def create_image(ds: "Dataset", data_element: "DataElement") -> "gdcm.Image":
"""Return a ``gdcm.Image``.
Parameters
----------
ds : dataset.Dataset
The :class:`~pydicom.dataset.Dataset` containing the Image
Pixel module.
data_element : gdcm.DataElement
The ``gdcm.DataElement`` *Pixel Data* element.
Returns
-------
gdcm.Image
"""
image = gdcm.Image()
number_of_frames = getattr(ds, 'NumberOfFrames', 1)
image.SetNumberOfDimensions(2 if number_of_frames == 1 else 3)
image.SetDimensions((ds.Columns, ds.Rows, number_of_frames))
image.SetDataElement(data_element)
pi_type = gdcm.PhotometricInterpretation.GetPIType(
ds.PhotometricInterpretation)
image.SetPhotometricInterpretation(gdcm.PhotometricInterpretation(pi_type))
ts_type = gdcm.TransferSyntax.GetTSType(
str.__str__(ds.file_meta.TransferSyntaxUID))
image.SetTransferSyntax(gdcm.TransferSyntax(ts_type))
pixel_format = gdcm.PixelFormat(ds.SamplesPerPixel, ds.BitsAllocated,
ds.BitsStored, ds.HighBit,
ds.PixelRepresentation)
image.SetPixelFormat(pixel_format)
if 'PlanarConfiguration' in ds:
image.SetPlanarConfiguration(ds.PlanarConfiguration)
return image
def create_image(dicom_dataset, data_element):
"""Create a gdcm.Image from a FileDataset and a gdcm.DataElement containing
PixelData (0x7fe0, 0x0010)
Parameters
----------
dicom_dataset : FileDataset
data_element : gdcm.DataElement
DataElement containing PixelData
Returns
-------
gdcm.Image
"""
image = gdcm.Image()
number_of_frames = getattr(dicom_dataset, 'NumberOfFrames', 1)
image.SetNumberOfDimensions(2 if number_of_frames == 1 else 3)
image.SetDimensions(
(dicom_dataset.Columns, dicom_dataset.Rows, number_of_frames))
image.SetDataElement(data_element)
pi_type = gdcm.PhotometricInterpretation.GetPIType(
dicom_dataset.PhotometricInterpretation)
image.SetPhotometricInterpretation(gdcm.PhotometricInterpretation(pi_type))
ts_type = gdcm.TransferSyntax.GetTSType(
str.__str__(dicom_dataset.file_meta.TransferSyntaxUID))
image.SetTransferSyntax(gdcm.TransferSyntax(ts_type))
pixel_format = gdcm.PixelFormat(dicom_dataset.SamplesPerPixel,
dicom_dataset.BitsAllocated,
dicom_dataset.BitsStored,
dicom_dataset.HighBit,
dicom_dataset.PixelRepresentation)
image.SetPixelFormat(pixel_format)
if 'PlanarConfiguration' in dicom_dataset:
image.SetPlanarConfiguration(dicom_dataset.PlanarConfiguration)
return image
def decompress(inFile, outFile):
print("Extract (or copy) %s to %s" % (inFile, outFile))
try:
reader = gdcm.ImageReader()
reader.SetFileName(inFile)
if not reader.Read():
raise Exception("Unable to read %s with gdcm.ImageReader()" %
inFile)
change = gdcm.ImageChangeTransferSyntax()
change.SetTransferSyntax(
gdcm.TransferSyntax(gdcm.TransferSyntax.ImplicitVRLittleEndian))
change.SetInput(reader.GetImage())
if not change.Change():
raise Exception(
"Unable to change %s with gdcm.ImageChangeTransferSyntax()" %
inFile)
writer = gdcm.ImageWriter()
writer.SetFileName(outFile)
writer.SetFile(reader.GetFile())
writer.SetImage(change.GetOutput())
if not writer.Write():
raise Exception("Unable to write %s with gdcm.ImageWriter()" %
outFile)
except Exception as e:
sys.stderr.write("%s, copying instead" % str(e))
if inFile is not outFile:
shutil.copyfile(inFile, outFile)
def decomp(file1, file2='temp_file_22.dcm', return_dcm=False):
#file1 = '/data/gabriel/TAVR/TAVR_Sample_Study/IM-0003-1528.dcm'#sys.argv[1] # input filename
