def convertData(self, plugin, loadable):
node = plugin.load(loadable)
dcmFile = loadable.files[0]
seriesNumber = self.dicomDatabase.fileValue(dcmFile, "0020,0011")
patientID = self.dicomDatabase.fileValue(dcmFile, "0010,0020")
studyDate = self.dicomDatabase.fileValue(dcmFile, "0008,0020")
studyTime = self.dicomDatabase.fileValue(dcmFile, "0008,0030")[0:4]
if node:
storageNode = node.CreateDefaultStorageNode()
studyID = '{}_{}_{}'.format(patientID, studyDate, studyTime)
dirName = os.path.join(self.outputDir, studyID, "RESOURCES",
seriesNumber, "Reconstructions")
xmlName = os.path.join(dirName, seriesNumber + '.xml')
try:
os.makedirs(dirName)
except:
pass
DICOMLib.DICOMCommand("dcm2xml", [dcmFile, xmlName]).start()
nrrdName = os.path.join(dirName, seriesNumber + ".nrrd")
# print(nrrdName)
storageNode.SetFileName(nrrdName)
storageNode.WriteData(node)
if self.copyDICOM:
fileCount = 0
dirName = os.path.join(self.outputDir, studyID, "RESOURCES",
seriesNumber, "DICOM")
try:
os.makedirs(dirName)
except:
pass
for dcm in loadable.files:
shutil.copy(dcm,
os.path.join(dirName, "%06d.dcm" % fileCount))
fileCount = fileCount + 1
else:
print('No node!')
def createDICOMFileForScene(self):
"""
Export the scene data:
- first to a directory using the utility in the mrmlScene
- create a zip file using the application logic
- create secondary capture based on the sample dataset
- add the zip file as a private creator tag
TODO: confirm that resulting file is valid - may need to change the CLI
to include more parameters or do a new implementation ctk/DCMTK
See:
http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Writing_DICOM
"""
# set up temp directories and files
self.dicomDirectory = tempfile.mkdtemp('', 'dicomExport', slicer.app.temporaryPath)
self.sceneDirectory = os.path.join(self.dicomDirectory,'scene')
os.mkdir(self.sceneDirectory) # known to be unique
self.imageFile = os.path.join(self.dicomDirectory, "scene.jpg")
self.zipFile = os.path.join(self.dicomDirectory, "scene.zip")
self.dumpFile = os.path.join(self.dicomDirectory, "dicom.dump")
self.sdbFile = os.path.join(self.dicomDirectory, "SlicerDataBundle.dcm")
# Clean up paths on Windows (some commands and operations are not performed properly with mixed slash and backslash)
self.dicomDirectory = self.dicomDirectory.replace('\\','/')
self.sceneDirectory = self.sceneDirectory.replace('\\','/') # otherwise invalid zip file is created on Windows (with the same size strangely)
self.imageFile = self.imageFile.replace('\\','/')
self.zipFile = self.zipFile.replace('\\','/')
self.dumpFile = self.dumpFile.replace('\\','/')
self.sdbFile = self.sdbFile.replace('\\','/')
# get the screen image
self.progress('Saving Image...')
image = ctk.ctkWidgetsUtils.grabWidget(slicer.util.mainWindow())
image.save(self.imageFile)
imageReader = vtk.vtkJPEGReader()
imageReader.SetFileName(self.imageFile)
imageReader.Update()
#add storage node for each storable node in the scene, add file name if file name doesn't exist
# TODO: this could be moved to appLogic.SaveSceneToSlicerDataBundleDirectory
lnodes = slicer.mrmlScene.GetNodesByClass("vtkMRMLLinearTransformNode")
lnodes.UnRegister(slicer.mrmlScene)
lnum = lnodes.GetNumberOfItems()
for itemNum in range(lnum):
print(itemNum)
node = lnodes.GetItemAsObject(itemNum)
snode = node.GetStorageNode()
if snode is None:
print("something is none")
snode = node.CreateDefaultStorageNode()
slicer.mrmlScene.AddNode(snode)
node.SetAndObserveStorageNodeID(snode.GetID())
if snode.GetFileName() is None:
snode.SetFileName(node.GetID()+".h5")
# save the scene to the temp dir
self.progress('Saving Scene...')
