def set_experiment_attrs(config, project, subject, experiment, key, value):
"""
Set the field for an MRSession
For example, datetodvd, findingsdate, findings
:param config: str
:param project: str
:param subject: str
:param experiment: str
:param key: str
:param value: str
:return: str
"""
config = xe.get_config(config)
session = xe.get_xnat_session(config)
api = config.get('api')
path = '{}/projects/{}/subjects/{}/experiments/{}'.format(api, project, subject, experiment)
xsi = 'xnat:mrSessionData'
field = 'xnat:mrSessionData/fields/field[name={}]/field'.format(key)
payload = {'xsiType': xsi, field: value}
return session.put(path, params=payload)
def set_experiment_attrs(config, project, subject, experiment, key, value):
"""
Set the field for an MRSession
For example, datetodvd, findingsdate, findings
:param config: str
:param project: str
:param subject: str
:param experiment: str
:param key: str
:param value: str
:return: str
"""
config = xe.get_config(config)
session = xe.get_xnat_session(config)
api = config.get('api')
path = '{}/projects/{}/subjects/{}/experiments/{}'.format(
api, project, subject, experiment)
xsi = 'xnat:mrSessionData'
field = 'xnat:mrSessionData/fields/field[name={}]/field'.format(key)
payload = {'xsiType': xsi, field: value}
return session.put(path, params=payload)
def main(args=None):
config = xe.get_config(args.config)
session = xe.get_xnat_session(config)
if args.update:
# Update the cache of XNAT Experiment XML files
xe.extract_experiment_xml(config, session, args.experimentsdir,
args.num_extract)
# extract info from the experiment XML files
experiment = xe.get_experiments_dir_info(args.experimentsdir)
experiment_df = xe.experiments_to_dataframe(experiment)
reading = xe.get_experiments_dir_reading_info(args.experimentsdir)
reading_df = xe.reading_to_dataframe(reading)
experiment_reading = inner_join_dataframes(experiment_df, reading_df)
# exclude phantoms, but include the traveling human phantoms
site_id_pattern = '[A-EX]-[0-9]{5}-[MFT]-[0-9]'
df = experiment_reading[experiment_reading.site_id.str.contains(
site_id_pattern)]
result = None
if args.report_type == 'no_findings_date':
# Findings are listed without a findings date
result = findings_date_empty(df)
if args.set_findings_date:
# Update the findings date to equal the date to dvd
update_findings_date(args.config, result)
elif args.report_type == 'no_findings':
# Findings is empty but a date is listed
result = findings_empty(df)
elif args.report_type == 'no_findings_or_date':
# Both the findings and findings date are empty
result = findings_and_date_empty(df)
if args.reset_datetodvd:
record = result[result.experiment_id == experiment]
project = record.project.values[0]
subject = record.subject_id.values[0]
experiment = args.reset_datetodvd
set_experiment_attrs(args.config, project, subject, experiment,
'datetodvd', 'none')
elif args.report_type == 'correct_dvd_date':
dates_df = pd.read_csv(args.file_to_reset_datetodvd)
result = pd.DataFrame(index=['Subject'],
columns=[
'project', 'subject_id', 'experiment_id',
'site_experiment_id', 'datetodvd',
'findingsdate'
])
result = result.fillna(0)
for subject in df['subject_id'].tolist():
if subject in dates_df['mri_xnat_sid'].tolist():
if args.verbose:
print "Checking for {}".format(subject)
eids = dates_df[dates_df['mri_xnat_sid'] ==
subject]['mri_xnat_eids'].tolist()
date = dates_df[dates_df['mri_xnat_sid'] ==
subject]['mri_datetodvd'].tolist()
if eids != []:
if len(eids[0]) == 13:
experiment = eids[0]
record = df[df.experiment_id == experiment]
record_date = record['datetodvd'].tolist()
if date != [] and record_date != []:
if record_date[0] != date[0] or type(
record_date[0]) != str():
project = record.project.values[0]
subject = record.subject_id.values[0]
experiment = record.experiment_id.values[0]
set_experiment_attrs(args.config, project,
subject, experiment,
'datetodvd', date[0])
elif len(eids[0]) == 27 or eids == None:
experiment = eids[0].split(" ")
for e in experiment:
record_date = record['datetodvd'].tolist()
record = df[df.experiment_id == e]
if date != [] and record_date != []:
if record_date[0] != date[0] or type(
record_date[0]) == str():
project = record.project.values[0]
subject = record.subject_id.values[0]
set_experiment_attrs(
args.config, project, subject, e,
'datetodvd', date[0])
elif args.report_type == 'no_findings_before_date':
# Findings and Findings Date is empty before a given date
if not args.before_date:
raise (Exception(
"Please set --before-date YYYY-MM-DD when running the no_findings_before_date report."
