Support array-type metadata fields in cubids group

cubids/constants.py

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

cubids/cubids.py

@@ -307,7 +307,6 @@ 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)
@@ -346,7 +345,6 @@ 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​
@@ -358,8 +356,6 @@ 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

@@ -16,9 +16,6 @@ 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
@@ -67,8 +64,6 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
-    Obliquity:
-      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       precision: 3
@@ -113,8 +108,6 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
-    Obliquity:
-      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       suggest_variant_rename: yes
@@ -158,8 +151,6 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
-    Obliquity:
-      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       precision: 3
@@ -204,8 +195,6 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
-    Obliquity:
-      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       precision: 3
@@ -250,8 +239,6 @@ derived_params:
       suggest_variant_rename: yes
     NumVolumes:
       suggest_variant_rename: yes
-    Obliquity:
-      suggest_variant_rename: yes
     VoxelSizeDim1:
       tolerance: 0.001
       precision: 3
@@ -311,6 +298,9 @@ 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:
@@ -350,6 +340,9 @@ 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:
@@ -389,6 +382,9 @@ 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:
@@ -428,6 +424,9 @@ 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:
@@ -479,6 +478,9 @@ 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
@@ -535,6 +537,9 @@ 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

@@ -352,7 +352,6 @@ 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()
@@ -364,7 +363,6 @@ 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")
@@ -373,7 +371,6 @@ 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
 
 
@@ -396,7 +393,6 @@ 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")
@@ -405,7 +401,6 @@ 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

cubids/tests/test_cubids.py

@@ -449,21 +449,6 @@ def _test__get_param_groups(cubids_instance):
     # Add assertions here
 
 
-def _test_round_params(cubids_instance):
-    """Test rounding parameters.
-
-    Parameters
-    ----------
-    cubids_instance : CuBIDS
-        An instance of the CuBIDS class.
-    """
-    param_group_df = pd.DataFrame({"param": [0.123456789]})
-    config = {"param": {"round": 3}}
-    modality = "bold"
-    rounded_params = cubids_instance.round_params(param_group_df, config, modality)
-    # Add assertions here
-
-
 def _test_get_sidecar_metadata(cubids_instance):
     """Test getting sidecar metadata.
 
@@ -477,21 +462,6 @@ def _test_get_sidecar_metadata(cubids_instance):
     # Add assertions here
 
 
-def _test_format_params(cubids_instance):
-    """Test formatting parameters.
-
-    Parameters
-    ----------
-    cubids_instance : CuBIDS
-        An instance of the CuBIDS class.
-    """
-    param_group_df = pd.DataFrame({"param": [0.123456789]})
-    config = {"param": {"format": "{:.2f}"}}
-    modality = "bold"
-    formatted_params = cubids_instance.format_params(param_group_df, config, modality)
-    # Add assertions here
-
-
 def _test__order_columns(cubids_instance):
     """Test ordering columns.