Formatting

Author: lguerard

src/imcflibs/imagej/bdv.py

@@ -133,7 +133,9 @@ def reference_channel(self, value):
         """
         # channel = int(value) - 1  # will raise a ValueError if cast fails
         self._use_channel = "channels=[use Channel %s]" % int(value)
-        log.debug("New reference channel setting: %s", self._use_channel)
+        log.debug(
+            "New reference channel setting: %s", self._use_channel
+        )
 
     def reference_illumination(self, value):
         """Set the reference illumination when using *Expert Grouping Options*.
@@ -149,8 +151,13 @@ def reference_illumination(self, value):
         value : int or int-like
             The illumination number to use for the grouping.
         """
-        self._use_illumination = "illuminations=[use Illumination %s]" % value
-        log.debug("New reference illumination setting: %s", self._use_illumination)
+        self._use_illumination = (
+            "illuminations=[use Illumination %s]" % value
+        )
+        log.debug(
+            "New reference illumination setting: %s",
+            self._use_illumination,
+        )
 
     def reference_tile(self, value):
         """Set the reference tile when using *Expert Grouping Options*.
@@ -184,7 +191,9 @@ def reference_timepoint(self, value):
             The timepoint number to use for the grouping.
         """
         self._use_timepoint = "timepoints=[use Timepoint %s]" % value
-        log.debug("New reference timepoint setting: %s", self._use_timepoint)
+        log.debug(
+            "New reference timepoint setting: %s", self._use_timepoint
+        )
 
     ### process-X methods
 
@@ -406,16 +415,22 @@ def fmt_acitt_options(self, input="process"):
         """
         input_type = ["process", "resave"]
         if input not in input_type:
-            raise ValueError("Invalue input type. Expected one of: %s" % input_type)
+            raise ValueError(
+                "Invalue input type. Expected one of: %s" % input_type
+            )
         parameters = [
             input + "_angle=" + self._angle_processing_option,
             input + "_channel=" + self._channel_processing_option,
-            input + "_illumination=" + self._illumination_processing_option,
+            input
+            + "_illumination="
+            + self._illumination_processing_option,
             input + "_tile=" + self._tile_processing_option,
             input + "_timepoint=" + self._timepoint_processing_option,
         ]
         parameter_string = " ".join(parameters).strip()
-        log.debug("Formatted 'process_X' options: <%s>", parameter_string)
+        log.debug(
+            "Formatted 'process_X' options: <%s>", parameter_string
+        )
         return parameter_string + " "
 
     def fmt_acitt_selectors(self):
@@ -435,12 +450,16 @@ def fmt_acitt_selectors(self):
         parameters = [
             self._angle_select if self._angle_select else "",
             self._channel_select if self._channel_select else "",
-            self._illumination_select if self._illumination_select else "",
+            self._illumination_select
+            if self._illumination_select
+            else "",
             self._tile_select if self._tile_select else "",
             self._timepoint_select if self._timepoint_select else "",
         ]
         parameter_string = " ".join(parameters).strip()
-        log.debug("Formatted 'processing_X' selectors: <%s>", parameter_string)
+        log.debug(
+            "Formatted 'processing_X' selectors: <%s>", parameter_string
+        )
         return parameter_string + " "
 
     def fmt_how_to_treat(self):
@@ -458,7 +477,9 @@ def fmt_how_to_treat(self):
             "how_to_treat_timepoints=" + self._treat_timepoints,
         ]
         parameter_string = " ".join(parameters).strip()
-        log.debug("Formatted 'how_to_treat_X' options: <%s>", parameter_string)
+        log.debug(
+            "Formatted 'how_to_treat_X' options: <%s>", parameter_string
+        )
         return parameter_string + " "
 
     def fmt_use_acitt(self):
@@ -473,13 +494,22 @@ def fmt_use_acitt(self):
         """
         parameters = [
             self._use_angle if self._treat_angles == "group" else "",
-            self._use_channel if self._treat_channels == "group" else "",
-            self._use_illumination if self._treat_illuminations == "group" else "",
+            self._use_channel
+            if self._treat_channels == "group"
+            else "",
+            self._use_illumination
+            if self._treat_illuminations == "group"
+            else "",
             self._use_tile if self._treat_tiles == "group" else "",
-            self._use_timepoint if self._treat_timepoints == "group" else "",
+            self._use_timepoint
+            if self._treat_timepoints == "group"
+            else "",
         ]
         parameter_string = " ".join(parameters).strip()
-        log.debug("Formatted expert grouping 'use' options: <%s>", parameter_string)
+        log.debug(
+            "Formatted expert grouping 'use' options: <%s>",
+            parameter_string,
+        )
         return parameter_string + " "
 
