v0.4.4

docs/source/conf.py

@@ -8,7 +8,7 @@
 project = 'mdreg'
 copyright = '2024, mdreg maintainers'
 author = 'mdreg maintainers'
-release = '0.4.3'
+release = '0.4.4'
 
 # -- Path setup --------------------------------------------------------------
 # If extensions (or modules to document with autodoc) are in another directory,

docs/source/releases/index.rst

@@ -11,6 +11,7 @@ Releases
 .. toctree::
    :maxdepth: 2
 
+   release_0.4.4
    release_0.4.3
    release_0.4.2
    release_0.4.1

docs/source/releases/release_0.4.4.rst

@@ -0,0 +1,20 @@
+mdreg 0.4.4
+===========
+
+Summary
+-------
+
+- Added error handling for elastix
+
+Contributors
+------------
+
+1 authors added to this release (alphabetically):
+
+- Steven Sourbron (`@plaresmedima <https://github.com/plaresmedima>`_)
+
+1 reviewers added to this release (alphabetically):
+
+- Steven Sourbron (`@plaresmedima <https://github.com/plaresmedima>`_)
+
+

pyproject.toml

@@ -6,7 +6,7 @@ requires = ['setuptools>=61.2']
 
 [project]
 name = "mdreg"
-version = "0.4.3"
+version = "0.4.4"
 dependencies = [
   'importlib-resources>=1.1.0',
   'tqdm',
@@ -50,7 +50,8 @@ keywords = ['python', "medical imaging", "motion correction", "registration"]
 requires-python = ">=3.6"
 
 [project.urls]
-"Homepage" = "https://github.com/QIB-Sheffield/mdreg"
+"Homepage" = "https://qib-sheffield.github.io/mdreg/"
+"Source Code" = "https://github.com/QIB-Sheffield/mdreg"
 
 [tool.setuptools]
 # ...

src/mdreg/elastix.py

@@ -1,5 +1,6 @@
 import __main__
 import os
+import warnings
 import multiprocessing
 import numpy as np
 from tqdm import tqdm
@@ -262,10 +263,16 @@ def _coreg_2d(source_large, target_large, spacing, downsample, log, mask,
     target_small.SetSpacing(spacing_small)
     source_small.SetOrigin(origin_small)
     target_small.SetOrigin(origin_small)
-    coreg_small, result_transform_parameters = itk.elastix_registration_method(
-        target_small, source_small,
-        parameter_object=params_obj, 
-        log_to_console=log)
+    try:
+        coreg_small, result_transform_parameters = itk.elastix_registration_method(
+            target_small, source_small,
+            parameter_object=params_obj, 
+            log_to_console=log)
+    except:
+        warnings.warn('Elastix coregistration failed. Returning zero '
+                      'deformation field. To find out the error, set log=True.')
+        deformation_field = np.zeros(source_large.shape + (len(source_large.shape), ))
+        return source_large.copy(), deformation_field
 
     # Get coregistered image at original size
     large_shape_x, large_shape_y = source_large.shape
@@ -331,10 +338,16 @@ def _coreg_3d(source_large, target_large, spacing, downsample, log, mask,
     target_small.SetSpacing(spacing_small)
     source_small.SetOrigin(origin_small)
     target_small.SetOrigin(origin_small)
-    coreg_small, result_transform_parameters = itk.elastix_registration_method(
-        target_small, source_small,
-        parameter_object=params_obj, 
-        log_to_console=log) # perform registration of downsampled image
+    try:
+        coreg_small, result_transform_parameters = itk.elastix_registration_method(
+            target_small, source_small,
+            parameter_object=params_obj, 
+            log_to_console=log) # perform registration of downsampled image
+    except:
+        warnings.warn('Elastix coregistration failed. Returning zero '
+                      'deformation field. To find out the error, set log=True.')
+        deformation_field = np.zeros(source_large.shape + (len(source_large.shape), ))
+        return source_large.copy(), deformation_field
 
     # Get coregistered image at original size
     result_transform_parameters.SetParameter(0, "Size", [str(large_shape_z), str(large_shape_y), str(large_shape_x)])