def __init__(self,
parent,
name=None,
appname="the application",
filename='preferences.txt'):
# Load the XRC file for our gui resources
res = XmlResource(util.GetResourcePath('preferences.xrc'))
self.dlgPreferences = res.LoadDialog(None, "PreferencesDialog")
self.dlgPreferences.Init(name, appname)
# Setup internal pubsub methods
pub.subscribe(self.SetPreferenceTemplate,
'preferences.updated.template')
pub.subscribe(self.SavePreferenceValues, 'preferences.updated.values')
# Setup user pubsub methods
pub.subscribe(self.GetPreferenceValue, 'preferences.requested.value')
pub.subscribe(self.GetPreferenceValues, 'preferences.requested.values')
pub.subscribe(self.SetPreferenceValue, 'preferences.updated.value')
# Initialize variables
self.preftemplate = []
self.values = {}
self.filename = os.path.join(guiutil.get_data_dir(), filename)
self.LoadPreferenceValues()
def __init__(self, parent):
self.parent = parent
# Set up pubsub
pub.subscribe(self.OnUpdatePatient, 'patient.updated.raw_data')
# Load the XRC file for our gui resources
self.res = XmlResource(util.GetBasePluginsPath('anonymize.xrc'))
def pluginLoader(parent):
"""Function to load the plugin."""
# Load the XRC file for our gui resources
res = XmlResource(util.GetBasePluginsPath('treeview.xrc'))
panelTreeView = res.LoadPanel(parent, 'pluginTreeView')
panelTreeView.Init(res)
return panelTreeView
def get_progress_dialog(parent, title="Loading..."):
"""Function to load the progress dialog."""
# Load the XRC file for our gui resources
res = XmlResource(util.GetResourcePath('guiutil.xrc'))
dialogProgress = res.LoadDialog(parent, 'ProgressDialog')
dialogProgress.Init(res, title)
return dialogProgress
def pluginLoader(parent):
"""Function to load the plugin."""
# Load the XRC file for our gui resources
res = XmlResource(util.GetBasePluginsPath("dvh.xrc"))
panelDVH = res.LoadPanel(parent, "pluginDVH")
panelDVH.Init(res)
return panelDVH
def __init__(self, parent):
self.parent = parent
# Set up pubsub
pub.subscribe(self.OnUpdatePatient, 'patient.updated.parsed_data')
# Load the XRC file for our gui resources
xrc = os.path.join(os.path.dirname(__file__), 'Analysis.xrc')
self.res = XmlResource(xrc)
def PluginManager(parent, plugins, pluginsDisabled):
"""Prepare to show the plugin manager dialog."""
# Load the XRC file for our gui resources
res = XmlResource(util.GetResourcePath('plugin.xrc'))
dlgPluginManager = res.LoadDialog(parent, "PluginManagerDialog")
dlgPluginManager.Init(plugins, pluginsDisabled)
# Show the dialog
dlgPluginManager.ShowModal()
class plugin:
"""Analyzes DVH."""
def __init__(self, parent):
self.parent = parent
# Set up pubsub
pub.subscribe(self.OnUpdatePatient, 'patient.updated.parsed_data')
# Load the XRC file for our gui resources
xrc = os.path.join(os.path.dirname(__file__), 'Analysis.xrc')
self.res = XmlResource(xrc)
def OnUpdatePatient(self, msg):
"""Update and load the patient data."""
self.data = msg.data
def pluginMenu(self, evt):
"""Method called after the panel has been initialized."""
panelAnalysis = self.res.LoadDialog(self.parent, "AnalysisPanel")
panelAnalysis.SetTitle("TG-101 Stereotactic Plan Analysis")
panelAnalysis.Init(self.data['structures'], self.data['dvhs'])
panelAnalysis.ShowModal()
return panelAnalysis
def OnDestroy(self, evt):
"""Unbind to all events before the plugin is destroyed."""
pub.unsubscribe(self.OnUpdatePatient)
class plugin:
def __init__(self, parent):
self.parent = parent
# Set up pubsub
pub.subscribe(self.OnUpdatePatient, 'patient.updated.raw_data')
# Load the XRC file for our gui resources
xrc = os.path.join(os.path.dirname(__file__), 'scaledose.xrc')
self.res = XmlResource(xrc)
def OnUpdatePatient(self, msg):
"""Update and load the patient data."""
