def save(self, viewInteractor):
path = self.paths[viewInteractor]
parentDirectory, name = os.path.split(path)
interactors = viewInteractor.interactionWidget.interactors
header = str(dicom.read_file(os.path.join(path, sorted(os.listdir(
path))[viewInteractor.volumeView.currentSlice])))
# get data from inputs
contrast = interactors[0].itemText(interactors[0].currentIndex())
orientation = interactors[1].itemText(interactors[1].currentIndex())
enhanced = interactors[2].isChecked()
poorQuality = interactors[3].isChecked()
review = interactors[4].isChecked()
derived = interactors[5].isChecked()
if derived:
derivedType = interactors[6].itemText(
interactors[6].currentIndex())
else:
derivedType = ""
comment = interactors[7].text()
# get data from header
seriesNumber = dcm.findSeriesNumber(header)
sequence = ' '.join(dcm.findSequence(header))
vendor = dcm.findVendor(header)
fieldStrength = dcm.findFieldStrength(header)
echoTime, inversionTime, repetitionTime = dcm.findTimeParameters(
header)
# get data from folder structure
directoryStem, date = os.path.split(self.workingDirectory)
_, identifier = os.path.split(directoryStem)
centerID, patientID = map(int, identifier.split('_'))
# save and rename
info = [str(seriesNumber), contrast, orientation]
uniqueIdentifier = '_'.join(map(str, [centerID, patientID, date,
seriesNumber]))
if enhanced:
info.insert(2, "CE")
if derived:
info.append(derivedType)
newName = '_'.join(info)
if newName == name:
if self.database is not None:
self.databaseCursor.execute(
'INSERT OR REPLACE INTO Series VALUES\
(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)',
(centerID, patientID, date, seriesNumber, contrast,
enhanced, orientation, sequence, derived, derivedType,
vendor, fieldStrength, echoTime, inversionTime,
repetitionTime, poorQuality, review, comment,
uniqueIdentifier))
self.database.commit()
return
newPath = os.path.join(parentDirectory, newName)
if os.path.exists(newPath):
review = True
if self.database is not None:
self.databaseCursor.execute(
'INSERT OR REPLACE INTO Series VALUES\
(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)',
(centerID, patientID, date, seriesNumber, contrast,
enhanced, orientation, sequence, derived, derivedType,
vendor, fieldStrength, echoTime, inversionTime,
repetitionTime, poorQuality, review, comment,
uniqueIdentifier))
self.database.commit()
return
else:
os.rename(path, newPath)
self.paths[viewInteractor] = newPath
if self.database is not None:
self.databaseCursor.execute(
'INSERT INTO Series VALUES\
(?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?,?)',
(centerID, patientID, date, seriesNumber, contrast,
enhanced, orientation, sequence, derived, derivedType,
vendor, fieldStrength, echoTime, inversionTime,
repetitionTime, poorQuality, review, comment,
uniqueIdentifier))
self.database.commit()
def setWorkingDirectory(self, workingDirectory):
self.workingDirectory = os.path.abspath(workingDirectory)
self.setWindowTitle(self.workingDirectory)
self.multiView.removeAllViews()
# working directory needs to contain DICOM folders
for dataset in os.listdir(self.workingDirectory):
datasetPath = os.path.join(self.workingDirectory, dataset)
if len(os.listdir(datasetPath)) < 200:
viewInteractor = view.VolumeViewInteraction(
data=dcm.volumeFromDCMDirectory(datasetPath),
interactionRows=2)
else:
viewInteractor = view.VolumeViewInteraction(
data=dcm.LazyDCMVolume(datasetPath),
interactionRows=2)
# get header
sliceNumber = viewInteractor.volumeView.currentSlice
path = os.path.join(datasetPath,
sorted(os.listdir(datasetPath))[sliceNumber])
header = str(dicom.read_file(path))
# set label
searches = ["Series Description", "Sequence Name", "Protocol Name"]
leftLabel = dcm.valueFromSearch(searches, header, True)
for search in searches:
if search in leftLabel.keys():
if leftLabel[search] != '':
leftLabel = leftLabel[search]
break
else:
leftLabel = ''
viewInteractor.interactionWidget.setLeftLabel(leftLabel)
# contrast combo box
contrast = dcm.findContrast(header)
sequence = dcm.findSequence(header)
if contrast == "T2" and "FLAIR" in sequence:
contrast = "FLAIR"
viewInteractor.interactionWidget.addComboBox(
sorted(dcm.allContrasts.keys() + ["UNKNOWN"]), contrast)
# orientation combo box
orientation = dcm.findOrientation(header)
if orientation == "UNKNOWN":
orientation = "ax"
viewInteractor.interactionWidget.addComboBox(
sorted(dcm.allOrientations))
# contrast agent checkbox
enhanced = dcm.isContrastEnhanced(header)
viewInteractor.interactionWidget.addCheckBox("CE", "left",
enhanced, 1)
# quality checkbox
viewInteractor.interactionWidget.addCheckBox("LQ", "left")
# review checkbox
viewInteractor.interactionWidget.addCheckBox("RVW", "left")
# derived checkbox
isDerived = dcm.isDerived(header)
viewInteractor.interactionWidget.addCheckBox("DRV", "left",
isDerived[0], 1)
viewInteractor.interactionWidget.interactors[-1].stateChanged.\
connect(self.onDerivedCheckBoxChanged)
# view header button
viewInteractor.interactionWidget.addButton("Header")
viewInteractor.interactionWidget.buttons[-1].clicked.connect(
self.onHeaderButtonClicked)
# save button
viewInteractor.interactionWidget.addButton("Save", 1)
viewInteractor.interactionWidget.buttons[-1].clicked.connect(
self.onSaveButtonClicked)
# derivatives combobox
derivativeOptions = []
for key in dcm.allDerivatives.keys():
derivativeOptions += dcm.allDerivatives[key]
default = 0
if contrast in isDerived[1].keys():
if len(isDerived[1][contrast]) == 1:
default = isDerived[1][contrast][0]
elif "other" in isDerived[1].keys():
if len(isDerived[1]["other"]) == 1:
default = isDerived[1]["other"][0]
viewInteractor.interactionWidget.addComboBox(derivativeOptions,
default, 1)
if isDerived[0]:
viewInteractor.interactionWidget.interactors[-1].show()
else:
viewInteractor.interactionWidget.interactors[-1].hide()
# comment line edit
viewInteractor.interactionWidget.addLineEdit(row=1)
# add view
self.paths[viewInteractor] = datasetPath
self.multiView.addView(viewInteractor)