Add cmd unigradicon-jacobian

.github/workflows/gpu-test-action.yml

@@ -13,10 +13,10 @@ jobs:
 
     steps:
     - uses: actions/checkout@v2
-    - name: Set up Python 3.7
+    - name: Set up Python 3.8
       uses: actions/setup-python@v2
       with:
-        python-version: 3.7
+        python-version: 3.8
     - name: Install dependencies
       run: |
         pip install -r requirements.txt

.github/workflows/test_readme_works.yml

@@ -11,7 +11,7 @@ jobs:
     strategy:
       max-parallel: 5
       matrix:
-        python-version: [ '3.7', '3.8', '3.9', '3.11', '3.12']
+        python-version: ['3.8', '3.9', '3.11', '3.12']
 
     steps:
     - uses: actions/checkout@v2
@@ -35,4 +35,5 @@ jobs:
             --transform=trans.hdf5 --warped_moving_out=warped_2_C01_1.nrrd --nearest_neighbor
         unigradicon-warp --fixed=RegLib_C01_2.nrrd --moving=RegLib_C01_1_foreground_mask.nii.gz \
             --transform=trans.hdf5 --warped_moving_out=warped_2_C01_1.nrrd --nearest_neighbor
+        unigradicon-jacobian --fixed=RegLib_C01_2.nrrd --transform=trans.hdf5 --jacob=jacobian.nii.gz
 

setup.cfg

@@ -18,7 +18,7 @@ classifiers =
 package_dir = 
     = src
 packages = find:
-python_requires = >=3.7
+python_requires = >=3.8
 
 install_requires = 
     icon_registration>=1.1.5
@@ -30,3 +30,4 @@ where = src
 console_scripts =
     unigradicon-register = unigradicon:main
     unigradicon-warp = unigradicon:warp_command
+    unigradicon-jacobian = unigradicon:compute_jacobian_map_command

src/unigradicon/__init__.py

@@ -386,9 +386,6 @@ def warp_command():
             use_reference_image=True,
             reference_image=fixed
             )
-
-    warped_moving_image = maybe_cast_back(warped_moving_image)
-
     itk.imwrite(warped_moving_image, args.warped_moving_out)
 
 def maybe_cast(img: itk.Image):
@@ -409,3 +406,34 @@ def maybe_cast(img: itk.Image):
 
     return img, maybe_cast_back
 
+def compute_jacobian_map_command():
+    import itk
+    import argparse
+    parser = argparse.ArgumentParser(description="Compute the Jacobian map of a given transform.")
+    parser.add_argument("--transform", required=True, type=str,
+                            help="The path to the transform file.")
+    parser.add_argument("--fixed", required=True, type=str,
+                            help="The path to the fixed image that has been used in the registration.")
+    parser.add_argument("--jacob", required=True, default=None, help="The path to the output Jacobian map, \
+                        e.g. /path/to/output_jacobian.nii.gz")
+    parser.add_argument("--log_jacob", required=False, default=None, help="The path to the output log Jacobian map. \
+                            If not specified, the log Jacobian map will not be saved.")
+    args = parser.parse_args()
+
+    transform_file = args.transform
+    fixed_img_file = args.fixed
+    transform = itk.transformread(transform_file)[0]
+    jacob = itk.displacement_field_jacobian_determinant_filter(
+        itk.transform_to_displacement_field_filter(
+            transform,
+            reference_image=itk.imread(fixed_img_file),
+            use_reference_image=True
+        )
+    )
+    itk.imwrite(jacob, args.jacob)
+
+    if args.log_jacob is not None:
+        log_jacob = itk.LogImageFilter.New(jacob)
+        log_jacob.Update()
+        log_jacob = log_jacob.GetOutput()
+        itk.imwrite(jacob, args.log_jacob)