self.data = msg.data
def pluginMenu(self, evt):
"""Scale DICOM RT dose data."""
dlgScaleDose = self.res.LoadDialog(self.parent, "ScaleDoseDialog")
dlgScaleDose.Init(self.data['rxdose'])
if dlgScaleDose.ShowModal() == wx.ID_OK:
oldRxDose = dlgScaleDose.oldRxDose
newRxDose = dlgScaleDose.newRxDose
# Initialize and start the scale dose thread
self.t = threading.Thread(target=self.ScaleDoseDataThread,
args=(self.data, oldRxDose, newRxDose,
self.UpdateData))
self.t.start()
else:
pass
dlgScaleDose.Destroy()
return
def ScaleDoseDataThread(self, data, oldRxDose, newRxDose, finishedFunc):
"""Scale the DICOM RT dose data."""
dosescale = float(newRxDose) / float(oldRxDose)
# Scale the Rx dose
data['rxdose'] = int(data['rxdose'] * dosescale)
rtdose = data['rtdose']
# Scale the Dose grid data
rtdose.DoseGridScaling = rtdose.DoseGridScaling * dosescale
# Scale the DVH data
if "DVHs" in rtdose:
for item in rtdose.DVHs:
item.DVHDoseScaling = item.DVHDoseScaling * dosescale
wx.CallAfter(finishedFunc, data)
def UpdateData(
self,
data,
):
"""Publish the updated patient data."""
pub.sendMessage('patient.updated.raw_data', data)
class plugin:
"""Calculates conformality of an isodose line to a structure."""
def __init__(self, parent):
self.parent = parent
# Set up pubsub
pub.subscribe(self.OnUpdatePatient, 'patient.updated.parsed_data')
# Load the XRC file for our gui resources
xrc = os.path.join(os.path.dirname(__file__), 'Conformality.xrc')
self.res = XmlResource(xrc)
def OnUpdatePatient(self, msg):
"""Update and load the patient data."""
self.data = msg.data
def pluginMenu(self, evt):
"""Method called after the panel has been initialized."""
panelConformality = self.res.LoadDialog(self.parent,
"ConformalityPanel")
panelConformality.SetTitle("SRS Conformality")
panelConformality.Init(self.data['structures'], self.data['dose'],
self.data['plan'], self.data['dvhs'])
panelConformality.ShowModal()
return panelConformality
def ImportDicom(parent):
"""Prepare to show the dialog that will Import DICOM and DICOM RT files."""
# Load the XRC file for our gui resources
res = XmlResource(util.GetResourcePath('dicomgui.xrc'))
dlgDicomImporter = res.LoadDialog(parent, "DicomImporterDialog")
dlgDicomImporter.Init(res)
# Show the dialog and return the result
if (dlgDicomImporter.ShowModal() == wx.ID_OK):
value = dlgDicomImporter.GetPatient()
#pub.sendMessage('patient.updated.raw_data', value)
else:
value = {}
# Block until the thread is done before destroying the dialog
if dlgDicomImporter:
dlgDicomImporter.t.join()
dlgDicomImporter.Destroy()
return value
def OnInit(self):
# no-op in wxPython2.8 and later: wx.InitAllImageHandlers()
wx.GetApp().SetAppName("dicompyler")
# Load the XRC file for our gui resources
self.res = XmlResource(util.GetResourcePath('main.xrc'))
# Use the native listctrl on Mac OS X
if guiutil.IsMac():
wx.SystemOptions.SetOptionInt("mac.listctrl.always_use_generic", 0)
dicompylerFrame = MainFrame(None, -1, "dicompyler", self.res)
self.SetTopWindow(dicompylerFrame)
dicompylerFrame.Show()
return 1
def open(self, sum):
"""
Start progress handler, set the number of steps, the operation will
take in sum. Will be called once before update()
is called several times
"""
if self.progDlg is None:
res = XmlResource.Get()
self.progDlg = res.LoadDialog(self.parent, "ProgressDialog")
self.progDlg.ctrls = XrcControls(self.progDlg)
self.progDlg.SetTitle(self.title)
self.currYieldStep = 1
self.progDlg.ctrls.text.SetLabel(self.msg)
self.progDlg.ctrls.gauge.SetRange(sum + self.addsteps)
self.progDlg.ctrls.gauge.SetValue(0)
self.progDlg.Show()
class plugin:
def __init__(self, parent):
self.parent = parent
# Set up pubsub
pub.subscribe(self.OnUpdatePatient, 'patient.updated.raw_data')
# Load the XRC file for our gui resources
self.res = XmlResource(util.GetBasePluginsPath('anonymize.xrc'))
def OnUpdatePatient(self, msg):
"""Update and load the patient data."""