 
@@ -517,7 +547,9 @@ class DefinitionOptions(object):
     def __init__(self):
         self._angle_definition = SINGLE_FILE % "angle"
         self._channel_definition = MULTI_SINGLE_FILE % "channel"
-        self._illumination_definition = SINGLE_FILE % "illumination direction"
+        self._illumination_definition = (
+            SINGLE_FILE % "illumination direction"
+        )
         self._tile_definition = MULTI_MULTI_FILE % "tile"
         self._timepoint_definition = SINGLE_FILE % "time-point"
 
@@ -538,7 +570,9 @@ def check_definition_option(self, value):
             "multi_single",
             "multi_multi",
         ]:
-            raise ValueError("Value must be one of single, multi_multi or multi_single")
+            raise ValueError(
+                "Value must be one of single, multi_multi or multi_single"
+            )
 
         return {
             "single": SINGLE_FILE,
@@ -584,7 +618,9 @@ def set_angle_definition(self, value):
         """
         choices = self.check_definition_option_ang_ill(value)
         self._angle_definition = choices[value] % "angle"
-        log.debug("New 'angle_definition' setting: %s", self._angle_definition)
+        log.debug(
+            "New 'angle_definition' setting: %s", self._angle_definition
+        )
 
     def set_channel_definition(self, value):
         """Set the value for the channel definition
@@ -596,7 +632,10 @@ def set_channel_definition(self, value):
         """
         choices = self.check_definition_option(value)
         self._channel_definition = choices[value] % "channel"
-        log.debug("New 'channel_definition' setting: %s", self._channel_definition)
+        log.debug(
+            "New 'channel_definition' setting: %s",
+            self._channel_definition,
+        )
 
     def set_illumination_definition(self, value):
         """Set the value for the illumination definition
@@ -607,9 +646,12 @@ def set_illumination_definition(self, value):
             One of `single`, `multi_single` or `multi_multi`.
         """
         choices = self.check_definition_option_ang_ill(value)
-        self._illumination_definition = choices[value] % "illumination direction"
+        self._illumination_definition = (
+            choices[value] % "illumination direction"
+        )
         log.debug(
-            "New 'illumination_definition' setting: %s", self._illumination_definition
+            "New 'illumination_definition' setting: %s",
+            self._illumination_definition,
         )
 
     def set_tile_definition(self, value):
@@ -622,7 +664,9 @@ def set_tile_definition(self, value):
         """
         choices = self.check_definition_option(value)
         self._tile_definition = choices[value] % "tile"
-        log.debug("New 'tile_definition' setting: %s", self._tile_definition)
+        log.debug(
+            "New 'tile_definition' setting: %s", self._tile_definition
+        )
 
     def set_timepoint_definition(self, value):
         """Set the value for the time_point_definition
@@ -634,7 +678,10 @@ def set_timepoint_definition(self, value):
         """
         choices = self.check_definition_option(value)
         self._timepoint_definition = choices[value] % "time-point"
-        log.debug("New 'timepoint_definition' setting: %s", self._timepoint_definition)
+        log.debug(
+            "New 'timepoint_definition' setting: %s",
+            self._timepoint_definition,
+        )
 
     def fmt_acitt_options(self):
         """Format Angle / Channel / Illumination / Tile / Timepoint options.
@@ -650,12 +697,15 @@ def fmt_acitt_options(self):
         parameters = [
             "multiple_angles=" + self._angle_definition,
             "multiple_channels=" + self._channel_definition,
-            "multiple_illuminations_directions=" + self._illumination_definition,
+            "multiple_illuminations_directions="
+            + self._illumination_definition,
             "multiple_tiles=" + self._tile_definition,
             "multiple_timepoints=" + self._timepoint_definition,
         ]
         parameter_string = " ".join(parameters).strip()
-        log.debug("Formatted 'multiple_X' options: <%s>", parameter_string)
+        log.debug(
+            "Formatted 'multiple_X' options: <%s>", parameter_string
+        )
         return parameter_string + " "
 
 
@@ -679,10 +729,14 @@ def check_processing_input(value, range_end):
         value = [value]
     # Check if all the elements of the value list are of the same type
     if not all(isinstance(x, type(value[0])) for x in value):
-        raise TypeError("Invalid input type. All the values should be of the same type")
+        raise TypeError(
+            "Invalid input type. All the values should be of the same type"
+        )
     if type(range_end) is int:
         if type(value[0]) is not int:
-            raise TypeError("Invalid input type. Expected an int for the range start")
+            raise TypeError(
+                "Invalid input type. Expected an int for the range start"
+            )
         elif len(value) != 1:
             raise ValueError(
                 "Invalid input type. Expected a single number for the range start"
@@ -720,7 +774,13 @@ def get_processing_settings(dimension, selection, value, range_end):
 