appLogic = slicer.app.applicationLogic()
appLogic.SaveSceneToSlicerDataBundleDirectory(self.sceneDirectory, imageReader.GetOutput())
# make the zip file
self.progress('Making zip...')
appLogic.Zip(self.zipFile, self.sceneDirectory)
zipSize = os.path.getsize(self.zipFile)
# now create the dicom file
# - create the dump (capture stdout)
# cmd = "dcmdump --print-all --write-pixel %s %s" % (self.dicomDirectory, self.referenceFile)
self.progress('Making dicom reference file...')
if not self.referenceFile:
# set reference file the first file found in the DICOM database
self.getFirstFileInDatabase()
# if there is still no reference file, then there are no files in the database, cannot continue
if not self.referenceFile:
logging.error('No reference file! DICOM database is empty')
return False
args = ['--print-all', '--write-pixel', self.dicomDirectory, self.referenceFile]
dump = DICOMLib.DICOMCommand('dcmdump', args).start()
# append this to the dumped output and save the result as self.dicomDirectory/dcm.dump
# with %s as self.zipFile and %d being its size in bytes
zipSizeString = "%d" % zipSize
# hack: encode the file zip file size as part of the creator string
# because none of the normal types (UL, DS, LO) seem to survive
# the dump2dcm step (possibly due to the Unknown nature of the private tag)
creatorString = "3D Slicer %s" % zipSizeString
candygram = """(cadb,0010) LO [%s] # %d, 1 PrivateCreator
(cadb,1008) LO [%s] # 4, 1 Unknown Tag & Data
(cadb,1010) OB =%s # %d, 1 Unknown Tag & Data
""" % (creatorString, len(creatorString), zipSizeString, self.zipFile, zipSize)
dump = str(dump) + candygram
logging.debug('dumping to: %s/dump.dcm' % self.dicomDirectory, 'w')
fp = open('%s/dump.dcm' % self.dicomDirectory, 'w')
fp.write(dump)
fp.close()
self.progress('Encapsulating Scene in DICOM Dump...')
args = [
'%s/dump.dcm' % self.dicomDirectory,
'%s/template.dcm' % self.dicomDirectory,
'--generate-new-uids', '--overwrite-uids', '--ignore-errors']
DICOMLib.DICOMCommand('dump2dcm', args).start()
# now create the Secondary Capture data set
# cmd = "img2dcm -k 'InstanceNumber=1' -k 'SeriesDescription=Slicer Data Bundle' -df %s/template.dcm %s %s" % (self.dicomDirectory, self.imageFile, self.sdbFile)
args = [
'-k', 'InstanceNumber=1',
'-k', 'StudyDescription=Slicer Scene Export',
'-k', 'SeriesDescription=Slicer Data Bundle',
'--dataset-from', '%s/template.dcm' % self.dicomDirectory,
self.imageFile, self.sdbFile]
self.progress('Creating DICOM Binary File...')
DICOMLib.DICOMCommand('img2dcm', args).start()
self.progress('Done')
return True
def createDICOMFileForScene(self, parameters):
"""
Export the scene data:
- first to a directory using the utility in the mrmlScene
- create a zip file using the application logic
- create secondary capture based on the sample dataset
- add the zip file as a private creator tag
TODO: confirm that resulting file is valid - may need to change the CLI
to include more parameters or do a new implementation ctk/DCMTK
See:
http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Writing_DICOM
"""
# set up temp directories and files
self.dicomDirectory = tempfile.mkdtemp('', 'dicomExport',
slicer.app.temporaryPath)
self.sceneDirectory = os.path.join(self.dicomDirectory, 'scene')
os.mkdir(self.sceneDirectory) # known to be unique
self.imageFile = os.path.join(self.dicomDirectory, "scene.jpg")
self.zipFile = os.path.join(self.dicomDirectory, "scene.zip")
self.dumpFile = os.path.join(self.dicomDirectory, "dicom.dump")
self.sdbFile = os.path.join(self.dicomDirectory,
"SlicerDataBundle.dcm")
# get the screen image
self.progress('Saving Image...')
