Fixed pre-commit

CBICA · Oct 14, 2024 · adc5f10 · adc5f10
1 parent d77facf
commit adc5f10
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Showing 5 changed files with 40 additions and 32 deletions.
diff --git a/NiChart_DLMUSE/CalcROIVol.py b/NiChart_DLMUSE/CalcROIVol.py
@@ -1,13 +1,14 @@
 import csv as csv
+import logging
 import os
 from typing import Any
-import logging
+
 import nibabel as nib
 import numpy as np
 import pandas as pd
 
 logger = logging.getLogger(__name__)
-logging.basicConfig(filename='pipeline.log', encoding='utf-8', level=logging.DEBUG)
+logging.basicConfig(filename="pipeline.log", encoding="utf-8", level=logging.DEBUG)
 
 
 def calc_roi_volumes(mrid: Any, in_img: Any, label_indices: Any) -> pd.DataFrame:

diff --git a/NiChart_DLMUSE/ReorientImage.py b/NiChart_DLMUSE/ReorientImage.py
@@ -1,14 +1,16 @@
+import logging
 import os
 from typing import Any
-import logging
+
 import nibabel as nib
 import pandas as pd
 from nibabel.orientations import axcodes2ornt, ornt_transform
 
 IMG_EXT = ".nii.gz"
 
 logger = logging.getLogger(__name__)
-logging.basicConfig(filename='pipeline.log', encoding='utf-8', level=logging.DEBUG)
+logging.basicConfig(filename="pipeline.log", encoding="utf-8", level=logging.DEBUG)
+
 
 def reorient_img(in_img: Any, ref: Any, out_img: Any) -> None:
     """

diff --git a/NiChart_DLMUSE/__main__.py b/NiChart_DLMUSE/__main__.py
@@ -152,7 +152,7 @@ def main() -> None:
                 device,
                 dlmuse_extra_args,
                 dlicv_extra_args,
-                i
+                i,
             ),
         )
         curr_thread.start()

diff --git a/NiChart_DLMUSE/dlmuse_pipeline.py b/NiChart_DLMUSE/dlmuse_pipeline.py
@@ -1,5 +1,6 @@
-import os
 import logging
+import os
+
 import pkg_resources  # type: ignore
 
 from .CalcROIVol import apply_create_roi_csv, combine_roi_csv
@@ -31,24 +32,25 @@
 )
 
 logger = logging.getLogger(__name__)
-logging.basicConfig(filename='pipeline.log', encoding='utf-8', level=logging.DEBUG)
+logging.basicConfig(filename="pipeline.log", encoding="utf-8", level=logging.DEBUG)
+
 
 def run_pipeline(
     in_data: str,
     out_dir: str,
     device: str,
     dlmuse_extra_args: str,
     dlicv_extra_args: str,
-    sub_fldr: int
+    sub_fldr: int,
 ) -> None:
     """
     NiChart pipeline
     """
-    logging.info(f'Starting the pipeline on folder {sub_fldr}')
-    logging.info(f'Detecting input images for batch [{sub_fldr}]...')
+    logging.info(f"Starting the pipeline on folder {sub_fldr}")
+    logging.info(f"Detecting input images for batch [{sub_fldr}]...")
     # Detect input images
     df_img = make_img_list(in_data)
-    logging.info(f'Detecting input images for batch [{sub_fldr}] done')
+    logging.info(f"Detecting input images for batch [{sub_fldr}] done")
 
     # Set init paths and envs
     out_dir = os.path.abspath(out_dir)
@@ -61,17 +63,17 @@ def run_pipeline(
 
     os.makedirs(working_dir, exist_ok=True)
 
-    logging.info(f'Reorient images to LPS for batch [{sub_fldr}]...')
+    logging.info(f"Reorient images to LPS for batch [{sub_fldr}]...")
     # Reorient image to LPS
     out_dir = os.path.join(working_dir, "s1_reorient_lps")
     ref = REF_ORIENT
     out_suff = SUFF_LPS
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
     apply_reorient_img(df_img, ref, out_dir, out_suff)
-    logging.info(f'Reorient images to LPS for batch [{sub_fldr}] done')
+    logging.info(f"Reorient images to LPS for batch [{sub_fldr}] done")
 
-    logging.info(f'Applying DLICV for batch [{sub_fldr}]...')
+    logging.info(f"Applying DLICV for batch [{sub_fldr}]...")
     # Apply DLICV
     in_dir = os.path.join(working_dir, "s1_reorient_lps")
     out_dir = os.path.join(working_dir, "s2_dlicv")
@@ -80,9 +82,9 @@ def run_pipeline(
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
     run_dlicv(in_dir, in_suff, out_dir, out_suff, device, dlicv_extra_args)
-    logging.info(f'Applying DLICV for batch [{sub_fldr}] done')
+    logging.info(f"Applying DLICV for batch [{sub_fldr}] done")
 
-    logging.info(f'Applying mask for batch [{sub_fldr}]...')
+    logging.info(f"Applying mask for batch [{sub_fldr}]...")
     # Mask image
     in_dir = os.path.join(working_dir, "s1_reorient_lps")
     mask_dir = os.path.join(working_dir, "s2_dlicv")
@@ -93,9 +95,9 @@ def run_pipeline(
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
     apply_mask_img(df_img, in_dir, in_suff, mask_dir, mask_suff, out_dir, out_suff)
-    logging.info(f'Applying mask for batch [{sub_fldr}] done')
+    logging.info(f"Applying mask for batch [{sub_fldr}] done")
 
