def GetDicomGroups(self, path, recursive):
if not const.VTK_WARNING:
log_path = utils.encode(
os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt'),
const.FS_ENCODE)
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
y = yGetDicomGroups(path, recursive)
for value_progress in y:
print(">>>>", value_progress)
if not self.running:
break
if isinstance(value_progress, tuple):
self.UpdateLoadFileProgress(value_progress)
else:
self.EndLoadFile(value_progress)
self.UpdateLoadFileProgress(None)
#Is necessary in the case user cancel
#the load, ensure that dicomdialog is closed
if (self.stoped):
self.UpdateLoadFileProgress(None)
self.stoped = False
def GetFilenameList(self):
# Should be called when user selects this group
# This list will be used to create the vtkImageData
# (interpolated)
if _has_win32api:
filelist = [win32api.GetShortPathName(dicom.image.file)
for dicom in
self.slices_dict.values()]
else:
filelist = [dicom.image.file for dicom in
self.slices_dict.values()]
# Sort slices using GDCM
#if (self.dicom.image.orientation_label != "CORONAL"):
#Organize reversed image
sorter = gdcm.IPPSorter()
sorter.SetComputeZSpacing(True)
sorter.SetZSpacingTolerance(1e-10)
try:
sorter.Sort([utils.encode(i, const.FS_ENCODE) for i in filelist])
except TypeError:
sorter.Sort(filelist)
filelist = sorter.GetFilenames()
# for breast-CT of koning manufacturing (KBCT)
if list(self.slices_dict.values())[0].parser.GetManufacturerName() == "Koning":
filelist.sort()
return filelist
def GetFilenameList(self):
# Should be called when user selects this group
# This list will be used to create the vtkImageData
# (interpolated)
if _has_win32api:
filelist = [win32api.GetShortPathName(dicom.image.file)
for dicom in
self.slices_dict.values()]
else:
filelist = [dicom.image.file for dicom in
self.slices_dict.values()]
# Sort slices using GDCM
if (self.dicom.image.orientation_label != "CORONAL"):
#Organize reversed image
sorter = gdcm.IPPSorter()
sorter.SetComputeZSpacing(True)
sorter.SetZSpacingTolerance(1e-10)
try:
sorter.Sort([utils.encode(i, const.FS_ENCODE) for i in filelist])
except TypeError:
sorter.Sort(filelist)
filelist = sorter.GetFilenames()
# for breast-CT of koning manufacturing (KBCT)
if list(self.slices_dict.values())[0].parser.GetManufacturerName() == "Koning":
filelist.sort()
return filelist
def GetDicomGroups(self, path, recursive):
if not const.VTK_WARNING:
log_path = utils.encode(os.path.join(const.USER_LOG_DIR, 'vtkoutput.txt'), const.FS_ENCODE)
fow = vtk.vtkFileOutputWindow()
fow.SetFileName(log_path)
ow = vtk.vtkOutputWindow()
ow.SetInstance(fow)
y = yGetDicomGroups(path, recursive)
for value_progress in y:
print(">>>>", value_progress)
if not self.running:
break
if isinstance(value_progress, tuple):
self.UpdateLoadFileProgress(value_progress)
else:
self.EndLoadFile(value_progress)
self.UpdateLoadFileProgress(None)
#Is necessary in the case user cancel
#the load, ensure that dicomdialog is closed
if(self.stoped):
self.UpdateLoadFileProgress(None)
self.stoped = False
def create_dicom_thumbnails(filename, window=None, level=None):
rvtk = vtkgdcm.vtkGDCMImageReader()
rvtk.SetFileName(utils.encode(filename, const.FS_ENCODE))
rvtk.Update()
img = rvtk.GetOutput()
if window is None or level is None:
_min, _max = img.GetScalarRange()
window = _max - _min
level = _min + window / 2
dx, dy, dz = img.GetDimensions()
if dz > 1:
thumbnail_paths = []
for i in range(dz):
img_slice = ExtractVOI(img, 0, dx-1, 0, dy-1, i, i+1)
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(img_slice)
colorer.SetWindow(window)
colorer.SetLevel(level)
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputData(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputData(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
thumbnail_paths.append(thumbnail_path)
return thumbnail_paths
else:
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(img)
colorer.SetWindow(window)
colorer.SetLevel(level)
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputData(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputData(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
return thumbnail_path
def run(self):
grouper = self.grouper
