def LoadPatientDataThread(ptdata):
"""Load the patient data."""
patient = {}
if not 'images' in ptdata:
#Look for DICOM data in the ptdata dictionary
for rtdatatype in ptdata.keys():
if isinstance(ptdata[rtdatatype], pydicom.dataset.FileDataset):
patient.update(dp(ptdata[rtdatatype]).GetDemographics())
break
if 'rtss' in ptdata:
d = dp(ptdata['rtss'])
s = d.GetStructures()
for k in s.keys():
s[k]['planes'] = d.GetStructureCoordinates(k)
s[k]['thickness'] = d.CalculatePlaneThickness(s[k]['planes'])
patient['structures'] = s
if 'images' in ptdata:
if not 'id' in patient:
patient.update(dp(ptdata['images'][0]).GetDemographics())
patient['images'] = []
for image in ptdata['images']:
patient['images'].append(dp(image))
return patient
def LoadPatientDataThread(self, parent, ptdata, progressFunc, updateFunc):
"""Thread to load the patient data."""
# Call the progress function to update the gui
wx.CallAfter(progressFunc, 0, 0, 'Processing patient data...')
patient = {}
if not 'images' in ptdata:
#Look for DICOM data in the ptdata dictionary
for rtdatatype in ptdata.keys():
if isinstance(ptdata[rtdatatype], pydicom.dataset.FileDataset):
patient.update(dp(ptdata[rtdatatype]).GetDemographics())
break
if 'rtss' in ptdata:
wx.CallAfter(progressFunc, 20, 100,
'Processing RT Structure Set...')
d = dp(ptdata['rtss'])
s = d.GetStructures()
for k in s.keys():
s[k]['planes'] = d.GetStructureCoordinates(k)
s[k]['thickness'] = d.CalculatePlaneThickness(s[k]['planes'])
patient['structures'] = s
if 'rtplan' in ptdata:
wx.CallAfter(progressFunc, 40, 100, 'Processing RT Plan...')
patient['plan'] = dp(ptdata['rtplan']).GetPlan()
if 'rtdose' in ptdata:
wx.CallAfter(progressFunc, 60, 100, 'Processing RT Dose...')
patient['dvhs'] = dp(ptdata['rtdose']).GetDVHs()
patient['dose'] = dp(ptdata['rtdose'])
if 'images' in ptdata:
wx.CallAfter(progressFunc, 80, 100, 'Processing Images...')
if not 'id' in patient:
patient.update(dp(ptdata['images'][0]).GetDemographics())
patient['images'] = []
for image in ptdata['images']:
patient['images'].append(dp(image))
if 'rxdose' in ptdata:
if not 'plan' in patient:
patient['plan'] = {}
patient['plan']['rxdose'] = ptdata['rxdose']
# if the min/max/mean dose was not present, calculate it and save it for each structure
wx.CallAfter(progressFunc, 90, 100, 'Processing DVH data...')
if ('dvhs' in patient) and ('structures' in patient):
# If the DVHs are not present, calculate them
i = 0
for key, structure in patient['structures'].items():
# Only calculate DVHs if they are not present for the structure
# or recalc all DVHs if the preference is set
if ((not (key in patient['dvhs'].keys()))
or (self.dvhRecalc == 'Always Recalculate DVH')):
# Only calculate DVHs for structures, not applicators
# and only if the dose grid is present
if ((structure['name'].startswith('Applicator'))
or (not "PixelData" in patient['dose'].ds)):
continue
wx.CallAfter(
progressFunc, 10 * i / len(patient['structures']) + 90,
100,
'Calculating DVH for ' + structure['name'] + '...')
# Limit DVH bins to 500 Gy due to high doses in brachy
dvh = dvhcalc.get_dvh(ptdata['rtss'], patient['dose'].ds,
key, 50000)
if len(dvh.counts):
patient['dvhs'][key] = dvh
i += 1
for key, dvh in patient['dvhs'].items():
dvh.rx_dose = patient['plan']['rxdose'] / 100
wx.CallAfter(progressFunc, 100, 100, 'Done')
wx.CallAfter(updateFunc, patient)
def LoadPatientDataThread(self, parent, ptdata, progressFunc, updateFunc):
"""Thread to load the patient data."""
