change structure

src/clinicaio/generators/caps/__init__.py

@@ -0,0 +1 @@
+from .generator import CAPSGenerator

src/clinicaio/utils/caps_generator/filename.py → src/clinicaio/generators/caps/filename.py

@@ -1,7 +1,7 @@
 from pathlib import Path
 from typing import Optional
 
-from clinicaio.utils.bids_entities import (
+from clinicaio.models.bids_entities import (
     DescriptionEntity,
     ResolutionEntity,
     SessionEntity,
@@ -10,10 +10,10 @@
     SUVREntity,
     TracerEntity,
 )
-from clinicaio.utils.caps import Description, Extension, Suffix
+from clinicaio.models.caps import Description, Extension, Suffix
 
 
-def get_caps_filename(
+def _get_caps_filename(
     subject: int,
     session: int,
     suffix: str,

src/clinicaio/utils/caps_generator/flair_linear.py → src/clinicaio/generators/caps/flair_linear.py

@@ -5,13 +5,13 @@
 import numpy as np
 from scipy.io import savemat
 
-from clinicaio.utils.bids_entities import SessionEntity, SubjectEntity
-from clinicaio.utils.caps import Extension, Resolution, Space, Suffix
+from clinicaio.models.bids_entities import SessionEntity, SubjectEntity
+from clinicaio.models.caps import Extension, Resolution, Space, Suffix
 
-from .filename import get_caps_filename
+from .filename import _get_caps_filename
 
 
-def build_flair_linear(
+def _build_flair_linear(
     root: Union[str, Path], subject: int, session: int, crop: bool = True
 ):
     """
@@ -34,7 +34,7 @@ def build_flair_linear(
     )
     directory.mkdir(parents=True, exist_ok=True)
 
-    uncropped_file = directory / get_caps_filename(
+    uncropped_file = directory / _get_caps_filename(
         subject,
         session,
         space=space,
@@ -44,7 +44,7 @@ def build_flair_linear(
     )
     nib.save(dummy_nifti_img, uncropped_file)
 
-    mat_file = directory / get_caps_filename(
+    mat_file = directory / _get_caps_filename(
         subject,
         session,
         space=space,
@@ -55,7 +55,7 @@ def build_flair_linear(
     savemat(mat_file, dummy_mat)
 
     if crop:
-        cropped_file = directory / get_caps_filename(
+        cropped_file = directory / _get_caps_filename(
             subject,
             session,
             space=space,

src/clinicaio/utils/caps_generator/generator.py → src/clinicaio/generators/caps/generator.py

@@ -2,12 +2,12 @@
 from pathlib import Path
 from typing import List, Union
 
-from clinicaio.utils.bids_entities import SessionEntity, SubjectEntity
-from clinicaio.utils.caps import Pipeline
+from clinicaio.models.bids_entities import SessionEntity, SubjectEntity
+from clinicaio.models.caps import Pipeline
 
-from .flair_linear import build_flair_linear
-from .pet_linear import build_pet_linear
-from .t1_linear import build_t1_linear
+from .flair_linear import _build_flair_linear
+from .pet_linear import _build_pet_linear
+from .t1_linear import _build_t1_linear
 
 
 class CAPSGenerator:
@@ -57,11 +57,11 @@ def build_pipeline(
         """
         pipeline = Pipeline(pipeline)
         if pipeline == Pipeline.T1_LINEAR:
-            builder = build_t1_linear
+            builder = _build_t1_linear
         elif pipeline == Pipeline.FLAIR_LINEAR:
-            builder = build_flair_linear
+            builder = _build_flair_linear
         elif pipeline == Pipeline.PET_LINEAR:
-            builder = build_pet_linear
+            builder = _build_pet_linear
         else:
             raise ValueError(f"pipeline {pipeline} is not yet implemented.")
 
