Merge branch 'dev' of https://github.com/matt-sd-watson/steinbock int…

…o dev
BodenmillerGroup · May 14, 2024 · 983bb19 · 983bb19
2 parents 8cf35de + 22ad48f
commit 983bb19
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Showing 3 changed files with 12 additions and 5 deletions.
diff --git a/requirements.txt b/requirements.txt
@@ -17,4 +17,4 @@ readimc==0.7.0
 scikit-image==0.19.3
 scipy==1.10.0
 tifffile==2023.1.23.1
-xtiff==0.7.9
+xtiff==0.7.9
diff --git a/steinbock/preprocessing/_cli/imc.py b/steinbock/preprocessing/_cli/imc.py
@@ -201,7 +201,9 @@ def panel_cmd(
 )
 @click_log.simple_verbosity_option(logger=steinbock_logger)
 @catch_exception(handle=SteinbockException)
-def images_cmd(mcd_dir, txt_dir, unzip, panel_file, hpf, img_dir, image_info_file, strict):
+def images_cmd(
+    mcd_dir, txt_dir, unzip, panel_file, hpf, img_dir, image_info_file, strict
+):
     channel_names = None
     if Path(panel_file).is_file():
         panel = io.read_panel(panel_file)
@@ -220,7 +222,12 @@ def images_cmd(mcd_dir, txt_dir, unzip, panel_file, hpf, img_dir, image_info_fil
         recovery_txt_file,
         recovered,
     ) in imc.try_preprocess_images_from_disk(
-        mcd_files, txt_files, channel_names=channel_names, hpf=hpf, unzip=unzip, strict=strict
+        mcd_files,
+        txt_files,
+        channel_names=channel_names,
+        hpf=hpf,
+        unzip=unzip,
+        strict=strict,
     ):
         img_file_stem = Path(mcd_or_txt_file).stem
         if acquisition is not None:

diff --git a/steinbock/preprocessing/imc.py b/steinbock/preprocessing/imc.py
@@ -441,7 +441,7 @@ def try_preprocess_images_from_disk(
                 channel_names=channel_names,
                 hpf=hpf,
                 unzip=unzip,
-                strict=strict
+                strict=strict,
             ):
                 yield Path(mcd_file), acquisition, img, recovery_txt_file, recovered
                 del img
@@ -461,7 +461,7 @@ def try_preprocess_images_from_disk(
                         channel_names=channel_names,
                         hpf=hpf,
                         unzip=unzip,
-                        strict=strict
+                        strict=strict,
                     ):
                         yield (
                             Path(mcd_file),