# Call the progress function to update the gui
wx.CallAfter(progressFunc, 0, 0, 'Processing patient data...')
patient = {}
if not 'images' in ptdata:
#Look for DICOM data in the ptdata dictionary
for rtdatatype in ptdata.keys():
if isinstance(ptdata[rtdatatype], pydicom.dataset.FileDataset):
patient.update(dp(ptdata[rtdatatype]).GetDemographics())
break
if 'rtss' in ptdata:
wx.CallAfter(progressFunc, 20, 100, 'Processing RT Structure Set...')
d = dp(ptdata['rtss'])
s = d.GetStructures()
for k in s.keys():
s[k]['planes'] = d.GetStructureCoordinates(k)
s[k]['thickness'] = d.CalculatePlaneThickness(s[k]['planes'])
patient['structures'] = s
if 'rtplan' in ptdata:
wx.CallAfter(progressFunc, 40, 100, 'Processing RT Plan...')
patient['plan'] = dp(ptdata['rtplan']).GetPlan()
if 'rtdose' in ptdata:
wx.CallAfter(progressFunc, 60, 100, 'Processing RT Dose...')
patient['dvhs'] = dp(ptdata['rtdose']).GetDVHs()
patient['dose'] = dp(ptdata['rtdose'])
if 'images' in ptdata:
wx.CallAfter(progressFunc, 80, 100, 'Processing Images...')
if not 'id' in patient:
patient.update(dp(ptdata['images'][0]).GetDemographics())
patient['images'] = []
for image in ptdata['images']:
patient['images'].append(dp(image))
if 'rxdose' in ptdata:
if not 'plan' in patient:
patient['plan'] = {}
patient['plan']['rxdose'] = ptdata['rxdose']
# if the min/max/mean dose was not present, calculate it and save it for each structure
wx.CallAfter(progressFunc, 90, 100, 'Processing DVH data...')
if ('dvhs' in patient) and ('structures' in patient):
# If the DVHs are not present, calculate them
i = 0
for key, structure in patient['structures'].items():
# Only calculate DVHs if they are not present for the structure
# or recalc all DVHs if the preference is set
if ((not (key in patient['dvhs'].keys())) or
(self.dvhRecalc == 'Always Recalculate DVH')):
# Only calculate DVHs for structures, not applicators
# and only if the dose grid is present
if ((structure['name'].startswith('Applicator')) or
(not "PixelData" in patient['dose'].ds)):
continue
wx.CallAfter(progressFunc,
10*i/len(patient['structures'])+90, 100,
'Calculating DVH for ' + structure['name'] +
'...')
# Limit DVH bins to 500 Gy due to high doses in brachy
dvh = dvhcalc.get_dvh(ptdata['rtss'], patient['dose'].ds, key, 50000)
if len(dvh.counts):
patient['dvhs'][key] = dvh
i += 1
for key, dvh in patient['dvhs'].items():
dvh.rx_dose = patient['plan']['rxdose'] / 100
wx.CallAfter(progressFunc, 100, 100, 'Done')
wx.CallAfter(updateFunc, patient)
def LoadPatientDataThread(self, parent, ptdata, progressFunc, updateFunc):
"""Thread to load the patient data."""
# Call the progress function to update the gui
wx.CallAfter(progressFunc, 0, 0, 'Processing patient data...')
patient = {}
if not 'images' in ptdata:
#Look for DICOM data in the ptdata dictionary
for rtdatatype in ptdata.keys():
if isinstance(ptdata[rtdatatype], pydicom.dataset.FileDataset):
patient.update(dp(ptdata[rtdatatype]).GetDemographics())
break
if 'rtss' in ptdata:
wx.CallAfter(progressFunc, 20, 100,
'Processing RT Structure Set...')
