Rename volume scripts

scripts/legacy/scil_apply_transform_to_image.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_volume_apply_transform import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_volume_apply_transform.py. Please change
+your existing pipelines accordingly.
+
+"""
+
+
+@deprecate_script("scil_apply_transform_to_image.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_count_non_zero_voxels.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_volume_count_non_zero_voxels import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_volume_count_non_zero_voxels.py.
+Please change your existing pipelines accordingly.
+
+"""
+
+
+@deprecate_script("scil_count_non_zero_voxels.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_crop_volume.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_volume_crop import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_volume_crop.py. Please change
+your existing pipelines accordingly.
+
+"""
+
+
+@deprecate_script("scil_crop_volume.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_flip_volume.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_volume_flip import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_volume_flip.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_flip_volume.py", DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_image_math.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_volume_math import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_volume_math.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_image_math.py", DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_remove_outliers_ransac.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_volume_remove_outliers_ransac import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_volume_remove_outliers_ransac.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_remove_outliers_ransac.py", DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_resample_volume.py

@@ -0,0 +1,22 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_volume_resample import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_volume_resample.py. Please change
+your existing pipelines accordingly.
+
+"""
+
+
+@deprecate_script("scil_resample_volume.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_reshape_to_reference.py

@@ -0,0 +1,21 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_volume_reshape_to_reference import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_volume_reshape_to_reference.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_reshape_to_reference.py",
+                  DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_snr_in_roi.py

@@ -0,0 +1,20 @@
+#!/usr/bin/env python3
+# -*- coding: utf-8 -*-
+
+from scilpy.io.deprecator import deprecate_script
+from scripts.scil_dwi_compute_snr import main as new_main
+
+
+DEPRECATION_MSG = """
+This script has been renamed scil_dwi_compute_snr.py.
+Please change your existing pipelines accordingly.
+"""
+
+
+@deprecate_script("scil_snr_in_roi.py", DEPRECATION_MSG, '1.7.0')
+def main():
+    new_main()
+
+
+if __name__ == "__main__":
+    main()

scripts/legacy/scil_split_volume_by_ids.py

@@ -2,18 +2,18 @@
 # -*- coding: utf-8 -*-
 
 from scilpy.io.deprecator import deprecate_script
-from scripts.scil_tracking_local import main as new_main
+from scripts.scil_labels_split_volume_by_ids import main as new_main
 
 
 DEPRECATION_MSG = """
-This script has been renamed scil_labels_split_volume_by_ids.
+This script has been renamed scil_labels_split_volume_by_ids.py.
 Now, all our scripts using labels start with scil_labels_...!
 
 Please change your existing pipelines accordingly.
 """
 
 
-@deprecate_script("scil_split_volume_by_is.py", DEPRECATION_MSG, '1.7.0')
+@deprecate_script("scil_split_volume_by_ids.py", DEPRECATION_MSG, '1.7.0')
 def main():
     new_main()
 

scripts/tests/test_snr_in_roi.py → scripts/tests/test_dwi_compute_snr.py

@@ -12,7 +12,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_snr_in_roi.py', '--help')
+    ret = script_runner.run('scil_dwi_compute_snr.py', '--help')
     assert ret.success
 
 
@@ -29,7 +29,7 @@ def test_snr(script_runner):
     noise_mask = os.path.join(get_home(), 'processing',
                               'small_roi_gm_mask.nii.gz')
 
-    ret = script_runner.run('scil_snr_in_roi.py', in_dwi,
+    ret = script_runner.run('scil_dwi_compute_snr.py', in_dwi,
                             in_bval, in_bvec, in_mask,
                             '--noise_mask', noise_mask,
                             '--b0_thr', '10')

scripts/tests/test_apply_transform_to_image.py → scripts/tests/test_volume_apply_transform.py

@@ -13,7 +13,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_apply_transform_to_image.py', '--help')
+    ret = script_runner.run('scil_volume_apply_transform.py', '--help')
     assert ret.success
 
 
@@ -25,7 +25,7 @@ def test_execution_bst(script_runner):
                          'fa.nii.gz')
     in_aff = os.path.join(get_home(), 'bst',
                           'output0GenericAffine.mat')
-    ret = script_runner.run('scil_apply_transform_to_image.py',
+    ret = script_runner.run('scil_volume_apply_transform.py',
                             in_model, in_fa, in_aff,
                             'template_lin.nii.gz', '--inverse')
     assert ret.success

scripts/tests/test_count_non_zero_voxels.py → scripts/tests/test_volume_count_non_zero_voxels.py

