "          + spec_FCA_sweep_dist   + "nm, "
+        if 'spec_FCA_t_loop' in locals():
+            globvar_AFMdata.spec_other += "t (exp): "       + spec_FCA_t_loop       + "min, "
+        if 'spec_FCA_t_tot' in locals():
+            globvar_AFMdata.spec_other += "t (tot): "       + spec_FCA_t_tot        + "min, "
+
+    #print(nanonis_file,
+    #      globvar_AFMdata.date,
+    #      globvar_AFMdata.spec_files,
+    #      globvar_AFMdata.spec_x_label,
+    #      globvar_AFMdata.spec_x_unit,
+    #      globvar_AFMdata.spec_y_label,
+    #      globvar_AFMdata.spec_y_unit,
+    #      globvar_AFMdata.spec_y_factor,
+    #      globvar_AFMdata.spec_points,
+    #      globvar_AFMdata.spec_feedback,
+    #      globvar_AFMdata.spec_acquisition,
+    #      globvar_AFMdata.spec_time,
+    #      globvar_AFMdata.spec_position,
+    #      globvar_AFMdata.spec_delay,
+    #      globvar_AFMdata.sweep_f0,
+    #      globvar_AFMdata.sweep_Q,
+    #      globvar_AFMdata.sweep_phase,
+    #      globvar_AFMdata.sweep_A_exec)
+
+    return list_X, list_Y
+
+
+
+# This is the definition, which prepares the spectra data. The
+# data is then directly send to the definition, which prepares the thumbnails.
+def prepare_SPECS_Nanonis_spectra_curves(nanonis_file):
+
+    initialize_AFM_data()
+
+    data_file_name = nanonis_file
+    data_file = os.path.join(globvar_AFMdir.working_directory,data_file_name)
+
+    list_X, list_Y = read_SPECS_Nanonis_spectra_data(data_file)
+    if list_X == [] or list_Y == []:
+        return False
+
+    i = 0
+    for list_x, list_y in zip(list_X, list_Y):
+
+        image_name, file_extension = os.path.splitext(nanonis_file)
+        # There has to be an 's', which is used to identify the thumb image as
+        # an spectroscopy thumb image!
+        image_name = image_name + "_" + "s%02d" % (i)
+
+        if globvar_ThumbPara.png:
+            image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                            image_name) + ".png"
+        else:
+            image_path = os.path.join(globvar_AFMdir.thumbnail_directory,
+                                            image_name) + ".jpeg"
+
+        if os.path.isfile(image_path):
+            return True
+
+        create_thumb_spectra([list_x],
+                             [list_y],
+                             i,
+                             image_name,
+                             image_path,
+                             globvar_AFMdata.spec_y_label[i])
+
+        i += 1
+
+    return True

