Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Jump to bottom

Intra links #285

Merged
merged 13 commits into from
Jul 27, 2023
Merged

Intra links #285

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
13 commits
Select commit Hold shift + click to select a range
8eb859f
implemented metadata links (or inheritance) between process parameter…
denisri Jul 24, 2023
d5497f5
removed debug print
denisri Jul 25, 2023
469793d
re-generated fake morphologist pipeline
denisri Jul 25, 2023
b401e8e
fixed test
denisri Jul 25, 2023
d1ae1ea
fixed fake morphologist test
denisri Jul 25, 2023
d7a5c86
also look for _meta_links in pipeline sub-schemas definitions
denisri Jul 25, 2023
de51a86
fix in unused code
denisri Jul 26, 2023
79eb0b3
fixes in brainvisa schemas
denisri Jul 26, 2023
2b89935
- pass initial metadata to modification functions
denisri Jul 27, 2023
b63b8d9
use initial metadata to restore values
denisri Jul 27, 2023
6e38277
fixed completion test
denisri Jul 27, 2023
760ed10
trying tests using python 3.10
denisri Jul 27, 2023
fd13b30
using python 3.10 doesn't help, back to 3.9
denisri Jul 27, 2023
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
220 changes: 188 additions & 32 deletions capsul/dataset.py
View file
Open in desktop

Large diffs are not rendered by default.

4 changes: 2 additions & 2 deletions capsul/pipeline/test/fake_morphologist/baladinnormalizationpipeline.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -15,15 +15,15 @@ def pipeline_definition(self):

# links
self.export_parameter("NormalizeBaladin", "anatomy_data", "t1mri", is_optional=False)
self.add_link("t1mri->ReorientAnatomy.t1mri")
self.add_link("t1mri->ConvertBaladinNormalizationToAIMS.source_volume")
self.add_link("t1mri->ReorientAnatomy.t1mri")
self.export_parameter("ConvertBaladinNormalizationToAIMS", "registered_volume", "template", is_optional=False)
self.add_link("template->NormalizeBaladin.anatomical_template")
self.export_parameter("ConvertBaladinNormalizationToAIMS", "set_transformation_in_source_volume", is_optional=False)
self.export_parameter("ReorientAnatomy", "allow_flip_initial_MRI", is_optional=False)
self.export_parameter("ReorientAnatomy", "commissures_coordinates", "ReorientAnatomy_commissures_coordinates", is_optional=True)
self.add_link("NormalizeBaladin.transformation_matrix->ConvertBaladinNormalizationToAIMS.read")
self.export_parameter("NormalizeBaladin", "transformation_matrix", "NormalizeBaladin_transformation_matrix", is_optional=True)
self.add_link("NormalizeBaladin.transformation_matrix->ConvertBaladinNormalizationToAIMS.read")
self.export_parameter("NormalizeBaladin", "normalized_anatomy_data", "NormalizeBaladin_normalized_anatomy_data", is_optional=True)
self.export_parameter("ConvertBaladinNormalizationToAIMS", "write", "ConvertBaladinNormalizationToAIMS_write", is_optional=True)
self.add_link("ConvertBaladinNormalizationToAIMS.write->ReorientAnatomy.transformation")
Expand Down
7 changes: 4 additions & 3 deletions capsul/pipeline/test/fake_morphologist/brainorientation.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -19,8 +19,8 @@ def pipeline_definition(self):
self.export_parameter("select_AC_PC_Or_Normalization", "switch", "select_AC_PC_Or_Normalization", is_optional=True)
self.export_parameter("Normalization", "t1mri", "T1mri", is_optional=False)
self.add_link("T1mri->StandardACPC.T1mri")
self.export_parameter("Normalization", "allow_flip_initial_MRI", is_optional=False)
self.add_link("allow_flip_initial_MRI->StandardACPC.allow_flip_initial_MRI")
self.export_parameter("StandardACPC", "allow_flip_initial_MRI", is_optional=False)
self.add_link("allow_flip_initial_MRI->Normalization.allow_flip_initial_MRI")
self.export_parameter("StandardACPC", "Normalised", "StandardACPC_Normalised", is_optional=True)
self.export_parameter("StandardACPC", "Anterior_Commissure", "StandardACPC_Anterior_Commissure", is_optional=True)
self.export_parameter("StandardACPC", "Posterior_Commissure", "StandardACPC_Posterior_Commissure", is_optional=True)
Expand Down Expand Up @@ -60,8 +60,8 @@ def pipeline_definition(self):
self.add_link("StandardACPC.reoriented_t1mri->select_AC_PC_Or_Normalization.StandardACPC_switch_reoriented_t1mri")
self.export_parameter("Normalization", "transformation", "normalization_transformation", weak_link=True, is_optional=True)
self.add_link("Normalization.transformation->TalairachFromNormalization.normalization_transformation")
self.add_link("Normalization.reoriented_t1mri->TalairachFromNormalization.t1mri")
self.add_link("Normalization.reoriented_t1mri->select_AC_PC_Or_Normalization.Normalization_switch_reoriented_t1mri")
self.add_link("Normalization.reoriented_t1mri->TalairachFromNormalization.t1mri")
self.export_parameter("Normalization", "normalized", "Normalization_normalized", weak_link=True, is_optional=True)
self.export_parameter("Normalization", "NormalizeFSL_NormalizeFSL_transformation_matrix", "Normalization_NormalizeFSL_NormalizeFSL_transformation_matrix", weak_link=True, is_optional=True)
self.export_parameter("Normalization", "NormalizeSPM_spm_transformation", "Normalization_NormalizeSPM_spm_transformation", weak_link=True, is_optional=True)
Expand Down Expand Up @@ -130,6 +130,7 @@ def pipeline_definition(self):
self.allow_flip_initial_MRI = False
self.StandardACPC_Normalised = 'No'
self.StandardACPC_remove_older_MNI_normalization = True
self.Normalization_select_Normalization_pipeline = 'NormalizeSPM'
self.Normalization_init_translation_origin = 0
self.Normalization_NormalizeFSL_alignment = 'Not Aligned but Same Orientation'
self.Normalization_NormalizeFSL_set_transformation_in_source_volume = True
Expand Down
8 changes: 4 additions & 4 deletions capsul/pipeline/test/fake_morphologist/fslnormalization.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -14,11 +14,11 @@ def pipeline_definition(self):
self.add_process("converter", "capsul.pipeline.test.fake_morphologist.aimsconverter.AimsConverter")

# links
self.export_parameter("ConvertFSLnormalizationToAIMS", "source_volume", "t1mri", is_optional=False)
self.add_link("t1mri->converter.read")
self.export_parameter("converter", "read", "t1mri", is_optional=False)
self.add_link("t1mri->ReorientAnatomy.t1mri")
self.export_parameter("NormalizeFSL", "anatomical_template", "template", is_optional=False)
self.add_link("template->ConvertFSLnormalizationToAIMS.registered_volume")
self.add_link("t1mri->ConvertFSLnormalizationToAIMS.source_volume")
self.export_parameter("ConvertFSLnormalizationToAIMS", "registered_volume", "template", is_optional=False)
self.add_link("template->NormalizeFSL.anatomical_template")
self.export_parameter("NormalizeFSL", "Alignment", "alignment", is_optional=False)
self.export_parameter("ConvertFSLnormalizationToAIMS", "set_transformation_in_source_volume", is_optional=False)
self.export_parameter("ReorientAnatomy", "allow_flip_initial_MRI", is_optional=False)
Expand Down
Loading