self.data = msg.data
def pluginMenu(self, evt):
"""Anonymize DICOM / DICOM RT data."""
dlgAnonymize = self.res.LoadDialog(self.parent, "AnonymizeDialog")
dlgAnonymize.Init()
if dlgAnonymize.ShowModal() == wx.ID_OK:
path = dlgAnonymize.path
name = str(dlgAnonymize.name)
patientid = str(dlgAnonymize.patientid)
privatetags = dlgAnonymize.privatetags
# If the path doesn't exist, create it
if not os.path.exists(path):
os.mkdir(path)
# Initialize the progress dialog
dlgProgress = guiutil.get_progress_dialog(
wx.GetApp().GetTopWindow(), "Anonymizing DICOM data...")
# Initialize and start the anonymization thread
self.t = threading.Thread(target=self.AnonymizeDataThread,
args=(self.data, path, name, patientid,
privatetags,
dlgProgress.OnUpdateProgress))
self.t.start()
# Show the progress dialog
dlgProgress.ShowModal()
dlgProgress.Destroy()
else:
pass
dlgAnonymize.Destroy()
return
def AnonymizeDataThread(self, data, path, name, patientid, privatetags,
progressFunc):
"""Anonmyize and save each DICOM / DICOM RT file."""
length = 0
for key in ['rtss', 'rtplan', 'rtdose']:
if data.has_key(key):
length = length + 1
if data.has_key('images'):
length = length + len(data['images'])
i = 1
if data.has_key('rtss'):
rtss = data['rtss']
wx.CallAfter(progressFunc, i, length,
'Anonymizing file ' + str(i) + ' of ' + str(length))
self.updateCommonElements(rtss, name, patientid, privatetags)
self.updateElement(rtss, 'SeriesDescription', 'RT Structure Set')
self.updateElement(rtss, 'StructureSetDate', '19010101')
self.updateElement(rtss, 'StructureSetTime', '000000')
if rtss.has_key('RTROIObservations'):
for item in rtss.RTROIObservations:
self.updateElement(item, 'ROIInterpreter', 'anonymous')
rtss.save_as(os.path.join(path, 'rtss.dcm'))
i = i + 1
if data.has_key('rtplan'):
rtplan = data['rtplan']
wx.CallAfter(progressFunc, i, length,
'Anonymizing file ' + str(i) + ' of ' + str(length))
self.updateCommonElements(rtplan, name, patientid, privatetags)
self.updateElement(rtplan, 'SeriesDescription', 'RT Plan')
self.updateElement(rtplan, 'RTPlanName', 'plan')
self.updateElement(rtplan, 'RTPlanDate', '19010101')
self.updateElement(rtplan, 'RTPlanTime', '000000')
if rtplan.has_key('ToleranceTables'):
for item in rtplan.ToleranceTables:
self.updateElement(item, 'ToleranceTableLabel',
'tolerance')
if rtplan.has_key('Beams'):
for item in rtplan.Beams:
self.updateElement(item, 'Manufacturer', 'manufacturer')
self.updateElement(item, 'InstitutionName', 'institution')
self.updateElement(item, 'InstitutionAddress', 'address')
self.updateElement(item, 'InstitutionalDepartmentName',
'department')
self.updateElement(item, 'ManufacturersModelName', 'model')
self.updateElement(item, 'TreatmentMachineName',
'txmachine')
if rtplan.has_key('TreatmentMachines'):
for item in rtplan.TreatmentMachines:
self.updateElement(item, 'Manufacturer', 'manufacturer')
self.updateElement(item, 'InstitutionName', 'vendor')
self.updateElement(item, 'InstitutionAddress', 'address')
self.updateElement(item, 'InstitutionalDepartmentName',
'department')
self.updateElement(item, 'ManufacturersModelName', 'model')
self.updateElement(item, 'DeviceSerialNumber', '0')
self.updateElement(item, 'TreatmentMachineName',
'txmachine')
if rtplan.has_key('Sources'):
for item in rtplan.Sources:
self.updateElement(item, 'SourceManufacturer',
'manufacturer')
self.updateElement(item, 'SourceIsotopeName', 'isotope')
rtplan.save_as(os.path.join(path, 'rtplan.dcm'))
i = i + 1
