Follow-ups from the coding session on 2025-03-11

src/imcflibs/imagej/misc.py

@@ -43,7 +43,7 @@
     -----
     `ij.IJ.showProgress` internally increments the given `cur` value by 1.
     """
     log.info(
         "Progress: %s / %s (%s)", cur + 1, final, (1.0 + cur) / final
     )
     IJ.showProgress(cur, final)
@@ -82,7 +82,7 @@
 
     hours, rem = divmod(end - start, 3600)
     minutes, seconds = divmod(rem, 60)
     return "{:0>2}:{:0>2}:{:05.2f}".format(
         int(hours), int(minutes), seconds
     )
 
@@ -120,18 +120,20 @@
     tuple of (float, float)
         Mean and standard deviation of the input list.
     """
-    filtered_list = filter(None, values_list)
+    filtered_list = [x for x in values_list if x is not None]
 
-    try:
-        mean = round(
-            sum(filtered_list) / len(filtered_list), round_decimals
-        )
-    except ZeroDivisionError:
-        mean = 0
-    tot = 0.0
-    for x in filtered_list:
-        tot = tot + (x - mean) ** 2
-    return [mean, (tot / (len(filtered_list))) ** 0.5]
+    if not filtered_list:
+        return 0, 0
+
+    mean = round(
+        sum(filtered_list) / len(filtered_list), round_decimals
+    )
+    variance = sum((x - mean) ** 2 for x in filtered_list) / len(
+        filtered_list
+    )
+    std_dev = round(variance**0.5, round_decimals)
+
+    return mean, std_dev
 
 
 def find_focus(imp):
@@ -166,7 +168,7 @@
     # Check if more than 1 channel
     # FUTURE Could be improved for multi channel
     if imp_dimensions[2] != 1:
         sys.exit(
             "Image has more than one channel, please reduce dimensionality"
         )
 
@@ -184,7 +186,7 @@
             # pix_array = pix_array*pix_array
 
             sumpix_array = sum(pix_array)
             var = sumpix_array / (
                 imp_dimensions[0] * imp_dimensions[1] * mean
             )
 
@@ -215,12 +217,12 @@
 
     # Ensure the sender and server are configured from Prefs
     if not sender:
         log.info(
             "Sender email is not configured. Please check IJ_Prefs.txt."
         )
         return
     if not server:
         log.info(
             "SMTP server is not configured. Please check IJ_Prefs.txt."
         )
         return
@@ -303,7 +305,7 @@
         Flag to request the formatted string to be returned instead of printing
         it to the log. By default False.
     """
     formatted = (
         time.strftime("%H:%M:%S", time.localtime())
         + ": "
         + message
@@ -505,21 +507,21 @@
     """
 
     # Check if the output file exists
     if not os.path.exists(out_file):
         # If the file does not exist, create it and write the header
         with open(out_file, "wb") as f:
             dict_writer = csv.DictWriter(
                 f, content[0].keys(), delimiter=";"
             )
             dict_writer.writeheader()
             dict_writer.writerows(content)
     else:
         # If the file exists, append the results
         with open(out_file, "ab") as f:
             dict_writer = csv.DictWriter(
                 f, content[0].keys(), delimiter=";"
             )
             dict_writer.writerows(content)
 
 
 def save_image_in_format(
@@ -583,20 +585,20 @@
     #                  /output/path/C2/image_title_series_001.ome.tif
     """
 
     out_ext = {}
     out_ext["ImageJ-TIF"] = ".tif"
     out_ext["ICS-1"] = ".ids"
     out_ext["ICS-2"] = ".ics"
     out_ext["OME-TIFF"] = ".ome.tif"
     out_ext["CellH5"] = ".ch5"
     out_ext["BMP"] = ".bmp"
 
     imp_to_use = []
     dir_to_save = []
 
     if split_channels:
         for channel in range(1, imp.getNChannels() + 1):
             imp_to_use.append(
                 Duplicator().run(
                     imp,
                     channel,
@@ -607,34 +609,34 @@
                     imp.getNFrames(),
                 )
             )
             dir_to_save.append(
                 os.path.join(out_dir, "C" + str(channel))
             )
     else:
         imp_to_use.append(imp)
         dir_to_save.append(out_dir)
 
     for index, current_imp in enumerate(imp_to_use):
         basename = imp.getShortTitle()
 
         out_path = os.path.join(
             dir_to_save[index],
             basename + "_series_" + str(series).zfill(pad_number),
         )
 
         if format == "ImageJ-TIF":
             pathtools.create_directory(dir_to_save[index])
             IJ.saveAs(current_imp, "Tiff", out_path + ".tif")
 
         elif format == "BMP":
             out_folder = os.path.join(out_dir, basename + os.path.sep)
             pathtools.create_directory(out_folder)
             StackWriter.save(current_imp, out_folder, "format=bmp")
 
         else:
             bf.export(current_imp, out_path + out_ext[format])
 
         current_imp.close()
 
 
 def pad_number(index, pad_length=2):
@@ -659,7 +661,7 @@
     >>> pad_number(42, 4)
     '0042'
     """
     return str(index).zfill(pad_length)
 
 
 def locate_latest_imaris(paths_to_check=None):
@@ -679,22 +681,22 @@
     -------
     str
     """
     if not paths_to_check:
         paths_to_check = [
             r"C:\Program Files\Bitplane\ImarisFileConverter ",
             r"C:\Program Files\Bitplane\Imaris ",
         ]
 
     imaris_paths = [""]
 
     for check in paths_to_check:
         hits = glob.glob(check + "*")
         imaris_paths += sorted(
             hits,
             key=lambda x: float(x.replace(check, "").replace(".", "")),
         )
 
     return imaris_paths[-1]
 
 
 def run_imarisconvert(file_path):
@@ -718,21 +720,21 @@
 
     """
 
     path_root, file_extension = os.path.splitext(file_path)
     if file_extension == ".ids":
         file_extension = ".ics"
         file_path = path_root + file_extension
 
     imaris_path = locate_latest_imaris()
 
     command = 'ImarisConvert.exe  -i "%s" -of Imaris5 -o "%s"' % (
         file_path,
         file_path.replace(file_extension, ".ims"),
     )
     log.debug("\n%s" % command)
     IJ.log("Converting to Imaris5 .ims...")
     result = subprocess.call(command, shell=True, cwd=imaris_path)
     if result == 0:
         IJ.log("Conversion to .ims is finished")
     else:
         IJ.log("Conversion failed with error code: %d" % result)