def TestRead(filename, verbose=False):
r = gdcm.Reader()
r.SetFileName(filename)
sucess = r.Read()
#if verbose: print r.GetFile()
if verbose: print r.GetFile().GetDataSet()
return sucess
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 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, filename):
self.image_reader = gdcm.ImageReader()
self.image_reader.SetFileName(filename)
self.reader = gdcm.Reader()
self.reader.SetFileName(filename)
if not self.reader.Read():
raise DicomFileReadFailed("{} dicom file read failed.".format(
filename))
self.dicom_file = self.reader.GetFile()
self.dicom_dataset = self.dicom_file.GetDataSet()
self.dicom_header = self.dicom_file.GetHeader()
if not self.image_reader.Read():
raise DicomImageReadFailed("{} image read failed.".format(
filename))
def TestModifyFields(filename):
outfilename = filename + ".rewrite"
r = gdcm.Reader()
r.SetFileName(filename)
sucess = r.Read()
#print r.GetFile().GetDataSet()
ds = r.GetFile().GetDataSet()
#print dir(ds)
# eg, let's remove a tag
removetag = gdcm.Tag(0x0043, 0x106f)
if ds.FindDataElement(removetag):
ds.Remove(removetag)
# let's replace a value:
replacetag = gdcm.Tag(0x0010, 0x0010)
if ds.FindDataElement(replacetag):
de = ds.GetDataElement(replacetag)
#print dir(de)
patname = "This^is^an^example"
vl = gdcm.VL(len(patname))
de.SetByteValue(patname, vl)
# let's insert a new dataelement
# <entry group="0012" element="0062" vr="CS" vm="1" name="Patient Identity Removed"/>
pir = gdcm.DataElement(gdcm.Tag(0x0012, 0x0062))
pir.SetVR(gdcm.VR(gdcm.VR.CS)) # specify the VR explicitely
yes = "YES"
pir.SetByteValue(yes, gdcm.VL(len(yes)))
ds.Insert(pir)
# try again but pretend we don't know the VR
# <entry group="0012" element="0063" vr="LO" vm="1-n" name="De-identification Method"/>
deidmethod = gdcm.Tag(0x0012, 0x0063)
# retrieve the supreme global instance, sum of all knowledge in da whole universe:
dicomdicts = gdcm.GlobalInstance.GetDicts()
dictel = dicomdicts.GetDictEntry(deidmethod)
#print dictel.GetVR()
deid = gdcm.DataElement(deidmethod)
deid.SetVR(dictel.GetVR())
methodstr = "Well known Company"
#deid.SetByteValue( methodstr, gdcm.VL(len(methodstr)) )
deid.SetByteValue(methodstr, gdcm.VL(len(methodstr)))
ds.Insert(deid)
#w = gdcm.Writer()
#w.SetFileName( outfilename )
#w.SetFile( r.GetFile() )
#sucess = w.Write()
return sucess
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 TestAnonymizer(filename, verbose=False):
r = gdcm.Reader()
r.SetFileName(filename)
sucess = r.Read()
if (not sucess): return 1
#print r.GetFile().GetDataSet()
ano = gdcm.Anonymizer()
ano.SetFile(r.GetFile())
# 1. Replace with another value
ano.Replace(gdcm.Tag(0x0010, 0x0010), "Test^Anonymize")
# 2. Remove a tag (even a SQ)
ano.Remove(gdcm.Tag(0x0008, 0x2112))
# 3. Make a tag empty
ano.Empty(gdcm.Tag(0x0008, 0x0070))
# Call the main function:
sucess = ano.RemovePrivateTags() # do it !
