Updated project files

README.md

@@ -44,6 +44,40 @@ mv fixed_image.nii.gz moving_image.nii.gz incoming
 apptainer exec docker://fnndsc/pl-images-register:latest images_register [--args] incoming outgoing
 ```
 
+If there is only one moving image, it will be registered onto the fixed image.
+If there are multiple moving images, each one will be registered to the fixed image separately.
+
+For multiple moving images, all of them should be placed in a folder, and the folder should be passed to the 
+parser under moving_images_folder.
+
+Example 1:
+
+Inputs: 
+```shell
+    input_dir/fixed_image.nii.gz
+    input_dir/moving_image.nii.gz 
+```
+Outputs:
+```shell
+    output_dir/moving_image_registered.nii.gz
+    output_dir/moving_image_transform.mat
+``` 
+Example 2:
+
+Inputs: 
+```shell
+    input_dir/fixed_image.nii.gz
+    input_dir/moving_images_folder/moving_image1.nii.gz, moving_image2.nii.gz, moving_image3.nii.gz, etc.
+```
+Outputs:
+```shell
+    output_dir/moving_images_folder/moving_image1_registered.nii.gz, moving_image2_registered.nii.gz, 
+        moving_image3.nii.gz, etc.
+    output_dir/moving_images_folder/moving_image1_transform.mat, moving_image2_transform.mat, 
+        moving_image3_transform.mat, etc.
+```
+Please not that all images (fixed, moving, registered) must be in nii.gz format.
+
 ## Development
 
 The registration algorithms are found in images_register.py module.

images_register.py

@@ -8,6 +8,7 @@
 # --------------------------------------------- ENVIRONMENT SETUP -----------------------------------------------------
 # Project imports:
 from registration_tools import rigid_registration
+from os_tools import sub_niftis
 
 # System imports:
 from os.path import join
@@ -36,24 +37,59 @@
                                     'the transformation matrix. The fixed, moving, and registered moving images '
                                     'are all in NIfTI format.',
                         formatter_class=ArgumentDefaultsHelpFormatter)
+
 # parser.add_argument('-V', '--version', action='version',
 #                     version=f'%(prog)s {__version__}')
 
+"""
+If there is only one moving image, it will be registered onto the fixed image.
+If there are multiple moving images, each one will be registered to the fixed image separately.
+
+For multiple moving images, all of them should be placed in a folder, and the folder should be passed to the 
+parser under moving_images_folder.
+
+Example 1:
+ 
+Inputs: 
+    input_dir/fixed_image.nii.gz
+    input_dir/moving_image.nii.gz 
+
+Outputs:
+    output_dir/moving_image_registered.nii.gz
+    output_dir/moving_image_transform.mat
+
+Example 2:
+
+Inputs: 
+    input_dir/fixed_image.nii.gz
+    input_dir/moving_images_folder/moving_image1.nii.gz, moving_image2.nii.gz, moving_image3.nii.gz, etc.
+
+Outputs:
+    output_dir/moving_images_folder/moving_image1_registered.nii.gz, moving_image2_registered.nii.gz, 
+        moving_image3.nii.gz, etc.
+    output_dir/moving_images_folder/moving_image1_transform.mat, moving_image2_transform.mat, 
+        moving_image3_transform.mat, etc.
+        
+Please not that all images (fixed, moving, registered) must be in nii.gz format.
+"""
+
 parser.add_argument('--fixed_image', type=str, default='fixed_image.nii.gz',
                     help='relative path to the fixed image in relation to input folder')
 parser.add_argument('--moving_image', type=str, default='moving_image.nii.gz',
-                    help='relative path to the moving image in relation to input folder')
-parser.add_argument('--registered_image', type=str, default='registered_image.nii.gz',
-                    help='relative path to the registered image in relation to output folder')
-parser.add_argument('--transform_matrix', type=str, default='transform.mat',
-                    help='relative path to the transformation matrix in relation to output folder')
+                    help='relative path to the moving image in relation to input folder.'
+                         'The moving image must be in .nii.gz format.')
+parser.add_argument('--moving_images_folder', type=str, default='None',
+                    help='relative path to the folder containing multiple moving images.'
+                         'Every image in this folder will be registered to the fixed image.'
+                         'All moving images must be in .nii.gz format.')
