def ProcessOneFilePublic(filename, outfilename, tmpfile):
gdcm.ImageHelper.SetForceRescaleInterceptSlope(True)
vtkreader = vtkgdcm.vtkGDCMImageReader()
vtkreader.SetFileName(filename)
vtkreader.Update()
cast = vtk.vtkImageCast()
cast.SetInput(vtkreader.GetOutput())
cast.SetOutputScalarTypeToUnsignedShort()
# vtkGDCMImageWriter does not support Sequence, so let's write a tmp file first:
# Some operation will actually be discarded (we simply need a temp storage)
vtkwriter = vtkgdcm.vtkGDCMImageWriter()
vtkwriter.SetFileName(tmpfile)
vtkwriter.SetMedicalImageProperties(vtkreader.GetMedicalImageProperties())
vtkwriter.SetDirectionCosines(vtkreader.GetDirectionCosines())
print "Format:", vtkreader.GetImageFormat()
vtkwriter.SetImageFormat(vtkreader.GetImageFormat())
vtkwriter.SetInput(cast.GetOutput())
#vtkwriter.Update()
vtkwriter.Write()
# ok now rewrite the exact same file as the original (keep all info)
# but use the Pixel Data Element from the written file
tmpreader = gdcm.ImageReader()
tmpreader.SetFileName(tmpfile)
if not tmpreader.Read():
sys.exit(1)
reader = gdcm.Reader()
reader.SetFileName(filename)
if not reader.Read():
sys.exit(1)
# Make sure to remove Slope/Rescale to avoid re-execution
ds = reader.GetFile().GetDataSet()
tags = [
gdcm.Tag(0x0028, 0x1052),
gdcm.Tag(0x0028, 0x1053),
gdcm.Tag(0x0028, 0x1053),
]
for tag in tags:
ds.Remove(tag)
writer = gdcm.ImageWriter()
writer.SetFileName(outfilename)
# Pass image from vtk written file
writer.SetImage(tmpreader.GetImage())
# pass dataset from initial 'reader'
writer.SetFile(reader.GetFile())
if not writer.Write():
sys.exit(1)
def ProcessOneFilePublic(filename, outfilename, tmpfile):
gdcm.ImageHelper.SetForceRescaleInterceptSlope(True)
vtkreader = vtkgdcm.vtkGDCMImageReader()
vtkreader.SetFileName( filename )
vtkreader.Update()
cast = vtk.vtkImageCast()
cast.SetInput( vtkreader.GetOutput() )
cast.SetOutputScalarTypeToUnsignedShort()
# vtkGDCMImageWriter does not support Sequence, so let's write a tmp file first:
# Some operation will actually be discarded (we simply need a temp storage)
vtkwriter = vtkgdcm.vtkGDCMImageWriter()
vtkwriter.SetFileName( tmpfile )
vtkwriter.SetMedicalImageProperties( vtkreader.GetMedicalImageProperties() )
vtkwriter.SetDirectionCosines( vtkreader.GetDirectionCosines() )
print "Format:",vtkreader.GetImageFormat()
vtkwriter.SetImageFormat( vtkreader.GetImageFormat() )
vtkwriter.SetInput( cast.GetOutput() )
#vtkwriter.Update()
vtkwriter.Write()
# ok now rewrite the exact same file as the original (keep all info)
# but use the Pixel Data Element from the written file
tmpreader = gdcm.ImageReader()
tmpreader.SetFileName( tmpfile )
if not tmpreader.Read():
sys.exit(1)
reader = gdcm.Reader()
reader.SetFileName( filename )
if not reader.Read():
sys.exit(1)
# Make sure to remove Slope/Rescale to avoid re-execution
ds = reader.GetFile().GetDataSet()
tags = [
gdcm.Tag(0x0028,0x1052),
gdcm.Tag(0x0028,0x1053),
gdcm.Tag(0x0028,0x1053),
]
for tag in tags:
ds.Remove( tag )
writer = gdcm.ImageWriter()
writer.SetFileName( outfilename )
# Pass image from vtk written file
writer.SetImage( tmpreader.GetImage() )
# pass dataset from initial 'reader'
writer.SetFile( reader.GetFile() )
if not writer.Write():
sys.exit(1)
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._writer = vtkgdcm.vtkGDCMImageWriter()