@@ -101,9 +101,13 @@ def remove_pipeline(
             raise ValueError(f"pipeline {pipeline} is not yet implemented.")
 
         full_dir = (
-            self.dir / "subjects" / SubjectEntity(subject) / SessionEntity(session) / directory
+            self.dir
+            / "subjects"
+            / SubjectEntity(subject)
+            / SessionEntity(session)
+            / directory
         )
         try:
             shutil.rmtree(full_dir)
-        except FileNotFoundError:   # there is not such subject/session for this pipeline
+        except FileNotFoundError:  # there is not such subject/session for this pipeline
             pass

src/clinicaio/utils/caps_generator/pet_linear.py → src/clinicaio/generators/caps/pet_linear.py

@@ -5,14 +5,14 @@
 import numpy as np
 from scipy.io import savemat
 
-from clinicaio.utils.bids_entities import SessionEntity, SubjectEntity
-from clinicaio.utils.caps import Extension, Resolution, Space, Suffix
-from clinicaio.utils.pet import SUVRReferenceRegion, Tracer
+from clinicaio.models.bids_entities import SessionEntity, SubjectEntity
+from clinicaio.models.caps import Extension, Resolution, Space, Suffix
+from clinicaio.models.pet import SUVRReferenceRegion, Tracer
 
-from .filename import get_caps_filename
+from .filename import _get_caps_filename
 
 
-def build_pet_linear(
+def _build_pet_linear(
     root: Union[str, Path],
     subject: int,
     session: int,
@@ -42,7 +42,7 @@ def build_pet_linear(
     )
     directory.mkdir(parents=True, exist_ok=True)
 
-    uncropped_file = directory / get_caps_filename(
+    uncropped_file = directory / _get_caps_filename(
         subject,
         session,
         tracer=trc,
@@ -55,7 +55,7 @@ def build_pet_linear(
     )
     nib.save(dummy_nifti_img, uncropped_file)
 
-    mat_file = directory / get_caps_filename(
+    mat_file = directory / _get_caps_filename(
         subject,
         session,
         tracer=trc,
@@ -66,7 +66,7 @@ def build_pet_linear(
     savemat(mat_file, dummy_mat)
 
     if crop:
-        cropped_file = directory / get_caps_filename(
+        cropped_file = directory / _get_caps_filename(
             subject,
             session,
             tracer=trc,
@@ -80,7 +80,7 @@ def build_pet_linear(
         nib.save(dummy_nifti_img, cropped_file)
 
     if save_pet_in_t1w_space:
-        nifti_file = directory / get_caps_filename(
+        nifti_file = directory / _get_caps_filename(
             subject,
             session,
             tracer=trc,

src/clinicaio/utils/caps_generator/t1_linear.py → src/clinicaio/generators/caps/t1_linear.py

@@ -5,13 +5,13 @@
 import numpy as np
 from scipy.io import savemat
 
-from clinicaio.utils.bids_entities import SessionEntity, SubjectEntity
-from clinicaio.utils.caps import Extension, Resolution, Space, Suffix
+from clinicaio.models.bids_entities import SessionEntity, SubjectEntity
+from clinicaio.models.caps import Extension, Resolution, Space, Suffix
 
-from .filename import get_caps_filename
+from .filename import _get_caps_filename
 
 
-def build_t1_linear(
+def _build_t1_linear(
     root: Union[str, Path], subject: int, session: int, crop: bool = True
 ):
     """
@@ -34,7 +34,7 @@ def build_t1_linear(
     )
     directory.mkdir(parents=True, exist_ok=True)
 
-    uncropped_file = directory / get_caps_filename(
+    uncropped_file = directory / _get_caps_filename(
         subject,
         session,
         space=space,
@@ -44,7 +44,7 @@ def build_t1_linear(
     )
     nib.save(dummy_nifti_img, uncropped_file)
 
-    mat_file = directory / get_caps_filename(
+    mat_file = directory / _get_caps_filename(
         subject,
         session,
         space=space,
@@ -55,7 +55,7 @@ def build_t1_linear(
     savemat(mat_file, dummy_mat)
 
     if crop:
-        cropped_file = directory / get_caps_filename(
+        cropped_file = directory / _get_caps_filename(
             subject,
             session,
             space=space,

tests/unittests/utils/caps_generator/test_filename.py → tests/unittests/generators/caps/test_filename.py

@@ -2,7 +2,7 @@
 
 import pytest
 
-from clinicaio.utils.caps_generator.filename import get_caps_filename
+from clinicaio.generators.caps.filename import _get_caps_filename
 