#file2 = file2#sys.argv[2] # output filename
if os.path.isfile(file2):
os.remove(file2)
reader = gdcm.ImageReader()
reader.SetFileName(file1)
reader.GetFile()
if not reader.Read():
sys.exit(1)
change = gdcm.ImageChangeTransferSyntax()
change.SetTransferSyntax(
gdcm.TransferSyntax(gdcm.TransferSyntax.ImplicitVRLittleEndian))
change.SetInput(reader.GetImage())
if not change.Change():
sys.exit(1)
writer = gdcm.ImageWriter()
writer.SetFileName(file2)
writer.SetFile(reader.GetFile())
writer.SetImage(change.GetOutput())
if not writer.Write():
sys.exit(1)
if return_dcm:
return pydicom.dcmread(file2, force=True)
else:
return pydicom.dcmread(file2, force=True).pixel_array
def cn(self, file1):
file2 = "tmp00.dcm" # output filename
reader = gdcm.ImageReader()
reader.SetFileName(file1)
reader.Read()
change = gdcm.ImageChangeTransferSyntax()
change.SetTransferSyntax(
gdcm.TransferSyntax(gdcm.TransferSyntax.ImplicitVRLittleEndian))
change.SetInput(reader.GetImage())
change.Change()
writer = gdcm.ImageWriter()
writer.SetFileName(file2)
writer.SetFile(reader.GetFile())
writer.SetImage(change.GetOutput())
writer.Write()
zz = pydicom.read_file("tmp00.dcm")
os.remove("tmp00.dcm")
return zz
def dc(inputFile, outputFile): reader = gdcm.ImageReader() reader.SetFileName(inputFile) if not reader.Read(): sys.exit(1) change = gdcm.ImageChangeTransferSyntax() change.SetTransferSyntax( gdcm.TransferSyntax(gdcm.TransferSyntax.ImplicitVRLittleEndian) ) change.SetInput( reader.GetImage() ) if not change.Change(): sys.exit(1) writer = gdcm.ImageWriter() writer.SetFileName(outputFile) writer.SetFile( reader.GetFile() ) writer.SetImage( change.GetOutput() ) if not writer.Write(): sys.exit(1)
def method2(file1, file2):
reader = gdcm.ImageReader()
reader.SetFileName(file1)
if not reader.Read():
sys.exit(1)
change = gdcm.ImageChangeTransferSyntax()
change.SetTransferSyntax(
gdcm.TransferSyntax(gdcm.TransferSyntax.ImplicitVRLittleEndian))
change.SetInput(reader.GetImage())
if not change.Change():
sys.exit(1)
writer = gdcm.ImageWriter()
writer.SetFileName(file2)
writer.SetFile(reader.GetFile())
writer.SetImage(change.GetOutput())
if not writer.Write():
raise ValueError
if __name__ == "__main__":
mypath='/home/vishnu/Projects/series-000001/'
oppath='/home/vishnu/Projects/output/'
onlyfiles = [f for f in listdir(mypath) if isfile(join(mypath, f))]
for files in onlyfiles:
file1= mypath+files
file2 = oppath+files
#file1 = sys.argv[1] # input filename
#file2 = sys.argv[2] # output filename
reader = gdcm.ImageReader()
reader.SetFileName( file1 )
if not reader.Read():
sys.exit(1)
change = gdcm.ImageChangeTransferSyntax()
change.SetTransferSyntax( gdcm.TransferSyntax(gdcm.TransferSyntax.ImplicitVRLittleEndian) )
change.SetInput( reader.GetImage() )
if not change.Change():
sys.exit(1)
writer = gdcm.ImageWriter()
writer.SetFileName( file2 )
writer.SetFile( reader.GetFile() )
writer.SetImage( change.GetOutput() )
if not writer.Write():
sys.exit(1)
def _rle_encode(src: bytes, **kwargs: Any) -> bytes:
"""Return RLE encoded image data from `src`.
Parameters
----------
src : bytes
The raw image frame data to be encoded.
**kwargs
Required parameters:
* `rows`: int
* `columns`: int
* `samples_per_pixel`: int
* `number_of_frames`: int
* `bits_allocated`: int
* `bits_stored`: int
* `pixel_representation`: int
* `photometric_interpretation`: str
Returns
-------
bytes
The encoded image data.
