Concerns last commit: I forgot to add 'import os' and to add some spaces.

- Nanonis files: ISO-8859-1 decoding implemented
- Nanonis => Multipass mode: first code lines

.gitignore

@@ -0,0 +1,2 @@
+AFM_thumbs/__pycache__/
+

AFM_thumbs.py

@@ -40,6 +40,14 @@
 #       First git visibility             : 2022/04/08, Clemens Barth
 #
 #
+#       2022/12/09
+#       ==========
+#       - Nanonis files: ISO-8859-1 decoding implemented (reading
+#         the header)
+#       - Nanonis - Multipass mode: first code lines inserted.
+#         Still to be done: title with "[Px]_" identifier for each
+#         image => This needs to be done in Channel.py.
+#
 #       2022/04/08
 #       ==========
 #       - First upload of AFM_thumbs.py onto our git server.

AFM_thumbs/Channel.py

@@ -33,6 +33,7 @@ from AFM_thumbs.Variables import globvar_color_dict
 from AFM_thumbs.Variables import globvar_spaces
 
 
+# _________________________________________________________________ Definitions
 
 def rename_channel(name):
 

AFM_thumbs/Linalg.py

@@ -119,7 +119,7 @@ def linalg_line_fit(size_x, size_y, data):
         xy = sum(line*x_vec)
 
         B  = scipy.mat([[xy],[y]])
-        c,resid,rank,sigma = linalg.lstsq(M,B)
+        c, resid, rank, sigma = linalg.lstsq(M, B)
 
         plane.append([i * c[0][0] + c[1][0] for i in range(size_x)])
 
@@ -198,7 +198,12 @@ def check_image_properties(data, data_file):
 
         list_nans = np.where(np.isnan(data))[0]
         data_clean = np.delete(data, list_nans)
-        data_mean = np.mean(data_clean)
+
+        # If all pixels are on NaN, then put the mean value onto 0.0.
+        if len(list_nans) == len(data):
+            data_mean = 0.0
+        else:
+            data_mean = np.mean(data_clean)
 
         for nan in list_nans:
             data[nan] = data_mean

AFM_thumbs/SPECS_Nanonis.py

@@ -26,6 +26,7 @@
 
 import sys
 import os
+import chardet
 import numpy as np
 
 from AFM_thumbs.Variables  import globvar_AFMdata
@@ -48,6 +49,22 @@ from AFM_thumbs.Channel    import plane_fit
 from AFM_thumbs.Channel    import rename_channel
 
 
+# ___________________________________________________________________ Constants
+
+
+# This is used for checking the channels in the 'Multipass mode'.
+multi_pass_ident = ["[P1]_",
+                    "[P2]_",
+                    "[P3]_",
+                    "[P4]_",
+                    "[P5]_",
+                    "[P6]_",
+                    "[P7]_",
+                    "[P8]_",
+                    "[P9]_",
+                   "[P10]_"]
+
+
 # _________________________________________________________________ Definitions
 
 def is_SPECS_Nanonis_file(directory, files):
@@ -76,14 +93,17 @@ def is_SPECS_Nanonis_file(directory, files):
 # an .sxm into the parameter class of AFM_thumbs.
 def read_SPECS_Nanonis_image_data(nanonis_file):
 
-    # # Print the entire header.
+    # Debug: Print the entire header.
-    # nanonis_file_path = os.path.join(globvar_AFMdir.working_directory, nanonis_file)
+    FLAG_debug = False
-    # nanonis_file_p = open(nanonis_file_path, "rb")
+    if FLAG_debug:
-    # line = ""
+        nanonis_file_path = os.path.join(globvar_AFMdir.working_directory, nanonis_file)
-    # while line!=b':SCANIT_END:':
+        nanonis_file_p = open(nanonis_file_path, "rb")
-    #     line = nanonis_file_p.readline().rstrip()
+        line = ""
-    #     print(line)
+        while line!=b':SCANIT_END:':
-    # nanonis_file_p.close()
+            line = nanonis_file_p.readline().rstrip()
+            print(line)
+        nanonis_file_p.close()
+        exit(-1)
 
     initialize_AFM_data()
 