reader = gdcm.ImageReader()
if _has_win32api:
try:
reader.SetFileName(
utils.encode(win32api.GetShortPathName(self.filepath),
const.FS_ENCODE))
except TypeError:
reader.SetFileName(win32api.GetShortPathName(self.filepath))
else:
try:
reader.SetFileName(utils.encode(self.filepath,
const.FS_ENCODE))
except TypeError:
reader.SetFileName(self.filepath)
if (reader.Read()):
file = reader.GetFile()
# Retrieve data set
dataSet = file.GetDataSet()
# Retrieve header
header = file.GetHeader()
stf = gdcm.StringFilter()
stf.SetFile(file)
field_dict = {}
data_dict = {}
tag = gdcm.Tag(0x0008, 0x0005)
ds = reader.GetFile().GetDataSet()
if ds.FindDataElement(tag):
encoding_value = str(
ds.GetDataElement(tag).GetValue()).split('\\')[0]
if encoding_value.startswith("Loaded"):
encoding = "ISO_IR 100"
else:
try:
encoding = const.DICOM_ENCODING_TO_PYTHON[
encoding_value]
except KeyError:
encoding = 'ISO_IR 100'
else:
encoding = "ISO_IR 100"
# Iterate through the Header
iterator = header.GetDES().begin()
while (not iterator.equal(header.GetDES().end())):
dataElement = iterator.next()
if not dataElement.IsUndefinedLength():
tag = dataElement.GetTag()
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not (utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = utils.decode(
data[1], encoding)
else:
data_dict[group][field] = "Invalid Character"
# Iterate through the Data set
iterator = dataSet.GetDES().begin()
while (not iterator.equal(dataSet.GetDES().end())):
dataElement = iterator.next()
if not dataElement.IsUndefinedLength():
tag = dataElement.GetTag()
# if (tag.GetGroup() == 0x0009 and tag.GetElement() == 0x10e3) \
# or (tag.GetGroup() == 0x0043 and tag.GetElement() == 0x1027):
# continue
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not (utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = utils.decode(
data[1], encoding, 'replace')
else:
data_dict[group][field] = "Invalid Character"
# -------------- To Create DICOM Thumbnail -----------
try:
data = data_dict[str(0x028)][str(0x1050)]
level = [float(value) for value in data.split('\\')][0]
data = data_dict[str(0x028)][str(0x1051)]
window = [float(value) for value in data.split('\\')][0]
except (KeyError, ValueError):
level = None
window = None
if _has_win32api:
thumbnail_path = imagedata_utils.create_dicom_thumbnails(
win32api.GetShortPathName(self.filepath), window, level)
else:
thumbnail_path = imagedata_utils.create_dicom_thumbnails(
self.filepath, window, level)
#------ Verify the orientation --------------------------------
img = reader.GetImage()
direc_cosines = img.GetDirectionCosines()
orientation = gdcm.Orientation()
try:
_type = orientation.GetType(tuple(direc_cosines))
except TypeError:
_type = orientation.GetType(direc_cosines)
label = orientation.GetLabel(_type)
# ---------- Refactory --------------------------------------
data_dict['invesalius'] = {'orientation_label': label}
# -------------------------------------------------------------
dict_file[self.filepath] = data_dict
#---------- Verify is DICOMDir -------------------------------
is_dicom_dir = 1
try:
if (data_dict[str(0x002)][str(0x002)] !=
"1.2.840.10008.1.3.10"): #DICOMDIR
is_dicom_dir = 0
except (KeyError):
is_dicom_dir = 0
if not (is_dicom_dir):
parser = dicom.Parser()
parser.SetDataImage(dict_file[self.filepath], self.filepath,
thumbnail_path)
dcm = dicom.Dicom()
#self.l.acquire()
dcm.SetParser(parser)
grouper.AddFile(dcm)
def run(self):
grouper = self.grouper
reader = gdcm.ImageReader()
if _has_win32api:
try:
reader.SetFileName(utils.encode(win32api.GetShortPathName(self.filepath),
const.FS_ENCODE))
except TypeError:
reader.SetFileName(win32api.GetShortPathName(self.filepath))
else:
try:
reader.SetFileName(utils.encode(self.filepath, const.FS_ENCODE))
except TypeError:
reader.SetFileName(self.filepath)
if (reader.Read()):
file = reader.GetFile()
# Retrieve data set
dataSet = file.GetDataSet()
# Retrieve header
header = file.GetHeader()
stf = gdcm.StringFilter()
stf.SetFile(file)
field_dict = {}
data_dict = {}
tag = gdcm.Tag(0x0008, 0x0005)
ds = reader.GetFile().GetDataSet()
if ds.FindDataElement(tag):
encoding_value = str(ds.GetDataElement(tag).GetValue()).split('\\')[0]
