Revert obliquity-related changes.

Author: tsalo

cubids/constants.py

@@ -29,12 +29,12 @@
         "SliceEncodingDirection",
         "DwellTime",
         "FlipAngle",
-        "ImageOrientationPatientDICOM",
         "MultibandAccelerationFactor",
         "RepetitionTime",
         "VolumeTiming",
         "NumberOfVolumesDiscardedByScanner",
         "NumberOfVolumesDiscardedByUser",
+        "Obliquity",
         "VoxelSizeDim1",
         "VoxelSizeDim2",
         "VoxelSizeDim3",

cubids/cubids.py

@@ -307,6 +307,7 @@ def add_nifti_info(self):
         the dataset using `datalad` before processing the files.
 
         Metadata added to the JSON sidecars includes:
+        - Obliquity
         - Voxel sizes (dimensions 1, 2, and 3)
         - Matrix dimensions (sizes of dimensions 1, 2, and 3)
         - Number of volumes (for 4D images)
@@ -345,6 +346,7 @@ def add_nifti_info(self):
                     continue
 
                 # get important info from niftis
+                obliquity = np.any(nb.affines.obliquity(img.affine) > 1e-4)
                 voxel_sizes = img.header.get_zooms()
                 matrix_dims = img.shape
                 # add nifti info to corresponding sidecars​
@@ -356,6 +358,8 @@ def add_nifti_info(self):
                     except Exception:
                         print("Error parsing this sidecar: ", sidecar)
 
+                    if "Obliquity" not in data.keys():
+                        data["Obliquity"] = str(obliquity)
                     if "VoxelSizeDim1" not in data.keys():
                         data["VoxelSizeDim1"] = float(voxel_sizes[0])
                     if "VoxelSizeDim2" not in data.keys():

cubids/data/config.yml

@@ -16,6 +16,9 @@ derived_params:
     # Number of volumes
     NumVolumes:
       suggest_variant_rename: yes
+    # Boolean indicating oblique acquisition
+    Obliquity:
+      suggest_variant_rename: yes
     # String describing image orientation (e.g., LAS+)
     ImageOrientation:
       suggest_variant_rename: yes
@@ -64,6 +67,8 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
+    Obliquity:
+      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       precision: 3
@@ -108,6 +113,8 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
+    Obliquity:
+      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       suggest_variant_rename: yes
@@ -151,6 +158,8 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
+    Obliquity:
+      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       precision: 3
@@ -195,6 +204,8 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
+    Obliquity:
+      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       precision: 3
@@ -239,6 +250,8 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
+    Obliquity:
+      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       precision: 3
@@ -298,9 +311,6 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
-    ImageOrientationPatientDICOM:
-      tolerance: 0.0001
-      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:
@@ -340,9 +350,6 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
-    ImageOrientationPatientDICOM:
-      tolerance: 0.0001
-      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:
@@ -382,9 +389,6 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
-    ImageOrientationPatientDICOM:
-      tolerance: 0.0001
-      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:
@@ -424,9 +428,6 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
-    ImageOrientationPatientDICOM:
-      tolerance: 0.0001
-      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:
@@ -478,9 +479,6 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
-    ImageOrientationPatientDICOM:
-      tolerance: 0.0001
-      suggest_variant_rename: yes
     LabelingDistance:
       tolerance: 0.1
       suggest_variant_rename: yes
@@ -537,9 +535,6 @@ sidecar_params:
       suggest_variant_rename: yes
     FlipAngle:
       suggest_variant_rename: yes
-    ImageOrientationPatientDICOM:
-      tolerance: 0.0001
-      suggest_variant_rename: yes
     MultibandAccelerationFactor:
       suggest_variant_rename: yes
     NumberOfVolumesDiscardedByScanner:

cubids/tests/test_bond.py

@@ -352,6 +352,7 @@ def test_add_nifti_info_datalad(tmp_path):
     summary_df = pd.read_table(summary_tsv)
     l_cols = summary_df.columns.tolist()
     assert "NumVolumes" not in l_cols
+    assert "Obliquity" not in l_cols
 
     # now add nifti info
     bod.add_nifti_info()
@@ -363,6 +364,7 @@ def test_add_nifti_info_datalad(tmp_path):
                 metadata = json.load(jsonr)
             found_fields.update(metadata.keys())
     assert "NumVolumes" in found_fields
+    assert "Obliquity" in found_fields
     assert "ImageOrientation" in found_fields
 
     # nifti_tsv_prefix = str(tmp_path / "nifti_tsvs")
@@ -371,6 +373,7 @@ def test_add_nifti_info_datalad(tmp_path):
     # nifti_summary_df = pd.read_table(nifti_summary_tsv)
     # nifti_l_cols = nifti_summary_df.columns.tolist()
     # assert 'NumVolumes' in nifti_l_cols
+    # assert 'Obliquity' in nifti_l_cols
     # assert 'ImageOrientation' in nifti_l_cols
 
 
@@ -393,6 +396,7 @@ def test_add_nifti_info_no_datalad(tmp_path):
                 metadata = json.load(jsonr)
             found_fields.update(metadata.keys())
     assert "NumVolumes" in found_fields
+    assert "Obliquity" in found_fields
     assert "ImageOrientation" in found_fields
 
     # tsv_prefix = str(tmp_path / "tsvs")
@@ -401,7 +405,7 @@ def test_add_nifti_info_no_datalad(tmp_path):
     # summary_df = pd.read_table(summary_tsv)
     # l_cols = summary_df.columns.tolist()
     # assert 'NumVolumes' in l_cols
-
+    # assert 'Obliquity' in l_cols
 
 # TODO: add tests that return an error for invalid merge
 

docs/example.rst

@@ -152,7 +152,7 @@ Adding NIfTI Information to JSON Sidecars
 
 Next, we seek to add more image parameters to our sidecars so that we can better define our Entity Sets.
 Historically, only a subset of parameters in the NIfTI image header have been included in a BIDS sidecar...
-Parameters such as image dimensions, number of volumes, and voxel sizes —
+Parameters such as image dimensions, number of volumes, image obliquity, and voxel sizes —
 all important data that can change how our pipelines will eventually run!
 
 To add them to the sidecar metadata, run:
@@ -317,7 +317,7 @@ This command will produce four tables that describe the dataset's heterogeneity
 By first examining ``v0_summary.tsv`` users are given the opportunity to conduct metadata
 quality assurance (QA).
 The file can help identify instances of incomplete, incorrect, or unusable parameter groups,
-based on acquisition fields such as dimension and voxel sizes, number of volumes, and more.
+based on acquisition fields such as dimension and voxel sizes, number of volumes, obliquity,and more.
 
 .. warning::