def tcia_tests():
# The TCIA interface is very slow, so uncomment to skip this one
#raise SkipTest
logger = logging.getLogger(tcia_tests.__name__)
# Test TCIA Instantiate
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('tcia', repos)
# source = TCIAInterface(address='https://services.cancerimagingarchive.net/services/v3/TCIA',
# api_key=os.environ['TCIA_API_KEY'])
# Apparently API key doesn't work for NLST b/c it is a private collection
# series = source.get_series_from_id('1.2.840.113654.2.55.4303894980888172655039251025765147023')
# source.download_archive(series, 'nlst_tmp_archive')
# Test TCIA Download
series = source.get_series_from_id('1.3.6.1.4.1.9328.50.4.15567')
source.download_archive(series, 'tcia_tmp_archive')
assert os.path.getsize('tcia_tmp_archive.zip') == 266582
os.remove('tcia_tmp_archive.zip')
# Test TCIA Copy
source.copy(series, source, 'tcia_tmp_archive')
assert os.path.getsize('tcia_tmp_archive.zip') == 266582
os.remove('tcia_tmp_archive.zip')
def xnat_bulk_edit():
# Example of bulk editing from spreadsheet
logger = logging.getLogger(xnat_bulk_edit.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
import csv
with open('/Users/derek/Desktop/protect3d.variables.csv', 'rbU') as csvfile:
propreader = csv.reader(csvfile)
propreader.next()
for row in propreader:
logger.info(', '.join(row))
subject_id = row[0]
new_subject_id = '{num:04d}'.format(num=int(subject_id))
logger.info(new_subject_id)
params = {'gender': row[1],
#'age': row[2],
'src': row[3],
'label': new_subject_id}
source.do_put('data/archive/projects/protect3d/subjects', subject_id, params=params)
def tcia_tests():
# The TCIA interface is very slow, so uncomment to skip this one
#raise SkipTest
logger = logging.getLogger(tcia_tests.__name__)
# Test TCIA Instantiate
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('tcia', repos)
# source = TCIAInterface(address='https://services.cancerimagingarchive.net/services/v3/TCIA',
# api_key=os.environ['TCIA_API_KEY'])
# Apparently API key doesn't work for NLST b/c it is a private collection
# series = source.get_series_from_id('1.2.840.113654.2.55.4303894980888172655039251025765147023')
# source.download_archive(series, 'nlst_tmp_archive')
# Test TCIA Download
series = source.get_series_from_id('1.3.6.1.4.1.9328.50.4.15567')
source.download_archive(series, 'tcia_tmp_archive')
assert os.path.getsize('tcia_tmp_archive.zip') == 266582
os.remove('tcia_tmp_archive.zip')
# Test TCIA Copy
source.copy(series, source, 'tcia_tmp_archive')
assert os.path.getsize('tcia_tmp_archive.zip') == 266582
os.remove('tcia_tmp_archive.zip')
def xnat_bulk_edit():
# Example of bulk editing from spreadsheet
logger = logging.getLogger(xnat_bulk_edit.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
import csv
with open('/Users/derek/Desktop/protect3d.variables.csv',
'rbU') as csvfile:
propreader = csv.reader(csvfile)
propreader.next()
for row in propreader:
logger.info(', '.join(row))
subject_id = row[0]
new_subject_id = '{num:04d}'.format(num=int(subject_id))
logger.info(new_subject_id)
params = {
'gender': row[1],
#'age': row[2],
'src': row[3],
'label': new_subject_id
}
source.do_put('data/archive/projects/protect3d/subjects',
subject_id,
params=params)
def test_montage_adv():
logger = logging.getLogger(test_montage_adv.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('montage', repos)
mrn = '000019477504'
q = '16397558'
r = source.do_get('api/v1/index/rad/search/rad',
params={
'q': '',
'patient_mrn': mrn
})
logger.debug(pprint(r))
exit()
r = source.find('study', q, 'rad')
# logger.debug(pprint(r))
qq = r.get('objects')[0].get('resource_uri')
logger.debug(qq)
r = source.do_get(qq)
logger.debug(pprint(r))
def dicom_tests():
logger = logging.getLogger(dicom_tests.__name__)
# Test DICOM Instantiate
from OrthancInterface import OrthancInterface