-    logging.info(f'Applying DLMUSE for batch [{sub_fldr}]...')
+    logging.info(f"Applying DLMUSE for batch [{sub_fldr}]...")
     # Apply DLMUSE
     in_dir = os.path.join(working_dir, "s3_masked")
     out_dir = os.path.join(working_dir, "s4_dlmuse")
@@ -104,9 +106,9 @@ def run_pipeline(
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
     run_dlmuse(in_dir, in_suff, out_dir, out_suff, device, dlmuse_extra_args)
-    logging.info(f'Applying DLMUSE for batch [{sub_fldr}] done')
+    logging.info(f"Applying DLMUSE for batch [{sub_fldr}] done")
 
-    logging.info(f'Relabeling DLMUSE for batch [{sub_fldr}]...')
+    logging.info(f"Relabeling DLMUSE for batch [{sub_fldr}]...")
     # Relabel DLMUSE
     in_dir = os.path.join(working_dir, "s4_dlmuse")
     out_dir = os.path.join(working_dir, "s5_relabeled")
@@ -124,9 +126,9 @@ def run_pipeline(
         LABEL_FROM,
         LABEL_TO,
     )
-    logging.info(f'Applying DLMUSE for batch [{sub_fldr}] done')
+    logging.info(f"Applying DLMUSE for batch [{sub_fldr}] done")
 
-    logging.info(f'Combining DLICV and MUSE masks for batch [{sub_fldr}]...')
+    logging.info(f"Combining DLICV and MUSE masks for batch [{sub_fldr}]...")
     # Combine DLICV and MUSE masks
     in_dir = os.path.join(working_dir, "s5_relabeled")
     mask_dir = os.path.join(working_dir, "s2_dlicv")
@@ -137,18 +139,18 @@ def run_pipeline(
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
     apply_combine_masks(df_img, in_dir, in_suff, mask_dir, mask_suff, out_dir, out_suff)
-    logging.info(f'Combining DLICV and MUSE masks for batch [{sub_fldr}] done')
+    logging.info(f"Combining DLICV and MUSE masks for batch [{sub_fldr}] done")
 
-    logging.info(f'Reorienting to initial orientation for batch [{sub_fldr}]...')
+    logging.info(f"Reorienting to initial orientation for batch [{sub_fldr}]...")
     # Reorient to initial orientation
     in_dir = os.path.join(working_dir, "s6_combined")
     out_dir = out_dir_final
     in_suff = SUFF_DLMUSE
     out_suff = SUFF_DLMUSE
     apply_reorient_to_init(df_img, in_dir, in_suff, out_dir, out_suff)
-    logging.info(f'Reorienting to initial orientation for batch [{sub_fldr}] done')
+    logging.info(f"Reorienting to initial orientation for batch [{sub_fldr}] done")
 
-    logging.info(f'Create ROI csv for batch [{sub_fldr}]...')
+    logging.info(f"Create ROI csv for batch [{sub_fldr}]...")
     # Create roi csv
     in_dir = out_dir_final
     out_dir = out_dir_final
@@ -157,13 +159,13 @@ def run_pipeline(
     apply_create_roi_csv(
         df_img, in_dir, in_suff, DICT_MUSE_SINGLE, DICT_MUSE_DERIVED, out_dir, out_suff
     )
-    logging.info(f'Create ROI csv for batch [{sub_fldr}] done')
+    logging.info(f"Create ROI csv for batch [{sub_fldr}] done")
 
-    logging.info(f'Combine ROI csv for batch [{sub_fldr}]...')
+    logging.info(f"Combine ROI csv for batch [{sub_fldr}]...")
     # Combine roi csv
     in_dir = out_dir_final
     out_dir = out_dir_final
     in_suff = SUFF_ROI
     out_name = OUT_CSV
     combine_roi_csv(df_img, in_dir, in_suff, out_dir, out_name)
-    logging.info(f'Combine ROI csv for batch [{sub_fldr}] done')
+    logging.info(f"Combine ROI csv for batch [{sub_fldr}] done")
diff --git a/NiChart_DLMUSE/utils.py b/NiChart_DLMUSE/utils.py
@@ -1,15 +1,16 @@
 import glob
+import logging
 import os
 import re
 from typing import Any
-import logging
+
 import numpy as np
 import pandas as pd
 
 LIST_IMG_EXT = [".nii", ".nii.gz"]
 
 logger = logging.getLogger(__name__)
-logging.basicConfig(filename='pipeline.log', encoding='utf-8', level=logging.DEBUG)
+logging.basicConfig(filename="pipeline.log", encoding="utf-8", level=logging.DEBUG)
 
 
 def get_basename(
@@ -114,7 +115,9 @@ def make_img_list(in_data: str) -> pd.DataFrame:
                 flag[i] = 1
         nii_files = nii_files[flag == 1]
 
-    logging.info(f"Detected {nii_files.shape[0]} images. Valid images are {len(nii_files)}...")
+    logging.info(
+        f"Detected {nii_files.shape[0]} images. Valid images are {len(nii_files)}..."  # type:ignore
+    )
     # Create a dataframe
     df_out = pd.DataFrame(data=nii_files, columns=["img_path"])
-Original file line number
+Diff line change
@@ Expand Up / @@ -152,7 +152,7 @@ def main() -> None: @@
                     device,
                     dlmuse_extra_args,
                     dlicv_extra_args,
-                    i
+                    i,
                 ),
             )
             curr_thread.start()
@@ Expand Down @@