if data.has_key('rtdose'):
rtdose = data['rtdose']
wx.CallAfter(progressFunc, i, length,
'Anonymizing file ' + str(i) + ' of ' + str(length))
self.updateCommonElements(rtdose, name, patientid, privatetags)
self.updateElement(rtdose, 'SeriesDescription', 'RT Dose')
rtdose.save_as(os.path.join(path, 'rtdose.dcm'))
i = i + 1
if data.has_key('images'):
images = data['images']
for n, image in enumerate(images):
wx.CallAfter(
progressFunc, i, length,
'Anonymizing file ' + str(i) + ' of ' + str(length))
self.updateCommonElements(image, name, patientid, privatetags)
self.updateElement(image, 'SeriesDate', '19010101')
self.updateElement(image, 'ContentDate', '19010101')
self.updateElement(image, 'SeriesTime', '000000')
self.updateElement(image, 'ContentTime', '000000')
self.updateElement(image, 'InstitutionName', 'institution')
self.updateElement(image, 'InstitutionAddress', 'address')
self.updateElement(image, 'InstitutionalDepartmentName',
'department')
modality = image.SOPClassUID.name.partition(
' Image Storage')[0]
image.save_as(
os.path.join(path,
modality.lower() + '.' + str(n) + '.dcm'))
i = i + 1
wx.CallAfter(progressFunc, length - 1, length, 'Done')
def updateElement(self, data, element, value):
"""Updates the element only if it exists in the original DICOM data."""
if element in data:
data.update({element: value})
def updateCommonElements(self, data, name, patientid, privatetags):
"""Updates the element only if it exists in the original DICOM data."""
if len(name):
self.updateElement(data, 'PatientsName', name)
if len(patientid):
self.updateElement(data, 'PatientID', patientid)
if privatetags:
data.remove_private_tags()
self.updateElement(data, 'OtherPatientIDs', patientid)
self.updateElement(data, 'OtherPatientNames', name)
self.updateElement(data, 'InstanceCreationDate', '19010101')
self.updateElement(data, 'InstanceCreationTime', '000000')
self.updateElement(data, 'StudyDate', '19010101')
self.updateElement(data, 'StudyTime', '000000')
self.updateElement(data, 'AccessionNumber', '')
self.updateElement(data, 'Manufacturer', 'manufacturer')
self.updateElement(data, 'ReferringPhysiciansName', 'physician')
self.updateElement(data, 'StationName', 'station')
self.updateElement(data, 'NameofPhysiciansReadingStudy', 'physician')
self.updateElement(data, 'OperatorsName', 'operator')
self.updateElement(data, 'PhysiciansofRecord', 'physician')
self.updateElement(data, 'ManufacturersModelName', 'model')
self.updateElement(data, 'PatientsBirthDate', '')
self.updateElement(data, 'PatientsSex', 'O')
self.updateElement(data, 'PatientsAge', '000Y')
self.updateElement(data, 'PatientsWeight', 0)
self.updateElement(data, 'PatientsSize', 0)
self.updateElement(data, 'PatientsAddress', 'address')
self.updateElement(data, 'AdditionalPatientHistory', '')
self.updateElement(data, 'EthnicGroup', 'ethnicity')
self.updateElement(data, 'StudyID', '1')
self.updateElement(data, 'DeviceSerialNumber', '0')
self.updateElement(data, 'SoftwareVersions', '1.0')
self.updateElement(data, 'ReviewDate', '19010101')
self.updateElement(data, 'ReviewTime', '000000')
self.updateElement(data, 'ReviewerName', 'anonymous')
class plugin:
def __init__(self, parent):
self.parent = parent
# Set up pubsub
pub.subscribe(self.OnUpdatePatient, "patient.updated.raw_data")
# Load the XRC file for our gui resources
self.res = XmlResource(util.GetBasePluginsPath("anonymize.xrc"))
def OnUpdatePatient(self, msg):
"""Update and load the patient data."""