     if selection == "single":
         processing_option = SINGLE % dimension
-        dimension_select = "processing_" + dimension + "=[" + dimension + " %s]" % value
+        dimension_select = (
+            "processing_"
+            + dimension
+            + "=["
+            + dimension
+            + " %s]" % value
+        )
 
     if selection == "multiple":
         processing_option = MULTIPLE % dimension
@@ -763,7 +823,9 @@ def backup_xml_files(source_directory, subfolder_name):
     pathtools.create_directory(xml_backup_directory)
     backup_subfolder = xml_backup_directory + "/%s" % (subfolder_name)
     pathtools.create_directory(backup_subfolder)
-    all_xml_files = pathtools.listdir_matching(source_directory, ".*\\.xml", regex=True)
+    all_xml_files = pathtools.listdir_matching(
+        source_directory, ".*\\.xml", regex=True
+    )
     os.chdir(source_directory)
     for xml_file in all_xml_files:
         shutil.copy2(xml_file, backup_subfolder)
@@ -823,7 +885,9 @@ def define_dataset_auto(
         dataset_save_path = result_folder
     if subsampling_factors:
         subsampling_factors = (
-            "manual_mipmap_setup subsampling_factors=" + subsampling_factors + " "
+            "manual_mipmap_setup subsampling_factors="
+            + subsampling_factors
+            + " "
         )
     else:
         subsampling_factors = ""
@@ -987,7 +1051,9 @@ def resave_as_h5(
         split_hdf5 = ""
 
     if subsampling_factors:
-        subsampling_factors = "subsampling_factors=" + subsampling_factors + " "
+        subsampling_factors = (
+            "subsampling_factors=" + subsampling_factors + " "
+        )
     else:
         subsampling_factors = " "
     if hdf5_chunk_sizes:
@@ -1077,10 +1143,13 @@ def phase_correlation_pairwise_shifts_calculation(
     file_info = pathtools.parse_path(project_path)
 
     if downsampling_xyz != "":
-        downsampling = "downsample_in_x=%s downsample_in_y=%s downsample_in_z=%s " % (
-            downsampling_xyz[0],
-            downsampling_xyz[1],
-            downsampling_xyz[2],
+        downsampling = (
+            "downsample_in_x=%s downsample_in_y=%s downsample_in_z=%s "
+            % (
+                downsampling_xyz[0],
+                downsampling_xyz[1],
+                downsampling_xyz[2],
+            )
         )
     else:
         downsampling = ""
@@ -1104,7 +1173,9 @@ def phase_correlation_pairwise_shifts_calculation(
     log.debug("Calculate pairwise shifts options: <%s>", options)
     IJ.run("Calculate pairwise shifts ...", str(options))
 
-    backup_xml_files(file_info["path"], "phase_correlation_shift_calculation")
+    backup_xml_files(
+        file_info["path"], "phase_correlation_shift_calculation"
+    )
 
 
 def filter_pairwise_shifts(
@@ -1216,7 +1287,9 @@ def optimize_and_apply_shifts(
         + processing_opts.fmt_how_to_treat()
     )
 
-    log.debug("Optimization and shifts application options: <%s>", options)
+    log.debug(
+        "Optimization and shifts application options: <%s>", options
+    )
     IJ.run("Optimize globally and apply shifts ...", str(options))
 
     backup_xml_files(file_info["path"], "optimize_and_apply_shifts")
@@ -1394,18 +1467,26 @@ def duplicate_transformations(
         target = "[All Channels]"
         source = str(channel_source - 1)
         if tile_source:
-            tile_apply = "apply_to_tile=[Single tile (Select from List)] "
-            tile_process = "processing_tile=[tile " + str(tile_source) + "] "
+            tile_apply = (
+                "apply_to_tile=[Single tile (Select from List)] "
+            )
+            tile_process = (
+                "processing_tile=[tile " + str(tile_source) + "] "
+            )
         else:
             tile_apply = "apply_to_tile=[All tiles] "
     elif transformation_type == "tile":
         apply = "[One tile to other tiles]"
         target = "[All Tiles]"
         source = str(tile_source)
         if channel_source:
-            chnl_apply = "apply_to_channel=[Single channel (Select from List)] "
+            chnl_apply = (
+                "apply_to_channel=[Single channel (Select from List)] "
+            )
             chnl_process = (
-                "processing_channel=[channel " + str(channel_source - 1) + "] "
+                "processing_channel=[channel "
+                + str(channel_source - 1)
+                + "] "
             )
         else:
             chnl_apply = "apply_to_channel=[All channels] "
@@ -1441,7 +1522,8 @@ def duplicate_transformations(
     IJ.run("Duplicate Transformations", str(options))
 
     backup_xml_files(
-        file_info["path"], "duplicate_transformation_" + transformation_type
+        file_info["path"],
+        "duplicate_transformation_" + transformation_type,
     )