AFM_thumbs/SPECS_Nanonis.txt

@@ -0,0 +1,571 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+#    Example for the complete header of a SPECS Nanonis '.sxm' file
+#    ==============================================================
+#
+#    :NANONIS_VERSION:
+#    2
+#    :SCANIT_TYPE:
+#                  FLOAT            MSBFIRST
+#    :REC_DATE:
+#     17.01.2021
+#    :REC_TIME:
+#    11:22:04
+#    :REC_TEMP:
+#          290.0000000000
+#    :ACQ_TIME:
+#            32.8
+#    :SCAN_PIXELS:
+#           256       256
+#    :SCAN_FILE:
+#    D:\Session_test\Session_first_time_test\Test0001.sxm
+#    :SCAN_TIME:
+#                 6.400E-2             6.400E-2
+#    :SCAN_RANGE:
+#               2.000000E-8           2.000000E-8
+#    :SCAN_OFFSET:
+#                 0.000000E+0         0.000000E+0
+#    :SCAN_ANGLE:
+#                0.000E+0
+#    :SCAN_DIR:
+#    up
+#    :BIAS:
+#                2.000E+0
+#    :Z-CONTROLLER:
+#    	Name	on	Setpoint	P-gain	I-gain	T-const
+#    	log Current	1	5.000E-11 A	2.000E-10 m	2.000E-7 m/s	1.000E-3 s
+#    :COMMENT:
+#    Aha, so geht das ...
+#    :NanonisMain>Session Path:
+#    D:\Session_test\Session_first_time_test
+#    :NanonisMain>SW Version:
+#    Generic 5e
+#    :NanonisMain>UI Release:
+#    10278
+#    :NanonisMain>RT Release:
+#    10278
+#    :NanonisMain>RT Frequency (Hz):
+#    20E+3
+#    :NanonisMain>Signals Oversampling:
+#    10
+#    :NanonisMain>Acquisition Period (s):
+#    20E-3
+#    :NanonisMain>Animations Period (s):
+#    20E-3
+#    :NanonisMain>Indicators Period (s):
+#    300E-3
+#    :NanonisMain>Measurements Period (s):
+#    500E-3
+#    :Bias>Bias (V):
+#    2E+0
+#    :Bias>Calibration (V/V):
+#    1E+0
+#    :Bias>Offset (V):
+#    0E+0
+#    :Current>Current (A):
+#    50.033E-12
+#    :Current>Calibration (A/V):
+#    5E-9
+#    :Current>Offset (A):
+#    0E+0
+#    :Current>Gain:
+#    Low
+#    :Piezo Configuration>Active Calib.:
+#    Default
+#    :Piezo Configuration>Calib. X (m/V):
+#    6E-9
+#    :Piezo Configuration>Calib. Y (m/V):
+#    6E-9
+#    :Piezo Configuration>Calib. Z (m/V):
+#    -6E-9
+#    :Piezo Configuration>HV Gain X:
+#    15
+#    :Piezo Configuration>HV Gain Y:
+#    15
+#    :Piezo Configuration>HV Gain Z:
+#    15
+#    :Piezo Configuration>Tilt X (deg):
+#    0
+#    :Piezo Configuration>Tilt Y (deg):
+#    0
+#    :Piezo Configuration>Curvature radius X (m):
+#    Inf
+#    :Piezo Configuration>Curvature radius Y (m):
+#    Inf
+#    :Piezo Configuration>2nd order corr X (V/m^2):
+#    0E+0
+#    :Piezo Configuration>2nd order corr Y (V/m^2):
+#    0E+0
+#    :Piezo Configuration>Drift X (m/s):
+#    0E+0
+#    :Piezo Configuration>Drift Y (m/s):
+#    0E+0
+#    :Piezo Configuration>Drift Z (m/s):
+#    0E+0
+#    :Piezo Configuration>Drift correction status (on/off):
+#    FALSE
+#    :Z-Controller>Z (m):
+#    39.1035E-9
+#    :Z-Controller>Controller name:
+#    log Current
+#    :Z-Controller>Controller status:
+#    ON
+#    :Z-Controller>Setpoint:
+#    50E-12
+#    :Z-Controller>Setpoint unit:
+#    A
+#    :Z-Controller>P gain:
+#    200E-12
+#    :Z-Controller>I gain:
+#    200E-9
+#    :Z-Controller>Time const (s):
+#    1E-3
+#    :Z-Controller>TipLift (m):
+#    0E+0
+#    :Z-Controller>Switch off delay (s):
+#    0E+0
+#    :Oscillation Control>differential input:
+#    FALSE
+#    :Oscillation Control>input 1/10:
+#    FALSE
+#    :Oscillation Control>Input Calibration (m/V):
+#    1E-6
+#    :Oscillation Control>Input Range (m):
+#    20.2162E-9
+#    :Oscillation Control>Center Frequency (Hz):
+#    200E+3
+#    :Oscillation Control>Range (Hz):
+#    9.53674E+0
+#    :Oscillation Control>Demod 1 Input:
+#    1
+#    :Oscillation Control>Demod 2 Input:
+#    1
+#    :Oscillation Control>Demod 3 Input:
+#    1
+#    :Oscillation Control>Demod 4 Input:
+#    1
+#    :Oscillation Control>Demod 1 Frequency:
+#    1
+#    :Oscillation Control>Demod 2 Frequency:
+#    1
+#    :Oscillation Control>Demod 3 Frequency:
+#    1
+#    :Oscillation Control>Demod 4 Frequency:
+#    1
+#    :Oscillation Control>Demod 1 Reference Phase (deg):
+#    0E+0
+#    :Oscillation Control>Demod 2 Reference Phase (deg):
+#    0E+0
+#    :Oscillation Control>Demod 3 Reference Phase (deg):
+#    0E+0
+#    :Oscillation Control>Demod 4 Reference Phase (deg):
+#    0E+0
+#    :Oscillation Control>Demod 1 Cut off frq (Hz):
+#    1.55k
+#    :Oscillation Control>Demod 2 Cut off frq (Hz):
+#    1.55k
+#    :Oscillation Control>Demod 3 Cut off frq (Hz):
+#    1.55k
+#    :Oscillation Control>Demod 4 Cut off frq (Hz):
+#    1.55k
+#    :Oscillation Control>Demod 1 Harmonic:
+#    1
+#    :Oscillation Control>Demod 2 Harmonic:
+#    1
+#    :Oscillation Control>Demod 3 Harmonic:
+#    1
+#    :Oscillation Control>Demod 4 Harmonic:
+#    1
+#    :Oscillation Control>Demod 1 Filter Order:
+#    2
+#    :Oscillation Control>Demod 2 Filter Order:
+#    2
+#    :Oscillation Control>Demod 3 Filter Order:
+#    2
+#    :Oscillation Control>Demod 4 Filter Order:
+#    2
+#    :Oscillation Control>Phase P gain (Hz/rad):
+#    151.8E-3
+#    :Oscillation Control>Phase I gain (Hz/rad/s):
+#    755.511E-3
+#    :Oscillation Control>Phase controller on:
+#    FALSE
+#    :Oscillation Control>FrequencyShift (Hz):
+#    0E+0
+#    :Oscillation Control>Amplitude Setpoint (m):
+#    1E-9
+#    :Oscillation Control>Amplitude P gain (V/nm):
+#    1.41747E+3
+#    :Oscillation Control>Amplitude I gain (V/nm/s):
+#    1.32194E+3
+#    :Oscillation Control>Amplitude controller on:
+#    FALSE
+#    :Oscillation Control>Excitation (V):
+#    1E-3
+#    :Oscillation Control>Output Ampl. Range (V):
+#    10
+#    :Oscillation Control>output off:
+#    FALSE
+#    :Oscillation Control>output add:
+#    TRUE
+#    :Oscillation Control>PLL-Setup Q-Factor:
+#    14.284E+3
+#    :Oscillation Control>PLL-Setup Demod. Bandwidth Amp (Hz):
+#    78.7927E-6
+#    :Oscillation Control>PLL-Setup Demod. Bandwidth Pha (Hz):
+#    8.69749E+0
+#    :Oscillation Control>PLL-Setup amplitude/excitation (m/V):
+#    7.94E-9
+#    :Scan>Scanfield:
+#    0E+0;0E+0;20E-9;20E-9;0E+0
+#    :Scan>series name:
+#    Test
+#    :Scan>channels:
+#    Current (A);Z (m)
+#    :Scan>pixels/line:
+#    256
+#    :Scan>lines:
+#    256
+#    :Scan>speed forw. (m/s):
+#    312.5E-9
+#    :Scan>speed backw. (m/s):
+#    312.5E-9
+#    :DATA_INFO:
+#    	Channel	Name	Unit	Direction	Calibration	Offset
+#    	14	Z	m	both	-9.000E-8	0.000E+0
+#    	0	Current	A	both	5.000E-9	0.000E+0
+#
+#    :SCANIT_END:
+
+#    Another one
+
+#    :NANONIS_VERSION:
+#    2
+#    :SCANIT_TYPE:
+#                  FLOAT            MSBFIRST
+#    :REC_DATE:
+#     05.02.2021
+#    :REC_TIME:
+#    19:40:42
+#    :REC_TEMP:
+#          290.0000000000
+#    :ACQ_TIME:
+#           288.5
+#    :SCAN_PIXELS:
+#           512       512
+#    :SCAN_FILE:
+#    D:\Data\sessions_Ag001\2021-02-03_cycle_13\m_0086.sxm
+#    :SCAN_TIME:
+#                 5.120E-1             5.120E-1
+#    :SCAN_RANGE:
+#               2.500000E-7           2.500000E-7
+#    :SCAN_OFFSET:
+#                 1.235544E-7         2.410663E-7
+#    :SCAN_ANGLE:
+#                0.000E+0
+#    :SCAN_DIR:
+#    down
+#    :BIAS:
+#                5.321E-1
+#    :Z-CONTROLLER:
+#    	Name	on	Setpoint	P-gain	I-gain	T-const
+#    	Frequency (neg)	1	-4.500E+1 Hz	6.983E-11 m/Hz	2.643E-8 m/Hz/s	2.643E-3 s
+#    :COMMENT:
+#
+#    :NanonisMain>Session Path:
+#    D:\Data\sessions_Ag001\2021-02-03_cycle_13
+#    :NanonisMain>SW Version:
+#    Generic 5e
+#    :NanonisMain>UI Release:
+#    10278
+#    :NanonisMain>RT Release:
+#    10278
+#    :NanonisMain>RT Frequency (Hz):
+#    20E+3
+#    :NanonisMain>Signals Oversampling:
+#    10
+#    :NanonisMain>Acquisition Period (s):
+#    20E-3
+#    :NanonisMain>Animations Period (s):
+#    20E-3
+#    :NanonisMain>Indicators Period (s):
+#    300E-3
+#    :NanonisMain>Measurements Period (s):
+#    10E-3
+#    :Bias>Bias (V):
+#    532.11E-3
+#    :Bias>Calibration (V/V):
+#    1E+0
+#    :Bias>Offset (V):
+#    0E+0
+#    :Current>Current (A):
+#    -132.953E-15
+#    :Current>Calibration (A/V):
+#    300E-12
+#    :Current>Offset (A):
+#    2.2182E-12
+#    :Current>Gain:
+#    High
+#    :Piezo Configuration>Active Calib.:
+#    Default
+#    :Piezo Configuration>Calib. X (m/V):
+#    10E-9
+#    :Piezo Configuration>Calib. Y (m/V):
+#    10E-9
+#    :Piezo Configuration>Calib. Z (m/V):
+#    10E-9
+#    :Piezo Configuration>HV Gain X:
+#    14
+#    :Piezo Configuration>HV Gain Y:
+#    14
+#    :Piezo Configuration>HV Gain Z:
+#    14
+#    :Piezo Configuration>Tilt X (deg):
+#    14.5234
+#    :Piezo Configuration>Tilt Y (deg):
+#    2.32116
+#    :Piezo Configuration>Curvature radius X (m):
+#    Inf
+#    :Piezo Configuration>Curvature radius Y (m):
+#    Inf
+#    :Piezo Configuration>2nd order corr X (V/m^2):
+#    0E+0
+#    :Piezo Configuration>2nd order corr Y (V/m^2):
+#    0E+0
+#    :Piezo Configuration>Drift X (m/s):
+#    0E+0
+#    :Piezo Configuration>Drift Y (m/s):
+#    0E+0
+#    :Piezo Configuration>Drift Z (m/s):
+#    0E+0
+#    :Piezo Configuration>Drift correction status (on/off):
+#    FALSE
+#    :Z-Controller>Z (m):
+#    136.55E-9
+#    :Z-Controller>Controller name:
+#    Frequency (neg)
+#    :Z-Controller>Controller status:
+#    ON
+#    :Z-Controller>Setpoint:
+#    -45E+0
+#    :Z-Controller>Setpoint unit:
+#    Hz
+#    :Z-Controller>P gain:
+#    69.8291E-12
+#    :Z-Controller>I gain:
+#    26.4252E-9
+#    :Z-Controller>Time const (s):
+#    2.64252E-3
+#    :Z-Controller>TipLift (m):
+#    0E+0
+#    :Z-Controller>Switch off delay (s):
+#    0E+0
+#    :Oscillation Control>differential input:
+#    TRUE
+#    :Oscillation Control>input 1/10:
+#    FALSE
+#    :Oscillation Control>Input Calibration (m/V):
+#    10E-9
+#    :Oscillation Control>Input Range (m):
+#    10E-9
+#    :Oscillation Control>Center Frequency (Hz):
+#    311.101E+3
+#    :Oscillation Control>Range (Hz):
+#    78.125E+3
+#    :Oscillation Control>Demod 1 Input:
+#    1
+#    :Oscillation Control>Demod 2 Input:
+#    1
+#    :Oscillation Control>Demod 3 Input:
+#    1
+#    :Oscillation Control>Demod 4 Input:
+#    1
+#    :Oscillation Control>Demod 1 Frequency:
+#    1
+#    :Oscillation Control>Demod 2 Frequency:
+#    1
+#    :Oscillation Control>Demod 3 Frequency:
+#    1
+#    :Oscillation Control>Demod 4 Frequency:
+#    1
+#    :Oscillation Control>Demod 1 Reference Phase (deg):
+#    88.88E+0
+#    :Oscillation Control>Demod 2 Reference Phase (deg):
+#    0E+0
+#    :Oscillation Control>Demod 3 Reference Phase (deg):
+#    0E+0
+#    :Oscillation Control>Demod 4 Reference Phase (deg):
+#    0E+0
+#    :Oscillation Control>Demod 1 Cut off frq (Hz):
+#    3.11k
+#    :Oscillation Control>Demod 2 Cut off frq (Hz):
+#    1.55k
+#    :Oscillation Control>Demod 3 Cut off frq (Hz):
+#    1.55k
+#    :Oscillation Control>Demod 4 Cut off frq (Hz):
+#    1.55k
+#    :Oscillation Control>Demod 1 Harmonic:
+#    1
+#    :Oscillation Control>Demod 2 Harmonic:
+#    1
+#    :Oscillation Control>Demod 3 Harmonic:
+#    1
+#    :Oscillation Control>Demod 4 Harmonic:
+#    1
+#    :Oscillation Control>Demod 1 Filter Order:
+#    2
+#    :Oscillation Control>Demod 2 Filter Order:
+#    2
+#    :Oscillation Control>Demod 3 Filter Order:
+#    2
+#    :Oscillation Control>Demod 4 Filter Order:
+#    2
+#    :Oscillation Control>Phase P gain (Hz/rad):
+#    1.67285E+0
+#    :Oscillation Control>Phase I gain (Hz/rad/s):
+#    57.6281E+0
+#    :Oscillation Control>Phase controller on:
+#    TRUE
+#    :Oscillation Control>FrequencyShift (Hz):
+#    -44.9015E+0
+#    :Oscillation Control>Amplitude Setpoint (m):
+#    300E-12
+#    :Oscillation Control>Amplitude P gain (V/nm):
+#    12.4425E+6
+#    :Oscillation Control>Amplitude I gain (V/nm/s):
+#    428.632E+6
+#    :Oscillation Control>Amplitude controller on:
+#    TRUE
+#    :Oscillation Control>Excitation (V):
+#    408.923E-6
+#    :Oscillation Control>Output Ampl. Range (V):
+#    0.1
+#    :Oscillation Control>output off:
+#    TRUE
+#    :Oscillation Control>output add:
+#    FALSE
+#    :Oscillation Control>PLL-Setup Q-Factor:
+#    27.721E+3
+#    :Oscillation Control>PLL-Setup Demod. Bandwidth Amp (Hz):
+#    392.6E+0
+#    :Oscillation Control>PLL-Setup Demod. Bandwidth Pha (Hz):
+#    95.847E+0
+#    :Oscillation Control>PLL-Setup amplitude/excitation (m/V):
+#    753.229E-9
+#    :Scan>Scanfield:
+#    123.554E-9;241.066E-9;250E-9;250E-9;0E+0
+#    :Scan>series name:
+#    m_
+#    :Scan>channels:
+#    Current (A);Z (m);OC D1 Amplitude (m);OC M1 Freq. Shift (Hz);OC M1 Excitation (V)
+#    :Scan>pixels/line:
+#    512
+#    :Scan>lines:
+#    512
+#    :Scan>speed forw. (m/s):
+#    488.281E-9
+#    :Scan>speed backw. (m/s):
+#    488.281E-9
+#    :Bias Spectroscopy>Sweep Start (V):
+#    -5E+0
+#    :Bias Spectroscopy>Sweep End (V):
+#    5E+0
+#    :Bias Spectroscopy>Num Pixel:
+#    256
+#    :Bias Spectroscopy>Z Avg time (s):
+#    50E-3
+#    :Bias Spectroscopy>Z offset (m):
+#    0E+0
+#    :Bias Spectroscopy>1st Settling time (s):
+#    5E-3
+#    :Bias Spectroscopy>Settling time (s):
+#    200E-6
+#    :Bias Spectroscopy>Integration time (s):
+#    100E-6
+#    :Bias Spectroscopy>End Settling time (s):
+#    5E-3
+#    :Bias Spectroscopy>Z control time (s):
+#    200E-3
+#    :Bias Spectroscopy>Max Slew rate (V/s):
+#    Inf
+#    :Bias Spectroscopy>backward sweep:
+#    FALSE
+#    :Bias Spectroscopy>Z-controller hold:
+#    TRUE
+#    :Bias Spectroscopy>Number of sweeps:
+#    1
+#    :Bias Spectroscopy>Channels:
+#    Current (A)
+#    :Bias Spectroscopy>Reset Bias:
+#    TRUE
+#    :Bias Spectroscopy>Record final Z:
+#    FALSE
+#    :Bias Spectroscopy>Lock-In run:
+#    FALSE
+#    :Z Spectroscopy>Initial Z-offset (m):
+#    1E-9
+#    :Z Spectroscopy>Sweep distance (m):
+#    -7E-9
+#    :Z Spectroscopy>Num Pixel:
+#    256
+#    :Z Spectroscopy>Z Avg time (s):
+#    50E-3
+#    :Z Spectroscopy>1st Settling time (s):
+#    5E-3
+#    :Z Spectroscopy>Settling time (s):
+#    200E-6
+#    :Z Spectroscopy>Integration time (s):
+#    100E-6
+#    :Z Spectroscopy>End Settling time (s):
+#    5E-3
+#    :Z Spectroscopy>Z control time (s):
+#    200E-3
+#    :Z Spectroscopy>Max Slew rate (V/s):
+#    Inf
+#    :Z Spectroscopy>backward sweep:
+#    TRUE
+#    :Z Spectroscopy>Number of sweeps:
+#    1
+#    :Z Spectroscopy>Channels:
+#    Current (A)
+#    :Z Spectroscopy>Time between fwd/bwd (s):
+#    0E+0
+#    :Z Spectroscopy>Record final Z:
+#    FALSE
+#    :Z Spectroscopy>Lock-In run:
+#    FALSE
+#    :Z Spectroscopy>Reset Z:
+#    TRUE
+#    :DATA_INFO:
+#    	Channel	Name	Unit	Direction	Calibration	Offset
+#    	14	Z	m	both	1.400E-7	0.000E+0
+#    	0	Current	A	both	3.000E-10	2.218E-12
+#    	17	OC_D1_Amplitude	m	both	1.000E-9	0.000E+0
+#    	18	OC_M1_Freq._Shift	Hz	both	7.812E+3	0.000E+0
+#    	19	OC_M1_Excitation	V	both	1.000E-2	0.000E+0
+#
+#    :SCANIT_END:

AFM_thumbs/Thumbs.py

@@ -0,0 +1,463 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+import sys
+import os
+import numpy as np
+import re
+
+# The following is a bit confusing but needed for crontab and ssh under Linux:
+# Matplotlib needs an X-Server, which does not exist when doing, e.g., ssh.
+# In the following we ask if the DISPLAY variable of the Linux system is set.
+# If this is not the case then we tell Python to do something special for
+# matplotlib (use of 'Agg')
+#
+# From: "http://stackoverflow.com/questions/4931376/
+# generating-matplotlib-graphs-without-a-running-x-server"
+# Other solution: matplotlib API, see "http://www.dalkescientific.com/writings/
+# diary/archive/2005/04/23/matplotlib_without_gui.html"
+if sys.platform == "linux2":
+    environ = os.environ
+    if "DISPLAY" not in environ:
+        import matplotlib as mpl
+        mpl.use('Agg')
+import matplotlib.pyplot as plt
+import matplotlib.lines  as mpllines
+from   matplotlib.colors import LinearSegmentedColormap
+
+from AFM_thumbs.Variables import globvar_AFMdata
+from AFM_thumbs.Variables import globvar_AFMdir
+from AFM_thumbs.Variables import globvar_ThumbPara
+from AFM_thumbs.Variables import globvar_thumb_size_x
+from AFM_thumbs.Variables import globvar_thumb_size_y
+from AFM_thumbs.Variables import globvar_thumb_text_width
+from AFM_thumbs.Variables import ID_abbreviations
+from AFM_thumbs.Channel import select_color
+from AFM_thumbs.Channel import invert
+from AFM_thumbs.Colour import reverse_colourmap
+
+# _________________________________________________________________ Definitions
+
+def create_thumb_images(data, image_nr, image_name, data_file_name):
+
+    # If there is a meaningful number in 'globvar_ThumbPara.rms':
+    if re.match("^\d+?\.\d+?$", globvar_ThumbPara.rms) != None:
+
+        # We reshape the array first because we can then better analyze the
+        # data for the contrast adjustment via the rms value.
+        datar = np.reshape(data, data.size)
+
+        # If there are regions in the image that are on the exact same value
+        # then discard them from the statistics analysis! This happens when,
+        # e.g., Nanonis images were not stored until the end of a scanning
+        # frame.
+        where = np.where(np.diff(datar) == 0)
+        # At least the length of a scanning line.
+        if len(where[0]) > float(globvar_AFMdata.x_pixel):
+            datar = np.delete(datar, where)
+
+        # Put the rms value into a float. The factor of 2.0 is to adapt old
+        # values.
+        rms = abs(float(globvar_ThumbPara.rms)) * 2.0
+        # Average value of the data array
+        aver = np.average(datar)
+        # Substrat the average value from the data and consider only the
+        # the absolute deviations from the average.
+        sub = np.abs(np.subtract(datar, aver))
+        # From the absolute deviations, calculate the mean and max value.
+        sub_aver = np.average(sub)
+        sub_max  = np.max(sub)
+
+        # Are there any spikes, so, values that overpass by a factor of 30?
+        index = np.argwhere(sub > 30.0 * sub_aver)
+        if index.size > 0:
+            # We reduce the rms value by a factor of 2.0.
+            rms = rms / 2.0
+            #print(image_nr, image_name, len(index))
+
+        # Cut the data on the top and bottom.
+        data = np.ma.clip(data, aver-sub_aver*rms, aver+sub_aver*rms)
+
+    # This deaktivates the interactive pyplot frame
+    # plt.ioff()
+
+    fig = plt.figure(figsize=(globvar_thumb_size_x, globvar_thumb_size_y))
+    frame = plt.subplot(111)
+
+    # Positioning of the image
+    plt.subplots_adjust(left=0.08,   bottom=None,
+                        right=0.99,  top=1.1,
+                        wspace=None, hspace=None)
+
+    # Image is put in
+    try:
+        float(globvar_AFMdata.x_size)
+    except ValueError:
+        globvar_AFMdata.x_size = "-100.0"
+
+    try:
+        float(globvar_AFMdata.y_size)
+    except ValueError:
+        globvar_AFMdata.y_size = "-100.0"
+
+    imgage = frame.imshow(data,extent=[0,abs(float(globvar_AFMdata.x_size)),
+                                       0,abs(float(globvar_AFMdata.y_size))])
+
+    # What kind of color scale do we have?
+    # Is it a pre-definied color from matplotlib, then it must be a string.
+    if type(select_color(image_nr, globvar_AFMdata.scandir[image_nr])) is str:
+        colormap = select_color(image_nr, globvar_AFMdata.scandir[image_nr])
+
+        if invert(image_nr,globvar_AFMdata.scandir[image_nr]):
+            colormap = reverse_colourmap("ListedColormap", colormap)
+
+    # If it is not a string, then it must be a color definied by ourselves,
+    # so go to here and transform this linear segment into a colormap.
+    else:
+        colormap = LinearSegmentedColormap("Colormap",select_color(image_nr,
+                                           globvar_AFMdata.scandir[image_nr]))
+
+        if invert(image_nr,globvar_AFMdata.scandir[image_nr]):
+            colormap = reverse_colourmap("LinearSegmentedColormap", colormap)
+
+    # Color scale
+    imgage.set_cmap(colormap)
+
+    if globvar_ThumbPara.peek:
+        imgage.set_clim(vmin=np.amin(data), vmax=np.amax(data))
+
+    # The colorbar
+    colorbar = fig.colorbar(imgage, shrink=0.65, aspect=30)
+    for t in colorbar.ax.get_yticklabels():
+        t.set_fontsize('x-small')
+
+    # The ticks and the size of the labels
+    plt.xticks(size = 'x-small')
+    plt.yticks(size = 'x-small')
+
+    # The ticks and their orientation
+    # ... at the bottom
+    lines = frame.get_xticklines()
+    labels = frame.get_xticklabels()
+    for line in lines:
+        line.set_marker(mpllines.TICKDOWN)
+    for label in labels:
+        label.set_y(-0.02)
+    # ... on the left
+    lines = frame.get_yticklines()
+    labels = frame.get_yticklabels()
+    for line in lines:
+        line.set_marker(mpllines.TICKLEFT)
+    for label in labels:
+        label.set_x(-0.02)
+
+    # Some text into the figure
+    # 1. Scanning direction to the bottom right
+    if globvar_AFMdata.scandir[image_nr] == "forward":
+        fig.text(0.83, 0.17, "forward",  fontsize=10)
+    if globvar_AFMdata.scandir[image_nr] == "backward":
+        fig.text(0.83, 0.17, "backward", fontsize=10)
+
+    # 2. Channel to the top right
+    fig.text(0.83, 0.95,
+             globvar_AFMdata.channel[image_nr] + " (" + \
+             globvar_AFMdata.unit[image_nr] + ")",
+             fontsize=11)
+
+    # 3. Text with parameters below the image
+    fig.text(0.035 + float(globvar_ThumbPara.text_x),
+             0.015 + float(globvar_ThumbPara.text_y),
+             image_text(image_name),
+             fontname=globvar_ThumbPara.font,
+             size=int(globvar_ThumbPara.text_size))
+
+    # 4. Average value below color scale
+    data_average = globvar_AFMdata.z_average
+    data_average = str(data_average)
+    data_average = data_average[:data_average.find(".")+2]
+    fig.text(0.83, 0.2,
+             "Aver. (raw)\n" + data_average + " (" + \
+             globvar_AFMdata.unit[image_nr] + ")",
+             fontsize=10)
+
+    # Save image now !
+    image_path = os.path.join(globvar_AFMdir.thumbnail_directory, image_name)
+
+    if globvar_ThumbPara.png:
+        image_path=image_path+".png"
+    else:
+        image_path=image_path+".jpeg"
+
+    plt.savefig(image_path, dpi=int(globvar_ThumbPara.res))
+
+    #plt.close('all')
+    plt.close(fig)
+    plt.clf()
+
+
+def image_text(image_name):
+
+    text_string = image_name + ", "
+
+    if globvar_ThumbPara.date and globvar_AFMdata.date != "":
+        text_string += "--"+globvar_AFMdata.date+"--, "
+    if globvar_ThumbPara.sizenm and globvar_AFMdata.x_size != "" and \
+        globvar_AFMdata.y_size != "":
+        text_string += "Size: " + globvar_AFMdata.x_size + "x" + \
+                        globvar_AFMdata.y_size + ", "
+    if globvar_ThumbPara.sizepx and globvar_AFMdata.x_pixel != "" and \
+        globvar_AFMdata.y_pixel != "":
+        text_string += "Pixl: " + globvar_AFMdata.x_pixel + "x" + \
+                        globvar_AFMdata.y_pixel + ", "
+    if globvar_ThumbPara.offset and globvar_AFMdata.x_off != "" and \
+        globvar_AFMdata.y_off != "":
+        text_string += "Off: " + globvar_AFMdata.x_off + "x" + \
+                        globvar_AFMdata.y_off + ", "
+    # SPECS Nanonis
+    # =============
+    # So far, there is no option(button). This needs to be implemented in future.
+    if globvar_AFMdata.res_freq != "":
+        text_string += "f0: " + globvar_AFMdata.res_freq + ", "
+    if globvar_ThumbPara.gain and globvar_AFMdata.gain != "":
+        text_string += "Gain: " + globvar_AFMdata.gain + ", "
+    if globvar_ThumbPara.gain and globvar_AFMdata.gain_int != "":
+        text_string += "IGain: " + globvar_AFMdata.gain_int + ", "
+    if globvar_ThumbPara.gain and globvar_AFMdata.gain_prop != "":
+        text_string += "PGain: " + globvar_AFMdata.gain_prop + ", "
+    if globvar_ThumbPara.gain and globvar_AFMdata.gain_signal != "":
+        text_string += "SigGain: " + globvar_AFMdata.gain_signal + ", "
+    if globvar_ThumbPara.gain and globvar_AFMdata.gain_xy != "":
+        text_string += "XYGain: " + globvar_AFMdata.gain_xy + ", "
+    if globvar_ThumbPara.gain and globvar_AFMdata.gain_z != "":
+        text_string += "ZGain: " + globvar_AFMdata.gain_z + ", "
+
+    # SPECS Nanonis
+    # =============
+    # So far, there is no option (button). This needs to be implemented
+    # in future.
+    if globvar_AFMdata.scan_updown != "":
+        text_string += globvar_AFMdata.scan_updown.capitalize() + " scan, "
+    if globvar_ThumbPara.speed and globvar_AFMdata.speed != "":
+        # For Dulcinea
+        if " Hz" in globvar_AFMdata.speed:
+            speed = globvar_AFMdata.speed
+            text_string += speed
+        # Otherwise: we now use the scan frequency as a speed because it is
+        # more readable. (2021-02-05)
+        else:
+            speed = float(globvar_AFMdata.speed) / float(globvar_AFMdata.x_size)
+            text_string += "Speed: %.2f" % speed + ", "
+    if globvar_ThumbPara.ampl and globvar_AFMdata.amplitude != "":
+        text_string += "Ampl: " + globvar_AFMdata.amplitude + ", "
+    if globvar_ThumbPara.angle and globvar_AFMdata.angle != "":
+        text_string += "Phi: " + globvar_AFMdata.angle + ", "
+    # Change 2017-06-25
+    # 1. Ugap and Feedback are listed at the end!
+    if globvar_ThumbPara.voltage and globvar_AFMdata.voltage != "":
+        text_string += "Ugap: " + globvar_AFMdata.voltage + ", "
+    if globvar_ThumbPara.feedback and globvar_AFMdata.feedback != "":
+        text_string += "FB: " + globvar_AFMdata.feedback
+
+    # This loop is for building a block of the text introducing some "\n"
+    zaehler1   = 0
+    zaehler2   = 0
+    text_block = ""
+
+    block_length = globvar_thumb_text_width + int(globvar_ThumbPara.text_block)
+
+    while (zaehler1 < len(text_string)):
+
+        if (text_string[zaehler1] == " "):
+            if (zaehler2 > block_length):
+                text_block = text_block + "\n"
+                zaehler2   = 0
+            else:
+                text_block = text_block + text_string[zaehler1]
+
+        else:
+            text_block = text_block + text_string[zaehler1]
+
+        zaehler1 +=1
+        zaehler2 +=1
+
+    return text_block
+
+
+# The function, which creates the thumbnails for spectra
+def create_thumb_spectra(x_data_list,
+                         y_data_list,
+                         image_nr,
+                         image_name,
+                         image_path,
+                         channel_name):
+
+    # Create figure
+    fig   = plt.figure(figsize=(globvar_thumb_size_x,
+                                globvar_thumb_size_y))
+
+    # Positioning of the graph inside the figure
+    plt.subplots_adjust(left=0.17,   bottom=0.3,
+                        right=0.95,  top=0.95,
+                        wspace=None, hspace=None)
+
+    # Plot the whole stuff
+    for x_data, y_data in zip(x_data_list, y_data_list):
+        plt.plot(x_data, y_data)
+
+    # Labels
+    plt.xlabel(globvar_AFMdata.spec_x_label[image_nr] + \
+                                " ("+globvar_AFMdata.spec_x_unit[image_nr]+")")
+    plt.ylabel(globvar_AFMdata.spec_y_label[image_nr] + \
+                                " ("+globvar_AFMdata.spec_y_unit[image_nr]+")")
+
+    if channel_name in ID_abbreviations:
+        channel_name = ID_abbreviations[channel_name]
+
+    # Some text ...
+    # 1. text below the spectra
+    fig.text(0.035 + float(globvar_ThumbPara.text_x),
+             0.035 + float(globvar_ThumbPara.text_y),
+             spectra_text(image_name,image_nr),
+             fontname=globvar_ThumbPara.font,
+             size=int(globvar_ThumbPara.text_size))
+
+    # The channel, measurement number or whatever to the bottom right
+    fig.text(0.92, 0.32,
+             channel_name,
+             fontsize=13,
+             horizontalalignment="right")
+    # The x, y, z(z_offset) position to the bottom left
+    if globvar_AFMdata.spec_position != []:
+        fig.text(0.92, 0.36,
+                 globvar_AFMdata.spec_position[image_nr],
+                 fontsize=13,
+                 horizontalalignment="right")
+
+    # Save image now !
+    plt.savefig(image_path, dpi=int(globvar_ThumbPara.res))
+    plt.close(fig)
+    plt.clf()
+    # Create a white thumbnail image. This is needed as a space filler for
+    # the pdfs afterwards ... . The 'white' thumbnail is created only once.
+    # Name: 'dummy_image.png'. The path to the thumbnail:
+    image_dummy_path=os.path.join(globvar_AFMdir.thumbnail_directory,
+                                  "dummy_image")
+    # If it does not exist, create it.
+    if not os.path.isfile(image_dummy_path+".jpeg"):
+        fig=plt.figure(figsize=(globvar_thumb_size_x,globvar_thumb_size_y))
+        plt.savefig(image_dummy_path, dpi=int(globvar_ThumbPara.res))
+        plt.close(fig)
+        plt.clf()
+
+    return True
+
+
+# The text below a spectrum. The routine has been modified on 2022-01-29,
+# for in particular the Nanonis spectroscopy.
+def spectra_text(image_name, channel):
+
+    # Cut the name if it has become too long!
+    if len(image_name) > 30:
+        image_name = image_name[:30] + "..."
+
+    text_string = image_name + ", "
+
+    if globvar_ThumbPara.date:
+        if globvar_AFMdata.date != "":
+            text_string += "--"+str(globvar_AFMdata.date)+"--, "
+
+    if globvar_AFMdata.spec_points != []:
+        if globvar_AFMdata.spec_points[channel] != "":
+            text_string += "Points: "+str(globvar_AFMdata.spec_points[channel])+", "
+
+    if globvar_AFMdata.spec_feedback != []:
+        if globvar_AFMdata.spec_feedback[channel] != "":
+            text_string += "Feedback: " + \
+                            str(globvar_AFMdata.spec_feedback[channel])+", "
+
+    if globvar_AFMdata.spec_acquisition != []:
+        if globvar_AFMdata.spec_acquisition[channel] != "":
+            text_string += "Acq.time: "+str(float(globvar_AFMdata.spec_acquisition \
+                                                        [channel])*1000.0)+"ms, "
+
+    if globvar_AFMdata.spec_delay != []:
+        if globvar_AFMdata.spec_delay[channel] != "":
+            text_string += "Delay: "+str(float(globvar_AFMdata.spec_delay \
+                                                        [channel])*1000.0)+"ms, "
+
+    if globvar_AFMdata.spec_time != []:
+        if globvar_AFMdata.spec_time[channel] != "":
+            text_string += "Time: "+str(globvar_AFMdata.spec_time[channel]) + "ms, "
+
+    if globvar_ThumbPara.gain:
+        if globvar_AFMdata.gain != "":
+            text_string += "Gain: "+str(globvar_AFMdata.gain)+", "
+    if globvar_ThumbPara.ampl:
+        if globvar_AFMdata.amplitude != "":
+            text_string += "Ampl: "+str(globvar_AFMdata.amplitude)+"nm, "
+
+    # Other spectroscopy data that shall be displayed.
+    if globvar_AFMdata.spec_other != None:
+        text_string += globvar_AFMdata.spec_other
+
+    # Change 2017-06-25
+    # 1. Ugap and Feedback are listed at the end!
+    if globvar_ThumbPara.voltage:
+        if globvar_AFMdata.voltage != "":
+            text_string += "Ugap: "+str(globvar_AFMdata.voltage)+", "
+    if globvar_ThumbPara.feedback:
+        if globvar_AFMdata.feedback != "":
+            text_string += "FB: "+str(globvar_AFMdata.feedback)
+
+    # This while loop is for building a block of the text introducing
+    # some "\n"
+    zaehler1   = 0
+    zaehler2   = 0
+    text_block = ""
+
+    block_length = 50
+
+    while (zaehler1 < len(text_string)):
+
+        if (text_string[zaehler1] == " "):
+            if (zaehler2 > block_length):
+                text_block = text_block + "\n"
+                zaehler2 = 0
+            else:
+                text_block = text_block + text_string[zaehler1]
+        else:
+            text_block = text_block + text_string[zaehler1]
+        zaehler1 +=1
+        zaehler2 +=1
+
+    # If some variables are simply not available, then it might be that there
+    # is a ',' at the end. Remove the ','.
+    if text_block[-1] == ',':
+         text_block = text_block[:-1]
+    if text_block[-2] == ',':
+         text_block = text_block[:-2]
+
+    return text_block