# NB NB NB: for now we're SWITCHING off the VTK-compatible
# Y-flip, until the X-mirror issues can be solved.
self._writer.SetFileLowerLeft(1)
module_utils.setup_vtk_object_progress(self, self._writer,
'Writing DICOM data')
self._caster = vtk.vtkImageCast()
self._caster.SetOutputScalarTypeToShort()
module_utils.setup_vtk_object_progress(self, self._caster,
'Casting DICOM data to short')
self._input_data = None
self._input_metadata = None
self._config.output_mode = 0
self._config.output_directory = ''
self._config.output_filename = ''
self._config.cast_to_short = True
config_list = [
('Output mode:', 'output_mode', 'base:int',
'radiobox', 'Output mode',
['Slice-per-file (directory)',
'Multi-slice per file (file)']),
('Output directory:', 'output_directory', 'base:str',
'dirbrowser',
'Directory that takes slice-per-file output'),
('Output filename:', 'output_filename', 'base:str',
'filebrowser',
'Output filename for multi-slice per file output.',
{'fileMode' : wx.SAVE,
'fileMask' : 'DICOM file (*.dcm)|*.dcm|'
'All files (*.*)|*.*'}
),
('Cast to short:', 'cast_to_short', 'base:bool',
'checkbox',
'Should the data be cast to signed 16-bit (short), '
'common for DICOM.')
]
ScriptedConfigModuleMixin.__init__(self, config_list,
{'Module (self)' : self})
self.sync_module_logic_with_config()
def __init__(self, module_manager):
ModuleBase.__init__(self, module_manager)
self._writer = vtkgdcm.vtkGDCMImageWriter()
# NB NB NB: for now we're SWITCHING off the VTK-compatible
# Y-flip, until the X-mirror issues can be solved.
self._writer.SetFileLowerLeft(1)
module_utils.setup_vtk_object_progress(self, self._writer,
'Writing DICOM data')
self._caster = vtk.vtkImageCast()
self._caster.SetOutputScalarTypeToShort()
module_utils.setup_vtk_object_progress(self, self._caster,
'Casting DICOM data to short')
self._input_data = None
self._input_metadata = None
self._config.output_mode = 0
self._config.output_directory = ''
self._config.output_filename = ''
self._config.cast_to_short = True
config_list = [
('Output mode:', 'output_mode', 'base:int', 'radiobox',
'Output mode',
['Slice-per-file (directory)', 'Multi-slice per file (file)']),
('Output directory:', 'output_directory', 'base:str', 'dirbrowser',
'Directory that takes slice-per-file output'),
('Output filename:', 'output_filename', 'base:str', 'filebrowser',
'Output filename for multi-slice per file output.', {
'fileMode': wx.SAVE,
'fileMask': 'DICOM file (*.dcm)|*.dcm|'
'All files (*.*)|*.*'
}),
('Cast to short:', 'cast_to_short', 'base:bool', 'checkbox',
'Should the data be cast to signed 16-bit (short), '
'common for DICOM.')
]
ScriptedConfigModuleMixin.__init__(self, config_list,
{'Module (self)': self})
self.sync_module_logic_with_config()
def PrintProgress(object, event):
assert event == "ProgressEvent"
print("Progress:", object.GetProgress())
if __name__ == "__main__":
try:
filename = os.sys.argv[1]
except:
# failure
print("Need a filename")
sys.exit(1)
# setup reader
r = vtkgdcm.vtkGDCMImageReader()
r.SetFileName(filename)
r.AddObserver("ProgressEvent", PrintProgress)
r.Update()
print(r.GetOutput())
# Write output
writer = vtkgdcm.vtkGDCMImageWriter()
writer.SetInput(r.GetOutput())
writer.SetMedicalImageProperties(r.GetMedicalImageProperties())
writer.SetFileName("TestvtkGDCMImageWriterPython.dcm")
writer.Write()
# Test succeed ?
#sys.exit(sucess != 1)
def PrintProgress(object, event):
assert event == "ProgressEvent"
print "Progress:", object.GetProgress()
if __name__ == "__main__":
try:
filename = os.sys.argv[1]
except:
# failure
print "Need a filename"
sys.exit(1)
# setup reader
r = vtkgdcm.vtkGDCMImageReader()
r.SetFileName( filename )
r.AddObserver("ProgressEvent", PrintProgress)
r.Update()
print r.GetOutput()
# Write output
writer = vtkgdcm.vtkGDCMImageWriter()
writer.SetInput( r.GetOutput() )
writer.SetMedicalImageProperties( r.GetMedicalImageProperties() )
writer.SetFileName( "TestvtkGDCMImageWriterPython.dcm" )
writer.Write()
