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[skip ci]
andreped · Sep 10, 2024 · a87de35 · a87de35
1 parent c094b28
commit a87de35
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Showing 2 changed files with 13 additions and 6 deletions.
diff --git a/vsi2tif/src/process.py b/vsi2tif/src/process.py
@@ -1,7 +1,8 @@
+import logging
 import os
-import traceback
 import shutil
-import logging
+import traceback
+
 from tqdm import tqdm
 
 from .benchmark import benchmark
@@ -22,12 +23,12 @@ def cellsens2tif_single(
 ) -> None:
 
     if int(plane) == -1:
-        image_folder = os.path.join(os.path.dirname(output_path), os.path.basename(output_path).replace('.tif', ''))
+        image_folder = os.path.join(os.path.dirname(output_path), os.path.basename(output_path).replace(".tif", ""))
         for s in range(50):
             try:
                 curr_output_path = os.path.join(image_folder, "plane_" + str(s) + "_" + os.path.basename(output_path))
                 cellsens2tif(input_path, curr_output_path, bfconvert, compression, tz, s, quality, max_mem, verbose)
-            except Exception as e:
+            except Exception:
                 logging.info("End of planes with value {}".format(s))
                 break
 
@@ -44,7 +45,7 @@ def cellsens2tif_single(
             shutil.copyfile(largest_file, output_path)
             if os.path.exists(image_folder):
                 shutil.rmtree(image_folder)
-        except Exception as e:
+        except Exception:
             logging.error("Issue cleaning up after all planes conversion.")
             logging.error(traceback.format_exc())
     else:

diff --git a/vsi2tif/vsi2tif.py b/vsi2tif/vsi2tif.py
@@ -13,7 +13,13 @@ def main():
     parser.add_argument("-b", "--bfconvert", help="path to bfconvert tool", required=True)
     parser.add_argument("-c", "--compression", help="compression technique for final image", default="jpeg")
     parser.add_argument("-s", "--tilesize", help="tile size to use during both conversion steps", default=1024)
-    parser.add_argument("-p", "--plane", help="which image plane to convert image from. If set to -1, all planes are converted and the largest is kept", default=0, type=int)
+    parser.add_argument(
+        "-p",
+        "--plane",
+        help="which image plane to convert image from. If set to -1, all planes are converted and the largest is kept",
+        default=0,
+        type=int,
+    )
     parser.add_argument("-q", "--quality", help="compression quality used with JPEG compression", default=85)
     parser.add_argument("-m", "--max-mem", help="set maximum memory in the java vm", default=32)
     parser.add_argument("-v", "--verbose", help="set verbosity level", default=1, type=int)