petpal 0.5.5__tar.gz → 0.5.6__tar.gz

{petpal-0.5.5 → petpal-0.5.6}/PKG-INFO

@@ -1,10 +1,9 @@
 Metadata-Version: 2.4
 Name: petpal
-Version: 0.5.5
+Version: 0.5.6
 Summary: PET-PAL (Positron Emission Tomography Processing and Analysis Library)
 Project-URL: Repository, https://github.com/PETPAL-WUSM/PETPAL.git
-Author: Bradley Judge
-Author-email: Furqan Dar <dar@wustl.edu>, Noah Goldman <noahg@wustl.edu>, Kenan Oestreich <kenan.oestreich@wustl.edu>
+Author-email: Noah Goldman <noahg@wustl.edu>, Bradley Judge <bjudge@wustl.edu>, Furqan Dar <dar@wustl.edu>, Kenan Oestreich <kenan.oestreich@wustl.edu>
 License-File: LICENSE
 Classifier: Development Status :: 2 - Pre-Alpha
 Classifier: Intended Audience :: Science/Research
@@ -45,7 +44,17 @@ Description-Content-Type: text/markdown
 
 ## Installation
 
-Currently, we only support building the package directly from source. Clone the repository using your preferred method. After navigating to the top-level directory (where `pyproject.toml` exists), we run the following command in the terminal:
+### Using Pip
+
+The simplest way to install PETPAL is using pip. First, ensure you are using Python version >=3.12. Then, run the following:
+
+```shell
+pip install petpal
+```
+
+### Build from source
+
+Clone the repository using your preferred method. After navigating to the top-level directory (where `pyproject.toml` exists), we run the following command in the terminal:
 
 ```shell
 pip install .  # Installs the package

{petpal-0.5.5 → petpal-0.5.6}/README.md

@@ -9,7 +9,17 @@
 
 ## Installation
 
-Currently, we only support building the package directly from source. Clone the repository using your preferred method. After navigating to the top-level directory (where `pyproject.toml` exists), we run the following command in the terminal:
+### Using Pip
+
+The simplest way to install PETPAL is using pip. First, ensure you are using Python version >=3.12. Then, run the following:
+
+```shell
+pip install petpal
+```
+
+### Build from source
+
+Clone the repository using your preferred method. After navigating to the top-level directory (where `pyproject.toml` exists), we run the following command in the terminal:
 
 ```shell
 pip install .  # Installs the package

{petpal-0.5.5 → petpal-0.5.6}/petpal/cli/cli_preproc.py

@@ -345,89 +345,84 @@ def main():
         preproc_parser.print_help()
         raise SystemExit('Exiting without command')
 
-    if len(args.motion_target)==1:
-        motion_target = args.motion_target[0]
+    if 'motion_target' in dir(args):
+        if len(args.motion_target)==1:
+            motion_target = args.motion_target[0]
+        else:
+            motion_target = args.motion_target
     else:
-        motion_target = args.motion_target
+        motion_target = None
 
     command = str(args.command).replace('-','_')
 