proxy = OrthancInterface(address='http://localhost:8043', name='3dlab-dev1')
source = DICOMInterface(proxy=proxy, name='3dlab-dev0+dcm')
# Test DICOM Subject Query
r = source.find('subject', {'PatientName': 'ZNE*'})[0]
assert r.subject_id == 'ZA4VSDAUSJQA6'
# Test DICOM Q/R/DL
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('3dlab-dev0+dcm', repos)
target = Interface.factory('3dlab-dev1', repos)
w = source.find('series', {'SeriesInstanceUID': '1.2.840.113654.2.55.4303894980888172655039251025765147023'})[0]
u = target.retrieve(w, source)[0]
target.copy(u, target, 'nlst_tmp_archive')
assert os.path.getsize('nlst_tmp_archive.zip') == 176070
os.remove('nlst_tmp_archive.zip')
def dicom_tests():
logger = logging.getLogger(dicom_tests.__name__)
# Test DICOM Instantiate
from OrthancInterface import OrthancInterface
proxy = OrthancInterface(address='http://localhost:8043',
name='3dlab-dev1')
source = DICOMInterface(proxy=proxy, name='3dlab-dev0+dcm')
# Test DICOM Subject Query
r = source.find('subject', {'PatientName': 'ZNE*'})[0]
assert r.subject_id == 'ZA4VSDAUSJQA6'
# Test DICOM Q/R/DL
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('3dlab-dev0+dcm', repos)
target = Interface.factory('3dlab-dev1', repos)
w = source.find(
'series', {
'SeriesInstanceUID':
'1.2.840.113654.2.55.4303894980888172655039251025765147023'
})[0]
u = target.retrieve(w, source)[0]
target.copy(u, target, 'nlst_tmp_archive')
assert os.path.getsize('nlst_tmp_archive.zip') == 176070
os.remove('nlst_tmp_archive.zip')
def test_orthanc_juniper():
logger = logging.getLogger(orthanc_tests2.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('deathstar+lsmaster', repos)
source.all_studies()
def test_orthanc_juniper():
logger = logging.getLogger(orthanc_tests2.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('deathstar+lsmaster', repos)
source.all_studies()
def bulk_age_deduction():
logger = logging.getLogger(test_xnat.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
s = source.subject_from_id('UOCA0008A', project_id='ava')
r = source.do_get('data/services/dicomdump?src=/archive/projects', s.project_id, 'subjects', s.subject_id, 'experiments', 'UOCA0008A&field=PatientAge', params={'field1': 'PatientAge', 'field': 'StudyDate'})
def bulk_age_deduction():
logger = logging.getLogger(test_xnat.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
s = source.subject_from_id('UOCA0008A', project_id='ava')
r = source.do_get('data/services/dicomdump?src=/archive/projects', s.project_id, 'subjects', s.subject_id, 'experiments', 'UOCA0008A&field=PatientAge', params={'field1': 'PatientAge', 'field': 'StudyDate'})
def bulk_upload():
logger = logging.getLogger(test_xnat.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
from glob import glob
worklist = glob('/Users/derek/Data/hydrocephalus_dicom/*.zip')
for fn in worklist[1:]:
source.upload_archive(None, fn, project_id='ava')
def bulk_upload():
logger = logging.getLogger(test_xnat.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
from glob import glob
worklist = glob('/Users/derek/Data/hydrocephalus_dicom/*.zip')
for fn in worklist[1:]:
source.upload_archive(None, fn, project_id='ava')
def tcia_mirror():
logger = logging.getLogger(tcia_tests.__name__)
# Test TCIA Instantiate
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('tcia', repos)
target = Interface.factory('xnat-dev', repos)
fn = '/Users/derek/Desktop/tcia-all-seriesInstanceUids1438444078500.csv'
import csv
with open(fn, 'rbU') as csvfile:
seriesreader = csv.reader(csvfile)
seriesreader.next()
i = 0
for row in seriesreader:
i = i + 1
if i <= 0: continue
if i > 5: break
logger.info(', '.join(row))
group = row[0]
# subject_id = row[1]
series_id = row[9]
item = source.series_from_id(series_id)
#source.download_data(item)
# Change vars for XNAT
item['collection'] = group
item.subject.project_id = 'tcia'
#target.upload_data(item)