@@ -97,7 +117,15 @@ def read_SPECS_Nanonis_image_data(nanonis_file):
     list_line = []
     while line_!=b':SCANIT_END:':
         line_ = nanonis_file_p.readline().rstrip()
-        list_line.append(line_.decode("utf-8"))
+
+        # If it is a special standard, like ISO-8859-1, then treat
+        # it as such.
+        encoding = chardet.detect(line_)['encoding']
+        if encoding == "ISO-8859-1":
+            line_ = line_.decode("iso-8859-1")
+            list_line.append(line_)
+        else:
+            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,
@@ -124,6 +152,7 @@ def read_SPECS_Nanonis_image_data(nanonis_file):
             globvar_AFMdata.date += ", " + line
         if ":SCAN_FILE:" in list_line[i]:
             i += 1
+            #print(list_line[i])
             line = list_line[i].rstrip().strip()
             globvar_AFMdata.datfile = [line]
         if ":SCAN_RANGE:" in list_line[i]:
@@ -229,6 +258,10 @@ def read_SPECS_Nanonis_image_data(nanonis_file):
                 if channel_name in channels_not_supported:
                     continue
 
+                # For the "Multipass mode": Cut the '[Px]_' prefix.
+                if channel_name[:5] in multi_pass_ident:
+                    channel_name = channel_name[5:]
+
                 # Assign the correct channel names
                 if channel_name == "Current":
                     channel_name = "I"

AFM_thumbs/Variables.py

@@ -24,6 +24,10 @@
 # DO NOT REMOVE THIS PREAMBLE !!!
 #
 
+import os
+import time
+import pathlib
+
 
 #
 #
@@ -47,27 +51,33 @@ globvar_configfile_path = "./AFM_thumbs/"
 #
 #
 # _____________________________________________________________________ to here
-#
-#
-#
 
 
+# ____________________________________________________________ Git hash version
 
+# Get the git hash version
+def get_git_revision(base_path):
+
+    git_dir = pathlib.Path(base_path) / '.git'
+
+    with (git_dir / 'HEAD').open('r') as head:
+        ref = head.readline().split(' ')[-1].strip()
+    with (git_dir / ref).open('r') as git_hash:
+        return git_hash.readline().strip()
 
 
 # ____________________________________________________________ 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            = "2022-04-09"
+globvar_year            = "2023-04-26"
-globvar_version         = "3.0.0"
+globvar_version         = "3.0.1111"
+globvar_git_version     = get_git_revision(os.path.join(os.path.dirname(__file__), "../"))
 
 globvar_spaces          = "    "
 globvar_name            = "AFM thumbs v" + globvar_version
@@ -85,14 +95,16 @@ globvar_note            = ("Version " + globvar_version + " (" +
                            "Contributions from:\n" +
                            globvar_contributions)
 
-globvar_console         = ("\n\n"+
+globvar_console         = ("\n\n"                                         +
-                           globvar_spaces +
+                           globvar_spaces                                 +
-                           globvar_name + "  -  " +
+                           globvar_name   + "  -  "                       +
-                           globvar_year + "\n" +
+                           globvar_year   + "\n"                          +
-                           globvar_spaces + "www.root-1.de\n\n" +
+                           globvar_spaces                                 +
-                           globvar_spaces + "Today: " +
+                           "GIT commit: " + globvar_git_version + "\n"    +
-                           time.strftime("%d-%m-%Y") +
+                           globvar_spaces + "www.root-1.de\n\n"           +
-                           ", Time: " +
+                           globvar_spaces + "Today: "                     +
+                           time.strftime("%d-%m-%Y")                      +
+                           ", Time: "                                     +
                            time.strftime("%H:%M:%S"))
 
 globvar_python_directory = "AFM_thumbs"

README.md

@@ -1,11 +1,16 @@
+## Important note
+Note that the pages here are currently under construction! Soon, we will will have a first version, including an extensive description of `AFM_thumbs.py`. Please, be patient. -- Clemens Barth (2022-04-20)
+
+
 # AFM_thumbs.py
 
 ## Introduction
 
-The python program AFM_thumbs creates a pdf file, which shows all SPM
+The python program `AFM_thumbs.py` creates a pdf file, which shows all SPM
 (Scanning Probe Microscopy: like AFM, STM, KPFM, etc.) images and relevant
-data stored in a directory. In first place, AFM_thumbs is interesting for
+spectroscopy data stored in a directory. In first place, `AFM_thumbs.py` 
-scientists, who would like to obtain an overview of their SPM data.
+is interesting for scientists, who would like to obtain an overview of 
+their SPM data.
 
 ## Supported SPM data