Nanonis: ISO-8859-1 and Multipass mode

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

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/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.
-    # 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()
+    # Debug: Print the entire header.
+    FLAG_debug = False
+    if FLAG_debug:
+        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()
+        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

@@ -66,8 +66,8 @@ globvar_contributions   = "Reinhard Olbrich (testing)\n" \
                           "Alexander v Schmidtsfeld (testing)\n" \
                           "..."
 
-globvar_year            = "2022-04-09"
-globvar_version         = "3.0.0"
+globvar_year            = "2022-12-09"
+globvar_version         = "3.00111"
 
 globvar_spaces          = "    "
 globvar_name            = "AFM thumbs v" + globvar_version