# Test succeed ?
#sys.exit(sucess != 1)
VTK_DATA_ROOT = vtkGetDataRoot() r = vtkgdcm.vtkGDCMImageReader() r.SetFileName( VTK_DATA_ROOT + "/Data/mr.001" ) r.Update() #print r.GetOutput() # Pixel Spacing # 0.78125, 0.78125, 0 # Image Position (Patient) # -13.3034, -80.8219, 119.178 # try to rewrite it: w = vtkgdcm.vtkGDCMImageWriter() w.SetInput( r.GetOutput() ) w.SetMedicalImageProperties( r.GetMedicalImageProperties() ) w.SetDirectionCosines( r.GetDirectionCosines() ) w.SetFileName( "mr.001.dcm" ) w.Write() # beach.tif #tiffreader = vtk.vtkTIFFReader() #tiffreader.SetFileName( VTK_DATA_ROOT + "/Data/beach.tif" ) #tiffreader.Update() # print tiffreader.GetOutput() # -> TIFF reader was apparently broken in VTK until some very recent # version and thus image appear upside down, unless you also update VTKData :( jpegreader = vtk.vtkJPEGReader()
def ProcessOneFilePrivate(filename, outfilename, tmpfile):
vtkreader = vtkgdcm.vtkGDCMImageReader()
vtkreader.SetFileName( filename )
vtkreader.Update()
# (2005,1409) DS 4 0.0
# (2005,140a) DS 16 1.52283272283272
# (2005,0014) LO 26 Philips MR Imaging DD 005
tag1 = gdcm.PrivateTag(0x2005,0x09,"Philips MR Imaging DD 005")
tag2 = gdcm.PrivateTag(0x2005,0x0a,"Philips MR Imaging DD 005")
# Need to access some private tags, reread the file (for now):
reader = gdcm.Reader()
reader.SetFileName( filename )
if not reader.Read():
sys.exit(1)
ds = reader.GetFile().GetDataSet()
el1 = ds.GetDataElement( tag1 )
el2 = ds.GetDataElement( tag2 )
#pf = gdcm.PythonFilter()
#pf.SetFile( reader.GetFile() )
#print el1.GetTag()
print el1.GetByteValue()
v1 = eval(el1.GetByteValue().GetBuffer())
print el2.GetByteValue()
v2 = eval(el2.GetByteValue().GetBuffer())
print v1
shift = v1
print v2
scale = v2
ss = vtk.vtkImageShiftScale()
ss.SetInput( vtkreader.GetOutput() )
# because VTK image shift / scale convention is inverted from DICOM make sure shift is 0
assert shift == 0
ss.SetShift( shift )
ss.SetScale( scale )
ss.SetOutputScalarTypeToUnsignedShort ()
ss.Update()
# vtkGDCMImageWriter does not support Sequence, so let's write a tmp file first:
# Some operation will actually be discarded (we simply need a temp storage)
vtkwriter = vtkgdcm.vtkGDCMImageWriter()
vtkwriter.SetFileName( tmpfile )
vtkwriter.SetMedicalImageProperties( vtkreader.GetMedicalImageProperties() )
vtkwriter.SetDirectionCosines( vtkreader.GetDirectionCosines() )
vtkwriter.SetImageFormat( reader.GetImageFormat() )
# do not pass shift/scale again
vtkwriter.SetInput( ss.GetOutput() )
#vtkwriter.Update()
vtkwriter.Write()
# ok now rewrite the exact same file as the original (keep all info)
# but use the Pixel Data Element from the written file
tmpreader = gdcm.ImageReader()
tmpreader.SetFileName( tmpfile )
if not tmpreader.Read():
sys.exit(1)
writer = gdcm.ImageWriter()
writer.SetFileName( outfilename )
# Pass image from vtk written file
writer.SetImage( tmpreader.GetImage() )
# pass dataset from initial 'reader'
writer.SetFile( reader.GetFile() )
if not writer.Write():
sys.exit(1)
def img2dcm(self, input_img, output, img_type, img_number):
if img_type == "jpg":
print "JPG"
image = vtk.vtkJPEGReader()
image.SetFileName(input_img)
image.Update()
elif img_type == "tif":
print "TIF"
image = vtk.vtkTIFFReader()
image.SetFileName(input_img)