+
+# ------------------------------------------- ChRIS PLUGIN WRAPPER ----------------------------------------------------
 
 # The main function of this *ChRIS* plugin is denoted by this ``@chris_plugin`` "decorator."
 # Some metadata about the plugin is specified here. There is more metadata specified in setup.py.
 #
 # documentation: https://fnndsc.github.io/chris_plugin/chris_plugin.html#chris_plugin
 
-# ------------------------------------------- ChRIS PLUGIN WRAPPER ----------------------------------------------------
 @chris_plugin(
     parser=parser,
     title='Images registration',
@@ -77,11 +113,23 @@ def main(options: Namespace, inputdir: Path, outputdir: Path):
     print(DISPLAY_TITLE)
 
     fixed_image_path = join(inputdir, options.fixed_image)
-    moving_image_path = join(inputdir, options.moving_image)
-    registered_image_path = join(outputdir, options.registered_image)
-    transform_matrix_path = join(outputdir, options.transform_matrix)
 
-    rigid_registration(fixed_image_path, moving_image_path, registered_image_path, transform_matrix_path)
+    if options.moving_images_folder == 'None':
+        moving_image_path = join(inputdir, options.moving_image)
+        registered_image_path = join(outputdir, options.moving_image.replace('.nii.gz', '_registered.nii.gz'))
+        transform_matrix_path = join(outputdir, options.moving_image.replace('.nii.gz', '_transform.mat'))
+
+        rigid_registration(fixed_image_path, moving_image_path, registered_image_path, transform_matrix_path)
+
+    else:
+        moving_images_list = sub_niftis(join(inputdir, options.moving_images_folder), complete_path=False)
+        for i, moving_image in enumerate(moving_images_list):
+            moving_image_path = join(inputdir, options.moving_images_folder, moving_image)
+            registered_image_path = join(outputdir, options.moving_images_folder,
+                                         options.moving_image.replace('.nii.gz', '_registered.nii.gz'))
+            transform_matrix_path = join(outputdir, options.moving_images_folder,
+                                          options.moving_image.replace('.nii.gz', '_transform.mat'))
+            rigid_registration(fixed_image_path, moving_image_path, registered_image_path, transform_matrix_path)
 
 # ------------------------------------------------ EXECUTE MAIN -------------------------------------------------------
 

os_tools.py

@@ -0,0 +1,65 @@
+"""
+Developed by Arman Avesta, MD, PhD
+FNNDSC | Boston Children's Hospital | Harvard Medical School
+
+This file contains functions to help with file & folder organization, parallel processing, and other operating system
+functionalities.
+"""
+
+# ----------------------------------------------- ENVIRONMENT SETUP ---------------------------------------------------
+# Project imports:
+
+# System imports:
+import os
+from os.path import join, dirname
+from typing import List
+
+# ---------------------------------------------- HELPER FUNCTIONS -----------------------------------------------------
+
+def subdirs(root: str, complete_path: bool = False, prefix: str = None, suffix: str = None, sort: bool = True) \
+        -> List[str]:
+    if complete_path:
+        func = os.path.join
+    else:
+        func = lambda x, y: y
+    res = [func(root, subdir) for subdir in os.listdir(root) if os.path.isdir(join(root, subdir))
+           and (prefix is None or subdir.startswith(prefix))
+           and (suffix is None or subdir.endswith(suffix))]
+    if sort:
+        res.sort()
+    return res
+
+
+def subfiles(root: str, complete_path: bool = True, prefix: str = None, suffix: str = None, sort: bool = True) \
+        -> List[str]:
+    if complete_path:
+        func = os.path.join
+    else:
+        func = lambda x, y: y
+    res = [func(root, subdir) for subdir in os.listdir(root) if os.path.isfile(join(root, subdir))
+           and (prefix is None or subdir.startswith(prefix))
+           and (suffix is None or subdir.endswith(suffix))]
+    if sort:
+        res.sort()
+    return res
+
+
+def sub_niftis(root: str, complete_path: bool = True, sort: bool = True) -> List[str]:
+    return subfiles(root, complete_path=complete_path, sort=sort, suffix='.nii.gz')
+
+
+
+def split_path(path: str) -> List[str]:
+    """
+    splits at each separator. This is different from os.path.split which only splits at last separator
+    """
+    return path.split(os.sep)
+
+
+# -------------------------------------------------- CODE TESTING -----------------------------------------------------
+
+if __name__ == '__main__':
+
+    path = '/Users/arman/projects/pl-images-register/data/nifti'
+    niftis_list = sub_niftis(path, complete_path=False)
+    print(niftis_list)