))
has_dvd_before_date = check_dvdtodate_before_date(
df, before_date=args.before_date)
result = findings_and_date_empty(has_dvd_before_date)
result.to_csv(args.outfile, index=False)
else:
raise (
NotImplementedError("The report you entered is not in the list."))
result.to_csv(args.outfile,
columns=[
'project', 'subject_id', 'experiment_id',
'site_experiment_id', 'datetodvd', 'findingsdate'
],
index=False)
if verbose:
pd.set_option('display.max_rows', len(result))
print("Total records found: {}".format(len(result)))
print(result[['experiment_id', 'site_experiment_id']])
pd.reset_option('display.max_rows')
print("Finished!")
def main(args=None):
# TODO: Handle when T1 and T2 are in separate session (i.e., rescan)
if args.update:
config = xe.get_config(args.config)
session = xe.get_xnat_session(config)
xe.extract_experiment_xml(config, session, args.experimentsdir,
args.num_extract)
# extract info from the experiment XML files
experiment = xe.get_experiments_dir_info(args.experimentsdir)
# Scan specific information
scan = xe.get_experiments_dir_scan_info(args.experimentsdir)
# Session info
reading = xe.get_experiments_dir_reading_info(args.experimentsdir)
df = xe.merge_experiments_scans_reading(experiment, scan, reading)
# exclude phantoms, including the traveling human phantoms
site_id_pattern = '[A-E]-[0-9]{5}-[MF]-[0-9]'
df = df[df.site_id.str.contains(site_id_pattern)]
# exclude subjects not part of study
df = df[df['subject_id'] != 'NCANDA_S00127']
if args.unknown:
print "Sessions that have not yet been quality controlled"
scanCheckList = pd.DataFrame()
required_scans = [
'ncanda-mprage-v1', 'ncanda-t1spgr-v1', 'ncanda-t2fse-v1',
'ncanda-dti6b500pepolar-v1', 'ncanda-dti30b400-v1',
'ncanda-dti60b1000-v1', 'ncanda-grefieldmap-v1', 'ncanda-rsfmri-v1'
]
for eid in df.experiment_id.drop_duplicates():
eid_df = df[df.experiment_id == eid]
eid_df = eid_df[~pd.isnull(eid_df['quality'])]
if not len(eid_df[eid_df['quality'] != 'unknown']):
print eid
else:
unknownScanDF = eid_df[eid_df['quality'] == 'unknown']
mandatoryCheck = unknownScanDF[unknownScanDF['scan_type'].isin(
required_scans)]
if len(mandatoryCheck):
scanCheckList = scanCheckList.append(mandatoryCheck)
print " "
print "Mandatory scans that have not yet been quality controlled"
pd.set_option('display.max_rows', len(scanCheckList))
print scanCheckList['scan_type']
sys.exit()
if args.ignore_window or args.session_notes or args.scan_notes:
if args.usable:
df = df[df['quality'] == 'usable']
columns = [
'site_id', 'subject_id', 'experiment_id', 'experiment_date',
'excludefromanalysis'
]
if args.ignore_window or args.scan_notes:
columns = columns + ['scan_id', 'scan_type', 'quality']
if args.scan_notes:
columns = columns + ['scan_note']
if args.session_notes:
columns = columns + ['note']
result = df[columns]
# print result
else:
df.loc[:, 'experiment_date'] = df.experiment_date.astype('datetime64')
result = pd.DataFrame()
for subject_id in df.subject_id.drop_duplicates():
subject_df = df[df.subject_id == subject_id]
# find the earliest exam date for each given subject
grouping = subject_df.groupby('subject_id')
baseline_date = grouping['experiment_date'].nsmallest(1)
baseline_df = subject_df[subject_df.experiment_date ==
baseline_date[0]]
# Find window for follow-up
day_min = pd.datetools.Day(n=args.min)
day_max = pd.datetools.Day(n=args.max)
followup_min = baseline_df.experiment_date + day_min
followup_max = baseline_df.experiment_date + day_max
df_min = subject_df.experiment_date > followup_min[0]
df_max = subject_df.experiment_date < followup_max[0]
followup_df = subject_df[df_min & df_max]
# Included followup sessions slightly outside window
included = ['NCANDA_E02615', 'NCANDA_E02860']
included_df = subject_df[subject_df.experiment_id.isin(included)]
if included_df.shape[0]:
followup_df = included_df
# Create report for baseline visit
if args.baseline:
followup_df = baseline_df
# filter for specific scan types
scan_type_pairs = get_scan_type_pairs(args.modality)
scan1 = scan_type_pairs.get('scan1')
scan2 = scan_type_pairs.get('scan2')
scan1_df = followup_df[followup_df.scan_type.isin(scan1)]
scan2_df = followup_df[followup_df.scan_type.isin(scan2)]
# Filter quality column
if args.usable:
scan1_selected = scan1_df[scan1_df.quality == 'usable']
scan2_selected = scan2_df[scan2_df.quality == 'usable']
else:
scan1_selected = scan1_df
scan2_selected = scan2_df
# report columns
columns = [
'site_id', 'subject_id', 'experiment_id', 'experiment_date',
'excludefromanalysis', 'note', 'scan_type', 'quality',
'scan_note'
]
scan1_recs = scan1_selected.loc[:, columns].to_records(index=False)
scan2_recs = scan2_selected.loc[:, columns].to_records(index=False)
scan1_report = pd.DataFrame(scan1_recs,
index=scan1_selected.experiment_id)
scan2_report = pd.DataFrame(scan2_recs,
index=scan2_selected.experiment_id)
scan1_scan2_report = scan1_report.join(
scan2_report[['scan_type', 'quality', 'scan_note']],
lsuffix='_scan1',
rsuffix='_scan2',
how='inner')
if scan1_scan2_report.shape[0]:
result = result.append(scan1_scan2_report)
#
# Write out results
#
# Remove any duplicate rows due to extra usable scan types (i.e., fieldmaps)
result = result.drop_duplicates()
result.to_csv(args.outfile, index=False)
def main(args=None):
config = xe.get_config(args.config)
session = xe.get_xnat_session(config)
if args.update:
# Update the cache of XNAT Experiment XML files
xe.extract_experiment_xml(config, session,
args.experimentsdir, args.num_extract)
# extract info from the experiment XML files
experiment = xe.get_experiments_dir_info(args.experimentsdir)
experiment_df = xe.experiments_to_dataframe(experiment)
reading = xe.get_experiments_dir_reading_info(args.experimentsdir)
reading_df = xe.reading_to_dataframe(reading)
experiment_reading = inner_join_dataframes(experiment_df, reading_df)
# exclude phantoms, but include the traveling human phantoms
site_id_pattern = '[A-EX]-[0-9]{5}-[MFT]-[0-9]'
df = experiment_reading[experiment_reading.site_id.str.contains(site_id_pattern)]
result = None
if args.report_type == 'no_findings_date':
# Findings are listed without a findings date
result = findings_date_empty(df)
if args.set_findings_date:
# Update the findings date to equal the date to dvd
update_findings_date(args.config, result)
elif args.report_type == 'no_findings':
# Findings is empty but a date is listed
result = findings_empty(df)
elif args.report_type == 'no_findings_or_date':
# Both the findings and findings date are empty
result = findings_and_date_empty(df)
if args.reset_datetodvd:
record = result[result.experiment_id == experiment]
project = record.project.values[0]
subject = record.subject_id.values[0]
experiment = args.reset_datetodvd
set_experiment_attrs(args.config, project, subject, experiment, 'datetodvd', 'none')
elif args.report_type == 'correct_dvd_date':
dates_df = pd.read_csv(args.file_to_reset_datetodvd)
result = pd.DataFrame(index=['Subject'], columns=['project', 'subject_id', 'experiment_id',
'site_experiment_id', 'datetodvd', 'findingsdate'])
result = result.fillna(0)
for subject in df['subject_id'].tolist():
if subject in dates_df['mri_xnat_sid'].tolist():
if args.verbose:
print "Checking for {}".format(subject)
eids = dates_df[dates_df['mri_xnat_sid'] == subject]['mri_xnat_eids'].tolist()
date = dates_df[dates_df['mri_xnat_sid'] == subject]['mri_datetodvd'].tolist()
if eids != []:
if len(eids[0]) == 13:
experiment = eids[0]
record = df[df.experiment_id == experiment]
record_date = record['datetodvd'].tolist()
if date != [] and record_date != []:
if record_date[0] != date[0] or type(record_date[0]) != str() :
project = record.project.values[0]
subject = record.subject_id.values[0]
experiment = record.experiment_id.values[0]
set_experiment_attrs(args.config, project, subject, experiment, 'datetodvd', date[0])
elif len(eids[0]) == 27 or eids == None:
experiment = eids[0].split(" ")
for e in experiment:
record_date = record['datetodvd'].tolist()
record = df[df.experiment_id == e]
if date != [] and record_date != []:
if record_date[0] != date[0] or type(record_date[0]) == str():
project = record.project.values[0]
subject = record.subject_id.values[0]
set_experiment_attrs(args.config, project, subject, e, 'datetodvd', date[0])
elif args.report_type == 'no_findings_before_date':
# Findings and Findings Date is empty before a given date
if not args.before_date:
raise(Exception("Please set --before-date YYYY-MM-DD when running the no_findings_before_date report."))