if (not sucess): return 1
# Check we can also change value from binary field
#ano.Replace( gdcm.Tag(0x0010,0x0010), "16", gdcm. )
# Let's check if our anonymization worked:
if verbose:
print(ano.GetFile().GetDataSet())
# So at that point r.GetFile() was modified, let's simply passed it to the Writer:
# First find a place where to write it out:
subdir = "TestAnonymizerPython"
tmpdir = gdcm.Testing.GetTempDirectory(subdir)
if not gdcm.System.FileIsDirectory(tmpdir):
gdcm.System.MakeDirectory(tmpdir)
# Ok directory does exist now, extract the name of the input file, and merge it in
# our newly created tmpdir:
outfilename = gdcm.Testing.GetTempFilename(filename, subdir)
w = gdcm.Writer()
w.SetFileName(outfilename)
w.SetFile(r.GetFile())
w.SetCheckFileMetaInformation(False)
sucess = w.Write()
if (not sucess): return 1
if verbose:
print("Success to write: %s" % outfilename)
return sucess
def anonymizeOneFile(self, fin, fout):
reader = gdcm.Reader()
reader.SetFileName(fin)
ret = reader.Read()
if not ret:
return (False, "File could not been read")
(ar, af) = self._anonymizeOneFile(reader.GetFile())
if not ar:
return (False, "Error while anonymizing")
writer = gdcm.Writer()
writer.SetFileName(fout)
writer.SetFile(af)
writer.Write()
return (True, "OK")
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 example1():
b = Gdcmanon.Gdcmanon(key = 'openssl/key.key', cert = 'openssl/cert.pem', \
salt = '55')
anon = b.getInstance()
r = gdcm.Reader()
r.SetFileName('input.dcm')
r.Read()
anon.SetFile(r.GetFile())
if not anon.BasicApplicationLevelConfidentialityProfile(
True): # False to decrypt
print("Error during anonymization", file=sys.stderr)
else:
w = gdcm.Writer()
w.SetFileName('out.dcm')
w.SetFile(anon.GetFile())
w.Write()
python GetPortionCSAHeader.py input.dcm
Footnote:
SIEMENS is not publishing any information on the CSA header. So any info extracted
is at your own risk.
"""
import sys
import gdcm
if __name__ == "__main__":
file = sys.argv[1]
r = gdcm.Reader()
r.SetFileName(file)
if not r.Read():
sys.exit(1)
ds = r.GetFile().GetDataSet()
csa_t1 = gdcm.CSAHeader()
csa_t2 = gdcm.CSAHeader()
#print csa
t1 = csa_t1.GetCSAImageHeaderInfoTag()
print t1
t2 = csa_t2.GetCSASeriesHeaderInfoTag()
print t2
# Let's do it for t1:
if ds.FindDataElement(t1):
csa_t1.LoadFromDataElement(ds.GetDataElement(t1))
def process_mrs_siemens_csa(dcm_dir):
# ###USE THIS FOR DICOM FILES THAT HAVE CSA HEADERS###
#
# # Make a top-level instance and hide in top left corner, get filepath
# root = Tkinter.Tk()
# root.geometry('0x0+0+0')
# root.attributes("-topmost", 1)
# dcm_dir = tkFileDialog.askdirectory(parent=root)
# root.attributes("-topmost", 0)
# root.destroy()
root_dir = os.path.abspath(os.path.join(dcm_dir, os.pardir))
pat_name = os.path.split(os.path.dirname(dcm_dir))[1]
f = file(root_dir + '/preproc_dump.txt', 'w')
l = []
for fname in glob.glob(dcm_dir + '/*.dcm'):
try:
d = dicom.read_file(fname, force="True")
# if d.SoftwareVersions[-3:]=="B17":
if (0x7fe1, 0x1010) in d:
d.DataPointColumns = len(d[0x7fe1, 0x1010].value) / 8
d.DataPointRows = 1
l.append([
fname,
int(d.SeriesNumber), d.AcquisitionNumber,
d.DataPointColumns, d.DataPointRows
])
except AttributeError:
print('...')
