successfully compress dicom pixel data

FNNDSC · Aug 29, 2024 · 9bae269 · 9bae269
1 parent d4d5956
commit 9bae269
Showing 1 changed file with 10 additions and 9 deletions.
diff --git a/dicommake.py b/dicommake.py
@@ -22,6 +22,7 @@
 from pydicom.uid            import ExplicitVRLittleEndian,JPEG2000, JPEG2000Lossless
 import pylibjpeg
 from pydicom.uid import RLELossless
+from pydicom.encaps import encapsulate
 LOG             = logger.debug
 logger_format = (
     "<green>{time:YYYY-MM-DD HH:mm:ss}</green> │ "
@@ -81,6 +82,11 @@
                     dest        = 'thread',
                     action      = 'store_true',
                     default     = False)
+parser.add_argument("--compress",
+                    help        = "if specified, compress the DICOM pixel data",
+                    dest        = 'compress',
+                    action      = 'store_true',
+                    default     = False)
 parser.add_argument('--version',
                     action      = 'version',
                     version     = f'%(prog)s {__version__}')
@@ -147,23 +153,18 @@ def npimage_get(image):
     # The below fix handles this.
     # We change the transfer syntax UID (https://github.com/pydicom/pydicom/issues/1109)
     ds.PixelData = np_image.tobytes()
-    ds.file_meta.TransferSyntaxUID = ExplicitVRLittleEndian
-
-
+    ds.file_meta.TransferSyntaxUID  = ExplicitVRLittleEndian
     ds.AcquisitionTime              = AcquisitionTime()
     ds.AcquisitionDate              = AcquisitionDate()
     ds.SeriesInstanceUID            = pydicom.uid.generate_uid()
     ds.SOPInstanceUID               = pydicom.uid.generate_uid()
 
     # NB! If this is not set, images will not render properly in Cornerstone
     ds.PlanarConfiguration          = 0
-    ds.compress(RLELossless)
-    # Recompress the image data using JPEG2000
-    # compressed_pixel_data = pylibjpeg.encode(np_image.tobytes(), transfer_syntax='JPEG2000')
 
-    # Update the DICOM dataset
-    # ds.PixelData = compressed_pixel_data
-    ds.file_meta.TransferSyntaxUID = JPEG2000
+    # Compress the pixel data
+    ds.compress(RLELossless)
+    ds.file_meta.TransferSyntaxUID = RLELossless
     return ds
 
 def doubly_map(x: PathMapper, y: PathMapper) -> Iterable[tuple[Path, Path, Path, Path]]: