[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

@@ -53,6 +53,7 @@ def _get_nvimgcodec_encoder():
     if _NVIMGCODEC_ENCODER is None:
         try:
             from nvidia import nvimgcodec
+
             _NVIMGCODEC_ENCODER = nvimgcodec.Encoder()
             logger.debug("Initialized global nvimgcodec.Encoder singleton")
         except ImportError:
@@ -70,6 +71,7 @@ def _get_nvimgcodec_decoder():
     if _NVIMGCODEC_DECODER is None:
         try:
             from nvidia import nvimgcodec
+
             _NVIMGCODEC_DECODER = nvimgcodec.Decoder()
             logger.debug("Initialized global nvimgcodec.Decoder singleton")
         except ImportError:
@@ -209,9 +211,10 @@ def dicom_to_nifti(series_dir, is_seg=False):
 
         try:
             from monai.transforms import LoadImage
+
             from monailabel.transform.reader import NvDicomReader
             from monailabel.transform.writer import write_itk
-            
+
             # Use NvDicomReader with LoadImage
             reader = NvDicomReader(reverse_indexing=True, use_nvimgcodec=True)
             loader = LoadImage(reader=reader, image_only=False)
@@ -552,9 +555,10 @@ def nifti_to_dicom_seg(
 
 
 def itk_image_to_dicom_seg(label, series_dir, template) -> str:
-    from monailabel.utils.others.generic import run_command
     import shutil
 