image.Update()
elif img_type == "bmp":
print "BMP"
image = vtk.vtkBMPReader()
image.SetFileName(input_img)
image.Allow8BitBMPOn()
image.Update()
elif img_type == "png":
print "PNG"
image = vtk.vtkPNGReader()
image.SetFileName(input_img)
image.SetDataSpacing(self.spacing)
image.Update()
elif img_type == "vti":
print "VTI"
image = vtk.vtkXMLImageDataReader()
image.SetFileName(input_img)
image.Update()
#if (orientation == 0):
image_pos = img_number * self.spacing[2]
image_localization = image_pos
# print image_pos, img_number, image.GetOutput().GetScalarRange()
img_clone = vtk.vtkImageData()
img_clone.DeepCopy(image.GetOutput())
img_clone.SetSpacing(self.spacing)
img_clone.Update()
# v = vtk.vtkImageViewer()
# v.SetInput(image.GetOutput())
# v.SetColorLevel(500)
# v.SetColorWindow(240)
# v.Render()
# time.sleep(3)
# a = vtk.vtkImageCast()
# a.SetOutputScalarTypeToUnsignedChar()
# a.SetInput(image.GetOutput())
# a.ClampOverflowOn()
# a.Update()
#b = vtk.vtkJPEGWriter()
#b.SetFileName("C:\\teste.jpg")
#b.SetInput(a.GetOutput())
#b.writer()
#spacing = image.GetOutput().GetSpacing()
#elif (orientation == 1):
# image_pos[0] = image_pos[0] + thickness
# image_localization = image_localization + thickness
# img_number = img_number + 1
#elif (orientation == 2):
# image_pos[1] = image_pos[1] + thickness
# image_localization = image_localization + thickness
# img_number = img_number + 1
pos = 0, 0, image_pos
print pos
# transform = vtk.vtkTransform()
# transform.Translate(pos)
# transform_filter = vtk.vtkImageReslice()
# transform_filter.SetInput(image.GetOutput())
# transform_filter.SetResliceTransform(transform)
# transform_filter.Update()
properties = vtk.vtkMedicalImageProperties()
properties.SetModality(self.modality)
properties.SetInstitutionName(self.institution)
properties.SetPatientName(self.patient)
properties.SetSliceThickness(str(self.spacing[2]))
properties.SetSeriesNumber(str(self.serie))
properties.SetImageNumber(str(img_number))
properties.SetPatientID(self.patient_id)
properties.SetStudyID(self.study_id)
properties.AddUserDefinedValue("Image Position (Patient)", "%.5f\\%.5f\\%.5f" %
(pos[0], pos[1], pos[2]))
properties.AddUserDefinedValue("Instance Number", str(img_number))
print str(img_number), properties.GetNumberOfUserDefinedValues()
writer = vtkgdcm.vtkGDCMImageWriter()
writer.SetInput(img_clone)
writer.SetStudyUID(self.study_uid)
writer.SetSeriesUID(self.series_uid)
writer.SetMedicalImageProperties(properties)
writer.SetFileName(output)
# writer.SetImageFormat(vtk.VTK_LUMINANCE)
writer.SetFileDimensionality(3)
writer.Write()
reader = gdcm.Reader()
reader.SetFileName(output)
reader.Read()
anon = gdcm.Anonymizer()
anon.SetFile(reader.GetFile())
anon.Replace(gdcm.Tag(0x0020, 0x0013), str(img_number))
anon.Replace(gdcm.Tag(0x0028, 0x0030), "%.6f\\%.6f" % (self.spacing[0],
self.spacing[1]))
writer = gdcm.Writer()
writer.SetFile(reader.GetFile())
writer.SetFileName(output)
writer.Write()
