Update registration wrapper

scripts/extension/registration/apply_registration.py

@@ -98,9 +98,16 @@ def apply_for_file(input_path, output_path,
                    transformation_file, fiji_executable,
                    elastix_directory, tmp_folder, n_threads):
 
-    # grrr design anti-pattern
+    assert os.path.exists(elastix_directory)
+    assert os.path.exists(tmp_folder)
+    assert os.path.exists(input_path)
+    assert os.path.exists(transformation_file)
+    assert os.path.exists(os.path.split(output_path)[0])
+
+    # transformix arguments need to be passed as one string,
+    # with individual arguments comma separated
     # the argument to transformaix needs to be one large comma separated string
-    transformix_argument = ["elastix_directory=\'%s\'" % elastix_directory,
+    transformix_argument = ["elastixDirectory=\'%s\'" % elastix_directory,
                             "workingDirectory=\'%s\'" % tmp_folder,
                             "inputImageFile=\'%s\'" % input_path,
                             "transformationFile=\'%s\'" % transformation_file,

test/registration/check_wrapper.py

@@ -9,8 +9,8 @@ from scripts.extension.registration import ApplyRegistrationLocal
 
 
 def check_wrapper():
-    in_path = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/stomach_target_prospr.tif'
-    out_path = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/stomach_target_prospr_registered'
+    in_path = '/g/kreshuk/pape/Work/my_projects/platy-browser-data/registration/9.9.9/images/ProSPr/Stomach_forRegistration.tif'
+    out_path = '/g/kreshuk/pape/Work/my_projects/dev-platy/test/registration/somach_prospr_registered'
 
     in_list = [in_path]
     out_list = [out_path]