if encoding_value.startswith("Loaded"):
encoding = "ISO_IR 100"
else:
try:
encoding = const.DICOM_ENCODING_TO_PYTHON[encoding_value]
except KeyError:
encoding = 'ISO_IR 100'
else:
encoding = "ISO_IR 100"
# Iterate through the Header
iterator = header.GetDES().begin()
while (not iterator.equal(header.GetDES().end())):
dataElement = iterator.next()
if not dataElement.IsUndefinedLength():
tag = dataElement.GetTag()
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not(utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = utils.decode(data[1], encoding)
else:
data_dict[group][field] = "Invalid Character"
# Iterate through the Data set
iterator = dataSet.GetDES().begin()
while (not iterator.equal(dataSet.GetDES().end())):
dataElement = iterator.next()
if not dataElement.IsUndefinedLength():
tag = dataElement.GetTag()
# if (tag.GetGroup() == 0x0009 and tag.GetElement() == 0x10e3) \
# or (tag.GetGroup() == 0x0043 and tag.GetElement() == 0x1027):
# continue
data = stf.ToStringPair(tag)
stag = tag.PrintAsPipeSeparatedString()
group = str(tag.GetGroup())
field = str(tag.GetElement())
tag_labels[stag] = data[0]
if not group in data_dict.keys():
data_dict[group] = {}
if not(utils.VerifyInvalidPListCharacter(data[1])):
data_dict[group][field] = utils.decode(data[1], encoding, 'replace')
else:
data_dict[group][field] = "Invalid Character"
# -------------- To Create DICOM Thumbnail -----------
try:
data = data_dict[str(0x028)][str(0x1050)]
level = [float(value) for value in data.split('\\')][0]
data = data_dict[str(0x028)][str(0x1051)]
window = [float(value) for value in data.split('\\')][0]
except(KeyError, ValueError):
level = None
window = None
if _has_win32api:
thumbnail_path = imagedata_utils.create_dicom_thumbnails(win32api.GetShortPathName(self.filepath), window, level)
else:
thumbnail_path = imagedata_utils.create_dicom_thumbnails(self.filepath, window, level)
#------ Verify the orientation --------------------------------
img = reader.GetImage()
direc_cosines = img.GetDirectionCosines()
orientation = gdcm.Orientation()
try:
_type = orientation.GetType(tuple(direc_cosines))
except TypeError:
_type = orientation.GetType(direc_cosines)
label = orientation.GetLabel(_type)
# ---------- Refactory --------------------------------------
data_dict['invesalius'] = {'orientation_label' : label}
# -------------------------------------------------------------
dict_file[self.filepath] = data_dict
#---------- Verify is DICOMDir -------------------------------
is_dicom_dir = 1
try:
if (data_dict[str(0x002)][str(0x002)] != "1.2.840.10008.1.3.10"): #DICOMDIR
is_dicom_dir = 0
except(KeyError):
is_dicom_dir = 0
if not(is_dicom_dir):
parser = dicom.Parser()
parser.SetDataImage(dict_file[self.filepath], self.filepath, thumbnail_path)
dcm = dicom.Dicom()
#self.l.acquire()
dcm.SetParser(parser)
grouper.AddFile(dcm)
def create_dicom_thumbnails(filename, window=None, level=None):
rvtk = vtkgdcm.vtkGDCMImageReader()
rvtk.SetFileName(utils.encode(filename, const.FS_ENCODE))
rvtk.Update()
img = rvtk.GetOutput()
if window is None or level is None:
_min, _max = img.GetScalarRange()
window = _max - _min
level = _min + window / 2
dx, dy, dz = img.GetDimensions()
if dz > 1:
thumbnail_paths = []
for i in range(dz):
img_slice = ExtractVOI(img, 0, dx-1, 0, dy-1, i, i+1)
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(img_slice)
colorer.SetWindow(window)
colorer.SetLevel(level)
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputData(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputData(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
thumbnail_paths.append(thumbnail_path)
return thumbnail_paths
else:
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputData(img)
colorer.SetWindow(window)
colorer.SetLevel(level)
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputData(colorer.GetOutput())
resample.SetAxisMagnificationFactor ( 0, 0.25 )
resample.SetAxisMagnificationFactor ( 1, 0.25 )
resample.SetAxisMagnificationFactor ( 2, 1 )
resample.Update()
thumbnail_path = tempfile.mktemp()
write_png = vtk.vtkPNGWriter()
write_png.SetInputData(resample.GetOutput())
write_png.SetFileName(thumbnail_path)
write_png.Write()
return thumbnail_path
