REF: remove diffusion images

TEST/NoseTests/test_image.py

@@ -2,7 +2,7 @@
 from unittest import TestCase
 
 from bidsmanager.base.group import Group
-from bidsmanager.base.image import Image, FunctionalImage, DiffusionImage
+from bidsmanager.base.image import Image
 from bidsmanager.read.image_reader import read_image_from_bids_path
 from bidsmanager.write.dataset_writer import write_json
 from bidsmanager.utils.utils import read_json
@@ -22,10 +22,12 @@ def test_change_acquisition(self):
         self.assertEqual(basename.replace("contrast", "postcontrast"), image.get_basename())
 
     def test_change_task_name(self):
-        image = FunctionalImage(modality="bold", task="prediction", run=3)
+        image = Image(modality="bold", task="prediction", run=3)
         basename = image.get_basename()
-        image.set_task_name("weatherprediction")
-        self.assertEqual(basename.replace("prediction", "weatherprediction"), image.get_basename())
+        new_task_name = "weatherprediction"
+        image.set_task_name(new_task_name)
+        self.assertEqual(basename.replace("prediction", new_task_name), image.get_basename())
+        self.assertEqual(image.get_task_name(), new_task_name)
 
     def test_write_changed_acquisition(self):
         tmp_file = "run-05_FLAIR.nii.gz"
@@ -129,7 +131,7 @@ def test_reconstruction(self):
         assert "rec-axial" in image.get_basename()
 
     def test_add_metadata_without_sidecar(self):
-        image = DiffusionImage(modality="dwi", bval_path="./bval", bvec_path="./bvec")
+        image = Image(modality="dwi", bval_path="./bval", bvec_path="./bvec")
         image.add_metadata("WellThoughtOutTest", False)
         image.set_path("./test.nii.gz")
         touch(image.get_path())

bidsmanager/base/image.py

@@ -6,7 +6,8 @@
 
 
 class Image(BIDSObject):
-    def __init__(self, sidecar_path=None, modality=None, extension=".nii", *inputs, **kwargs):
+    def __init__(self, sidecar_path=None, modality=None, extension=".nii", bval_path=None, bvec_path=None,
+                 *inputs, **kwargs):
         self._session = None
         self._subject = None
         self._group = None
@@ -21,6 +22,8 @@ def __init__(self, sidecar_path=None, modality=None, extension=".nii", *inputs,
         self._modality = modality
         self._type = "Image"
         self._extension = extension
+        self._bval_path = bval_path
+        self._bvec_path = bvec_path
 
     def get_basename(self):
         return "_".join(self.get_subject_session_keys(keys=self.get_image_keys())) + self.get_extension()
@@ -167,6 +170,7 @@ def update(self, move=False):
             self.set_path(os.path.join(os.path.dirname(self.get_path()), self.get_basename()))
         update_file(self._previous_path, self._path, move=move)
         self.update_sidecar(move=move)
+        self.update_diffusion_files(move=move)
 
     def update_sidecar(self, move=False):
         if self._sidecar_metadata:
@@ -218,22 +222,6 @@ def _set_key_attribute(self, attribute, value):
     def get_sidecar_path(self):
         return self.sidecar_path
 
-
-class FunctionalImage(Image):
-    def __init__(self, *inputs, **kwargs):
-        super(FunctionalImage, self).__init__(*inputs, **kwargs)
-
-    def is_match(self, task_name=None, **kwargs):
-        return (not task_name or task_name == self.get_task_name()) and super(FunctionalImage, self).is_match(**kwargs)
-
-
-class DiffusionImage(Image):
-    def __init__(self, bval_path, bvec_path, *inputs, **kwargs):
-        super(DiffusionImage, self).__init__(*inputs, **kwargs)
-        self._bval_path = bval_path
-        self._bvec_path = bvec_path
-        self._modality = "dwi"
-
     def get_bval_path(self):
         return self._bval_path
 
@@ -250,12 +238,19 @@ def update_bvec(self, move=False):
         update_file(self._bvec_path, tmp_bvec_file, move=move)
         self._bvec_path = tmp_bvec_file
 
-    def update(self, *args, **kwargs):
-        super(DiffusionImage, self).update(*args, **kwargs)
+    def update_diffusion_files(self, move=False):
         if self._bval_path:
-            self.update_bval(*args, **kwargs)
+            self.update_bval(move=move)
         if self._bvec_path:
-            self.update_bvec(*args, **kwargs)
+            self.update_bvec(move=move)
+
+
+class FunctionalImage(Image):
+    def __init__(self, *inputs, **kwargs):
+        super(FunctionalImage, self).__init__(*inputs, **kwargs)
+
+    def is_match(self, task_name=None, **kwargs):
+        return (not task_name or task_name == self.get_task_name()) and super(FunctionalImage, self).is_match(**kwargs)
 
 
 image_entities = ("task", "acq", "ce", "dir", "rec",  "run", "echo")

bidsmanager/read/dicom_reader.py

@@ -11,7 +11,7 @@
 
 from ..base.subject import Subject
 from ..base.dataset import DataSet
-from ..base.image import DiffusionImage
+from ..base.image import Image
 from ..base.base import BIDSObject
 from ..base.session import Session
 from ..utils.image_utils import load_image
@@ -224,7 +224,7 @@ def convert_dicoms(dicom_objects):
 
 def convert_dwi_dicom(in_file):
     nifti_file, bval_file, bvec_file, sidecar_file = dcm2niix_dwi(in_file)
-    return DiffusionImage(path=nifti_file, bval_path=bval_file, bvec_path=bvec_file, sidecar_path=sidecar_file)
+    return Image(path=nifti_file, bval_path=bval_file, bvec_path=bvec_file, sidecar_path=sidecar_file)
 
 
 def dcm2niix_dwi(in_file):

bidsmanager/utils/image_utils.py

@@ -1,4 +1,4 @@
-from bidsmanager.base.image import FunctionalImage, Image, DiffusionImage
+from bidsmanager.base.image import FunctionalImage, Image
 
 
 def load_image(path_to_image, modality=None, acquisition=None, task_name=None, run_number=None, path_to_sidecar=None,
@@ -9,11 +9,7 @@ def load_image(path_to_image, modality=None, acquisition=None, task_name=None, r
                                sidecar_path=path_to_sidecar,
                                metadata=metadata,
                                **entities)
-    elif modality == "dwi":
-        return DiffusionImage(bval_path=bval_path, bvec_path=bvec_path, path=path_to_image, modality=modality,
-                              sidecar_path=path_to_sidecar,
-                              metadata=metadata,
-                              **entities)
     else:
         return Image(modality=modality, path=path_to_image,
-                     sidecar_path=path_to_sidecar, metadata=metadata, **entities)
+                     sidecar_path=path_to_sidecar, metadata=metadata, bval_path=bval_path, bvec_path=bvec_path,
+                     **entities)