AFM_thumbs/ToolTip.py

@@ -0,0 +1,77 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+# This class implements Tooltips for Tkinter
+# Original source: http://www.voidspace.org.uk/python/weblog/arch_d7_2006_07_01.shtml
+
+from tkinter import *
+
+class ToolTip(object):
+
+    def __init__(self, widget):
+        self.widget = widget
+        self.tipwindow = None
+        self.id = None
+        self.x = self.y = 0
+
+    def showtip(self, text):
+        "Display text in tooltip window"
+        self.text = text
+        if self.tipwindow or not self.text:
+            return
+        x, y, cx, cy = self.widget.bbox("insert")
+        x = x + self.widget.winfo_rootx() + 27
+        y = y + cy + self.widget.winfo_rooty() +27
+        self.tipwindow = tw = Toplevel(self.widget)
+        tw.wm_overrideredirect(1)
+        tw.wm_geometry("+%d+%d" % (x, y))
+        try:
+            # For Mac OS
+            tw.tk.call("::tk::unsupported::MacWindowStyle",
+                       "style", tw._w,
+                       "help", "noActivates")
+        except TclError:
+            pass
+        label = Label(tw, text=self.text, justify=LEFT,
+                      background="#ffffe0", relief=SOLID, borderwidth=1,
+                      font=("tahoma", "8", "normal"))
+        label.pack(ipadx=1)
+
+    def hidetip(self):
+        tw = self.tipwindow
+        self.tipwindow = None
+        if tw:
+            tw.destroy()
+
+def create_tool_tip(widget, text):
+    toolTip = ToolTip(widget)
+    def enter(event):
+        toolTip.showtip(text)
+    def leave(event):
+        toolTip.hidetip()
+    widget.bind('<Enter>', enter)
+    widget.bind('<Leave>', leave)
+    widget.bind('<Button-1>', leave)