except IOError:
print 'no such file'
for nlist in range(0, len(l)):
if l[nlist][2] == 1:
try:
d = dicom.read_file(l[nlist][0], force='TRUE')
# d.SpectroscopyAcquisitionDataColumns = lambda: None
# d.SpectroscopyAcquisitionDataColumns = d.DataPointColumns
d.SpectroscopyAcquisitionDataColumns = l[nlist][3]
# d.ProtocolName=str(d.ProtocolName).replace (" ","_")
# d.ProtocolName="HELIX"
# p1 = subprocess.Popen(["gdcmdump", "-C",l[nlist][0]], stdout=subprocess.PIPE, stderr=subprocess.PIPE)
# csa1 = p1.communicate()[0]
# d.ProtocolName=csa1.split("tProtocolName")[1].split("\t")[2].split("\r")[0].split('"')[2]
# print >>f, 'file: '+l[nlist][0]+'\tSeries: '+d.ProtocolName
#print(l[nlist][0])
# if d.WaterReferencedPhaseCorrection =="YES":
# ecc_str = 'ECC'
# else:
# ecc_str = 'NO_ECC'
ecc_str = 'NO_ECC'
# fname_new=(str(d.SeriesNumber)+'_'+str(d.ProtocolName).replace (" ","_").replace("/","_")+'_'+str(1)+'_'+ecc_str)
# if not os.path.exists(root_dir + '/' + pat_name + '_PREPROC_LCM'):
# os.makedirs(root_dir + '/' + pat_name + '_PREPROC_LCM')
# d.save_as(root_dir + '/' + pat_name + '_PREPROC_LCM/' + fname_new)
series = l[nlist][1]
npts = l[nlist][3]
avg = 0
for plist in range(0, len(l)):
if l[plist][1] == series:
avg = avg + 1
print(avg)
fname_new = (
str(d.SeriesNumber) + '_' +
str(d.ProtocolName).replace(" ", "_").replace("/", "_") +
'_' + str(avg) + '_' + ecc_str)
spec_data = np.zeros(shape=(avg * npts * 2))
n = []
for k in np.arange(0, npts):
n.append(
struct.unpack('f',
d[0x7fe1,
0x1010].value[4 * k:4 * k + 4])[0])
spec_data[0:(npts * 2)] = array.array('f', d[0x7fe1,
0x1010].value)
# spec_data[0:(npts*2)]=d.SpectroscopyData
for plist in range(0, len(l)):
if l[plist][1] == series:
print(l[plist][0])
try:
d_sub = dicom.read_file(l[plist][0])
# d_sub.ProtocolName=str(d_sub.PatientName).replace (" ","_")
nsub = int(l[plist][2] - 1)
spec_data[(nsub * npts *
2):((nsub + 1) * npts *
2)] = array.array(
'f', d_sub[0x7fe1,
0x1010].value)
print >> f, 'file: ' + l[plist][
0] + '\tSeries: ' + d_sub.ProtocolName
print(l[plist][0])
except AttributeError:
print('...')
except IOError:
print 'no such file'
except InvalidDicomError:
print 'Invalid Dicom file'
spec_data_dummy = np.zeros(
d.SpectroscopyAcquisitionDataColumns * avg * 2)
spec_data_dummy[0:d.SpectroscopyAcquisitionDataColumns * avg *
2:2] = spec_data[
1:d.SpectroscopyAcquisitionDataColumns *
avg * 2:2]
spec_data_dummy[1:d.SpectroscopyAcquisitionDataColumns * avg *
2:2] = spec_data[
0:d.SpectroscopyAcquisitionDataColumns *
avg * 2:2]
d.SpectroscopyData = list(spec_data_dummy)
r = gdcm.Reader()
r.SetFileName(str(l[nlist][0]))
r.Read()
ds = r.GetFile().GetDataSet()
csa_h1 = gdcm.CSAHeader()
csa1 = csa_h1.GetCSAImageHeaderInfoTag()
print csa1
if ds.FindDataElement(csa1):
csa_h1.LoadFromDataElement(ds.GetDataElement(csa1))
d.EffectiveEchoTime = float(
str(csa_h1.GetCSAElementByName("EchoTime").GetValue()))
d.RepetitionTime = float(
str(
csa_h1.GetCSAElementByName(
"RepetitionTime").GetValue()))
d.TransmitterFrequency = float(
str(
csa_h1.GetCSAElementByName(
"ImagingFrequency").GetValue()))
d.SpectralWidth = 1e9 / float(
str(
csa_h1.GetCSAElementByName(
"RealDwellTime").GetValue()))
d.EchoTime = d.EffectiveEchoTime
seqtype = str(
csa_h1.GetCSAElementByName(
"SequenceName").GetValue()).split("*")[1]
if seqtype == 'svs_st':
d.VolumeLocalizationTechnique = 'STEAM'
elif seqtype == 'svs_se':
d.VolumeLocalizationTechnique = 'PRESS'
if not os.path.exists(root_dir + '/' + pat_name +
'_PREPROC_LCM'):
os.makedirs(root_dir + '/' + pat_name + '_PREPROC_LCM')
# if not os.path.exists(root_dir + '/' + pat_name + '_LCM_Results'):
# os.makedirs(root_dir + '/' + pat_name + '_LCM_Results')
d.save_as(root_dir + '/' + pat_name + '_PREPROC_LCM/' +
fname_new)
except AttributeError:
print('...')
except IOError:
print 'no such file...'
except InvalidDicomError:
print 'Invalid Dicom file'
f.close()
print('DONE!')
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)
