Python XnatUtils.get_full_object方法代码示例

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
def edit_session_date(xnat, session_info):
    date = session_info['label'].split('_')[-1]
    date = '{}-{}-{}'.format(date[:4], date[4:6], date[6:])
    print("%s - %s" % (session_info['label'], date))
    if session_info['date'] == date:
        print ' already set up.'
    else:
        session_obj = XnatUtils.get_full_object(xnat, session_info)
        session_obj.attrs.set('date', date)

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
def sessions_delete():
    """Delete sessions on XNAT."""
    for session in LI_SESSIONS:
        print ' - deleting session: %s' % session['label']
        session_obj = XnatUtils.get_full_object(XNAT, session)
        if session_obj.exists():
            try:
                session_obj.delete()
            except:
                print "exception but let's continue"

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
def set_session_age(session_info):
    """Set age for session."""
    if not session_info['age'] or ARGS.force:
        session_obj = XnatUtils.get_full_object(XNAT, session_info)
        xsitype_sess = session_obj.attrs.get('xsiType')
        yob = session_obj.parent().attrs.get('yob')
        if not yob:
            print 'Skipping the session because yob not set.'
        else:
            yob = "%s-01-01" % yob
            years = years_between(yob, session_info['date'])
            age = '%.2f' % years
            session_obj.attrs.set('%s/%s' % (xsitype_sess, 'age'), age)
            print 'Age set to %s for %s.' % (age, session['label'])
    else:
        print 'Already set to %s for %s' % (session_info['age'],
                                            session['label'])

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
def zip_resources(xnat, args):
    """
    Loop through the project scans to zip files.

    :param xnat: interface from dax related to pyxnat
    :param args: arguments from parse_args
    """
    # set a directory where the files are download
    directory = os.path.abspath(XnatUtils.makedir(args.directory))

    list_scans = XnatUtils.list_project_scans(xnat, args.project)
    print("INFO: Filtering list of scans to keep scans with resources.")
    if not args.force:
        for resource in args.resources.split(','):
            list_scans = filter(lambda x: resource in x['resources'],
                                list_scans)

    # if sessions, filter:
    if args.sessions:
        list_scans = filter(
            lambda x: x['session_label'] in args.sessions.split(','),
            list_scans)

    # filtering last sessions:
    list_scans = sorted(list_scans, key=lambda k: k['session_label'])
    if args.lastsess:
        list_scans = remove_sessions_processed(list_scans, args.lastsess)

    number_scans = len(list_scans)
    print("INFO: Converting the %s scans found." % (number_scans))
    for index, scan in enumerate(list_scans):
        message = ' * {ind}/{tot} -- Session: {sess} -- Scan: {scan}'
        print(message.format(ind=index + 1,
                             tot=number_scans,
                             sess=scan['session_label'],
                             scan=scan['ID']))
        scan_obj = XnatUtils.get_full_object(xnat, scan)
        if scan_obj.exists():
            for resource in args.resources.split(','):
                zip_resource(scan_obj.resource(resource), directory,
                             resource, args.no_delete, args.no_big)

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
        if args.subjects:
            li_scans = XnatUtils.filter_list_dicts_regex(
                           li_scans, 'subject_label', args.subjects.split(','))
        li_scans = sorted(li_scans, key=lambda k: k['session_label'])
        for scan_d in li_scans:
            if scan_d['ID'] == 'n004':
                print (' -> converting session: %s /scan: %s'
                       % (scan_d['session_label'], scan_d['ID']))
                if 'IMG' in scan_d['resources']:
                    if 'NIFTI' not in scan_d['resources'] or args.force:
                        tmp_dir = os.path.join(args.directory,
                                               scan_d['session_label'],
                                               scan_d['ID'])
                        if not os.path.isdir(tmp_dir):
                            os.makedirs(tmp_dir)
                        scan_obj = XnatUtils.get_full_object(xnat, scan_d)
                        # Download:
                        files = XnatUtils.download_files_from_obj(
                                                tmp_dir, scan_obj.resource('IMG'))
                        if len(files) > 1 and args.zip_fdf:
                            zipping_files(scan_obj, os.path.dirname(files[0]))