self.data = msg
def pluginMenu(self, evt):
"""Anonymize DICOM / DICOM RT data."""
dlgAnonymize = self.res.LoadDialog(self.parent, "AnonymizeDialog")
dlgAnonymize.Init()
if dlgAnonymize.ShowModal() == wx.ID_OK:
path = dlgAnonymize.path
name = str(dlgAnonymize.name)
patientid = str(dlgAnonymize.patientid)
privatetags = dlgAnonymize.privatetags
# If the path doesn't exist, create it
if not os.path.exists(path):
os.mkdir(path)
# Initialize the progress dialog
dlgProgress = guiutil.get_progress_dialog(
wx.GetApp().GetTopWindow(), "Anonymizing DICOM data..."
)
# Initialize and start the anonymization thread
self.t = threading.Thread(
target=self.AnonymizeDataThread,
args=(
self.data,
path,
name,
patientid,
privatetags,
dlgProgress.OnUpdateProgress,
),
)
self.t.start()
# Show the progress dialog
dlgProgress.ShowModal()
dlgProgress.Destroy()
else:
pass
dlgAnonymize.Destroy()
return
def AnonymizeDataThread(
self, data, path, name, patientid, privatetags, progressFunc
):
"""Anonmyize and save each DICOM / DICOM RT file."""
length = 0
for key in ["rtss", "rtplan", "rtdose"]:
if key in data:
length = length + 1
if "images" in data:
length = length + len(data["images"])
i = 1
if "rtss" in data:
rtss = data["rtss"]
wx.CallAfter(
progressFunc,
i,
length,
"Anonymizing file " + str(i) + " of " + str(length),
)
self.updateCommonElements(rtss, name, patientid, privatetags)
self.updateElement(rtss, "SeriesDescription", "RT Structure Set")
self.updateElement(rtss, "StructureSetDate", "19010101")
self.updateElement(rtss, "StructureSetTime", "000000")
if "RTROIObservations" in rtss:
for item in rtss.RTROIObservations:
self.updateElement(item, "ROIInterpreter", "anonymous")
rtss.save_as(os.path.join(path, "rtss.dcm"))
i = i + 1
if "rtplan" in data:
rtplan = data["rtplan"]
wx.CallAfter(
progressFunc,
i,
length,
"Anonymizing file " + str(i) + " of " + str(length),
)
self.updateCommonElements(rtplan, name, patientid, privatetags)
self.updateElement(rtplan, "SeriesDescription", "RT Plan")
self.updateElement(rtplan, "RTPlanName", "plan")
self.updateElement(rtplan, "RTPlanDate", "19010101")
self.updateElement(rtplan, "RTPlanTime", "000000")
if "ToleranceTables" in rtplan:
for item in rtplan.ToleranceTables:
self.updateElement(item, "ToleranceTableLabel", "tolerance")
if "Beams" in rtplan:
for item in rtplan.Beams:
self.updateElement(item, "Manufacturer", "manufacturer")
self.updateElement(item, "InstitutionName", "institution")
self.updateElement(item, "InstitutionAddress", "address")
self.updateElement(
item, "InstitutionalDepartmentName", "department"
)
self.updateElement(item, "ManufacturersModelName", "model")
self.updateElement(item, "TreatmentMachineName", "txmachine")
if "TreatmentMachines" in rtplan:
for item in rtplan.TreatmentMachines:
self.updateElement(item, "Manufacturer", "manufacturer")
self.updateElement(item, "InstitutionName", "vendor")
self.updateElement(item, "InstitutionAddress", "address")
self.updateElement(
item, "InstitutionalDepartmentName", "department"
)
self.updateElement(item, "ManufacturersModelName", "model")
self.updateElement(item, "DeviceSerialNumber", "0")
self.updateElement(item, "TreatmentMachineName", "txmachine")
if "Sources" in rtplan:
for item in rtplan.Sources:
self.updateElement(item, "SourceManufacturer", "manufacturer")
self.updateElement(item, "SourceIsotopeName", "isotope")