AFM_thumbs/Variables.py

@@ -0,0 +1,648 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+
+#
+#
+# __________ Change the name and path of the config file  ___________ from here
+#
+#
+#
+globvar_configfile      = "Config_AFM_thumbs.conf"
+globvar_configfile_path = "./AFM_thumbs/"
+
+# Example for Linux
+# globvar_configfile_path = "/home/user/bin/AFM_thumbs/"
+# globvar_configfile      = "Config_AFM_thumbs.conf"
+#
+# Example for Windows
+# globvar_configfile_path = "C:\Users\Username\Desktop\AFmThumbnails\" \
+#                           "AFM_thumbs"
+# globvar_configfile      = "Config_AFM_thumbs.conf"
+
+#
+#
+#
+# _____________________________________________________________________ to here
+#
+#
+#
+
+
+
+
+
+# ____________________________________________________________ Global variables
+
+#    DO NOT CHANGE ANYTHING BELOW, OTHERWISE YOU KNOW WHAT TO DO !
+
+import time
+
+globvar_contributions   = "Reinhard Olbrich (testing)\n" \
+                          "Matthias Temmen (testing)\n" \
+                          "Alexander v Schmidtsfeld (testing)\n" \
+                          "..."
+
+globvar_year            = "2022-03-02"
+globvar_version         = "3.001"
+
+globvar_spaces          = "    "
+globvar_name            = "AFM thumbs v" + globvar_version
+globvar_bar_title       = (globvar_name + "  -  " +
+                           globvar_year)
+globvar_note            = ("Version " + globvar_version + " (" +
+                           globvar_year + ")\n"
+                           "www.development.root-1.de\n\n" +
+                           "Coordinated by:\n\n" +
+                           "Clemens Barth\n" +
+                           "(barth@root-1.de)\n\n" +
+                           "    and\n\n" +
+                           "Niklas Rethmann " +
+                           "(nrethmann@uni-osnabrueck.de)\n\n"+
+                           "Contributions from:\n" +
+                           globvar_contributions)
+
+globvar_console         = ("\n\n"+
+                           globvar_spaces +
+                           globvar_name + "  -  " +
+                           globvar_year + "\n" +
+                           globvar_spaces + "www.root-1.de\n\n" +
+                           globvar_spaces + "Today: " +
+                           time.strftime("%d-%m-%Y") +
+                           ", Time: " +
+                           time.strftime("%H:%M:%S"))
+
+globvar_python_directory = "AFM_thumbs"
+globvar_default_config = "Config_default.conf"
+
+globvar_thumb_size_x = 5.0
+globvar_thumb_size_y = 6.0
+globvar_thumb_text_width = 40
+
+globvar_timepassed_1 = ("\n" +
+                        globvar_spaces +
+                        "Overall passed time: ")
+globvar_timepassed_2 = "--- %d days --- %d hours --- %d minutes " + \
+                       "--- %0.3f seconds ---\n\n"
+
+# _______________________________________________________________ SPECS Nanonis
+
+SPECS_Nanonis_images_must_exist = ".sxm"
+SPECS_Nanonis_spectroscopy_must_exist = ".dat"
+
+# _______________________________________________________________ Omicron SCALA
+
+Omicron_SCALA_must_exist = ".par"
+Omicron_SCALA_forward  = ".tf"
+Omicron_SCALA_backward = ".tb"
+
+# ____________________________________________________________ Nanotec DULCINEA
+
+Nanotec_DULCINEA_must_exist = ".f.top"
+Nanotec_DULCINEA_forward  = ".f."
+Nanotec_DULCINEA_backward = ".b."
+Nanotec_DULCINEA_suffix = ["f.top","f.ch4","f.ch5","f.ch6","f.ch7","f.ch8",
+                           "b.top","b.ch4","b.ch5","b.ch6","b.ch7","b.ch8",
+                           ".f.1st.Auxfeed", ".f.2nd.Auxfeed",
+                           ".b.1st.Auxfeed", ".b.2nd.Auxfeed"]
+
+# _________________________________________________________________________ RHK
+
+RHK_must_exist = [".SM4", ".sm4"]
+RHK_all_directions = ["all", "All", "ALL", "A", "a"]
+RHK_forward_direction = ["forward", "Forward", "FORWARD", "for",
+                         "For", "FOR", "f", "F"]
+RHK_backward_direction = ["backward", "Backward", "BACKWARD",
+                          "back", "Back", "BACK", "b", "B"]
+
+
+RHK_message_direction = "    --- Some RHK files could be detected! ---\n\n" \
+                        "Choose scan direction: (f)orward" \
+                        ", (b)ackward, (a)ll: "
+# ____________________________________________________________________ Tooltips
+
+# Arrangement
+TT_n_col = "Number of images in a column \n\n\
+This option lets you specific how \n\
+many images have to be in a column \n\n"
+
+TT_n_row = "Number of images in arow \n\n\
+This option lets you specific how \n\
+many images have to be in a row \n\n"
+
+TT_rms = "Contrast (times rms value) \n\n\
+This option lets you specific the \n\
+contrast of the images"
+
+TT_res = "Image resolution factor (in percent) \n\n\
+This option lets you specific the \n\
+resolution of the images"
+
+TT_qual = "Image quality \n\n\
+This option lets you specific the \n\
+quality of the images"
+
+# Position
+TT_size         = "Font size \n\n\
+This option lets you specific the \n\
+font size of the image text"
+
+TT_dx_pos       = "dX position (in percent) \n\n\
+This option lets you shift the  \n\
+image text left or right"
+
+TT_dy_pos       = "dY position (in percent) \n\n\
+This option lets you shift the  \n\
+image text up or down"
+
+TT_dw           = "dWidth of text (in characters) \n\n\
+This option lets you specific the \n\
+width of the image text."
+
+# Specification
+TT_file_ex      = "This option lets you specific which \n\
+format should be considered"
+
+TT_master_dir   = "This option lets you specific which \n\
+folders should be considered. \n\
+Should only be used together with the \"All sub-directories\" option"
+
+TT_filename = "This option lets you specific which \n\
+files should be considered."
+
+# Param
+TT_date     = "Include date and time \n\
+in the image text"
+
+TT_size_nm  = "Include size in nanometer \n\
+in the image text"
+
+TT_size_px  = "Include size in pixel \n\
+in the image text"
+
+TT_off      = "Include offset in nanometer \n\
+in the image text"
+
+TT_vol      = "Includes voltage (Volt) \n\
+in the image text"
+
+TT_feed     = "Includes feedback\n\
+in the image text"
+
+TT_loop     = "Includes loop gain\n\
+in the image text"
+
+TT_speed    = "Include acquisition speed in s/line \n\
+in the image text"
+
+TT_amp      = "Include amplitude\n\
+in the image text"
+
+TT_angle    = "Include angle in degree \n\
+in the image text"
+
+# Other
+TT_thumb_before = "Delete thumbs before all \n\n\
+With this option enabled, the thumbnail directory \n\
+will be deleted before a pdf thumbnail is created."
+
+TT_thumb_after  = "Delete thumbs after all \n\n\
+With this option enabled, the thumbnail directory \n\
+will be deleted after a pdf thumbnail has been created."
+
+TT_extra_dir    = "Extra directory \n\n\
+Creates extra WSxM and Gwyddion directories. \n\
+Two new directories are created in the directory one level above.\n\
+The directory structure(s) of the AFM data is(are) conserved."
+
+TT_pdfs         = "Replace existing pdfs \n\n\
+Existing pdf files are replaced by new ones."
+
+TT_subdirs      = "All sub-directories \n\n\
+All subdirectories of the selected directory (Button 'Choose directory')\n\
+are also considered. The respective pdf files are placed into the\n\
+directory one level above."
+
+TT_png          = "Create images in png format \n\n\
+Change the image format of the thumbnails from jpeg to png."
+
+TT_spektral     = " Include spectras \n\n\
+With this option images of spectra are included\n\
+into the pdf file."
+
+TT_peek         = " Set color scale to peek-peek \n\n\
+This option permits setting the color scale of the \n\
+images to peek-to-peek values."
+
+TT_minimum_on_zero = " Set minimum value on zero \n\n\
+This option permits setting the minimum value of \n\
+the images onto zero."
+
+TT_Reich        = "Reichling Special Options \n\n\
+This option triggers the following features: \n\
+        - Colour for Kelvin images is set to gray \n\
+        - One df image is inverted"
+
+# _____________________________________________________________________ For all
+
+ID_topography = r"[Tt]op(ograph(y|ie))?|TOP(OGRAPH(Y|IE))?|[Zz]"
+ID_amplitude = r"[Aa]mplitude|AMPLITUDE|[Aa]mpl?\.?|AMPL?\.?"
+ID_kelvin = r"[Kk]el(vin)?|KEL(VIN)?"
+ID_kelvin_err = r"[Ee]rr(or)?|ERR(OR)?|[Ll]1[Xx]|KELVIN_ERR"
+ID_df = r"[Dd][Ff]"
+ID_df_fil = r"[Ff]iltered|FILTERED"
+ID_dissipation = r"[Dd](issipation)?|DISSIPATION|[Dd]amp|DAMP|[Pp][Ll][Ll]"
+ID_excitation = r"[Ee]xcitation|EXCITATION"
+ID_ext1 = r"[Ee]xt(ernal)?( )?1|[Ee]XT(ERNALl)?( )?1"
+ID_ext2 = r"[Ee]xt(ernal)?( )?2|[Ee]XT(ERNALl)?( )?2"
+ID_phase = r"[Pp]ha(se)?|PHA(SE)?"
+
+ID_list = [ID_topography, ID_amplitude,   ID_kelvin,     ID_kelvin_err, ID_df,
+           ID_df_fil,     ID_dissipation, ID_excitation, ID_ext1,       ID_ext2,
+           ID_phase]
+
+ID_abbreviations = {"Topography" : "Z", "filtered df":"df_fil", "Amplitude":"A",
+                    "Dissipation": "D", "Kelvin Error": "KPFM_err",
+                    "Ext 1": "Ext1", "Ext 2": "Ext2", "Excitation": "A_ext",
+                    "Phase": "Phase", "Kelvin": "KPFM", "DF_DIG": "df",
+                    "EXT": "Ext", "EXT1": "Ext1", "EXT2": "Ext2"}
+
+# ______________________________________________________________________ Colors
+
+# Colors: see http://matplotlib.org/examples/color/colormaps_reference.html
+# Note that many other colours still exist, pre-defined!
+
+globvar_ttk_Combobox = 10
+
+globvar_color_options = ["Grey", "Red", "Red2", "Blue", "Blue2", "Green",
+                         "ReiGreen", "Yellow", "Gold",
+                         "Orange", "Purples",
+                         "BlueGreen", "GreenBlu",
+                         "BluePurple", "PurpleBlue", "PupleRed", "RedPurple",
+                         "OrangeRed",
+                         "PurpleBlueGreen",
+                         "Gnuplot", "Gnuplot2", "Ocean", "Rainbow",
+                         "Gist_rainbow", "HSV", "Gist_stern", "Jet",
+                         "Hot", "AFMhot", "Bone", "Gist_heat"]
+
+# This red is very nice and also ...
+Color_Red = {'red':  ((0.0,  0.0, 0.0),
+                      (0.333,  0.6, 0.6),
+                      (0.666,  1.0, 1.0),
+                      (1.0,  1.0, 1.0)),
+            'green': ((0.0,  0.0, 0.0),
+                      (0.333,  0.0, 0.0),
+                      (0.666,  0.0, 0.0),
+                      (1.0,  1.0, 1.0)),
+            'blue':  ((0.0,  0.0, 0.0),
+                      (0.333,  0.0, 0.0),
+                      (0.666,  0.0, 0.0),
+                      (1.0,  1.0, 1.0))}
+
+# ... this yellow, ...
+Color_Yellow = {'red':  ((0.0,  0.0, 0.0),
+                         (0.333,  0.7, 0.7),
+                         (0.666,  1.0, 1.0),
+                         (1.0,  1.0, 1.0)),
+               'green': ((0.0,  0.0, 0.0),
+                         (0.333,  0.8, 0.8),
+                         (0.666,  1.0, 1.0),
+                         (1.0,  1.0, 1.0)),
+               'blue':  ((0.0,  0.0, 0.0),
+                         (0.333,  0.0, 0.0),
+                         (0.666,  0.0, 0.0),
+                         (1.0,  1.0, 1.0))}
+
+# ... this blue, ...
+Color_Blue = {'red':  ((0.0,  0.0, 0.0),
+                       (0.3,  0.0, 0.0),
+                       (0.7,  0.9, 0.9),
+                       (1.0,  1.0, 1.0)),
+             'green': ((0.0,  0.0, 0.0),
+                       (0.3,  0.0, 0.0),
+                       (0.7,  0.9, 0.9),
+                       (1.0,  1.0, 1.0)),
+             'blue':  ((0.0,  0.0, 0.0),
+                       (0.7,  0.9, 0.9),
+                       (1.0,  1.0, 1.0))}
+
+# ... gold and of course ...
+Color_Gold = {'red':  ((0.0,  0.0, 0.0),
+                       (0.333,  0.545098039216, 0.545098039216),