                        if len(files) == 1 and files[0].endswith('.zip'):
                            fdf_dir = os.path.dirname(files[0])
                            os.system('unzip -d %s -j %s > /dev/null'
                                      % (fdf_dir, files[0]))
                            os.remove(files[0])
                            files = get_files_list(fdf_dir, '.fdf',
                                                   add_procpar=True)

                        # Convert:

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
try:
    xnat = XnatUtils.get_interface(host=HOST)

    if ASSESSOR:
        li_assessors = [XnatUtils.select_assessor(xnat, ASSESSOR)]
        sys.stdout.write('Renaming resources %s to %s for assessor %s'
                         % (OLD_RESOURCE, NEW_RESOURCE, ASSESSOR))
    else:
        li_assessors = XnatUtils.list_project_assessors(xnat, PROJECT)
        sys.stdout.write('Renaming resources %s to %s for assessor type %s\n'
                         % (OLD_RESOURCE, NEW_RESOURCE, ASSESSOR_TYPE))

    for assessor in li_assessors:
        sys.stdout.write(' - assessor: %s ...\n' % assessor['label'])
        assessors = XnatUtils.get_full_object(xnat, assessor)
        old_res = assessors.resource(OLD_RESOURCE)
        files = None
        if old_res.exists():
            files = XnatUtils.download_files_from_obj(TMP_DIR, old_res)
            if files:
                new_res = assessors.resource(NEW_RESOURCE)
                XnatUtils.upload_files_to_obj(files, new_res)
                if new_res.exists():
                    old_res.delete()
                    sys.stdout.write('   renamed.\n')
                for f in files:
                    os.remove(f)

    print "DONE -- See y'all"
except Exception as e:

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
def make_preview_nifti(xnat, options):
    """generate previewe for a project on XNAT."""
    # make directory
    if not os.path.exists(options.directory):
        os.makedirs(options.directory)

    # list of scans for the project
    list_scans = XnatUtils.list_project_scans(xnat, options.project)
    # filter the list to keep scans with DICOM and no NIFTI
    if not options.force:
        print "Filtering scans to keep scans with NIFTI but no SNAPSHOTS."
        list_scans = filter(lambda x: 'NIFTI' in x['resources'] and
                                      'SNAPSHOTS' not in x['resources'],
                            list_scans)
    # if sessions, filter:
    if options.sessions:
        list_scans = filter(
            lambda x: x['session_label'] in options.sessions.split(','),
            list_scans)
    number_scans = len(list_scans)
    for index, scan in enumerate(sorted(list_scans,
                                        key=lambda k: k['session_label'])):
        message = ' * {index}/{total} -- Session: {session} -- Scan: {scan}'
        print message.format(index=index+1,
                             total=number_scans,
                             session=scan['session_label'],
                             scan=scan['ID'])
        scan_obj = XnatUtils.get_full_object(xnat, scan)

        res_obj = scan_obj.resource(options.resource)
        if res_obj.exists() and len(res_obj.files().get()) > 0:
            if options.force and scan_obj.resource("SNAPSHOTS").exists():
                scan_obj.resource("SNAPSHOTS").delete()
            print "   --> downloading "+options.resource+" ..."
            filename = XnatUtils.download_biggest_file_from_obj(
                                            options.directory, res_obj)
            if not filename:
                print '    - warning: '+options.resource+' -- no files.'
            else:
                if filename.endswith('.nii.gz'):
                    os.system('gzip -d '+filename)
                    filename = filename[:-3]
                fname = os.path.basename(filename).split('.')[0] + "_sm.gif"
                smgif = os.path.join(options.directory, fname)
                fname = os.path.basename(filename).split('.')[0] + "_lg.gif"
                lggif = os.path.join(options.directory, fname)

                status = generate_preview(filename, smgif, lggif)