# print spacing, pos, image.GetOutput().GetScalarRange()
# writer = ivDicom.DicomWriter()
# writer.SetFileName(output)
# writer.SaveIsNew(image.GetOutput())
#
# writer.SetAcquisitionModality(self.modality)
# writer.SetInstitutionName(self.institution)
# writer.SetStudyID(self.study_uid)
# writer.SetPatientID(self.patient_id)
# writer.SetPatientName(self.patient)
# writer.SetImageThickness(self.spacing[2])
# writer.SetImageSeriesNumber(self.serie)
# writer.SetImageNumber(img_number)
# writer.SetImagePosition(pos)
# writer.SetImageLocation(image_localization)
# writer.SetPixelSpacing(self.spacing[:2])
# writer.Save()
print "Written", input_img, "->", output
VTK_DATA_ROOT = vtkGetDataRoot()
r = vtkgdcm.vtkGDCMImageReader()
r.SetFileName(VTK_DATA_ROOT + "/Data/mr.001")
r.Update()
#print r.GetOutput()
# Pixel Spacing
# 0.78125, 0.78125, 0
# Image Position (Patient)
# -13.3034, -80.8219, 119.178
# try to rewrite it:
w = vtkgdcm.vtkGDCMImageWriter()
w.SetInput(r.GetOutput())
w.SetMedicalImageProperties(r.GetMedicalImageProperties())
w.SetDirectionCosines(r.GetDirectionCosines())
w.SetFileName("mr.001.dcm")
w.Write()
# beach.tif
#tiffreader = vtk.vtkTIFFReader()
#tiffreader.SetFileName( VTK_DATA_ROOT + "/Data/beach.tif" )
#tiffreader.Update()
# print tiffreader.GetOutput()
# -> TIFF reader was apparently broken in VTK until some very recent
# version and thus image appear upside down, unless you also update VTKData :(
jpegreader = vtk.vtkJPEGReader()
def ProcessOneFilePrivate(filename, outfilename, tmpfile):
vtkreader = vtkgdcm.vtkGDCMImageReader()
vtkreader.SetFileName(filename)
vtkreader.Update()
# (2005,1409) DS 4 0.0
# (2005,140a) DS 16 1.52283272283272
# (2005,0014) LO 26 Philips MR Imaging DD 005
tag1 = gdcm.PrivateTag(0x2005, 0x09, "Philips MR Imaging DD 005")
tag2 = gdcm.PrivateTag(0x2005, 0x0a, "Philips MR Imaging DD 005")
# Need to access some private tags, reread the file (for now):
reader = gdcm.Reader()
reader.SetFileName(filename)
if not reader.Read():
sys.exit(1)
ds = reader.GetFile().GetDataSet()
el1 = ds.GetDataElement(tag1)
el2 = ds.GetDataElement(tag2)
#pf = gdcm.PythonFilter()
#pf.SetFile( reader.GetFile() )
#print el1.GetTag()
print el1.GetByteValue()
v1 = eval(el1.GetByteValue().GetBuffer())
print el2.GetByteValue()
v2 = eval(el2.GetByteValue().GetBuffer())
print v1
shift = v1
print v2
scale = v2
ss = vtk.vtkImageShiftScale()
ss.SetInput(vtkreader.GetOutput())
# because VTK image shift / scale convention is inverted from DICOM make sure shift is 0
assert shift == 0
ss.SetShift(shift)
ss.SetScale(scale)
ss.SetOutputScalarTypeToUnsignedShort()
ss.Update()
# vtkGDCMImageWriter does not support Sequence, so let's write a tmp file first:
# Some operation will actually be discarded (we simply need a temp storage)
vtkwriter = vtkgdcm.vtkGDCMImageWriter()
vtkwriter.SetFileName(tmpfile)
vtkwriter.SetMedicalImageProperties(vtkreader.GetMedicalImageProperties())
vtkwriter.SetDirectionCosines(vtkreader.GetDirectionCosines())
vtkwriter.SetImageFormat(reader.GetImageFormat())
# do not pass shift/scale again
vtkwriter.SetInput(ss.GetOutput())
#vtkwriter.Update()
vtkwriter.Write()
# ok now rewrite the exact same file as the original (keep all info)
# but use the Pixel Data Element from the written file
tmpreader = gdcm.ImageReader()
tmpreader.SetFileName(tmpfile)
if not tmpreader.Read():
sys.exit(1)
writer = gdcm.ImageWriter()
writer.SetFileName(outfilename)
# Pass image from vtk written file
writer.SetImage(tmpreader.GetImage())
# pass dataset from initial 'reader'
writer.SetFile(reader.GetFile())
if not writer.Write():
sys.exit(1)