-    if command=='weighted_series_sum':
-        useful_functions.weighted_series_sum(input_image_4d_path=args.input_img,
-                                             out_image_path=args.out_img,
-                                             half_life=args.half_life,
-                                             start_time=args.start_time,
-                                             end_time=args.end_time,
-                                             verbose=True)
-
-    if command=='auto_crop':
-        image_operations_4d.SimpleAutoImageCropper(input_image_path=args.input_img,
-                                                   out_image_path=args.out_img,
-                                                   thresh_val=args.thresh_val,
-                                                   verbose=True)
-
-    if command=='motion_correction':
-        motion_corr.motion_corr(input_image_4d_path=args.input_img,
+    match command:
+        case 'weighted_series_sum':
+            useful_functions.weighted_series_sum(input_image_4d_path=args.input_img,
+                                                 out_image_path=args.out_img,
+                                                 half_life=args.half_life,
+                                                 start_time=args.start_time,
+                                                 end_time=args.end_time,
+                                                 verbose=True)
+        case 'auto_crop':
+            image_operations_4d.SimpleAutoImageCropper(input_image_path=args.input_img,
+                                                    out_image_path=args.out_img,
+                                                    thresh_val=args.thresh_val,
+                                                    verbose=True)
+        case 'motion_correction':
+            motion_corr.motion_corr(input_image_4d_path=args.input_img,
+                                    out_image_path=args.out_img,
+                                    motion_target_option=motion_target,
+                                    verbose=True,
+                                    type_of_transform=args.transform_type,
+                                    half_life=args.half_life)
+        case 'register_pet':
+            register.register_pet(input_reg_image_path=args.input_img,
                                 out_image_path=args.out_img,
+                                reference_image_path=args.anatomical,
                                 motion_target_option=motion_target,
                                 verbose=True,
-                                type_of_transform=args.transform_type,
                                 half_life=args.half_life)
-    if command=='register_pet':
-        register.register_pet(input_reg_image_path=args.input_img,
-                              out_image_path=args.out_img,
-                              reference_image_path=args.anatomical,
-                              motion_target_option=motion_target,
-                              verbose=True,
-                              half_life=args.half_life)
-
-    if command=='write_tacs_old':
-        regional_tac_extraction.write_tacs(input_image_path=args.input_img,
-                                           out_tac_dir=args.out_tac_dir,
-                                           segmentation_image_path=args.segmentation,
-                                           label_map_path=args.label_map_path,
-                                           verbose=True)
-
-    if command=='write_tacs':
-        tac_obj = regional_tac_extraction.WriteRegionalTacs(input_image_path=args.input_img,
-                                                  segmentation_path=args.segmentation,
-                                                  label_map=args.label_map)
-        tac_obj(out_tac_prefix=args.patid,
-                out_tac_dir=args.out_tac_dir,
-                one_tsv_per_region=not args.excel)
-
-    if command=='warp_pet_atlas':
-        register.warp_pet_atlas(input_image_path=args.input_img,
-                                anat_image_path=args.anatomical,
-                                atlas_image_path=args.reference_atlas,
-                                out_image_path=args.out_img,
-                                verbose=True)
-
-    if command=='gauss_blur':
-        image_operations_4d.gauss_blur(input_image_path=args.input_img,
-                                       blur_size_mm=args.blur_size_mm,
+        case 'write_tacs_old':
+            regional_tac_extraction.write_tacs(input_image_path=args.input_img,
+                                            out_tac_dir=args.out_tac_dir,
+                                            segmentation_image_path=args.segmentation,
+                                            label_map_path=args.label_map_path,
+                                            verbose=True)
+        case 'write_tacs':
+            tac_obj = regional_tac_extraction.WriteRegionalTacs(input_image_path=args.input_img,
+                                                    segmentation_path=args.segmentation,
+                                                    label_map=args.label_map)
+            tac_obj(out_tac_prefix=args.patid,
+                    out_tac_dir=args.out_tac_dir,
+                    one_tsv_per_region=not args.excel)
+        case 'warp_pet_atlas':
+            register.warp_pet_to_atlas(input_image_path=args.input_img,
+                                       anat_image_path=args.anatomical,
+                                       atlas_image_path=args.reference_atlas,
                                        out_image_path=args.out_img,
-                                       verbose=True,
-                                       use_fwhm=True)
-
-    if command=='suvr':
-        image_operations_4d.suvr(input_image_path=args.input_img,
-                                 out_image_path=args.out_img,
-                                 segmentation_image_path=args.segmentation,
-                                 ref_region=args.ref_region)
-
-    if command=='windowed_motion_corr':
-        motion_corr.windowed_motion_corr_to_target(input_image_path=args.input_img,
-                                                   out_image_path=args.out_img,
-                                                   motion_target_option=motion_target,
-                                                   w_size=args.window_size,
-                                                   type_of_transform=args.transform_type)
-
-    if command=='rescale_image':
-        input_img = ants.image_read(filename=args.input_img)
-        out_img = image_operations_4d.rescale_image(input_image=input_img,
-                                                    rescale_constant=args.scale_factor)
-        ants.image_write(image=out_img, filename=args.out_img)
+                                       verbose=True)
+        case 'gauss_blur':
+            image_operations_4d.gauss_blur(input_image_path=args.input_img,
+                                        blur_size_mm=args.blur_size_mm,
+                                        out_image_path=args.out_img,
+                                        verbose=True,
+                                        use_fwhm=True)
+        case 'suvr':
+            image_operations_4d.suvr(input_image_path=args.input_img,
+                                     out_image_path=args.out_img,
+                                     segmentation_image_path=args.segmentation,
+                                     ref_region=args.ref_region)
+        case 'windowed_motion_corr':
+            motion_corr.windowed_motion_corr_to_target(input_image_path=args.input_img,
+                                                    out_image_path=args.out_img,
+                                                    motion_target_option=motion_target,
+                                                    w_size=args.window_size,
+                                                    type_of_transform=args.transform_type)
+        case 'rescale_image':
+            input_img = ants.image_read(filename=args.input_img)
+            out_img = image_operations_4d.rescale_image(input_image=input_img,
+                                                        rescale_constant=args.scale_factor)
+            ants.image_write(image=out_img, filename=args.out_img)
 
 if __name__ == "__main__":
     main()

{petpal-0.5.5 → petpal-0.5.6}/pyproject.toml

@@ -4,12 +4,12 @@ build-backend = "hatchling.build"
 
 [project]
 name = "petpal"
-version = "0.5.5"
+version = "0.5.6"
 description = "PET-PAL (Positron Emission Tomography Processing and Analysis Library)"
 authors = [
-    {name = "Furqan Dar", email = "dar@wustl.edu"},
-    {name = "Bradley Judge"},
     {name = "Noah Goldman", email = "noahg@wustl.edu"},
+    {name = "Bradley Judge", email = "bjudge@wustl.edu"},
+    {name = "Furqan Dar", email = "dar@wustl.edu"},
     {name = "Kenan Oestreich", email = "kenan.oestreich@wustl.edu"}
 ]
 requires-python = ">= 3.12" # At least Python 3.12
@@ -47,7 +47,6 @@ classifiers = [  # These are added to PyPI package when published; Used for sear
 
 [project.scripts]
     petpal-preproc = "petpal.cli.cli_preproc:main"
-    petpal-bids = "petpal.cli.cli_bids:main"
     petpal-tac-interpolate = "petpal.cli.cli_tac_interpolation:main"
     petpal-graph-plot = "petpal.cli.cli_graphical_plots:main"
     petpal-graph-analysis = "petpal.cli.cli_graphical_analysis:main"