pixmap = qt.QPixmap.grabWidget(slicer.util.mainWindow())
pixmap.save(self.imageFile)
imageReader = vtk.vtkJPEGReader()
imageReader.SetFileName(self.imageFile)
imageReader.Update()
# save the scene to the temp dir
self.progress('Saving Scene...')
appLogic = slicer.app.applicationLogic()
appLogic.SaveSceneToSlicerDataBundleDirectory(self.sceneDirectory,
imageReader.GetOutput())
# make the zip file
self.progress('Making zip...')
appLogic.Zip(self.zipFile, self.sceneDirectory)
zipSize = os.path.getsize(self.zipFile)
# now create the dicom file
# - create the dump (capture stdout)
# cmd = "dcmdump --print-all --write-pixel %s %s" % (self.dicomDirectory, self.referenceFile)
self.progress('Making dicom reference file...')
if not self.referenceFile:
self.parametersFromStudy()
args = [
'--print-all', '--write-pixel', self.dicomDirectory,
self.referenceFile
]
dump = DICOMLib.DICOMCommand('dcmdump', args).start()
# append this to the dumped output and save the result as self.dicomDirectory/dcm.dump
# with %s as self.zipFile and %d being its size in bytes
zipSizeString = "%d" % zipSize
candygram = """(cadb,0010) LO [3D Slicer Lollipop] # %d, 1 PrivateCreator
(cadb,1008) UL [%s] # 4, 1 Unknown Tag & Data
(cadb,1010) OB =%s # %d, 1 Unknown Tag & Data
""" % (len('3D Slicer Lollipop'), zipSizeString, self.zipFile, zipSize)
dump = dump + candygram
fp = open('%s/dump.dcm' % self.dicomDirectory, 'w')
fp.write(dump)
fp.close()
self.progress('Encapsulating Scene in DICOM Dump...')
args = [
'%s/dump.dcm' % self.dicomDirectory,
'%s/template.dcm' % self.dicomDirectory, '--generate-new-uids',
'--overwrite-uids', '--ignore-errors'
]
DICOMLib.DICOMCommand('dump2dcm', args).start()
# now create the Secondary Capture data set
# cmd = "img2dcm -k 'InstanceNumber=1' -k 'SeriesDescription=Slicer Data Bundle' -df %s/template.dcm %s %s" % (self.dicomDirectory, self.imageFile, self.sdbFile)
args = [
'-k', 'InstanceNumber=1', '-k',
'StudyDescription=Slicer Scene Export', '-k',
'SeriesDescription=Slicer Data Bundle', '--dataset-from',
'%s/template.dcm' % self.dicomDirectory, self.imageFile,
self.sdbFile
]
self.progress('Creating DICOM Binary File...')
DICOMLib.DICOMCommand('img2dcm', args).start()
self.progress('Done')
return True
import DICOMLib, sys, slicer, os
dcmfile = sys.argv[1]
dcmdump = DICOMLib.DICOMCommand('dcmdump', [dcmfile])
dump = str(dcmdump.start()).replace("\\r", "\r").replace("\\n",
"\n").splitlines()
found_private_tag = False
for line in dump:
line = line.split(' ')
if line[0] == '(2001,1003)':
if line[-1] == "DiffusionBFactor":
found_private_tag = True
break
if not found_private_tag:
raise Exception("Could not find 'DiffusionBFactor' "
"private tag reading file '%s' using 'dcmdump' !" %
dcmfile)
def createDICOMFileForScene(self):
"""
Export the scene data:
- first to a directory using the utility in the mrmlScene
- create a zip file using the application logic
- create secondary capture based on the sample dataset
- add the zip file as a private creator tag
TODO: confirm that resulting file is valid - may need to change the CLI
to include more parameters or do a new implementation ctk/DCMTK
See:
http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Writing_DICOM
"""
# set up temp directories and files
if self.saveDirectoryPath is None:
self.saveDirectoryPath = tempfile.mkdtemp('', 'dicomExport',
slicer.app.temporaryPath)
self.zipFile = os.path.join(self.saveDirectoryPath, "scene.zip")
self.dumpFile = os.path.join(self.saveDirectoryPath, "dump.dcm")
self.templateFile = os.path.join(self.saveDirectoryPath,
"template.dcm")
self.sdbFile = os.path.join(self.saveDirectoryPath,
"SlicerDataBundle.dcm")
if self.studyDescription is None:
self.studyDescription = 'Slicer Scene Export'
if self.seriesDescription is None:
self.seriesDescription = 'Slicer Data Bundle'
# get the screen image if not specified
if self.imageFile is None:
self.progress('Saving Image...')