d = dp(ptdata['rtss'])
s = d.GetStructures()
for k in s.keys():
s[k]['planes'] = d.GetStructureCoordinates(k)
s[k]['thickness'] = d.CalculatePlaneThickness(s[k]['planes'])
patient['structures'] = s
if 'rtplan' in ptdata:
wx.CallAfter(progressFunc, 40, 100, 'Processing RT Plan...')
patient['plan'] = dp(ptdata['rtplan']).GetPlan()
if 'rtdose' in ptdata:
wx.CallAfter(progressFunc, 60, 100, 'Processing RT Dose...')
patient['dvhs'] = dp(ptdata['rtdose']).GetDVHs()
patient['dose'] = dp(ptdata['rtdose'])
if 'images' in ptdata:
wx.CallAfter(progressFunc, 80, 100, 'Processing Images...')
if not 'id' in patient:
patient.update(dp(ptdata['images'][0]).GetDemographics())
patient['images'] = []
for image in ptdata['images']:
patient['images'].append(dp(image))
if 'rxdose' in ptdata:
if not 'plan' in patient:
patient['plan'] = {}
patient['plan']['rxdose'] = ptdata['rxdose']
# if the min/max/mean dose was not present, calculate it and save it for each structure
wx.CallAfter(progressFunc, 90, 100, 'Processing DVH data...')
if ('dvhs' in patient) and ('structures' in patient):
# If the DVHs are not present, calculate them
i = 0
# Grabbing patient ID
dvh_patientID = ptdata['rtdose'].PatientID
csv_filename = str(dvh_patientID) + '.csv'
dvh_csv_list = []
# maximum dose of all ROIs
max_roi_dose = 0
# csv Header
csv_header = []
for key, structure in patient['structures'].items():
# Initialize a list for dvh exporting to csv
dvh_roi_list = []
# Only calculate DVHs if they are not present for the structure
# or recalc all DVHs if the preference is set
if ((not (key in patient['dvhs'].keys()))
or (self.dvhRecalc == 'Always Recalculate DVH')):
# Only calculate DVHs for structures, not applicators
# and only if the dose grid is present
if ((structure['name'].startswith('Applicator'))
or (not "PixelData" in patient['dose'].ds)):
continue
wx.CallAfter(
progressFunc, 10 * i / len(patient['structures']) + 90,
100,
'Calculating DVH for ' + structure['name'] + '...')
# Limit DVH bins to 500 Gy due to high doses in brachy
dvh = dvhcalc.get_dvh(ptdata['rtss'], patient['dose'].ds,
key, 50000)
# Retrieve roi name
dvh_roiName = dvh.name
# Retrieve roi dvh volume
dvh_roiVolume = dvh.volume
# Append info
dvh_roi_list.append(dvh_patientID)
dvh_roi_list.append(dvh_roiName)
dvh_roi_list.append(dvh_roiVolume)
#
dvh_roiDose = dvh.relative_volume.counts
for i in range(0, len(dvh_roiDose), 10):
dvh_roi_list.append(dvh_roiDose[i])
if i > max_roi_dose:
max_roi_dose = i
dvh_csv_list.append(dvh_roi_list)
if len(dvh.counts):
patient['dvhs'][key] = dvh
i += 1
csv_header.append('Hash ID')
csv_header.append('ROI')
csv_header.append('Volume (mL)')
for i in range(0, max_roi_dose + 1, 10):
csv_header.append(str(i) + 'cGy')
pddf_csv = pd.DataFrame(dvh_csv_list, columns=csv_header).round(2)
pddf_csv.fillna(0.0, inplace=True)
pddf_csv.set_index('Hash ID', inplace=True)
if not os.path.exists(self.path + '/CSV'):
os.makedirs(self.path + '/CSV')
pddf_csv.to_csv(self.path + '/CSV/' + 'DVH_' + csv_filename)
for key, dvh in patient['dvhs'].items():
dvh.rx_dose = patient['plan']['rxdose'] / 100
wx.CallAfter(progressFunc, 100, 100, 'Done')
wx.CallAfter(updateFunc, patient)