def generateCustomDicomFiles(self, studySeriesSopUIDsTuple,
customFieldsDictionary, sourceDcmFile,
destFolder):
dcmReader = DicomReader(sourceDcmFile)
patientName = customFieldsDictionary['PATIENT_NAME']
patientID = customFieldsDictionary['PATIENT_ID']
accessionNumber = customFieldsDictionary['ACCESSION_NUMBER']
for uids in studySeriesSopUIDsTuple:
studyUID = uids[0]
seriesUID = uids[1]
sopUID = uids[2]
destFile = destFolder + '/' + sopUID + '.' + patientID + '.dcm'
substitutionList = []
substitutionList.append(['PatientsName', patientName])
substitutionList.append(['PatientID', patientID])
substitutionList.append(['AccessionNumber', accessionNumber])
substitutionList.append(['StudyInstanceUID', studyUID])
substitutionList.append(['SeriesInstanceUID', seriesUID])
substitutionList.append(['SOPInstanceUID', sopUID])
substitutionList.append(['MediaStorageSOPInstanceUID', sopUID])
# file meta
success = dcmReader.saveAs(destFile, substitutionList)
return success
def _findKosFile(self, retreivedFilesDirectory):
for file in os.listdir(retreivedFilesDirectory):
filePath = retreivedFilesDirectory + '/' + file;
if(DicomReader().isValidDcmFile(filePath)):
kosDcm = DicomReader(filePath);
if kosDcm.containsKosSequence():
return kosDcm;
return None;
def _findKosFile(self, retreivedFilesDirectory):
for file in os.listdir(retreivedFilesDirectory):
filePath = retreivedFilesDirectory + '/' + file;
if(DicomReader().isValidDcmFile(filePath)):
kosDcm = DicomReader(filePath);
if kosDcm.containsKosSequence():
return kosDcm;
return None;
def _findNonKosDicomFiles(self, retreivedFilesDirectory):
dcms = [];
for file in os.listdir(retreivedFilesDirectory):
filePath = retreivedFilesDirectory + '/' + file;
if(DicomReader().isValidDcmFile(filePath)):
dcm = DicomReader(filePath);
if not dcm.containsKosSequence():
dcms.append(dcm);
return dcms;
def _findNonKosDicomFiles(self, retreivedFilesDirectory):
dcms = [];
for file in os.listdir(retreivedFilesDirectory):
filePath = retreivedFilesDirectory + '/' + file;
if(DicomReader().isValidDcmFile(filePath)):
dcm = DicomReader(filePath);
if not dcm.containsKosSequence():
dcms.append(dcm);
return dcms;
def generateCustomDicomFiles(self, studySeriesSopUIDsTuple, customFieldsDictionary, sourceDcmFile, destFolder):
dcmReader = DicomReader(sourceDcmFile);
patientName = customFieldsDictionary['PATIENT_NAME'];
patientID = customFieldsDictionary['PATIENT_ID'];
accessionNumber = customFieldsDictionary['ACCESSION_NUMBER'];
for uids in studySeriesSopUIDsTuple:
studyUID = uids[0];
seriesUID = uids[1];
sopUID = uids[2];
destFile = destFolder + '/' + sopUID + '.' + patientID + '.dcm';
substitutionList = [];
substitutionList.append(['PatientsName', patientName]);
substitutionList.append(['PatientID', patientID]);
substitutionList.append(['AccessionNumber', accessionNumber]);
substitutionList.append(['StudyInstanceUID', studyUID]);
substitutionList.append(['SeriesInstanceUID', seriesUID]);
substitutionList.append(['SOPInstanceUID', sopUID]);
substitutionList.append(['MediaStorageSOPInstanceUID', sopUID]); # file meta
success = dcmReader.saveAs(destFile, substitutionList);
return success;
print('Getting Patient Diagnosis From %s' % (patients_csv))
for index, row in data.iterrows():
if row['cancer'] == 0:
patient_diagnosis[row['id']] = np.array([1,0])
else:
patient_diagnosis[row['id']] = np.array([0,1])
# Resample the images not found in the resampled directory.
# This will take some time.
for i in range(len(processPatientArray)):
patient_name = processPatientArray[i].split(file_split)[-1]
print('[%d/%d]\tPatient %s' % (i+1, len(processPatientArray), patient_name))
print('\tReading Slices...')
slices = DicomReader.readFromDir(processPatientArray[i])
print('\tConverting to hu...')
image = DicomReader.convertHounsfield(slices)
print('\tDownsizing...')
resampled_image = ImageMath.downsize(image, downsize_shape)
print('\tReshaping Slices...')
resampled_image = ImageMath.chunkify(resampled_image, slice_target=slice_count)
print('\tExtracting Lung Data...')
lungs = DicomReader.segmentLungMask(resampled_image, False)
print('\tNormalizing...')
lungs = ImageMath.normalize(lungs)
def _extractSopInstanceUID(self, dcmFileName):
if DicomReader().isValidDcmFile(dcmFileName):
dcm = DicomReader(dcmFileName);
return dcm.getSopInstanceUID();
def _extractSopInstanceUID(self, dcmFileName):
if DicomReader().isValidDcmFile(dcmFileName):
dcm = DicomReader(dcmFileName);
return dcm.getSopInstanceUID();
def __init__(self, path):
DicomReader(path).read()
class DicomWorker:
def __init__(self, path):
DicomReader(path).read()
if __name__ == "__main__":
ap = argparse.ArgumentParser(
description="",
formatter_class=argparse.ArgumentDefaultsHelpFormatter
)
#apg = ap.add_argument_group(title="Input Output")
#apg.add_argument("-i", "--input", help="Input 7 Segment Image", type=str, default="7SegInput.png")
#apg.add_argument("-o", "--output", help="Output 7 Segment Font", type=str, default="7SegOutput.bmp")
#apg.add_argument("-b", "--background", help="Background color", type=int, nargs=3, default=[3, 17, 34])
#apg.add_argument("-c", "--color", help="Segment color", type=int, nargs=3, default=[255, 255, 0])
#apg.add_argument("-r", "--rainbow", help="Segment color", action='store_true')
#apg.add_argument("-s", "--skewness", help="Italic factor", type=float, default=0)
#args = ap.parse_args(sys.argv[1:])
dw = DicomReader("/data/image/tcia/110/")
imageVtk = VtkImageHelper()
print(dw.getImageInformation())
test = imageVtk.createVtkMarchingCube(dw.getArrayDicom(), dw.getImageInformation())
writer = vtk.vtkXMLPolyDataWriter()
writer.SetFileName("/home/christoph/test.vtp")
writer.SetInputData(test)
writer.Write()
