def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._input_mmd = None
self._output_mmd = MedicalMetaData()
self._output_mmd.medical_image_properties = \
vtk.vtkMedicalImageProperties()
self._output_mmd.direction_cosines = \
vtk.vtkMatrix4x4()
# if the value (as it appears in mk.vtk_kit.constants.mipk)
# appears in the dict, its value refers to the user supplied
# value. when the user resets a field, that key is removed
# from the dict
self._config.new_value_dict = {}
# this is the list of relevant properties
self.mip_attr_l = \
module_kits.vtk_kit.constants.medical_image_properties_keywords
# this will be used to keep track of changes made to the prop
# grid before they are applied to the config
self._grid_value_dict = {}
self._view_frame = None
self.sync_module_logic_with_config()
def __init__(self, module_manager):
# initialise our base class
ModuleBase.__init__(self, module_manager)
self._input_mmd = None
self._output_mmd = MedicalMetaData()
self._output_mmd.medical_image_properties = \
vtk.vtkMedicalImageProperties()
self._output_mmd.direction_cosines = \
vtk.vtkMatrix4x4()
# if the value (as it appears in mk.vtk_kit.constants.mipk)
# appears in the dict, its value refers to the user supplied
# value. when the user resets a field, that key is removed
# from the dict
self._config.new_value_dict = {}
# this is the list of relevant properties
self.mip_attr_l = \
module_kits.vtk_kit.constants.medical_image_properties_keywords
# this will be used to keep track of changes made to the prop
# grid before they are applied to the config
self._grid_value_dict = {}
self._view_frame = None
self.sync_module_logic_with_config()
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
def execute_module(self):
if self._config.output_mode == 0:
# slice-per-file mode
if not os.path.isdir(self._config.output_directory):
raise RuntimeError('Please specify a valid output directory.')
# generate filenamelist with as many entries as there are
# z-slices
self._input_data.UpdateInformation() # shouldn't be nec.
z_len = self._input_data.GetDimensions()[2]
odir = self._config.output_directory
fn_list = [
os.path.join(odir, 'im%05d.dcm' % (i, ))
for i in range(1, z_len + 1)
]
fn_sa = vtk.vtkStringArray()
[fn_sa.InsertNextValue(fn) for fn in fn_list]
self._writer.SetFileNames(fn_sa)
self._writer.SetFileDimensionality(2)
else: # output_mode == 1, multi-slices per file
if not self._config.output_filename:
raise RuntimeError('Please specify an output filename.')
self._writer.SetFileName(self._config.output_filename)
self._writer.SetFileDimensionality(3)
# now setup the common stuff
mip = vtk.vtkMedicalImageProperties()
try:
mip.DeepCopy(self._input_metadata.medical_image_properties)
except AttributeError:
# this simply means that we have no input metadata
pass
self._writer.SetMedicalImageProperties(mip)
try:
self._writer.SetDirectionCosines(
self._input_metadata.direction_cosines)
except AttributeError:
# we have no input metadata, set the default
# identity matrix
m = vtk.vtkMatrix4x4()
self._writer.SetDirectionCosines(m)
if self._config.cast_to_short:
self._caster.SetInput(self._input_data)
# if we don't call this update, it crashes on Windows with
# GDCM 2.0.5, and everything else shortly before DeVIDE
# 8.5. The crash is inside the vtkGDCMImageWriter.
self._caster.Update()
self._writer.SetInput(self._caster.GetOutput())
else:
# just to be sure
self._caster.SetInput(None)
self._writer.SetInput(self._input_data)
self._writer.Write()
def execute_module(self):
if self._config.output_mode == 0:
# slice-per-file mode
if not os.path.isdir(self._config.output_directory):
raise RuntimeError(
'Please specify a valid output directory.')
# generate filenamelist with as many entries as there are
# z-slices
self._input_data.UpdateInformation() # shouldn't be nec.
z_len = self._input_data.GetDimensions()[2]
odir = self._config.output_directory
fn_list = [os.path.join(odir,'im%05d.dcm' % (i,))
for i in range(1, z_len+1)]
fn_sa = vtk.vtkStringArray()
[fn_sa.InsertNextValue(fn) for fn in fn_list]
self._writer.SetFileNames(fn_sa)
self._writer.SetFileDimensionality(2)
else: # output_mode == 1, multi-slices per file
if not self._config.output_filename:
raise RuntimeError(
'Please specify an output filename.')
self._writer.SetFileName(self._config.output_filename)
self._writer.SetFileDimensionality(3)
# now setup the common stuff
mip = vtk.vtkMedicalImageProperties()
try:
mip.DeepCopy(self._input_metadata.medical_image_properties)
except AttributeError:
# this simply means that we have no input metadata
pass
self._writer.SetMedicalImageProperties(mip)
try:
self._writer.SetDirectionCosines(
self._input_metadata.direction_cosines)
except AttributeError:
# we have no input metadata, set the default
# identity matrix
m = vtk.vtkMatrix4x4()
self._writer.SetDirectionCosines(m)
if self._config.cast_to_short:
self._caster.SetInput(self._input_data)
# if we don't call this update, it crashes on Windows with
# GDCM 2.0.5, and everything else shortly before DeVIDE
# 8.5. The crash is inside the vtkGDCMImageWriter.
self._caster.Update()
self._writer.SetInput(self._caster.GetOutput())
else:
# just to be sure
self._caster.SetInput(None)
self._writer.SetInput(self._input_data)
self._writer.Write()