target.do_put('data/archive/projects',
item.subject.project_id,
'subjects',
item.subject.subject_id.replace('.', '_'),
params={
'group': item['collection'],
'yob': item.subject['yob'],
'gender': item.subject['gender']
})
pass
def test_xnat():
logger = logging.getLogger(bulk_folder_upload.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
count = source.all_studies()
slack_addr = repos['rih3dlab']['address']
payload = {"text": "<http://xnat-dev.cloudapp.net:8080/xnat|xnat> currently contains {0} studies.".format(count)}
requests.post(slack_addr, json=payload)
def test_montage():
logger = logging.getLogger(test_montage.__name__)
# Test DICOM Q/R/DL
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('montage', repos)
# Look in collection "rad" for query string "fracture"
r = source.find('study', 'fracture', 'rad')
assert(r['meta']['total_count'] > 1400000)
# Test shared juniper session cookies
source2 = Interface.factory('montage', repos)
# Look in collection "rad" for query string "fracture"
r = source2.find('study', 'fracture', 'rad')
assert(r['meta']['total_count'] > 1400000)
def test_montage():
logger = logging.getLogger(test_montage.__name__)
# Test DICOM Q/R/DL
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('montage', repos)
# Look in collection "rad" for query string "fracture"
r = source.find('study', 'fracture', 'rad')
assert (r['meta']['total_count'] > 1400000)
# Test shared juniper session cookies
source2 = Interface.factory('montage', repos)
# Look in collection "rad" for query string "fracture"
r = source2.find('study', 'fracture', 'rad')
assert (r['meta']['total_count'] > 1400000)
def bulk_folder_upload():
logger = logging.getLogger(bulk_folder_upload.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
source.all_studies()
base_dir = '/Users/derek/Data/ATACH_I'
subject_worklist = glob('%s/*' % base_dir)
logger.info(subject_worklist)
i = 0
for subject_dir in subject_worklist:
subsubject_worklist = glob('%s/*' % subject_dir)
for subsubject_dir in subsubject_worklist:
study_worklist = glob('%s/*' % subsubject_dir)
#logger.info(study_worklist)
for study_dir in study_worklist:
i = i+1
#logger.info(study_dir)
if 'scene' in study_dir.lower(): continue
# get a dcm file to figure out the subject name, study id, and session type...
session_worklist = glob('%s/*' % study_dir)
session_dir = session_worklist[0]
instance_worklist = glob('%s/*' % session_dir)
instance_file = instance_worklist[0]
ds = dicom.read_file(instance_file)
#logger.info(ds)
orig_subject_id = ds.PatientID
num = int(re.search(r'\d+', orig_subject_id).group())
suffix_res = re.search(r'[A-Za-z]+', orig_subject_id)
if suffix_res:
suffix = suffix_res.group().upper()
if suffix == 'TIER':
# Special case for silly ATACH mis-labelling
if orig_subject_id.endswith('1'):
suffix = 'T1'
elif orig_subject_id.endswith('2'):
num = 172
suffix = 'T2'
else:
suffix = ''
subject_id = '{num:04d}{suffix}'.format(num=int(num), suffix=str(suffix))
study_id = ds.AccessionNumber
study_date_str = ds.StudyDate
age_str = ds.get('PatientsAge')
if study_date_str and age_str:
yob = deduce_yob(study_date_str, age_str)
else:
yob = None
logger.info('%s : %s : %s' % (subject_id, study_id, yob))
if i<=1:
continue
# source.upload_archive(None, study_dir, project_id='atach3d', study_id=study_id, subject_id=subject_id)
source.upload_archive(None, 'tmp.zip', project_id='atach3d', study_id=study_id, subject_id=subject_id)
if yob:
source.do_put('data/archive/projects/atach3d/subjects', subject_id, params={'yob': yob})
# TODO: Need to consider 'asserts' for xnat testing
s = source.subject_from_id('my_patient2', 'mtp01')
source.do_get('data/archive/projects/mtp01/subjects/my_patient2', params={'format': 'json', 'yob': '1971'})
t = DicomStudy(subject_id='my_patient3',
project_id='mtp01')
source.upload_archive(t, 'tcia_tmp_archive1.zip')
logger.info(s)