+    from monailabel.utils.others.generic import run_command
+
     command = "itkimage2segimage"
     if not shutil.which(command):
         error_msg = (
@@ -648,35 +652,35 @@ def transcode_dicom_to_htj2k(
 ) -> str:
     """
     Transcode DICOM files to HTJ2K (High Throughput JPEG 2000) lossless compression.
-    
+
     HTJ2K is a faster variant of JPEG 2000 that provides better compression performance
     for medical imaging applications. This function uses nvidia-nvimgcodec for encoding
     with batch processing for improved performance. All transcoding is performed using
     lossless compression to preserve image quality.
-    
+
     The function operates in three phases:
     1. Load all DICOM files and prepare pixel arrays
     2. Batch encode all images to HTJ2K in parallel
     3. Save encoded data back to DICOM files
-    
+
     Args:
         input_dir: Path to directory containing DICOM files to transcode
         output_dir: Path to output directory for transcoded files. If None, creates temp directory
         num_resolutions: Number of resolution levels (default: 6)
         code_block_size: Code block size as (height, width) tuple (default: (64, 64))
         verify: If True, decode output to verify correctness (default: False)
-        
+
     Returns:
         Path to output directory containing transcoded DICOM files
-        
+
     Raises:
         ImportError: If nvidia-nvimgcodec or pydicom are not available
         ValueError: If input directory doesn't exist or contains no DICOM files
-        
+
     Example:
         >>> output_dir = transcode_dicom_to_htj2k("/path/to/dicoms")
         >>> # Transcoded files are now in output_dir with lossless HTJ2K compression
-        
+
     Note:
         Requires nvidia-nvimgcodec to be installed:
             pip install nvidia-nvimgcodec-cu{XX}[all]
@@ -685,7 +689,7 @@ def transcode_dicom_to_htj2k(
     import glob
     import shutil
     from pathlib import Path
-    
+
     # Check for nvidia-nvimgcodec
     try:
         from nvidia import nvimgcodec
@@ -695,134 +699,136 @@ def transcode_dicom_to_htj2k(
             "Install it with: pip install nvidia-nvimgcodec-cu{XX}[all] "
             "(replace {XX} with your CUDA version, e.g., cu13)"
         )
-    
+
     # Validate input
     if not os.path.exists(input_dir):
         raise ValueError(f"Input directory does not exist: {input_dir}")
-    
+
     if not os.path.isdir(input_dir):
         raise ValueError(f"Input path is not a directory: {input_dir}")
-    
+
     # Get all DICOM files
     dicom_files = []
     for pattern in ["*.dcm", "*"]:
         dicom_files.extend(glob.glob(os.path.join(input_dir, pattern)))
-    
+
     # Filter to actual DICOM files
     valid_dicom_files = []
     for file_path in dicom_files:
         if os.path.isfile(file_path):
             try:
                 # Quick check if it's a DICOM file
-                with open(file_path, 'rb') as f:
+                with open(file_path, "rb") as f:
                     f.seek(128)
                     magic = f.read(4)
-                    if magic == b'DICM':
+                    if magic == b"DICM":
                         valid_dicom_files.append(file_path)
             except Exception:
                 continue
-    
+
     if not valid_dicom_files:
         raise ValueError(f"No valid DICOM files found in {input_dir}")
-    
+
     logger.info(f"Found {len(valid_dicom_files)} DICOM files to transcode")
-    
+
     # Create output directory
     if output_dir is None:
         output_dir = tempfile.mkdtemp(prefix="htj2k_")
     else:
         os.makedirs(output_dir, exist_ok=True)
-    
+
     # Create encoder and decoder instances (reused for all files)
     encoder = _get_nvimgcodec_encoder()
     decoder = _get_nvimgcodec_decoder() if verify else None
-    
+
     # HTJ2K Transfer Syntax UID - Lossless Only
     # 1.2.840.10008.1.2.4.201 = HTJ2K Lossless Only
     target_transfer_syntax = "1.2.840.10008.1.2.4.201"
     quality_type = nvimgcodec.QualityType.LOSSLESS
     logger.info("Using lossless HTJ2K compression")
-    
+
     # Configure JPEG2K encoding parameters
     jpeg2k_encode_params = nvimgcodec.Jpeg2kEncodeParams()
     jpeg2k_encode_params.num_resolutions = num_resolutions
     jpeg2k_encode_params.code_block_size = code_block_size
     jpeg2k_encode_params.bitstream_type = nvimgcodec.Jpeg2kBitstreamType.JP2
     jpeg2k_encode_params.prog_order = nvimgcodec.Jpeg2kProgOrder.LRCP
     jpeg2k_encode_params.ht = True  # Enable High Throughput mode
-    
+
     encode_params = nvimgcodec.EncodeParams(
         quality_type=quality_type,
         jpeg2k_encode_params=jpeg2k_encode_params,
     )
-    
+
     start_time = time.time()
     transcoded_count = 0
     skipped_count = 0
     failed_count = 0
-    
+
     # Phase 1: Load all DICOM files and prepare pixel arrays for batch encoding
     logger.info("Phase 1: Loading DICOM files and preparing pixel arrays...")
     dicom_datasets = []
     pixel_arrays = []
     files_to_encode = []
-    
+
     for i, input_file in enumerate(valid_dicom_files, 1):
         try:
             # Read DICOM
             ds = pydicom.dcmread(input_file)
-            
+
             # Check if already HTJ2K
-            current_ts = getattr(ds, 'file_meta', {}).get('TransferSyntaxUID', None)
-            if current_ts and str(current_ts).startswith('1.2.840.10008.1.2.4.20'):
+            current_ts = getattr(ds, "file_meta", {}).get("TransferSyntaxUID", None)
+            if current_ts and str(current_ts).startswith("1.2.840.10008.1.2.4.20"):
                 logger.debug(f"[{i}/{len(valid_dicom_files)}] Already HTJ2K: {os.path.basename(input_file)}")
                 # Just copy the file
                 output_file = os.path.join(output_dir, os.path.basename(input_file))
                 shutil.copy2(input_file, output_file)
                 skipped_count += 1
                 continue
-            
+
             # Use pydicom's pixel_array to decode the source image
             # This handles all transfer syntaxes automatically
