diff --git a/dicommake.py b/dicommake.py index 460562d..08cd8ca 100644 --- a/dicommake.py +++ b/dicommake.py @@ -36,7 +36,7 @@ -__version__ = '2.3.3' +__version__ = '2.3.4' DISPLAY_TITLE = r""" _ _ _ _ @@ -103,7 +103,7 @@ def preamble_show(options: Namespace) -> None: LOG("%25s: [%s]" % (k, v)) LOG("") -def image_intoDICOMinsert(image: Image.Image, ds: pydicom.Dataset) -> pydicom.Dataset: +def image_intoDICOMinsert(image: Image.Image, ds: pydicom.Dataset, compress: bool) -> pydicom.Dataset: """ Insert the "image" into the DICOM chassis "ds" and update/adapt DICOM tags where necessary. Also create a new @@ -160,9 +160,10 @@ def npimage_get(image): # NB! If this is not set, images will not render properly in Cornerstone ds.PlanarConfiguration = 0 - # Compress the pixel data - ds.compress(RLELossless) - ds.file_meta.TransferSyntaxUID = RLELossless + if compress: + # 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]]: @@ -314,7 +315,7 @@ def allIO_findExplicitly(options: Namespace, inputdir: Path, outputdir: Path) \ d_ret['outputIMG'] = [Path(y) for y in sorted([str(x) for x in l_outputIMG])] return d_ret -def files_unspool(d_paths:dict[str, Any]) -> Iterator[tuple[Path, Path, Path]]: +def files_unspool(d_paths:dict[str, Any], compress: bool) -> Iterator[tuple[Path, Path, Path, bool]]: """ This implements an Iterator over the lists passed in d_paths, and is ultimately used as a mapper in the main method. @@ -328,7 +329,7 @@ def files_unspool(d_paths:dict[str, Any]) -> Iterator[tuple[Path, Path, Path]]: for dcm_in, img_in, dcm_out in zip( d_paths['d_IO']['inputDCM'], d_paths['d_IO']['inputIMG'], d_paths['d_IO']['outputDCM']): - yield dcm_in, img_in, dcm_out + yield dcm_in, img_in, dcm_out, compress def imageNames_areSame(imgfile:Path, dcmfile:Path) -> bool: """ @@ -356,16 +357,18 @@ def imagePaths_process(*args) -> None: dcm_in:Path = args[0][0] img_in:Path = args[0][1] dcm_out:Path = args[0][2] + b_compress:bool = args[0][3] except: dcm_in:Path = args[0] img_in:Path = args[1] dcm_out:Path = args[2] + b_compress: bool = args[3] if imageNames_areSame(img_in, dcm_in): image:Image.Image = Image.open(str(img_in)) DICOM:pydicom.Dataset = pydicom.dcmread(str(dcm_in)) LOG("Processing %s using %s" % (dcm_in.name, img_in.name)) - image_intoDICOMinsert(image, DICOM).save_as(str(dcm_out)) + image_intoDICOMinsert(image, DICOM, b_compress).save_as(str(dcm_out)) LOG("Saved %s" % dcm_out) @chris_plugin( @@ -398,7 +401,7 @@ def main(options: Namespace, inputdir: Path, outputdir: Path) -> int: """ # pudb.set_trace() d_paths:dict[str, Any] = env_setupAndCheck(options, inputdir, outputdir) - mapper: Iterator[tuple[Path, Path, Path]] = files_unspool(d_paths) + mapper: Iterator[tuple[Path, Path, Path, bool]] = files_unspool(d_paths, options.compress) if int(options.thread): # While the "thread" implies "threading", we actually use # a ProcessPoolExecutor since the single threaded GIL actually @@ -411,7 +414,7 @@ def main(options: Namespace, inputdir: Path, outputdir: Path) -> int: pass else: for dcm_in, img_in, dcm_out in mapper: - imagePaths_process(dcm_in, img_in, dcm_out) + imagePaths_process(dcm_in, img_in, dcm_out, options.compress) return 0