# Need to test:
# 1. xnat-dev is up
# 2. mtp01 is empty
# 3. can upload a study to mtp01 w correct subject name, study name, etc.
# 4. can download the study from mtp01
pass
def bulk_folder_upload():
logger = logging.getLogger(bulk_folder_upload.__name__)
from tithonus import read_yaml
repos = read_yaml('repos.yaml')
source = Interface.factory('xnat-dev', repos)
source.all_studies()
base_dir = '/Users/derek/Data/ATACH_I'
subject_worklist = glob('%s/*' % base_dir)
logger.info(subject_worklist)
i = 0
for subject_dir in subject_worklist:
subsubject_worklist = glob('%s/*' % subject_dir)
for subsubject_dir in subsubject_worklist:
study_worklist = glob('%s/*' % subsubject_dir)
#logger.info(study_worklist)
for study_dir in study_worklist:
i = i + 1
#logger.info(study_dir)
if 'scene' in study_dir.lower(): continue
# get a dcm file to figure out the subject name, study id, and session type...
session_worklist = glob('%s/*' % study_dir)
session_dir = session_worklist[0]
instance_worklist = glob('%s/*' % session_dir)
instance_file = instance_worklist[0]
ds = pydicom.read_file(instance_file)
#logger.info(ds)
orig_subject_id = ds.PatientID
num = int(re.search(r'\d+', orig_subject_id).group())
suffix_res = re.search(r'[A-Za-z]+', orig_subject_id)
if suffix_res:
suffix = suffix_res.group().upper()
if suffix == 'TIER':
# Special case for silly ATACH mis-labelling
if orig_subject_id.endswith('1'):
suffix = 'T1'
elif orig_subject_id.endswith('2'):
num = 172
suffix = 'T2'
else:
suffix = ''
subject_id = '{num:04d}{suffix}'.format(num=int(num),
suffix=str(suffix))
study_id = ds.AccessionNumber
study_date_str = ds.StudyDate
age_str = ds.get('PatientsAge')
if study_date_str and age_str:
yob = deduce_yob(study_date_str, age_str)
else:
yob = None
logger.info('%s : %s : %s' % (subject_id, study_id, yob))
if i <= 1:
continue
# source.upload_archive(None, study_dir, project_id='atach3d', study_id=study_id, subject_id=subject_id)
source.upload_archive(None,
'tmp.zip',
project_id='atach3d',
study_id=study_id,
subject_id=subject_id)
if yob:
source.do_put('data/archive/projects/atach3d/subjects',
subject_id,
params={'yob': yob})
# TODO: Need to consider 'asserts' for xnat testing
s = source.subject_from_id('my_patient2', 'mtp01')
source.do_get('data/archive/projects/mtp01/subjects/my_patient2',
params={
'format': 'json',
'yob': '1971'
})
t = DicomStudy(subject_id='my_patient3', project_id='mtp01')
source.upload_archive(t, 'tcia_tmp_archive1.zip')
logger.info(s)
# Need to test:
# 1. xnat-dev is up
# 2. mtp01 is empty
# 3. can upload a study to mtp01 w correct subject name, study name, etc.
# 4. can download the study from mtp01
pass