+                       (0.666,  0.803921568627, 0.803921568627),
+                       (1.0,  1.0, 1.0)),
+             'green': ((0.0,  0.0, 0.0),
+                       (0.333,  0.458823529412, 0.458823529412),
+                       (0.666,  0.678431372549, 0.678431372549),
+                       (1.0,  1.0, 1.0)),
+             'blue':  ((0.0,  0.0, 0.0),
+                       (0.333,  0.0, 0.0),
+                       (0.666,  0.0, 0.0),
+                       (1.0,  1.0, 1.0))}
+
+# ... the famous green colour from the Michael Reichling group.
+Color_ReiGreen = {'red':  ((0.0,  0.0, 0.0),
+                           (0.381166,  0.0, 0.0),
+                           (0.672646,  0.471014, 0.471014),
+                           (1.0,  1.0, 1.0)),
+                'green':    ((0.0,  0.0, 0.0),
+                           (0.381166,  0.381166, 0.381166),
+                           (0.672646,  0.672646, 0.672646),
+                           (1.0,  1.0, 1.0)),
+                'blue':     ((0.0,  0.0, 0.0),
+                           (0.381166,  0.0, 0.0),
+                           (0.672646,  0.0, 0.0),
+                           (1.0,  1.0, 1.0))}
+
+Color_list = ["Greys_r", "Reds_r", Color_Red, "Blues_r", Color_Blue, "Greens_r",
+              Color_ReiGreen, Color_Yellow, Color_Gold,
+              "Oranges_r", "Purples_r",
+              "BuGn_r", "GnBu_r",
+              "BuPu_r", "PuBu_r", "PuRd_r", "RdPu_r",
+              "OrRd_r",
+              "PuBuGn_r",
+              "gnuplot", "gnuplot2", "ocean", "rainbow",
+              "gist_rainbow", "hsv", "gist_stern", "jet",
+              "hot", "afmhot", "bone", "gist_heat"]
+
+globvar_color_dict = {name:color for name, color in \
+                      zip(globvar_color_options, Color_list)}
+
+# ___________________________________________________________________ Fonts
+
+globvar_fonts = ['Courier', 'Courier New', 'Arial', 'FreeSans']
+
+globvar_bad_fonts = ['NotoColorEmoji.ttf']
+
+# ___________________________________________________________________ Classes
+
+class CLASSparameters(object):
+    def __init__(self, row, col, rms, res, font,
+                       thumbs_before, thumbs_after, peek, minimum_on_zero,
+                       png, date, sizenm,
+                       sizepx, offset, voltage, feedback, gain,
+                       speed, ampl, text_block, text_block_height,
+                       text_size, pdfs, text_x, text_y, angle,
+                       extra_direct, extension, masterdir, filename, jpeg,
+                       channel_names, thumbs, line_fit, plane_fit, invert,
+                       colors, geometry_x, geometry_y, spektra):
+        self.row = row
+        self.col = col
+        self.rms = rms
+        self.res = res
+        self.font = font
+        self.thumbs_before = thumbs_before
+        self.thumbs_after = thumbs_after
+        self.peek = peek
+        self.minimum_on_zero = minimum_on_zero
+        self.png = png
+        self.date = date
+        self.sizenm = sizenm
+        self.sizepx = sizepx
+        self.offset = offset
+        self.voltage = voltage
+        self.feedback = feedback
+        self.gain = gain
+        self.speed = speed
+        self.ampl = ampl
+        self.text_block = text_block
+        self.text_block_height = text_block_height
+        self.text_size = text_size
+        self.pdfs = pdfs
+        self.text_x = text_x
+        self.text_y = text_y
+        self.angle = angle
+        self.extra_direct = extra_direct
+        self.extension = extension
+        self.masterdir = masterdir
+        self.filename = filename
+        self.jpeg = jpeg
+        self.channel_names = channel_names
+        self.thumbs = thumbs
+        self.line_fit = line_fit
+        self.plane_fit = plane_fit
+        self.invert = invert
+        self.colors = colors
+        self.geometry_x = geometry_x
+        self.geometry_y = geometry_y
+        self.spektra = spektra
+
+class CLASSdir(object):
+    def __init__(self, working_directory, pdf_path,
+                 thumbnail_directory, data_directory_name):
+        self.working_directory = working_directory
+        self.pdf_path = pdf_path
+        self.thumbnail_directory = thumbnail_directory
+        self.data_directory_name = data_directory_name
+
+
+class CLASSdata(object):
+    __slots__ = ('date', 'x_size', 'y_size', 'x_pixel', 'y_pixel',
+                 'x_off', 'y_off',
+                 'voltage', 'measurement_type', 'feedback',
+                 'gain', 'gain_prop', 'gain_int', 'gain_xy',
+                 'gain_signal', 'gain_z',
+                 'speed', 'amplitude', 'angle', 'scan_updown',
+                 'sweep_f0', 'sweep_phase', 'sweep_A_exec', 'sweep_Q',
+                 'NONE',
+                 'datfile', 'channel', 'unit',
+                 'z_average', 'z_calibration', 'z_factor', 'z_offset', 'z_min',
+                 'z_max', 'res_freq', 'z_amplitude',
+                 'scandir', 'spec_x_unit', 'spec_x_label',
+                 'spec_y_unit', 'spec_y_label', 'spec_y_factor',
+                 'spec_points', 'spec_feedback', 'spec_acquisition',
+                 'spec_delay', 'spec_time', 'spec_position', 'spec_files',
+                 'spec_other')
+    def __init__(self,
+                 date,
+                 x_size,
+                 y_size,
+                 x_pixel,
+                 y_pixel,
+                 x_off,
+                 y_off,
+                 voltage,
+                 measurement_type,
+                 feedback,
+                 gain,
+                 gain_prop,
+                 gain_int,
+                 gain_xy,
+                 gain_signal,
+                 gain_z,
+                 speed,
+                 res_freq,
+                 amplitude,
+                 angle,
+                 scan_updown,
+                 sweep_f0,
+                 sweep_phase,
+                 sweep_A_exec,
+                 sweep_Q,
+                 #
+                 # From here to end: lists
+                 #
+                 NONE,
+                 datfile,
+                 channel,
+                 unit,
+                 z_average,
+                 z_calibration,
+                 z_factor,
+                 z_offset,
+                 z_min,
+                 z_max,
+                 z_amplitude,
+                 scandir,
+                 spec_x_unit,
+                 spec_x_label,
+                 spec_y_unit,
+                 spec_y_label,
+                 spec_y_factor,
+                 spec_points,
+                 spec_feedback,
+                 spec_acquisition,
+                 spec_delay,
+                 spec_time,
+                 spec_position,
+                 spec_files,
+                 spec_other):
+        self.date = date
+        self.x_size = x_size
+        self.y_size = y_size
+        self.x_pixel = x_pixel
+        self.y_pixel = y_pixel
+        self.x_off = x_off
+        self.y_off = y_off
+        self.voltage = voltage
+        self.measurement_type = measurement_type # SPECS Nanonis
+        self.feedback = feedback                 # I, df, etc.
+        self.gain = gain                         # SCALA
+        self.gain_prop = gain_prop               # DULCINEA
+        self.gain_int  = gain_int                # DULCINEA
+        self.gain_xy = gain_xy                   # DULCINEA
+        self.gain_signal = gain_signal           # DULCINEA
+        self.gain_z = gain_z                     # DULCINEA
+        self.speed = speed
+        self.res_freq = res_freq
+        self.amplitude = amplitude
+        self.angle = angle
+        self.scan_updown = scan_updown           # SPECS Nanonis
+        self.sweep_f0 = sweep_f0                 # SPECS Nanonis
+        self.sweep_phase = sweep_phase           # SPECS Nanonis
+        self.sweep_A_exec = sweep_A_exec         # SPECS Nanonis
+        self.sweep_Q = sweep_Q                   # SPECS Nanonis
+        self.NONE = NONE                         # This is a dummy ...
+        #
+        # From here to end: lists
+        #
+        self.datfile = datfile
+        self.channel = channel
+        self.unit = unit
+        self.z_average = z_average               # float, is set during runtime
+        self.z_calibration = z_calibration
+        self.z_factor = z_factor                 # DULCINEA, not used
+        self.z_offset = z_offset                 # SPECS Nanonis
+        self.z_amplitude = z_amplitude
+        self.z_min = z_min                       # DULCINEA, not used
+        self.z_max = z_max                       # DULCINEA, not used
+        self.scandir = scandir
+        self.spec_x_unit = spec_x_unit
+        self.spec_x_label = spec_x_label
+        self.spec_y_unit = spec_y_unit
+        self.spec_y_label = spec_y_label
+        self.spec_y_factor = spec_y_factor
+        self.spec_points = spec_points
+        self.spec_feedback = spec_feedback
+        self.spec_acquisition = spec_acquisition
+        self.spec_delay = spec_delay
+        self.spec_time = spec_time
+        self.spec_position = spec_position
+        self.spec_files = spec_files
+        self.spec_other = spec_other             # This can be used for any properties.
+
+class CLASSLinalg(object):
+    __slots__ = ('plane_M512', 'plane_M1024',
+                 'plane_x_vec512', 'plane_y_vec512',
+                 'plane_x_vec1024', 'plane_y_vec1024',
+                 'line_M512', 'line_M1024',
+                 'line_x_vec512', 'line_x_vec1024')
+    def __init__(self, plane_M512, plane_M1024,
+                       plane_x_vec512, plane_y_vec512,
+                       plane_x_vec1024, plane_y_vec1024,
+                       line_M512, line_M1024,
+                       line_x_vec512,line_x_vec1024):
+        self.plane_M512  = plane_M512
+        self.plane_M1024 = plane_M1024
+        self.plane_x_vec512  = plane_x_vec512
+        self.plane_y_vec512  = plane_y_vec512
+        self.plane_x_vec1024 = plane_x_vec1024
+        self.plane_y_vec1024 = plane_y_vec1024
+        self.line_M512 = line_M512
+        self.line_M1024 = line_M1024
+        self.line_x_vec512 = line_x_vec512
+        self.line_x_vec1024 = line_x_vec1024
+
+
+# The next 2 classes are used specifically for the RHK routine.
+class CLASSRHK_position_counter(object):
+    def __init__(self, position):
+        self.position = position
+
+    def add(self):
+        self.position += 1
+
+class CLASSRHK_direction_request(object):
+    def __init__(self, direction = all):
+        self.direction = direction
+
+class CLASSRHK_true(object):
+    def __init__(self, true = False):
+        self.true = true
+
+globvar_LINALG = CLASSLinalg(None,None,None,None,None,None,None,None,None,None)
+
+# The global variables 'globvar_AFMdata' and 'globvar_ThumbPara' are created!
+globvar_AFMdata = CLASSdata(None,None,None,None,None,None,None,None,None,None,
+                            None,None,None,None,None,None,None,None,None,None,
+                            None,None,None,None,None,None,
+                            [],[],[], None, [],[],[],[],[],[],[],
+                            [],[],[],[],[],[],[],[], [], [], [], [], None)
+
+globvar_AFMdir  = CLASSdir(None,None,None,None)
+
+globvar_ThumbPara = CLASSparameters(None, None, None, None, None,
+                           False, False, False, False, False, False,
+                           False, False, False, False, False,
+                           False, False, False,
+                           0, 0, 0, False, 0, 0, False,
+                           False, None, None, None, 0,
+                           [], [], [], [], [], [],
+                           [], [], None)
+
+# For RHK
+RHK_PositionCounter = CLASSRHK_position_counter(None)
+RHK_special = CLASSRHK_true(False)

AFM_thumbs/Variables.py~

@@ -0,0 +1,568 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#
+
+
+#
+#
+# __________ Change the name and path of the config file  ___________ from here
+#
+#
+#
+globvar_configfile      = "Config_AFM_thumbs.conf"
+globvar_configfile_path = "./AFM_thumbs/"
+
+"""
+Example for Linux
+globvar_configfile_path = "/home/user/bin/AFM_thumbs/" 
+globvar_configfile      = "Config_AFM_thumbs.conf"
+
+Example for Windows
+globvar_configfile_path = "C:\Users\Username\Desktop\AFmThumbnails\" \
+                          "AFM_thumbs"
+globvar_configfile      = "Config_AFM_thumbs.conf"
+"""
+#
+#
+#
+# _____________________________________________________________________ to here
+#
+#
+#
+
+
+
+
+
+# ____________________________________________________________ Global variables
+
+#    DO NOT CHANGE ANYTHING BELOW, OTHERWISE YOU KNOW WHAT TO DO !
+
+import time
+
+globvar_year            = "2016-01-15"
+globvar_version         = "2.2"
+
+globvar_spaces          = "    "
+globvar_name            = "AFM thumbs v" + globvar_version
+globvar_bar_title       = (globvar_name + "   " + 
+                           globvar_year)
+globvar_note            = ("Coordinated by:\n\nClemens Barth\n" +
+                           "(barth@root-1.de)\n\n" +
+                           "    and\n\n" +
+                           "Niklas Rethmann (nrethmann@uni-osnabrueck.de)\n\n"+                    
+                           globvar_year + "\n\n"
+                           "www.root-1.de")
+globvar_console         = ("\n\n"+
+                           globvar_spaces +
+                               globvar_name + 
+                               "" + 
+                               globvar_year + "\n" + 
+                           globvar_spaces + "www.root-1.de\n" +
+                           globvar_spaces + "Date: " + 
+                               time.strftime("%d-%m-%Y") + 
+                               ", Time: " +
+                               time.strftime("%H:%M:%S"))
+
+globvar_python_directory = "AFM_thumbs"
+globvar_default_config = "Config_default.conf"
+
+globvar_thumb_size_x = 5.0
+globvar_thumb_size_y = 5.0
+globvar_thumb_text_width = 50
+
+globvar_timepassed_1 = ("\n" +
+                        globvar_spaces + 
+                        "Overall passed time: ")
+globvar_timepassed_2 = "--- %d days --- %d hours --- %d minutes " + \
+                       "--- %0.3f seconds ---\n\n"
+
+# _______________________________________________________________ Omicron SCALA
+
+Omicron_SCALA_must_exist = ".par"
+Omicron_SCALA_forward  = ".tf"
+Omicron_SCALA_backward = ".tb"
+
+# ____________________________________________________________ Nanotec DULCINEA
+
+Nanotec_DULCINEA_must_exist = ".f.top"
+Nanotec_DULCINEA_forward  = ".f."
+Nanotec_DULCINEA_backward = ".b."
+Nanotec_DULCINEA_suffix = ["f.top","f.ch4","f.ch5","f.ch6","f.ch7","f.ch8", 
+                           "b.top","b.ch4","b.ch5","b.ch6","b.ch7","b.ch8",
+                           ".f.1st.Auxfeed", ".f.2nd.Auxfeed",
+                           ".b.1st.Auxfeed", ".b.2nd.Auxfeed"]
+                           
+# _________________________________________________________________________ RHK
+                           
+RHK_must_exist = [".SM4", ".sm4"]
+RHK_all_directions = ["all", "All", "ALL", "A", "a"]
+RHK_forward_direction = ["forward", "Forward", "FORWARD", "for", 
+                         "For", "FOR", "f", "F"]
+RHK_backward_direction = ["backward", "Backward", "BACKWARD", 
+                          "back", "Back", "BACK", "b", "B"]
+
+
+RHK_message_direction = "    --- Some RHK files could be detected! ---\n\n" \
+                        "Choose scan direction: (f)orward" \
+                        ", (b)ackward, (a)ll: "
+# ____________________________________________________________________ Tooltips
+
+# Arrangement
+TT_n_col = "Number of images in a column \n\n\
+This option lets you specific how \n\
+many images have to be in a column \n\n"
+
+TT_n_row = "Number of images in arow \n\n\
+This option lets you specific how \n\
+many images have to be in a row \n\n"
+
+TT_rms = "Contrast (times rms value) \n\n\
+This option lets you specific the \n\
+contrast of the images"
+
+TT_res = "Image resolution factor (in percent) \n\n\
+This option lets you specific the \n\
+resolution of the images"
+
+TT_qual = "Image quality \n\n\
+This option lets you specific the \n\
+quality of the images"
+
+# Position
+TT_size         = "Font size \n\n\
+This option lets you specific the \n\
+font size of the image text"
+
+TT_dx_pos       = "dX position (in percent) \n\n\
+This option lets you shift the  \n\
+image text left or right"
+
+TT_dy_pos       = "dY position (in percent) \n\n\
+This option lets you shift the  \n\
+image text up or down"
+
+TT_dw           = "dWidth of text (in characters) \n\n\
+This option lets you specific the \n\
+width of the image text."
+
+# Specification
+TT_file_ex      = "This option lets you specific which \n\
+format should be considered"
+
+TT_master_dir   = "This option lets you specific which \n\
+folders should be considered. \n\
+Should only be used together with the \"All sub-directories\" option" 
+
+TT_filename = "This option lets you specific which \n\
+files should be considered."
+
+# Param
+TT_date     = "Include date and time \n\
+in the image text"
+
+TT_size_nm  = "Include size in nanometer \n\
+in the image text"
+
+TT_size_px  = "Include size in pixel \n\
+in the image text"
+
+TT_off      = "Include offset in nanometer \n\
+in the image text"
+
+TT_vol      = "Includes voltage (Volt) \n\
+in the image text"
+
+TT_feed     = "Includes feedback\n\
+in the image text"
+
+TT_loop     = "Includes loop gain\n\
+in the image text"
+
+TT_speed    = "Include acquisition speed in s/line \n\
+in the image text"
+
+TT_amp      = "Include amplitude\n\
+in the image text"
+
+TT_angle    = "Include angle in degree \n\
+in the image text"
+
+# Other
+TT_thumb_before = "Delete thumbs before all \n\n\
+With this option enabled, the thumbnail directory \n\
+will be deleted before a pdf thumbnail is created."
+                    
+TT_thumb_after  = "Delete thumbs after all \n\n\
+With this option enabled, the thumbnail directory \n\
+will be deleted after a pdf thumbnail has been created."
+
+TT_extra_dir    = "Extra directory \n\n\
+Creates extra WSxM and Gwyddion directories. \n\
+Two new directories are created in the directory one level above.\n\
+The directory structure(s) of the AFM data is(are) conserved."
+
+TT_pdfs         = "Replace existing pdfs \n\n\
+Existing pdf files are replaced by new ones."
+
+TT_subdirs      = "All sub-directories \n\n\
+All subdirectories of the selected directory (Button 'Choose directory')\n\
+are also considered. The respective pdf files are placed into the\n\
+directory one level above."
+
+TT_png          = "Create images in png format \n\n\
+Change the image format of the thumbnails from jpeg to png."
+
+TT_spektral     = " Include spectras \n\n\
+With this option images of spectra are included\n\
+into the pdf file."
+
+TT_peek         = " Set color scale to peek-peek \n\n\
+This option permits setting the color scale of the \n\
+images to peek-to-peek values."
+
+TT_minimum_on_zero = " Set minimum value on zero \n\n\
+This option permits setting the minimum value of \n\
+the images onto zero."
+                 
+TT_Reich        = "Reichling Special Options \n\n\
+This option triggers the following features: \n\
+        - Colour for Kelvin images is set to gray \n\
+        - One df image is inverted"
+
+# _____________________________________________________________________ For all
+                            
+ID_topography = r"[Tt]op(ograph(y|ie))?|TOP(OGRAPH(Y|IE))?|[Zz]"
+ID_amplitude = r"[Aa]mplitude|AMPLITUDE|[Aa]mpl?\.?|AMPL?\.?"
+ID_kelvin = r"[Kk]el(vin)?|KEL(VIN)?"
+ID_kelvin_err = r"[Ee]rr(or)?|ERR(OR)?|[Ll]1[Xx]"
+ID_df = r"[Dd][Ff]"
+ID_df_fil = r"[Ff]iltered|FILTERED"
+ID_dissipation = r"[Dd](issipation)?|DISSIPATION|[Dd]amp|DAMP|[Pp][Ll][Ll]"
+ID_excitation = r"[Ee]xcitation|EXCITATION"
+ID_ext1 = r"[Ee]xt(ernal)?( )?1|[Ee]XT(ERNALl)?( )?1"
+ID_ext2 = r"[Ee]xt(ernal)?( )?2|[Ee]XT(ERNALl)?( )?2"
+ID_phase = r"[Pp]ha(se)?|PHA(SE)?"
+
+ID_list = [ID_topography, ID_amplitude, ID_kelvin, ID_kelvin_err, ID_df, 
+           ID_df_fil, ID_dissipation, ID_excitation, ID_ext1, ID_ext2, ID_phase]
+           
+ID_abbreviations = {"Topography" : "Z", "filtered df":"df_fil", "Amplitude":"A",
+                    "Dissipation": "D", "Kelvin Error": "KPFM_err", 
+                    "Ext 1": "Ext1", "Ext 2": "Ext2", "Excitation": "A_ext",
+                    "Phase": "Phase", "Kelvin": "KPFM", "DF_DIG": "df",
+                    "EXT": "Ext", "EXT1": "Ext1", "EXT2": "Ext2"}
+
+# ______________________________________________________________________ Colors
+
+# Colors: see http://matplotlib.org/examples/color/colormaps_reference.html
+# Note that many other colours still exist, pre-defined!
+
+globvar_ttk_Combobox = 10
+
+globvar_color_options = ["Grey", "Red", "Red2", "Blue", "Blue2", "Green", 
+                         "ReiGreen", "Yellow", "Gold",
+                         "Orange", "Purples", 
+                         "BlueGreen", "GreenBlu",
+                         "BluePurple", "PurpleBlue", "PupleRed", "RedPurple",
+                         "OrangeRed",
+                         "PurpleBlueGreen",
+                         "Gnuplot", "Gnuplot2", "Ocean", "Rainbow", 
+                         "Gist_rainbow", "HSV", "Gist_stern", "Jet",
+                         "Hot", "AFMhot", "Bone", "Gist_heat"]
+
+# This red is very nice and also ...
+Color_Red = {'red':  ((0.0,  0.0, 0.0),
+                   (0.333,  0.6, 0.6),
+                   (0.666,  1.0, 1.0),
+                   (1.0,  1.0, 1.0)),
+         'green': ((0.0,  0.0, 0.0),
+                   (0.333,  0.0, 0.0),
+                   (0.666,  0.0, 0.0),
+                   (1.0,  1.0, 1.0)),
+         'blue':  ((0.0,  0.0, 0.0),
+                   (0.333,  0.0, 0.0),
+                   (0.666,  0.0, 0.0),
+                   (1.0,  1.0, 1.0))}
+                   
+# ... this yellow, ...
+Color_Yellow = {'red':  ((0.0,  0.0, 0.0),
+                   (0.333,  0.7, 0.7),
+                   (0.666,  1.0, 1.0),
+                   (1.0,  1.0, 1.0)),
+         'green': ((0.0,  0.0, 0.0),
+                   (0.333,  0.8, 0.8),
+                   (0.666,  1.0, 1.0),
+                   (1.0,  1.0, 1.0)),
+         'blue':  ((0.0,  0.0, 0.0),
+                   (0.333,  0.0, 0.0),
+                   (0.666,  0.0, 0.0),
+                   (1.0,  1.0, 1.0))}
+                   
+# ... this blue, ...                   
+Color_Blue = {'red':  ((0.0,  0.0, 0.0),
+                   (0.3,  0.0, 0.0),
+                   (0.7,  0.9, 0.9),
+                   (1.0,  1.0, 1.0)),
+         'green': ((0.0,  0.0, 0.0),
+                   (0.3,  0.0, 0.0),
+                   (0.7,  0.9, 0.9),
+                   (1.0,  1.0, 1.0)),
+         'blue':  ((0.0,  0.0, 0.0),
+                   (0.7,  0.9, 0.9),
+                   (1.0,  1.0, 1.0))}
+
+# ... gold and of course ...
+Color_Gold = {'red':  ((0.0,  0.0, 0.0),
+                   (0.333,  0.545098039216, 0.545098039216),
+                   (0.666,  0.803921568627, 0.803921568627),
+                   (1.0,  1.0, 1.0)),
+         'green': ((0.0,  0.0, 0.0),
+                   (0.333,  0.458823529412, 0.458823529412),
+                   (0.666,  0.678431372549, 0.678431372549),
+                   (1.0,  1.0, 1.0)),
+         'blue':  ((0.0,  0.0, 0.0),
+                   (0.333,  0.0, 0.0),
+                   (0.666,  0.0, 0.0),
+                   (1.0,  1.0, 1.0))}
+
+# ... the green colour from the Michael Reichling group.
+Color_ReiGreen = {'red':  ((0.0,  0.0, 0.0),
+                            (0.381166,  0.0, 0.0),
+                            (0.672646,  0.471014, 0.471014),
+                            (1.0,  1.0, 1.0)),
+                  'green': ((0.0,  0.0, 0.0),
+                            (0.381166,  0.381166, 0.381166),
+                            (0.672646,  0.672646, 0.672646),
+                            (1.0,  1.0, 1.0)),
+                  'blue':  ((0.0,  0.0, 0.0),
+                            (0.381166,  0.0, 0.0),
+                            (0.672646,  0.0, 0.0),
+                            (1.0,  1.0, 1.0))}
+                   
+Color_list = ["Greys_r", "Reds_r", Color_Red, "Blues_r", Color_Blue, "Greens_r",
+              Color_ReiGreen, Color_Yellow, Color_Gold,
+              "Oranges_r", "Purples_r", 
+              "BuGn_r", "GnBu_r", 
+              "BuPu_r", "PuBu_r", "PuRd_r", "RdPu_r",
+              "OrRd_r",
+              "PuBuGn_r",
+              "gnuplot", "gnuplot2", "ocean", "rainbow", 
+              "gist_rainbow", "hsv", "gist_stern", "jet",
+              "hot", "afmhot", "bone", "gist_heat"]
+              
+globvar_color_dict = {name:color for name, color in \
+                      zip(globvar_color_options, Color_list)}
+                                        
+# ___________________________________________________________________ Fonts                                         
+
+globvar_fonts = ['Courier', 'Courier New', 'Arial', 'FreeSans']
+# ___________________________________________________________________ Classes  
+                   
+class CLASSparameters(object):
+    def __init__(self, row, col, rms, res, font,
+                       thumbs_before, thumbs_after, peek, minimum_on_zero, 
+                       png, date, sizenm, 
+                       sizepx, offset, voltage, feedback, gain, 
+                       speed, ampl, text_block, text_block_height, 
+                       text_size, pdfs, text_x, text_y, angle, 
+                       extra_direct, extension, masterdir, filename, jpeg,
+                       channel_names, thumbs, line_fit, plane_fit, invert, 
+                       colors, geometry_x, geometry_y, spektra):
+        self.row = row 
+        self.col = col
+        self.rms = rms 
+        self.res = res 
+        self.font = font
+        self.thumbs_before = thumbs_before 
+        self.thumbs_after = thumbs_after 
+        self.peek = peek
+        self.minimum_on_zero = minimum_on_zero    
+        self.png = png
+        self.date = date 
+        self.sizenm = sizenm 
+        self.sizepx = sizepx 
+        self.offset = offset 
+        self.voltage = voltage 
+        self.feedback = feedback 
+        self.gain = gain 
+        self.speed = speed 
+        self.ampl = ampl 
+        self.text_block = text_block 
+        self.text_block_height = text_block_height 
+        self.text_size = text_size 
+        self.pdfs = pdfs 
+        self.text_x = text_x 
+        self.text_y = text_y 
+        self.angle = angle
+        self.extra_direct = extra_direct 
+        self.extension = extension 
+        self.masterdir = masterdir
+        self.filename = filename
+        self.jpeg = jpeg
+        self.channel_names = channel_names
+        self.thumbs = thumbs
+        self.line_fit = line_fit
+        self.plane_fit = plane_fit 
+        self.invert = invert
+        self.colors = colors
+        self.geometry_x = geometry_x
+        self.geometry_y = geometry_y
+        self.spektra = spektra
+        
+class CLASSdir(object):
+    def __init__(self, working_directory, pdf_path, 
+                 thumbnail_directory, data_directory_name):
+        self.working_directory = working_directory
+        self.pdf_path = pdf_path
+        self.thumbnail_directory = thumbnail_directory
+        self.data_directory_name = data_directory_name        
+        
+
+class CLASSdata(object):
+    __slots__ = ('date', 'x_size', 'y_size', 'x_pixel', 'y_pixel', 
+                 'x_off', 'y_off', 
+                 'voltage', 'feedback', 
+                 'gain', 'gain_prop', 'gain_int', 'gain_xy', 
+                 'gain_signal', 'gain_z',
+                 'speed', 'amplitude', 'angle', 'NONE',
+                 'datfile', 'channel', 'unit', 
+                 'z_average', 'z_calibration', 'z_factor', 'z_min', 
+                 'z_max', 'z_amplitude', 
+                 'scandir', 'spec_x_unit', 'spec_x_label', 
+                 'spec_y_unit', 'spec_y_label', 'spec_y_factor',
+                 'spec_points', 'spec_feedback', 'spec_acquisition', 
+                 'spec_delay')
+    def __init__(self, date, x_size, y_size, x_pixel, y_pixel, x_off, y_off, 
+                 voltage, feedback, 
+                 gain, gain_prop, gain_int, gain_xy, gain_signal, gain_z,
+                 speed, amplitude, angle, NONE,
+                 datfile, channel, unit, 
+                 z_average, z_calibration, z_factor, z_min, z_max, z_amplitude, 
+                 scandir, spec_x_unit, spec_x_label, 
+                 spec_y_unit, spec_y_label, spec_y_factor,
+                 spec_points, spec_feedback, spec_acquisition, spec_delay):
+        self.date = date
+        self.x_size = x_size
+        self.y_size = y_size
+        self.x_pixel = x_pixel
+        self.y_pixel = y_pixel
+        self.x_off = x_off
+        self.y_off = y_off
+        self.voltage = voltage
+        self.feedback = feedback
+        self.gain = gain # SCALA
+        self.gain_prop = gain_prop # DULCINEA
+        self.gain_int  = gain_int # DULCINEA
+        self.gain_xy = gain_xy # DULCINEA
+        self.gain_signal = gain_signal # DULCINEA
+        self.gain_z = gain_z # DULCINEA
+        self.speed = speed
+        self.amplitude = amplitude
+        self.angle = angle
+        self.NONE = NONE # This is a dummy ...
+        # From here to end: lists
+        self.datfile = datfile 
+        self.channel = channel
+        self.unit = unit
+        self.z_average = z_average # float, is determined during runtime
+        self.z_calibration = z_calibration
+        self.z_factor = z_factor # DULCINEA, not used so far
+        self.z_amplitude = z_amplitude
+        self.z_min = z_min # DULCINEA, not used so far
+        self.z_max = z_max # DULCINEA, not used so far
+        self.scandir = scandir
+        self.spec_x_unit = spec_x_unit    
+        self.spec_x_label = spec_x_label     
+        self.spec_y_unit = spec_y_unit
+        self.spec_y_label = spec_y_label
+        self.spec_y_factor = spec_y_factor      
+        self.spec_points = spec_points
+        self.spec_feedback = spec_feedback
+        self.spec_acquisition = spec_acquisition
+        self.spec_delay = spec_delay             
+      
+      
+class CLASSLinalg(object):
+    __slots__ = ('plane_M512', 'plane_M1024', 
+                 'plane_x_vec512', 'plane_y_vec512', 
+                 'plane_x_vec1024', 'plane_y_vec1024',
+                 'line_M512', 'line_M1024', 
+                 'line_x_vec512', 'line_x_vec1024')
+    def __init__(self, plane_M512, plane_M1024, 
+                       plane_x_vec512, plane_y_vec512, 
+                       plane_x_vec1024, plane_y_vec1024,
+                       line_M512, line_M1024,
+                       line_x_vec512,line_x_vec1024):
+        self.plane_M512  = plane_M512
+        self.plane_M1024 = plane_M1024  
+        self.plane_x_vec512  = plane_x_vec512
+        self.plane_y_vec512  = plane_y_vec512 
+        self.plane_x_vec1024 = plane_x_vec1024
+        self.plane_y_vec1024 = plane_y_vec1024
+        self.line_M512 = line_M512
+        self.line_M1024 = line_M1024
+        self.line_x_vec512 = line_x_vec512
+        self.line_x_vec1024 = line_x_vec1024
+
+
+# The next 2 classes are used specifically for the RHK routine.        
+class CLASSRHK_position_counter(object):
+    def __init__(self, position):
+        self.position = position
+            
+    def add(self):
+        self.position += 1
+            
+class CLASSRHK_direction_request(object):
+    def __init__(self, direction = all):
+        self.direction = direction
+        
+class CLASSRHK_true(object):
+    def __init__(self, true = False):
+        self.true = true
+
+                
+globvar_LINALG = CLASSLinalg(None,None,None,None,None,None,None,None,None,None)        
+
+globvar_AFMdata = CLASSdata(None,None,None,None,None,None,None,None,None,None,
+                     None,None,None,None,None,None,None,None, None,
+                     [],[],[], None, [],[],[],[],[],[],[],
+                     [],[],[],[],[],[],[],[])   
+                               
+globvar_AFMdir  = CLASSdir(None,None,None,None)
+
+globvar_ThumbPara = CLASSparameters(None, None, None, None, None,
+                           False, False, False, False, False, False,
+                           False, False, False, False, False,
+                           False, False, False, 
+                           0, 0, 0, False, 0, 0, False, 
+                           False, None, None, None, 0,
+                           [], [], [], [], [], [],
+                           [], [], None)
+
+# For RHK
+RHK_PositionCounter = CLASSRHK_position_counter(None)
+RHK_special = CLASSRHK_true(False)