@@ -13,13 +13,13 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_count_non_zero_voxels.py', '--help')
+    ret = script_runner.run('scil_volume_count_non_zero_voxels.py', '--help')
     assert ret.success
 
 
 def test_execution_others(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_img = os.path.join(get_home(), 'others',
                           'rgb.nii.gz')
-    ret = script_runner.run('scil_count_non_zero_voxels.py', in_img)
+    ret = script_runner.run('scil_volume_count_non_zero_voxels.py', in_img)
     assert ret.success

scripts/tests/test_flip_volume.py → scripts/tests/test_volume_flip.py

@@ -13,14 +13,14 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_flip_volume.py', '--help')
+    ret = script_runner.run('scil_volume_flip.py', '--help')
     assert ret.success
 
 
 def test_execution_surface_vtk_fib(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_fa = os.path.join(get_home(), 'surface_vtk_fib',
                          'fa.nii.gz')
-    ret = script_runner.run('scil_flip_volume.py', in_fa, 'fa_flip.nii.gz',
+    ret = script_runner.run('scil_volume_flip.py', in_fa, 'fa_flip.nii.gz',
                             'x')
     assert ret.success

scripts/tests/test_image_math.py → scripts/tests/test_volume_math.py

@@ -12,7 +12,7 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_image_math.py', '--help')
+    ret = script_runner.run('scil_volume_math.py', '--help')
     assert ret.success
 
 
@@ -24,23 +24,23 @@ def test_execution_add(script_runner):
                             'brainstem_174.nii.gz')
     in_img_3 = os.path.join(get_home(), 'atlas',
                             'brainstem_175.nii.gz')
-    ret = script_runner.run('scil_image_math.py', 'addition',
+    ret = script_runner.run('scil_volume_math.py', 'addition',
                             in_img_1, in_img_2, in_img_3, 'brainstem.nii.gz')
     assert ret.success
 
 
 def test_execution_low_thresh(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_img = os.path.join(get_home(), 'atlas', 'brainstem.nii.gz')
-    ret = script_runner.run('scil_image_math.py', 'lower_threshold',
+    ret = script_runner.run('scil_volume_math.py', 'lower_threshold',
                             in_img, '1', 'brainstem_bin.nii.gz')
     assert ret.success
 
 
 def test_execution_low_mult(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_img = os.path.join(get_home(), 'atlas', 'brainstem_bin.nii.gz')
-    ret = script_runner.run('scil_image_math.py', 'multiplication',
+    ret = script_runner.run('scil_volume_math.py', 'multiplication',
                             in_img, '16', 'brainstem_unified.nii.gz')
     assert ret.success
 
@@ -53,7 +53,7 @@ def test_execution_concatenate(script_runner):
     in_img_4 = os.path.join(get_home(), 'atlas', 'ids', '13.nii.gz')
     in_img_5 = os.path.join(get_home(), 'atlas', 'ids', '17.nii.gz')
     in_img_6 = os.path.join(get_home(), 'atlas', 'ids', '18.nii.gz')
-    ret = script_runner.run('scil_image_math.py', 'concatenate',
+    ret = script_runner.run('scil_volume_math.py', 'concatenate',
                             in_img_1, in_img_2, in_img_3, in_img_4, in_img_5,
                             in_img_6, 'concat_ids.nii.gz')
     assert ret.success
@@ -65,7 +65,7 @@ def test_execution_concatenate_4D(script_runner):
     in_img_2 = os.path.join(get_home(), 'atlas', 'ids', '8_10.nii.gz')
     in_img_3 = os.path.join(get_home(), 'atlas', 'ids', '12.nii.gz')
     in_img_4 = os.path.join(get_home(), 'atlas', 'ids', '8_10.nii.gz')
-    ret = script_runner.run('scil_image_math.py', 'concatenate',
+    ret = script_runner.run('scil_volume_math.py', 'concatenate',
                             in_img_1, in_img_2, in_img_3, in_img_4,
                             'concat_ids_4d.nii.gz')
     assert ret.success

scripts/tests/test_remove_outliers_ransac.py → scripts/tests/test_volume_remove_outliers_ransac.py

@@ -12,14 +12,14 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_remove_outliers_ransac.py', '--help')
+    ret = script_runner.run('scil_volume_remove_outliers_ransac.py', '--help')
     assert ret.success
 
 
 def test_execution_processing(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_ad = os.path.join(get_home(), 'processing',
                          'ad.nii.gz')
-    ret = script_runner.run('scil_remove_outliers_ransac.py', in_ad,
+    ret = script_runner.run('scil_volume_remove_outliers_ransac.py', in_ad,
                             'ad_ransanc.nii.gz')
     assert ret.success

scripts/tests/test_resample_volume.py → scripts/tests/test_volume_resample.py

@@ -13,14 +13,14 @@
 
 
 def test_help_option(script_runner):
-    ret = script_runner.run('scil_resample_volume.py', '--help')
+    ret = script_runner.run('scil_volume_resample.py', '--help')
     assert ret.success
 
 
 def test_execution_others(script_runner):
     os.chdir(os.path.expanduser(tmp_dir.name))
     in_img = os.path.join(get_home(), 'others',
                           'fa.nii.gz')
-    ret = script_runner.run('scil_resample_volume.py', in_img,
+    ret = script_runner.run('scil_volume_resample.py', in_img,
                             'fa_resample.nii.gz', '--voxel_size', '2')
     assert ret.success