             source_pixel_array = ds.pixel_array
-            
+
             # Ensure it's a numpy array
             if not isinstance(source_pixel_array, np.ndarray):
                 source_pixel_array = np.array(source_pixel_array)
-            
+
             # Add channel dimension if needed (nvimgcodec expects shape like (H, W, C))
             if source_pixel_array.ndim == 2:
                 source_pixel_array = source_pixel_array[:, :, np.newaxis]
-            
+
             # Store for batch encoding
             dicom_datasets.append(ds)
             pixel_arrays.append(source_pixel_array)
             files_to_encode.append(input_file)
-            
+
             if i % 50 == 0 or i == len(valid_dicom_files):
                 logger.info(f"Loading progress: {i}/{len(valid_dicom_files)} files loaded")
-                
+
         except Exception as e:
             logger.error(f"[{i}/{len(valid_dicom_files)}] Error loading {os.path.basename(input_file)}: {e}")
             failed_count += 1
             continue
-    
+
     if not pixel_arrays:
         logger.warning("No images to encode")
         return output_dir
-    
+
     # Phase 2: Batch encode all images to HTJ2K
     logger.info(f"Phase 2: Batch encoding {len(pixel_arrays)} images to HTJ2K...")
     encode_start = time.time()
-    
+
     try:
         encoded_htj2k_images = encoder.encode(
             pixel_arrays,
             codec="jpeg2k",
             params=encode_params,
         )
         encode_time = time.time() - encode_start
-        logger.info(f"Batch encoding completed in {encode_time:.2f} seconds ({len(pixel_arrays)/encode_time:.1f} images/sec)")
+        logger.info(
+            f"Batch encoding completed in {encode_time:.2f} seconds ({len(pixel_arrays)/encode_time:.1f} images/sec)"
+        )
     except Exception as e:
         logger.error(f"Batch encoding failed: {e}")
         # Fall back to individual encoding
@@ -839,70 +845,67 @@ def transcode_dicom_to_htj2k(
             except Exception as e2:
                 logger.error(f"Failed to encode image {idx}: {e2}")
                 encoded_htj2k_images.append(None)
-    
+
     # Phase 3: Save encoded data back to DICOM files
     logger.info("Phase 3: Saving encoded DICOM files...")
     save_start = time.time()
-    
+
     for idx, (ds, encoded_data, input_file) in enumerate(zip(dicom_datasets, encoded_htj2k_images, files_to_encode)):
         try:
             if encoded_data is None:
                 logger.error(f"Skipping {os.path.basename(input_file)} - encoding failed")
                 failed_count += 1
                 continue
-            
+
             # Encapsulate encoded frames for DICOM
             new_encoded_frames = [bytes(encoded_data)]
             encapsulated_pixel_data = pydicom.encaps.encapsulate(new_encoded_frames)
             ds.PixelData = encapsulated_pixel_data
-            
+
             # Update transfer syntax UID
             ds.file_meta.TransferSyntaxUID = pydicom.uid.UID(target_transfer_syntax)
-            
+
             # Save to output directory
             output_file = os.path.join(output_dir, os.path.basename(input_file))
             ds.save_as(output_file)
-            
+
             # Verify if requested
             if verify:
                 ds_verify = pydicom.dcmread(output_file)
                 pixel_data = ds_verify.PixelData
                 data_sequence = pydicom.encaps.decode_data_sequence(pixel_data)
                 images_verify = decoder.decode(
                     data_sequence,
-                    params=nvimgcodec.DecodeParams(
-                        allow_any_depth=True,
-                        color_spec=nvimgcodec.ColorSpec.UNCHANGED
-                    ),
+                    params=nvimgcodec.DecodeParams(allow_any_depth=True, color_spec=nvimgcodec.ColorSpec.UNCHANGED),
                 )
                 image_verify = np.array(images_verify[0].cpu()).squeeze()
-                
+
                 if not np.allclose(image_verify, ds_verify.pixel_array):
                     logger.warning(f"Verification failed for {os.path.basename(input_file)}")
                     failed_count += 1
                     continue
-            
+
             transcoded_count += 1
-            
+
             if (idx + 1) % 50 == 0 or (idx + 1) == len(dicom_datasets):
                 logger.info(f"Saving progress: {idx + 1}/{len(dicom_datasets)} files saved")
-                
+
         except Exception as e:
             logger.error(f"Error saving {os.path.basename(input_file)}: {e}")
             failed_count += 1
             continue
-    
+
     save_time = time.time() - save_start
     logger.info(f"Saving completed in {save_time:.2f} seconds")
-    
+
     elapsed_time = time.time() - start_time
-    
+
     logger.info(f"Transcoding complete:")
     logger.info(f"  Total files: {len(valid_dicom_files)}")
     logger.info(f"  Successfully transcoded: {transcoded_count}")
     logger.info(f"  Already HTJ2K (copied): {skipped_count}")
     logger.info(f"  Failed: {failed_count}")
     logger.info(f"  Time elapsed: {elapsed_time:.2f} seconds")
     logger.info(f"  Output directory: {output_dir}")
-    
+
     return output_dir

monailabel/transform/reader.py

@@ -55,11 +55,11 @@ def _get_nvimgcodec_decoder():
     """Get or create a thread-local nvimgcodec decoder singleton."""
     if not has_nvimgcodec:
         raise RuntimeError("nvimgcodec is not available. Cannot create decoder.")
-    
-    if not hasattr(_thread_local, 'decoder') or _thread_local.decoder is None:
+
+    if not hasattr(_thread_local, "decoder") or _thread_local.decoder is None:
         _thread_local.decoder = nvimgcodec.Decoder()
         logger.debug(f"Initialized thread-local nvimgcodec.Decoder for thread {threading.current_thread().name}")
-    
+
     return _thread_local.decoder
 
 

tests/integration/radiology_serverless/__init__.py

@@ -8,4 +8,3 @@
 # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 # See the License for the specific language governing permissions and
 # limitations under the License.
-