has_dvd_before_date = check_dvdtodate_before_date(df, before_date=args.before_date)
result = findings_and_date_empty(has_dvd_before_date)
result.to_csv(args.outfile, index=False)
else:
raise(NotImplementedError("The report you entered is not in the list."))
result.to_csv(args.outfile,
columns=['project', 'subject_id', 'experiment_id',
'site_experiment_id', 'datetodvd', 'findingsdate'],
index=False)
if verbose:
pd.set_option('display.max_rows', len(result))
print("Total records found: {}".format(len(result)))
print(result[['experiment_id', 'site_experiment_id']])
pd.reset_option('display.max_rows')
print("Finished!")
def main(args=None):
# TODO: Handle when T1 and T2 are in separate session (i.e., rescan)
if args.update:
config = xe.get_config(args.config)
session = xe.get_xnat_session(config)
xe.extract_experiment_xml(config, session,
args.experimentsdir, args.num_extract)
# extract info from the experiment XML files
experiment = xe.get_experiments_dir_info(args.experimentsdir)
# Scan specific information
scan = xe.get_experiments_dir_scan_info(args.experimentsdir)
# Session info
reading = xe.get_experiments_dir_reading_info(args.experimentsdir)
df = xe.merge_experiments_scans_reading(experiment, scan, reading)
# exclude phantoms, including the traveling human phantoms
site_id_pattern = '[A-E]-[0-9]{5}-[MF]-[0-9]'
df = df[df.site_id.str.contains(site_id_pattern)]
# convert to date type
df.loc[:, 'experiment_date'] = df.experiment_date.astype('datetime64')
result = pd.DataFrame()
for subject_id in df.subject_id.drop_duplicates():
subject_df = df[df.subject_id == subject_id]
# find the earliest exam date for each given subject
grouping = subject_df.groupby('subject_id')
baseline_date = grouping['experiment_date'].nsmallest(1)
baseline_df = subject_df[subject_df.experiment_date == baseline_date[0]]
# Find window for follow-up
day_min = pd.datetools.Day(n=args.min)
day_max = pd.datetools.Day(n=args.max)
followup_min = baseline_df.experiment_date + day_min
followup_max = baseline_df.experiment_date + day_max
df_min = subject_df.experiment_date > followup_min[0]
df_max = subject_df.experiment_date < followup_max[0]
followup_df = subject_df[df_min & df_max]
# Included followup sessions slightly outside window
included = ['NCANDA_E02615', 'NCANDA_E02860']
included_df = subject_df[subject_df.experiment_id.isin(included)]
if included_df.shape[0]:
followup_df = included_df
# Create report for baseline visit
if args.baseline:
followup_df = baseline_df
# filter for specific scan types
scan_type_pairs = get_scan_type_pairs(args.modality)
scan1 = scan_type_pairs.get('scan1')
scan2 = scan_type_pairs.get('scan2')
scan1_df = followup_df[followup_df.scan_type.isin(scan1)]
scan2_df = followup_df[followup_df.scan_type.isin(scan2)]
# Filter quality column
if args.usable :
scan1_selected = scan1_df[scan1_df.quality == 'usable']
scan2_selected = scan2_df[scan2_df.quality == 'usable']
else :
scan1_selected = scan1_df
scan2_selected = scan2_df
# report columns
columns = ['site_id', 'subject_id', 'experiment_id', 'experiment_date',
'excludefromanalysis', 'note', 'scan_type', 'quality',
'scan_note']
scan1_recs = scan1_selected.loc[:, columns].to_records(index=False)
scan2_recs = scan2_selected.loc[:, columns].to_records(index=False)
scan1_report = pd.DataFrame(scan1_recs,
index=scan1_selected.experiment_id)
