Merge pull request #58 from CBICA/spiros-dev

Documentation update

.github/workflows/pre-commit.yml

@@ -3,7 +3,7 @@ name: pre-commit
 on:
   pull_request:
   push:
-    branches: [main]
+    branches: ["main", "spiros-dev"]
 
 jobs:
   pre-commit:

.github/workflows/sphinx-docs.yml

@@ -1,7 +1,7 @@
 name: Deploy static content to Pages
 on:
   push:
-    branches: ["main"]
+    branches: ["main", "spiros-dev"]
 
 jobs:
   build-docs:

NiChart_DLMUSE/CalcROIVol.py

@@ -11,9 +11,19 @@
 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:
+def calc_roi_volumes(mrid: Any, in_img: Any, label_indices: np.ndarray) -> pd.DataFrame:
     """
     Creates a dataframe with the volumes of rois
+
+    :param mrid: the input mrid
+    :type mrid: Any
+    :param in_img: the input image
+    :type in_img: niftii image
+    :param label_indices: passed label indices
+    :type label_indices: np.ndarray
+
+    :return: Dataframe with details of images
+    :rtype: pd.DataFrame
     """
 
     # Keep input lists as arrays
@@ -56,6 +66,14 @@ def calc_roi_volumes(mrid: Any, in_img: Any, label_indices: Any) -> pd.DataFrame
 def append_derived_rois(df_in: pd.DataFrame, derived_roi_map: Any) -> pd.DataFrame:
     """
     Calculates a dataframe with the volumes of derived rois.
+
+    :param df_in: the passed dataframe
+    :type df_in: pd.DataFrame
+    :param derived_roi_map: derived roi map file
+    :type derived_roi_map: Any
+
+    :return: ROI dataframe
+    :rtype: pd.DataFrame
     """
 
     # Read derived roi map file to a dictionary
@@ -91,6 +109,17 @@ def create_roi_csv(
 ) -> None:
     """
     Creates a csv file with the results of the roi calculations
+
+    :param mrid: the input mrid
+    :type mrid: Any
+    :param in_roi: the input ROI
+    :type in_roi: Any
+    :param map_derived_roi: derived roi map file
+    :type map_derived_roi: Any
+    :param out_csv: output csv filename
+    :type out_csv: str
+
+    :rtype: None
     """
 
     # Calculate MUSE ROIs
@@ -122,6 +151,19 @@ def apply_create_roi_csv(
 ) -> None:
     """
     Apply roi volume calc to all images
+
+    :param df_img: the passed dataframe
+    :type df_img: pd.DataFrame
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
@@ -140,6 +182,19 @@ def combine_roi_csv(
 ) -> None:
     """
     Combine csv files
+
+    :param df_img: passed dataframe
+    :type df_img: pd.DataFrame
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_name: the desired output filename
+    :type out_name: str
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)

NiChart_DLMUSE/MaskImage.py

@@ -66,10 +66,16 @@ def calc_bbox_with_padding(img: np.ndarray, perc_pad: int = 10) -> np.ndarray:
     return bcoors
 
 
-def mask_img(in_img: Any, mask_img: Any, out_img: Any) -> None:
+def mask_img(in_img: Any, mask_img: Any, out_img: str) -> None:
     """
     Applies the input mask to the input image
     Crops the image around the mask
+
+    :param in_img: the passed image
+    :param mask_img: the input mask
+    :param out_img: the output filename
+    :type out_img: str
+    :rtype: None
     """
 
     # Read input image and mask
@@ -99,9 +105,16 @@ def mask_img(in_img: Any, mask_img: Any, out_img: Any) -> None:
     nii_out.to_filename(out_img)
 
 
-def combine_masks(dlmuse_mask: Any, dlicv_mask: Any, out_img: Any) -> None:
+def combine_masks(dlmuse_mask: Any, dlicv_mask: Any, out_img: str) -> None:
     """'
     Combine icv and muse masks
+
+    :param dlmuse_mask: The passed dlmuse mask
+    :param dlicv_mask: The passed dlicv mask
+    :param out_img: the output filename
+    :type out_img: str
+
+    :rtype: None
     """
 
     # Read input images
@@ -146,6 +159,21 @@ def apply_mask_img(
 ) -> None:
     """
     Apply reorientation to all images
+
+    :param df_img: The passed dataframe
+    :type df_img: pd.DataFrame
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the passed input suffix
+    :type in_suff: str
+    :param mask_dir: the passed mask directory
+    :type mask_dir: str
+    :param out_dir: the passed output directory
+    :type out_dir: str
+    :param out_suff: the passed output suffix
+    :type out_suff: str
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
@@ -170,6 +198,23 @@ def apply_combine_masks(
 ) -> None:
     """
     Apply reorientation to all images
+
+    :param df_img: the passed dataframe
+    :type df_img: pd.DataFrame
+    :param dlmuse_dir: the passed dlmuse directory
+    :type dlmuse_dir: str
+    :param dlmuse_suff: the passed dlmuse suffix
+    :type dlmuse_suff: str
+    :param dlicv_dir: the passed dlicv directory
+    :type dlicv_dir: str
+    :param dlicv_suff: the passed dlicv suffix
+    :type dlicv_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)