 
 @pytest.mark.parametrize(
@@ -38,6 +38,6 @@
     ],
 )
 def test_get_caps_filename(args, expected_output):
-    filename = get_caps_filename(**args)
+    filename = _get_caps_filename(**args)
     assert isinstance(filename, Path)
     assert str(filename) == expected_output

tests/unittests/utils/caps_generator/test_flair_linear.py → tests/unittests/generators/caps/test_flair_linear.py

@@ -1,7 +1,7 @@
 import shutil
 from pathlib import Path
 
-from clinicaio.utils.caps_generator.flair_linear import build_flair_linear
+from clinicaio.generators.caps.flair_linear import _build_flair_linear
 
 
 def test_build_flair_linear():
@@ -11,7 +11,7 @@ def test_build_flair_linear():
     if test_dir.exists():
         shutil.rmtree(test_dir)
 
-    build_flair_linear(root=test_dir, subject=2, session=3)
+    _build_flair_linear(root=test_dir, subject=2, session=3)
     assert (
         pipeline_dir
         / "sub-002_ses-M003_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_FLAIR.nii.gz"
@@ -26,7 +26,7 @@ def test_build_flair_linear():
 
     shutil.rmtree(test_dir)
 
-    build_flair_linear(root=test_dir, subject=2, session=3, crop=False)
+    _build_flair_linear(root=test_dir, subject=2, session=3, crop=False)
     assert not (
         pipeline_dir
         / "sub-002_ses-M003_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_FLAIR.nii.gz"

tests/unittests/utils/caps_generator/test_generator.py → tests/unittests/generators/caps/test_generator.py

@@ -1,7 +1,7 @@
 import shutil
 from pathlib import Path
 
-from clinicaio.utils.caps_generator.generator import CAPSGenerator
+from clinicaio.generators.caps.generator import CAPSGenerator
 
 
 def test_caps_generator():

tests/unittests/utils/caps_generator/test_pet_linear.py → tests/unittests/generators/caps/test_pet_linear.py

@@ -1,7 +1,7 @@
 import shutil
 from pathlib import Path
 
-from clinicaio.utils.caps_generator.pet_linear import build_pet_linear
+from clinicaio.generators.caps.pet_linear import _build_pet_linear
 
 
 def test_build_pet_linear():
@@ -11,7 +11,7 @@ def test_build_pet_linear():
     if test_dir.exists():
         shutil.rmtree(test_dir)
 
-    build_pet_linear(
+    _build_pet_linear(
         root=test_dir,
         subject=2,
         session=3,
@@ -32,7 +32,7 @@ def test_build_pet_linear():
 
     shutil.rmtree(test_dir)
 
-    build_pet_linear(
+    _build_pet_linear(
         root=test_dir,
         subject=2,
         session=3,

tests/unittests/utils/caps_generator/test_t1_linear.py → tests/unittests/generators/caps/test_t1_linear.py

@@ -1,7 +1,7 @@
 import shutil
 from pathlib import Path
 
-from clinicaio.utils.caps_generator.t1_linear import build_t1_linear
+from clinicaio.generators.caps.t1_linear import _build_t1_linear
 
 
 def test_build_t1_linear():
@@ -11,7 +11,7 @@ def test_build_t1_linear():
     if test_dir.exists():
         shutil.rmtree(test_dir)
 
-    build_t1_linear(root=test_dir, subject=2, session=3, crop=True)
+    _build_t1_linear(root=test_dir, subject=2, session=3, crop=True)
     assert (
         pipeline_dir
         / "sub-002_ses-M003_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_T1w.nii.gz"
@@ -25,7 +25,7 @@ def test_build_t1_linear():
 
     shutil.rmtree(test_dir)
 
-    build_t1_linear(root=test_dir, subject=2, session=3, crop=False)
+    _build_t1_linear(root=test_dir, subject=2, session=3, crop=False)
     assert not (
         pipeline_dir
         / "sub-002_ses-M003_space-MNI152NLin2009cSym_desc-Crop_res-1x1x1_T1w.nii.gz"