self.imageFile = os.path.join(self.saveDirectoryPath, "scene.jpg")
image = ctk.ctkWidgetsUtils.grabWidget(slicer.util.mainWindow())
image.save(self.imageFile)
imageReader = vtk.vtkJPEGReader()
imageReader.SetFileName(self.imageFile)
imageReader.Update()
# Clean up paths on Windows (some commands and operations are not performed properly with mixed slash and backslash)
self.saveDirectoryPath = self.saveDirectoryPath.replace('\\', '/')
self.imageFile = self.imageFile.replace('\\', '/')
self.zipFile = self.zipFile.replace('\\', '/')
self.dumpFile = self.dumpFile.replace('\\', '/')
self.templateFile = self.templateFile.replace('\\', '/')
self.sdbFile = self.sdbFile.replace('\\', '/')
# save the scene to the temp dir
self.progress('Saving scene into MRB...')
if not slicer.mrmlScene.WriteToMRB(self.zipFile,
imageReader.GetOutput()):
logging.error('Failed to save scene into MRB file: ' +
self.zipFile)
return False
zipSize = os.path.getsize(self.zipFile)
# now create the dicom file
# - create the dump (capture stdout)
# cmd = "dcmdump --print-all --write-pixel %s %s" % (self.saveDirectoryPath, self.referenceFile)
self.progress('Making dicom reference file...')
logging.info('Using reference file ' + str(self.referenceFile))
args = [
'--print-all', '--write-pixel', self.saveDirectoryPath,
self.referenceFile
]
dumpByteArray = DICOMLib.DICOMCommand('dcmdump', args).start()
dump = str(dumpByteArray.data(), encoding='utf-8')
# append this to the dumped output and save the result as self.saveDirectoryPath/dcm.dump
# with %s as self.zipFile and %d being its size in bytes
zipSizeString = "%d" % zipSize
# hack: encode the file zip file size as part of the creator string
# because none of the normal types (UL, DS, LO) seem to survive
# the dump2dcm step (possibly due to the Unknown nature of the private tag)
creatorString = "3D Slicer %s" % zipSizeString
candygram = """(cadb,0010) LO [%s] # %d, 1 PrivateCreator
(cadb,1008) LO [%s] # 4, 1 Unknown Tag & Data
(cadb,1010) OB =%s # %d, 1 Unknown Tag & Data
""" % (creatorString, len(creatorString), zipSizeString, self.zipFile, zipSize)
dump = dump + candygram
logging.debug('dumping to: %s' % self.dumpFile)
fp = open(self.dumpFile, 'w')
fp.write(dump)
fp.close()
self.progress('Encapsulating scene in DICOM dump...')
args = [
self.dumpFile, self.templateFile, '--generate-new-uids',
'--overwrite-uids', '--ignore-errors'
]
DICOMLib.DICOMCommand('dump2dcm', args).start()
# now create the Secondary Capture data set
# cmd = "img2dcm -k 'InstanceNumber=1' -k 'SeriesDescription=Slicer Data Bundle' -df %s/template.dcm %s %s" % (self.saveDirectoryPath, self.imageFile, self.sdbFile)
args = [
'-k', 'InstanceNumber=1', '-k',
'StudyDescription=%s' % str(self.studyDescription), '-k',
'SeriesDescription=%s' % str(self.seriesDescription),
'--dataset-from', self.templateFile, self.imageFile, self.sdbFile
]
argIndex = 6
for key, value in self.optionalTags.items():
args.insert(argIndex, '-k')
tagNameValue = f'{str(key)}={str(value)}'
args.insert(argIndex + 1, tagNameValue)
argIndex += 2
self.progress('Creating DICOM binary file...')
