class DicomParser:
"""Class for parsing DICOM files."""
def __init__(self, **kwargs):
"""Initialize with url to DICOM server."""
self.server = DicomServer(**kwargs)
def get_info(self, patient):
"""Return main DICOM tags from Orthanc."""
url = os.path.join('patients', patient)
return self.server.api(url)['MainDicomTags']
def radiation_total_dose(self, patient_id):
"""Calculate total dose in Gy of treatment plan."""
# TODO: write method here
return
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
"""
Created on Thu May 10 22:21:15 2018
@author: Michal
"""
"""Extract data form DICOM server and store in mongo."""
import os
from pymongo import MongoClient
from dicom_server import DicomServer
from dicom_parser import DicomParser
# Instantiate server object
server = DicomServer()
# Check that DICOM server is working
print 'Checking if server is working...'
print 'Should get response 200, got response {}'.format(server.echo())
# Search DICOM server using DicomServer methods
patients = server.api('patients')
# Store data in mongo
# Create connection to database
client = MongoClient(os.getenv('MONGODB_URL'))
db = client.get_default_database()
"""Extract data form DICOM server and store in mongo."""
import os
from pymongo import MongoClient
from dicom_server import DicomServer
from dicom_parser import DicomParser
# Instantiate server object
server = DicomServer()
# Check that DICOM server is working
print 'Checking if server is working...'
print 'Should get response 200, got response {}'.format(server.echo())
# Search DICOM server using DicomServer methods
# Find total number of patients
patients = server.api('patients')
print 'There are {} patients'.format(len(patients))
# Get the DICOM PatientID associated with each Orthanc patient id
for patient in patients:
url = os.path.join('patients', patient)
patient_id = server.api(url)['MainDicomTags']['PatientID']
print 'Orthanc patient id: {}, DICOM PatientID: {}'.format(
patient, patient_id)
# Find total number of male patients
query = {'PatientSex': 'M'}
print 'Searching for: {}'.format(query)
male_patients = server.find(query, level='Patient')
print 'There are {} male patients'.format(len(male_patients))
def __init__(self, **kwargs):
"""Initialize with url to DICOM server."""
self.server = DicomServer(**kwargs)
class DicomParser:
"""Class for parsing DICOM files."""
def __init__(self, **kwargs):
"""Initialize with url to DICOM server."""
self.server = DicomServer(**kwargs)
def get_info(self, patient):
"""Return main DICOM tags from Orthanc."""
url = os.path.join('patients', patient)
return self.server.api(url)['MainDicomTags']
def radiation_total_dose(self, patient):
"""Calculate total dose in Gy of treatment plan."""
url = os.path.join('patients', patient)
PatientID = self.server.api(url)['MainDicomTags']['PatientID']
studies = self.server.api(url)['Studies']
BeamDoses = 0
for study in studies:
series = []
flat_series_list = []
studies_url = os.path.join('studies',study)
series.append(self.server.api(studies_url)['Series'])
for sublist in series:
for item in sublist:
flat_series_list.append(item)
for a_series in flat_series_list:
instances = []
flat_instances_list = []
series_url = os.path.join('series',a_series)
if self.server.api(series_url)['MainDicomTags']['Modality'] == 'RTPLAN':
instances.append(self.server.api(series_url)['Instances'])
for sublist in instances:
for item in sublist:
flat_instances_list.append(item)
for instance in flat_instances_list:
instance_tags = self.server.api(os.path.join('instances', instance, 'simplified-tags'))
beam_sequences = []
if 'FractionGroupSequence' in instance_tags.keys():
for i in instance_tags['FractionGroupSequence']:
beam_sequences.append(i['ReferencedBeamSequence'])
beam_seqs_flattened = []
for j in beam_sequences:
for item in j:
beam_seqs_flattened.append(item)
for k in beam_seqs_flattened:
BeamDoses = BeamDoses + float(k['BeamDose'])
return {'PatientID':PatientID,'radiation_total_dose':BeamDoses}
"""Delete all patients store in DICOM server."""
import os
import requests
from dicom_server import DicomServer
# Instantiate server object
server = DicomServer()
# Get patient hashes
patients = server.api('patients')
for patient in patients:
url = os.path.join(os.getenv('DICOM_URL'), 'patients', patient)
r = requests.delete(url)
if r.status_code == 200:
print 'Successfully deleted: {}'.format(patient)
else:
print 'Failed to delete: {}'.format(patient)
print 'Status code: {}'.format(r.status_code)