def TestStringFilter(filename, verbose=False):
r = gdcm.Reader()
r.SetFileName(filename)
success = r.Read()
if (not success): return 1
file = r.GetFile()
ds = file.GetDataSet()
# Change gdcm struct into something swig can digest:
pds = gdcm.PythonDataSet(ds)
sf = gdcm.StringFilter()
pds.Start() # Make iterator go at beginning
dic1 = {}
dic2 = {}
sf.SetFile(file) # extremely important
while (not pds.IsAtEnd()):
t = str(pds.GetCurrent().GetTag())
res = sf.ToStringPair(pds.GetCurrent().GetTag())
dic2[t] = res[1]
dic1[res[0]] = res[1]
pds.Next()
#print dic1
#print dic2
try:
print "Pixel Representation=", dic2['(0028,0103)']
except KeyError:
print "Tag not found in dataset"
return 0
def __init__(self, dcm_path):
try:
self.dcm_path = dcm_path
pygdcm.gdcm_Reader = gdcm.ImageReader()
pygdcm.gdcm_Reader.SetFileName(self.dcm_path)
file = pygdcm.gdcm_Reader.GetFile()
self.dataset = file.GetDataSet()
self.strFilter = gdcm.StringFilter()
self.strFilter.SetFile(pygdcm.gdcm_Reader.GetFile())
self.image_u16 = []
except Exception as e:
print(traceback.print_exc())
return
def _read_all_tags(self, filename):
r = gdcm.Reader(filename)
r.Read()
f = r.GetFile()
ds = file.GetDataSet()
pds = gdcm.PythonDataSet(ds)
sf = gdcm.StringFilter()
pds.Start() # Make iterator go at begining
dic = {}
sf.SetFile(f) # extremely important
while (not pds.IsAtEnd()):
res = sf.ToStringPair(pds.GetCurrent().GetTag())
dic[res[0]] = res[1]
pds.Next()
return dic
def __init__(self, fname):
self.fname = fname
self.file_name, self.file_extension = os.path.splitext(fname)
reader = gdcm.Reader()
reader.SetFileName(fname)
if not reader.Read():
raise InvalidDicom("Not a valid DICOM file")
self._file = reader.GetFile()
self._header = self._file.GetHeader()
self._dataset = self._file.GetDataSet()
self._str_filter = gdcm.StringFilter()
self._str_filter.SetFile(self._file)
self._image = None
self._anon_obj = None
self._errors = None
self._warnings = None
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()
reader.SetFileName(self.filepath)
if (reader.Read()):
file = reader.GetFile()
# Retrieve data set
dataSet = file.GetDataSet()
# Retrieve header
header = file.GetHeader()
stf = gdcm.StringFilter()
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()
stf.SetFile(file)
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] = data[1].decode(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()
stf.SetFile(file)
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] = data[1].decode(
encoding, 'replace')
else:
data_dict[group][field] = "Invalid Character"
# -------------- To Create DICOM Thumbnail -----------
rvtk = vtkgdcm.vtkGDCMImageReader()
rvtk.SetFileName(self.filepath)
rvtk.Update()
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):
level = 300.0
window = 2000.0
colorer = vtk.vtkImageMapToWindowLevelColors()
colorer.SetInputConnection(rvtk.GetOutputPort())
colorer.SetWindow(float(window))
colorer.SetLevel(float(level))
colorer.SetOutputFormatToRGB()
colorer.Update()
resample = vtk.vtkImageResample()
resample.SetInputConnection(colorer.GetOutputPort())
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.SetInputConnection(resample.GetOutputPort())
write_png.SetFileName(thumbnail_path)
write_png.Write()
#------ 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)
# If the reader fails to read the file, we should stop !
if not r.Read():
print ("Not a valid DICOM file")
# Get the DICOM File structure
file = r.GetFile()
# Get the DataSet part of the file
dataset = file.GetDataSet()
# Ok let's print it !
#print dataset
# Use StringFilter to print a particular Tag:
sf = gdcm.StringFilter()
sf.SetFile(r.GetFile())
# Check if Attribute exist
#print dataset.FindDataElement(gdcm.Tag(0x0008, 0x2218))
# Let's print it as string pair:
#print sf.ToStringPair(gdcm.Tag(0x18, 0x1110))[1]
#prints just the value for this dicom element
#print sf.ToStringPair(gdcm.Tag(0x28, 0x0030))[1]
#this is just a function to test getting the user inputted acc# to query the database.
#TODO: This function will be rewrittent to get the dicom header from the database using the
#user inputted accession number.