rtplan.save_as(os.path.join(path, "rtplan.dcm"))
i = i + 1
if "rtdose" in data:
rtdose = data["rtdose"]
wx.CallAfter(
progressFunc,
i,
length,
"Anonymizing file " + str(i) + " of " + str(length),
)
self.updateCommonElements(rtdose, name, patientid, privatetags)
self.updateElement(rtdose, "SeriesDescription", "RT Dose")
rtdose.save_as(os.path.join(path, "rtdose.dcm"))
i = i + 1
if "images" in data:
images = data["images"]
for n, image in enumerate(images):
wx.CallAfter(
progressFunc,
i,
length,
"Anonymizing file " + str(i) + " of " + str(length),
)
self.updateCommonElements(image, name, patientid, privatetags)
self.updateElement(image, "SeriesDate", "19010101")
self.updateElement(image, "ContentDate", "19010101")
self.updateElement(image, "SeriesTime", "000000")
self.updateElement(image, "ContentTime", "000000")
self.updateElement(image, "InstitutionName", "institution")
self.updateElement(image, "InstitutionAddress", "address")
self.updateElement(image, "InstitutionalDepartmentName", "department")
modality = image.SOPClassUID.name.partition(" Image Storage")[0]
image.save_as(
os.path.join(path, modality.lower() + "." + str(n) + ".dcm")
)
i = i + 1
wx.CallAfter(progressFunc, length - 1, length, "Done")
def updateElement(self, data, element, value):
"""Updates the element only if it exists in the original DICOM data."""
if element in data:
data.update({element: value})
def updateCommonElements(self, data, name, patientid, privatetags):
"""Updates the element only if it exists in the original DICOM data."""
if len(name):
self.updateElement(data, "PatientsName", name)
if len(patientid):
self.updateElement(data, "PatientID", patientid)
if privatetags:
data.remove_private_tags()
self.updateElement(data, "OtherPatientIDs", patientid)
self.updateElement(data, "OtherPatientNames", name)
self.updateElement(data, "InstanceCreationDate", "19010101")
self.updateElement(data, "InstanceCreationTime", "000000")
self.updateElement(data, "StudyDate", "19010101")
self.updateElement(data, "StudyTime", "000000")
self.updateElement(data, "AccessionNumber", "")
self.updateElement(data, "Manufacturer", "manufacturer")
self.updateElement(data, "ReferringPhysiciansName", "physician")
self.updateElement(data, "StationName", "station")
self.updateElement(data, "NameofPhysiciansReadingStudy", "physician")
self.updateElement(data, "OperatorsName", "operator")
self.updateElement(data, "PhysiciansofRecord", "physician")
self.updateElement(data, "ManufacturersModelName", "model")
self.updateElement(data, "PatientsBirthDate", "")
self.updateElement(data, "PatientsSex", "O")
self.updateElement(data, "PatientsAge", "000Y")
self.updateElement(data, "PatientsWeight", 0)
self.updateElement(data, "PatientsSize", 0)
self.updateElement(data, "PatientsAddress", "address")
self.updateElement(data, "AdditionalPatientHistory", "")
self.updateElement(data, "EthnicGroup", "ethnicity")
self.updateElement(data, "StudyID", "1")
self.updateElement(data, "DeviceSerialNumber", "0")
self.updateElement(data, "SoftwareVersions", "1.0")
self.updateElement(data, "ReviewDate", "19010101")
self.updateElement(data, "ReviewTime", "000000")
self.updateElement(data, "ReviewerName", "anonymous")
def get_resource():
filename = os.path.join(os.getcwd(), os.path.dirname(__file__),
'hachoir_wx.xrc')
return XmlResource(filename)