"""
# Check the parameters are valid for RLE encoding with GDCM
samples_per_pixel: int = kwargs['samples_per_pixel']
bits_allocated: int = kwargs['bits_allocated']
# Bug up to v3.0.9 (Apr 2021) in handling 32-bit, 3 sample/px data
gdcm_version = [int(c) for c in gdcm.Version.GetVersion().split('.')]
if gdcm_version < [3, 1, 0]:
if bits_allocated == 32 and samples_per_pixel == 3:
raise RuntimeError(
"The 'gdcm' plugin is unable to RLE encode 32-bit, 3 "
"samples/px data with GDCM v3.0.9 or older")
if bits_allocated > 32:
raise ValueError(
f"The 'gdcm' plugin is unable to encode {bits_allocated}-bit data")
# Create a gdcm.Image with the uncompressed `src` data
image = _create_gdcm_image(src, **kwargs)
# Converts an image to match the set transfer syntax
converter = gdcm.ImageChangeTransferSyntax()
# Set up the converter with the intended transfer syntax...
ts = gdcm.TransferSyntax.GetTSType(kwargs['transfer_syntax_uid'])
converter.SetTransferSyntax(gdcm.TransferSyntax(ts))
# ...and image to be converted
converter.SetInput(image)
# Perform the conversion, returns bool
# 'PALETTE COLOR' and a lossy transfer syntax will return False
result = converter.Change()
if not result:
raise RuntimeError(
"An error occurred with the 'gdcm' plugin: "
"ImageChangeTransferSyntax.Change() returned a failure result")
# The converted image as gdcm.Image
# Weirdly, reusing `image` as the variable name causes a segfault here
output = converter.GetOutput()
# The element's value is the encapsulated encoded pixel data
seq = output.GetDataElement().GetSequenceOfFragments()
# RLECodec::Code() uses only 1 fragment per frame
if seq is None or seq.GetNumberOfFragments() != 1:
# Covers both no sequence and unexpected number of fragments
raise RuntimeError(
"An error occurred with the 'gdcm' plugin: unexpected number of "
"fragments found in the 'Pixel Data'")
fragment: str = seq.GetFragment(0).GetByteValue().GetBuffer()
return fragment.encode("utf-8", "surrogateescape")
def _create_gdcm_image(src: bytes, **kwargs: Any) -> "gdcm.Image":
"""Return a gdcm.Image from the `src`.
Parameters
----------
src : bytes
The raw image frame data to be encoded.
**kwargs
Required parameters:
* `rows`: int
* `columns`: int
* `samples_per_pixel`: int
* `number_of_frames`: int
* `bits_allocated`: int
* `bits_stored`: int
* `pixel_representation`: int
* `photometric_interpretation`: str
Returns
-------
gdcm.Image
An Image containing the `src` as a single uncompressed frame.
"""
rows = kwargs['rows']
columns = kwargs['columns']
samples_per_pixel = kwargs['samples_per_pixel']
number_of_frames = kwargs['number_of_frames']
pixel_representation = kwargs['pixel_representation']
bits_allocated = kwargs['bits_allocated']
bits_stored = kwargs['bits_stored']
photometric_interpretation = kwargs['photometric_interpretation']
pi = gdcm.PhotometricInterpretation.GetPIType(photometric_interpretation)
# GDCM's null photometric interpretation gets used for invalid values
if pi == gdcm.PhotometricInterpretation.PI_END:
raise ValueError(
"An error occurred with the 'gdcm' plugin: invalid photometric "
f"interpretation '{photometric_interpretation}'")
# `src` uses little-endian byte ordering
ts = gdcm.TransferSyntax.ImplicitVRLittleEndian
image = gdcm.Image()
image.SetNumberOfDimensions(2)
image.SetDimensions((columns, rows, 1))
image.SetPhotometricInterpretation(gdcm.PhotometricInterpretation(pi))
image.SetTransferSyntax(gdcm.TransferSyntax(ts))
pixel_format = gdcm.PixelFormat(samples_per_pixel, bits_allocated,
bits_stored, bits_stored - 1,
pixel_representation)
image.SetPixelFormat(pixel_format)
if samples_per_pixel > 1:
# Default `src` is planar configuration 0 (i.e. R1 G1 B1 R2 G2 B2)
image.SetPlanarConfiguration(0)
# Add the Pixel Data element and set the value to `src`
elem = gdcm.DataElement(gdcm.Tag(0x7FE0, 0x0010))
elem.SetByteStringValue(src)
image.SetDataElement(elem)
return cast("gdcm.Image", image)
def _rle_encode(src: bytes, **kwargs: Any) -> bytes:
"""Return RLE encoded image data from `src`.