scan2_report = pd.DataFrame(scan2_recs,
index=scan2_selected.experiment_id)
scan1_scan2_report = scan1_report.join(scan2_report[['scan_type',
'quality',
'scan_note']],
lsuffix='_scan1',
rsuffix='_scan2',
how='inner')
if scan1_scan2_report.shape[0]:
result = result.append(scan1_scan2_report)
# Remove any duplicate rows due to extra usable scan types (i.e., fieldmaps)
result = result.drop_duplicates()
result.to_csv(args.outfile, index=False)
def main(args=None):
# TODO: Handle when T1 and T2 are in separate session (i.e., rescan)
if args.update:
config = xe.get_config(args.config)
session = xe.get_xnat_session(config)
xe.extract_experiment_xml(config, session, args.experimentsdir,
args.num_extract)
# extract info from the experiment XML files
experiment = xe.get_experiments_dir_info(args.experimentsdir)
scan = xe.get_experiments_dir_scan_info(args.experimentsdir)
reading = xe.get_experiments_dir_reading_info(args.experimentsdir)
df = xe.merge_experiments_scans_reading(experiment, scan, reading)
# exclude phantoms, including the traveling human phantoms
site_id_pattern = '[A-E]-[0-9]{5}-[MF]-[0-9]'
df = df[df.site_id.str.contains(site_id_pattern)]
# convert to date type
df.loc[:, 'experiment_date'] = df.experiment_date.astype('datetime64')
result = pd.DataFrame()
for subject_id in df.subject_id.drop_duplicates():
subject_df = df[df.subject_id == subject_id]
# find the earliest exam date for each given subject
baseline_date = subject_df.groupby(
'subject_id')['experiment_date'].nsmallest(1)
baseline_df = subject_df[subject_df.experiment_date ==
baseline_date[0]]
# Find window for follow-up
followup_min = baseline_df.experiment_date + pd.datetools.Day(
n=args.min)
followup_max = baseline_df.experiment_date + pd.datetools.Day(
n=args.max)
followup_df = subject_df[
(subject_df.experiment_date > followup_min[0])
& (subject_df.experiment_date < followup_max[0])]
# Included followup sessions slightly outside window
included = ['NCANDA_E02615', 'NCANDA_E02860']
included_df = subject_df[subject_df.experiment_id.isin(included)]
if included_df.shape[0]:
followup_df = included_df
# Create report for baseline visit
if args.baseline:
followup_df = baseline_df
# filter for specific scan types
scan_type_pairs = get_scan_type_pairs(args.modality)
scan1 = scan_type_pairs.get('scan1')
scan2 = scan_type_pairs.get('scan2')
scan1_df = followup_df[followup_df.scan_type.isin(scan1)]
scan2_df = followup_df[followup_df.scan_type.isin(scan2)]
# Filter quality column
scan1_usable = scan1_df[scan1_df.quality == 'usable']
scan2_usable = scan2_df[scan2_df.quality == 'usable']
# report columns
columns = [
'site_id', 'subject_id', 'experiment_id', 'scan_type',
'experiment_date', 'quality', 'excludefromanalysis', 'note'
]
scan1_recs = scan1_usable.loc[:, columns].to_records(index=False)
scan2_recs = scan2_usable.loc[:, columns].to_records(index=False)
scan1_report = pd.DataFrame(scan1_recs,
index=scan1_usable.experiment_id)
scan2_report = pd.DataFrame(scan2_recs,
index=scan2_usable.experiment_id)
scan1_scan2_report = scan1_report.join(
scan2_report[['scan_type', 'quality']],
lsuffix='_scan1',
rsuffix='_scan2',
how='inner')
if scan1_scan2_report.shape[0]:
result = result.append(scan1_scan2_report)
# Remove any duplicate rows due to extra usable scan types (i.e., fieldmaps)
result = result.drop_duplicates()
result.to_csv(args.outfile, index=False)