AFM_thumbs/__init__.py

@@ -0,0 +1,25 @@
+# ##### BEGIN GPL LICENSE BLOCK #####
+#
+#  This program is free software; you can redistribute it and/or
+#  modify it under the terms of the GNU General Public License
+#  as published by the Free Software Foundation; either version 2
+#  of the License, or (at your option) any later version.
+#
+#  This program is distributed in the hope that it will be useful,
+#  but WITHOUT ANY WARRANTY; without even the implied warranty of
+#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+#  GNU General Public License for more details.
+#
+#  You should have received a copy of the GNU General Public License
+#  along with this program; if not, write to the Free Software Foundation,
+#  Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
+#
+# ##### END GPL LICENSE BLOCK #####
+#
+# This is part of the python program 'AFM_thumbs'. Please, read the
+# full licence text and other comments in the file 'AFM_thumbs.py'
+#
+# Dr. Clemens Barth (barth@root-1.de), project manager.
+#
+# DO NOT REMOVE THIS PREAMBLE !!!
+#

Config_AFM_thumbs_noline.log

@@ -0,0 +1,48 @@
+
+
+    AFM thumbs v2.4  -  2021-02-05
+    www.root-1.de
+
+    Today: 05-02-2021, Time: 14:36:10
+
+
+
+    Attention: The config file
+    ./Config_AFM_thumbs_noline.conf
+    does not exist!
+    The default config file 'AFM_thumbs/Config_default.conf' is now used!
+    If you have your own config file, put in the correct file name and path
+    in 'AFM_thumbs/Variables.py' => 'globvar_configfile' and 'globvar_configfile_path'
+
+    Config file: /media/cle/Daten/Data/X -- 2021/Programming/Python_AFM_thumbs/AFM_thumbs/Aktuelle_version/AFM_thumbs/Config_default.conf
+
+
+    Directories that will be considered:
+    /media/cle/Daten/Data/X -- 2021/rawdata/NANONIS/X -- session_demo/2021-01-18
+    /media/cle/Daten/Data/X -- 2021/rawdata/NANONIS/X -- session_demo/Session_first_time_test
+    /media/cle/Daten/Data/X -- 2021/rawdata/NANONIS/sessions_Ag001/2021-02-03_cycle_13
+    /media/cle/Daten/Data/X -- 2021/rawdata/NANONIS/sessions_Ceria/2021-02-01_ceria_10min_550C_10min_1
+    /media/cle/Daten/Data/X -- 2021/rawdata/NANONIS/sessions_Cu111/2021-01-14_sputtering_cycle_48_b
+
+
+
+       I'm working in the directory
+       /media/cle/Daten/Data/X -- 2021/rawdata/NANONIS/X -- session_demo/2021-01-18
+       right now ...
+
+       ... SPECS Nanonis spectras are stored as thumbs ...
+       ... SPECS Nanonis images are stored as thumbs ...
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift
+        Channel not found: OC_M1_Freq._Shift

Utilities/Linux/Ubuntu_unity/AFM_thumbs.desktop

@@ -0,0 +1,7 @@
+[Desktop Entry]
+Type=Application
+Terminal=true
+Name=AFM_thumbs
+Icon=/home/<username>/bin/AFM_thumbs/AFM_thumbs_icon.png
+Exec=/usr/bin/python /home/<username>/bin/AFM_thumbs/AFM_thumbs.py
+

Utilities/Windows/Create_Windows_shortcut.bat

@@ -0,0 +1,35 @@
+@echo off & setlocal
+
+:: Source: http://www.administrator.de/forum/verkn%C3%BCpfung-auf-desktop-per-batch-anlegen-155061.html
+
+:: Zielpfad
+set "zielpfad=%userprofile%\Desktop"
+
+::Name der Verknüpfung (ohne ".lnk")
+set "progtitel=AFM_thumbs Starter"
+::Speicherort der Programmdatei (wird auch für "Ausführen in:" verwendet)
+set "progdir=%cd%"
+set "progexe=Windows Batch Starter.bat"
+::Kommentar
+set "beschreibung=Run AFM_thumbs.py"
+::Icon
+set "iconpath=%progdir%\AFM_thumbs Icon.ico"
+
+::Bei Bedarf Ordner erstellen:
+md "%zielpfad%" 2>nul
+md "%progdir%" 2>nul
+
+::temporäres VBScript erzeugen ...
+ >%temp%\MakeShortCut.vbs echo Set objShell=WScript.CreateObject("Wscript.Shell")
+>>%temp%\MakeShortCut.vbs echo Set objShortcut=objShell.CreateShortcut("%zielpfad%\%progtitel%.lnk")
+>>%temp%\MakeShortCut.vbs echo objShortcut.TargetPath="%progdir%\%progexe%"
+>>%temp%\MakeShortCut.vbs echo objShortcut.Description="%beschreibung%"
+>>%temp%\MakeShortCut.vbs echo objShortcut.WorkingDirectory="%progdir%"
+>>%temp%\MakeShortCut.vbs echo objShortcut.IconLocation = "C:\Users\Niklas\Documents\Python Scripts\AFM_thumbs_v1.7x_04.10.14\AFM_thumbs Icon.ico"
+>>%temp%\MakeShortCut.vbs echo objShortcut.Save
+
+::... ausführen ...
+cscript //nologo %temp%\MakeShortCut.vbs
+
+::... und wieder löschen.
+del %temp%\MakeShortCut.vbs

Utilities/Windows/Windows_batch_starter.bat

@@ -0,0 +1,3 @@
+@echo off
+
+cmd /C "python AFM_thumbs.py"