Parameters
----------
src : bytes
The raw image frame data to be encoded.
**kwargs
Required parameters:
* `rows`: int
* `columns`: int
* `samples_per_pixel`: int
* `number_of_frames`: int
* `bits_allocated`: int
* `bits_stored`: int
* `pixel_representation`: int
* `photometric_interpretation`: str
Returns
-------
bytes
The encoded image data.
"""
# Check the parameters are valid for RLE encoding with GDCM
rows = kwargs['rows']
columns = kwargs['columns']
samples_per_pixel = kwargs['samples_per_pixel']
number_of_frames = kwargs['number_of_frames']
pixel_representation = kwargs['pixel_representation']
bits_allocated = kwargs['bits_allocated']
bits_stored = kwargs['bits_stored']
photometric_interpretation = kwargs['photometric_interpretation']
# Bug up to v3.0.9 (Apr 2021) in handling 32-bit, 3 sample/px data
gdcm_version = [int(c) for c in gdcm.Version.GetVersion().split('.')]
if gdcm_version < [3, 0, 10]:
if bits_allocated == 32 and samples_per_pixel == 3:
raise RuntimeError(
"The 'gdcm' plugin is unable to RLE encode 32-bit, 3 "
"samples/px data with GDCM v3.0.9 or older"
)
if bits_allocated > 32:
raise ValueError(
f"The 'gdcm' plugin is unable to encode {bits_allocated}-bit data"
)
# Create a gdcm.Image with the uncompressed `src` data
pi = gdcm.PhotometricInterpretation.GetPIType(
photometric_interpretation
)
# GDCM's null photometric interpretation gets used for invalid values
if pi == gdcm.PhotometricInterpretation.PI_END:
raise ValueError(
"An error occurred with the 'gdcm' plugin: invalid photometric "
f"interpretation '{photometric_interpretation}'"
)
# `src` uses little-endian byte ordering
ts = gdcm.TransferSyntax.ImplicitVRLittleEndian
# Must use ImageWriter().GetImage() to create a gdcmImage
# also have to make sure `writer` doesn't go out of scope
writer = gdcm.ImageWriter()
image = writer.GetImage()
image.SetNumberOfDimensions(2)
image.SetDimensions((columns, rows, 1))
image.SetPhotometricInterpretation(
gdcm.PhotometricInterpretation(pi)
)
image.SetTransferSyntax(gdcm.TransferSyntax(ts))
pixel_format = gdcm.PixelFormat(
samples_per_pixel,
bits_allocated,
bits_stored,
bits_stored - 1,
pixel_representation
)
image.SetPixelFormat(pixel_format)
if samples_per_pixel > 1:
# Default `src` is planar configuration 0 (i.e. R1 G1 B1 R2 G2 B2)
image.SetPlanarConfiguration(0)
# Add the Pixel Data element and set the value to `src`
elem = gdcm.DataElement(gdcm.Tag(0x7FE0, 0x0010))
elem.SetByteStringValue(src)
image.SetDataElement(elem)
# Converts an image to match the set transfer syntax
converter = gdcm.ImageChangeTransferSyntax()
# Set up the converter with the intended transfer syntax...
rle = gdcm.TransferSyntax.GetTSType(kwargs['transfer_syntax_uid'])
converter.SetTransferSyntax(gdcm.TransferSyntax(rle))
# ...and image to be converted
converter.SetInput(image)
# Perform the conversion, returns bool
# 'PALETTE COLOR' and a lossy transfer syntax will return False
result = converter.Change()
if not result:
raise RuntimeError(
"An error occurred with the 'gdcm' plugin: "
"ImageChangeTransferSyntax.Change() returned a failure result"
)
# A new gdcmImage with the converted pixel data element
image = converter.GetOutput()
# The element's value is the encapsulated encoded pixel data
seq = image.GetDataElement().GetSequenceOfFragments()
# RLECodec::Code() uses only 1 fragment per frame
if seq is None or seq.GetNumberOfFragments() != 1:
# Covers both no sequence and unexpected number of fragments
raise RuntimeError(
"An error occurred with the 'gdcm' plugin: unexpected number of "
"fragments found in the 'Pixel Data'"
)
fragment = seq.GetFragment(0).GetByteValue().GetBuffer()
return cast(bytes, fragment.encode("utf-8", "surrogateescape"))
