[pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

Author: pre-commit-ci[bot]

monailabel/datastore/utils/convert.py

@@ -27,6 +27,7 @@
 
 try:
     import highdicom as hd
+
     HIGHDICOM_AVAILABLE = True
 except ImportError:
     HIGHDICOM_AVAILABLE = False
@@ -92,29 +93,29 @@ def binary_to_image(reference_image, label, dtype=np.uint8, file_ext=".nii.gz"):
 
 def _extract_label_info(label, label_info):
     """Extract unique labels and model info from label file.
-    
+
     Args:
         label: Path to NIfTI label file
         label_info: List of dictionaries containing segment information
-        
+
     Returns:
         tuple: (unique_labels, model_name) or (None, None) if empty
     """
     # Load label file using SimpleITK (consistent with conversion pipeline)
     mask = SimpleITK.ReadImage(label)
     label_array = SimpleITK.GetArrayFromImage(mask)
-    
+
     # Extract unique non-zero labels
     unique_labels = np.unique(label_array).astype(np.int_)
     unique_labels = unique_labels[unique_labels != 0]
-    
+
     info = label_info[0] if label_info and 0 < len(label_info) else {}
     model_name = info.get("model_name", "AIName")
-    
+
     if not unique_labels.size:
         logger.warning("No non-zero labels found in segmentation")
         return None, None
-    
+
     return unique_labels, model_name
 
 
@@ -137,15 +138,15 @@ def _highdicom_nifti_to_dicom_seg(
     # Input validation
     if label_info is None:
         label_info = []
-    
+
     if not os.path.exists(label):
         logger.error(f"Label file not found: {label}")
         return ""
-    
+
     if not os.path.exists(series_dir):
         logger.error(f"Series directory not found: {series_dir}")
         return ""
-    
+
     # Extract label information
     unique_labels, model_name = _extract_label_info(label, label_info)
     if unique_labels is None:
@@ -229,7 +230,7 @@ def _highdicom_nifti_to_dicom_seg(
 
     # Get consistent timestamp for all DICOM attributes
     dt_now = datetime.datetime.now()
-    
+
     # DICOM series number is 4 digits max (0-9999)
     MAX_SERIES_NUMBER = 9999
     series_number = int(dt_now.strftime("%H%M%S")) % (MAX_SERIES_NUMBER + 1)
@@ -319,15 +320,15 @@ def _itk_nifti_to_dicom_seg(series_dir, label, label_info) -> str:
     # Input validation
     if label_info is None:
         label_info = []
-    
+
     if not os.path.exists(label):
         logger.error(f"Label file not found: {label}")
         return ""
-    
+
     if not os.path.exists(series_dir):
         logger.error(f"Series directory not found: {series_dir}")
         return ""
-    
+
     # Extract label information (reuse helper function)
     unique_labels, model_name = _extract_label_info(label, label_info)
     if unique_labels is None:
@@ -344,7 +345,7 @@ def _itk_nifti_to_dicom_seg(series_dir, label, label_info) -> str:
 
         # Check if custom segmentAttribute is provided
         segment_attr = info.get("segmentAttribute")
-        
+
         if segment_attr:
             # Use custom attribute as-is
             segment_descriptions.append(segment_attr)
@@ -379,12 +380,12 @@ def _itk_nifti_to_dicom_seg(series_dir, label, label_info) -> str:
 
     # Extract metadata from label_info (use first segment's metadata for study-level info)
     first_info = label_info[0] if label_info and len(label_info) > 0 else {}
-    
+
     # Get timestamp-based series number (consistent with highdicom implementation)
     dt_now = datetime.datetime.now()
     MAX_SERIES_NUMBER = 9999
     series_number = int(dt_now.strftime("%H%M%S")) % (MAX_SERIES_NUMBER + 1)
-    
+
     # Build ITK template with extracted or sensible default values
     template = {
         "ContentCreatorName": first_info.get("creator", "MONAI Label"),
@@ -452,7 +453,7 @@ def nifti_to_dicom_seg(
 
 def _dcmqi_nifti_to_dicom_seg(label, series_dir, template) -> str:
     """Convert NIfTI to DICOM SEG using dcmqi's itkimage2segimage command-line tool.
-    
+
     This is a low-level wrapper around the dcmqi itkimage2segimage tool.
     Called by _itk_nifti_to_dicom_seg() as the actual conversion implementation.
     """
@@ -524,21 +525,21 @@ def dicom_seg_to_itk_image(label, output_ext=".seg.nrrd"):
 
     # Convert to SimpleITK image
     image = SimpleITK.GetImageFromArray(volume.array)
-    
+
     # Convert spacing from highdicom to SimpleITK order
     # highdicom: (slice, row, column) for axes (0, 1, 2)
     # SimpleITK: (x, y, z) = (column, row, slice)
     # Therefore: reverse the spacing tuple
     sitk_spacing = tuple(reversed(volume.spacing))
     image.SetSpacing(sitk_spacing)
-    
+
     # Set origin and direction if available
-    if hasattr(volume, 'position') and volume.position is not None:
+    if hasattr(volume, "position") and volume.position is not None:
         # Origin (position) is in LPS physical coordinates for voxel (0,0,0)
         # Both highdicom and SimpleITK use the same coordinate system, so no conversion needed
         image.SetOrigin(volume.position)
-        
-    if hasattr(volume, 'direction') and volume.direction is not None:
+
+    if hasattr(volume, "direction") and volume.direction is not None:
         # Direction matrix columns need reordering
         # highdicom: columns are [slice_dir, row_dir, col_dir] = [z, y, x]
         # SimpleITK: columns must be [x_dir, y_dir, z_dir]