DICOMLib.DICOMCommand('img2dcm', args).start()
self.progress('Deleting temporary files...')
os.remove(self.zipFile)
os.remove(self.dumpFile)
os.remove(self.templateFile)
self.progress('Done')
return True
def createDICOMFileForScene(self, parameters):
"""
Export the scene data:
- first to a directory using the utility in the mrmlScene
- create a zip file using python utility
- create secondary capture based on the sample dataset
- add the zip file as a private creator tag
TODO: confirm that resulting file is valid - may need to change the CLI
to include more parameters or do a new implementation ctk/DCMTK
See:
http://sourceforge.net/apps/mediawiki/gdcm/index.php?title=Writing_DICOM
"""
# set up temp directories and files
self.dicomDirectory = tempfile.mkdtemp('', 'dicomExport', slicer.app.temporaryPath)
self.sceneDirectory = os.path.join(self.dicomDirectory,'scene')
os.mkdir(self.sceneDirectory) # known to be unique
self.imageFile = os.path.join(self.dicomDirectory, "scene.jpg")
self.zipFile = os.path.join(self.dicomDirectory, "scene.zip")
self.dumpFile = os.path.join(self.dicomDirectory, "dicom.dump")
self.sdbFile = os.path.join(self.dicomDirectory, "SlicerDataBundle.dcm")
# get the screen image
pixmap = qt.QPixmap.grabWidget(slicer.util.mainWindow())
pixmap.save(self.imageFile)
imageReader = vtk.vtkJPEGReader()
imageReader.SetFileName(self.imageFile)
imageReader.Update()
# save the scene to the temp dir
appLogic = slicer.app.applicationLogic()
appLogic.SaveSceneToSlicerDataBundleDirectory(self.sceneDirectory, imageReader.GetOutput())
# make the zip file
zip = zipfile.ZipFile( self.zipFile, "w", zipfile.ZIP_DEFLATED )
start = len(self.sceneDirectory) + 1
for root, subdirs, files in os.walk(self.sceneDirectory):
for f in files:
filePath = os.path.join(root,f)
archiveName = filePath[start:]
zip.write(filePath, archiveName)
zip.close()
zipSize = os.path.getsize(self.zipFile)
# now create the dicom file
# - create the dump (capture stdout)
# cmd = "dcmdump --print-all --write-pixel %s %s" % (self.dicomDirectory, self.referenceFile)
if not self.referenceFile:
self.parametersFromStudy()
args = ['--print-all', '--write-pixel', self.dicomDirectory, self.referenceFile]
dump = DICOMLib.DICOMCommand('dcmdump', args).start()
# append this to the dumped output and save the result as self.dicomDirectory/dcm.dump
#with %s as self.zipFile and %d being its size in bytes
candygram = """(cadb,0010) LO [3D Slicer Candygram] # 20, 1 PrivateCreator
(cadb,1008) OB =%s # %d, 1 Unknown Tag & Data
""" % (self.zipFile, zipSize)
dump = dump + candygram
fp = open('%s/dump.dcm' % self.dicomDirectory, 'w')
fp.write(dump)
fp.close()
# cmd = "dump2dcm %s/dump.dcm %s/template.dcm" % (self.dicomDirectory, self.dicomDirectory)
args = ['%s/dump.dcm' % self.dicomDirectory, '%s/template.dcm' % self.dicomDirectory]
DICOMLib.DICOMCommand('dump2dcm', args).start()
# now create the SC data set
# cmd = "img2dcm -k 'InstanceNumber=1' -k 'SeriesDescription=Slicer Data Bundle' -df %s/template.dcm %s %s" % (self.dicomDirectory, self.imageFile, self.sdbFile)
args = ['-k', 'InstanceNumber=1', '-k', 'SeriesDescription=Slicer Data Bundle',
'-df', '%s/template.dcm' % self.dicomDirectory,
self.imageFile, self.sdbFile]
DICOMLib.DICOMCommand('img2dcm', args).start()