NiChart_DLMUSE/RelabelROI.py

@@ -11,10 +11,21 @@ def relabel_rois(
 ) -> None:
     """
     Convert labels in input roi image to new labels based on the mapping
-    print()
     The mapping file should contain numeric indices for the mapping
-    irint()
     between the input roi image (from) and output roi image (to)
+
+    :param in_img: the passed image
+    :type in_img: niftii image
+    :param roi_map: the passed roi map
+    :type roi_map: str
+    :param label_from: input roi image
+    :type label_from: Any
+    :param label_to: output roi image
+    :type label_to: Any
+    :param out_img: the desired filename for the output image
+    :type out_img: str
+
+    :rtype: None
     """
 
     # Read image
@@ -52,6 +63,25 @@ def apply_relabel_rois(
 ) -> None:
     """
     Apply relabeling to all images
+
+    :param df_img: the passed dataframe
+    :type df_img: pd.DataFrame
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+    :param roi_map: the roi map
+    :type roi_map: Any
+    :param label_from: input roi image
+    :type label_from: Any
+    :param label_to: output roi image
+    :type label_to: Any
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)

NiChart_DLMUSE/ReorientImage.py

@@ -12,9 +12,16 @@
 logging.basicConfig(filename="pipeline.log", encoding="utf-8", level=logging.DEBUG)
 
 
-def reorient_img(in_img: Any, ref: Any, out_img: Any) -> None:
+def reorient_img(in_img: Any, ref: Any, out_img: str) -> None:
     """
     Reorient image
+
+    :param in_img: the input image
+    :type in_img: niftii image
+    :param out_img: the desired filename for the output image
+    :type out_img: str
+
+    :rtype: None
     """
     if os.path.exists(out_img):
         logging.info("Out file exists, skip reorientation ...")
@@ -50,6 +57,15 @@ def apply_reorient_img(
 ) -> None:
     """
     Apply reorientation to all images
+
+    :param df_img: the passed dataframe
+    :type df_img: pd.DataFrame
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suffix: the output suffix
+    :type out_suffix: str
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)
@@ -61,10 +77,23 @@ def apply_reorient_img(
 
 
 def apply_reorient_to_init(
-    df_img: pd.DataFrame, in_dir: str, in_suff: Any, out_dir: str, out_suff: str
+    df_img: pd.DataFrame, in_dir: str, in_suff: str, out_dir: str, out_suff: str
 ) -> None:
     """
     Apply reorientation to init img to all images
+
+    :param df_img: the passed dataframe
+    :type df_img: pd.DataFrame
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :param in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+
+    :rtype: None
     """
     if not os.path.exists(out_dir):
         os.makedirs(out_dir)

NiChart_DLMUSE/SegmentImage.py

@@ -6,12 +6,30 @@
 
 def run_dlicv(
     in_dir: str,
-    in_suff: Any,
+    in_suff: str,
     out_dir: str,
-    out_suff: Any,
+    out_suff: str,
     device: str,
     extra_args: str = "",
 ) -> None:
+    """
+    Run dlicv with the passed images
+
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+    :param device: cuda/mps for GPU acceleration otherwise cpu
+    :type device: str
+    :param extra_args: extra arguments for DLICV package
+    :type extra_args: str
+
+    :rtype: None
+    """
     # Call DLICV
     os.system(f"DLICV -i {in_dir} -o {out_dir} -device {device} " + extra_args)
 
@@ -28,6 +46,24 @@ def run_dlmuse(
     device: str,
     extra_args: str = "",
 ) -> None:
+    """
+    Run dlmuse with the passed images
+
+    :param in_dir: the input directory
+    :type in_dir: str
+    :param in_suff: the input suffix
+    :type in_suff: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param out_suff: the output suffix
+    :type out_suff: str
+    :param device: cuda/mps for GPU acceleration otherwise cpu
+    :type device: str
+    :param extra_args: extra arguments for DLMUSE package
+    :type extra_args: str
+
+    :rtype: None
+    """
     # Call DLMUSE
     os.system(f"DLMUSE -i {in_dir} -o {out_dir} -device {device} " + extra_args)
 

NiChart_DLMUSE/dlmuse_pipeline.py

@@ -45,6 +45,21 @@ def run_pipeline(
 ) -> None:
     """
     NiChart pipeline
+
+    :param in_data: the input directory
+    :type in_data: str
+    :param out_dir: the output directory
+    :type out_dir: str
+    :param device: conda/mps for GPU acceleration otherwise cpu
+    :type device: str
+    :param dlmuse_extra_args: extra arguments for DLMUSE package
+    :type dlmuse_extra_args: str
+    :param dlicv_extra_args: extra arguments for DLICV package
+    :type dlicv_extra_args: str
+    :param sub_fldr: the number of subfolders(default = 1)
+    :type sub_fldr: int
+
+    :rtype: None
     """
     logging.info(f"Starting the pipeline on folder {sub_fldr}")
     logging.info(f"Detecting input images for batch [{sub_fldr}]...")