                if not status:
                    print '   --> GIF FAILED'
                else:
                    if os.path.isfile(smgif):
                        print '   --> GIF Made / upload to XNAT...'
                        scan_obj.resource('SNAPSHOTS').file('snap_t.gif')\
                                .put(smgif, 'GIF', 'THUMBNAIL')
                        scan_obj.resource('SNAPSHOTS').file('snap.gif')\
                                .put(lggif, 'GIF', 'ORIGINAL')
                    else:
                        print '   --> GIF FAILED'

                    if os.path.isfile(smgif):
                        os.remove(smgif)
                        os.remove(lggif)

                if os.path.isfile(filename):
                    os.remove(filename)
        else:
            print("    - ERROR : issue with resource %s: no file or resource. "
                  % (options.resource))

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
def convert_DICOM():
    """Loop through the project scans to convert DICOM to NIFTI."""
    list_scans = XnatUtils.list_project_scans(XNAT, OPTIONS.project)
    # filter the list to keep scans with DICOM and no NIFTI
    if not OPTIONS.force:
        print "Filtering list of scans to keep scans with DICOM but no NIFTI."
        list_scans = filter(
         lambda x: 'DICOM' in x['resources'] and 'NIFTI' not in x['resources'],
         list_scans)
    else:
        print "Filtering list of scans to keep scans with DICOM."
        list_scans = filter(lambda x: 'DICOM' in x['resources'], list_scans)
    # if sessions, filter:
    if OPTIONS.sessions:
        list_scans = filter(
            lambda x: x['session_label'] in OPTIONS.sessions.split(','),
            list_scans)
    number_scans = len(list_scans)
    print "Converting the %s scans found." % (number_scans)
    for index, scan in enumerate(sorted(list_scans,
                                        key=lambda k: k['session_label'])):
        message = ' * {index}/{total} -- Session: {session} -- Scan: {scan}'
        print message.format(index=index+1,
                             total=number_scans,
                             session=scan['session_label'],
                             scan=scan['ID'])
        need_to_zip = False
        scan_obj = XnatUtils.get_full_object(XNAT, scan)
        if scan_obj.exists() and \
           len(scan_obj.resource('DICOM').files().get()) > 0:
            print "   --> downloading DICOM ..."
            fpaths = XnatUtils.download_files_from_obj(
                        OPTIONS.directory,
                        scan_obj.resource("DICOM"))
            if not fpaths:
                print '    - warning: DICOM -- no files.'
            else:
                if OPTIONS.force and scan_obj.resource('NIFTI').exists():
                    scan_obj.resource('NIFTI').delete()

                dcm_dir = os.path.join(OPTIONS.directory, 'DICOM')
                if len(fpaths) > 1:
                    need_to_zip = True

                if len(fpaths) == 1 and fpaths[0].endswith('.zip'):
                    if not os.path.exists(dcm_dir):
                        os.makedirs(dcm_dir)
                    os.system('unzip -d %s -j %s > /dev/null' % (dcm_dir,
                                                                 fpaths[0]))
                    os.remove(fpaths[0])
                dicom_files = get_dicom_list(dcm_dir)

                if dicom_files:
                    # Check for duplicate dicoms:
                    if OPTIONS.check_dcm:
                        check_duplicate_slices_dicom(dicom_files)
                    # convert dcm to nii
                    conversion_status = dcm2nii(dicom_files[0])

                    if not conversion_status:
                        # Convert dcm via dcmdjpeg
                        dcmdjpeg(dcm_dir)
                        # try again dcm2nii
                        dcm_fpath = os.path.join(dcm_dir, 'final_1.dcm')
                        conversion_status = dcm2nii(dcm_fpath)

                    # Check if Nifti created:
                    nii_li = [f for f in os.listdir(dcm_dir)
                              if f.endswith('.nii.gz') or f.endswith('.nii')]
                    if not nii_li:
                        print "    - warning: dcm to nii failed with \
conversion dcmjpeg. no upload."
                    else:
                        # UPLOADING THE RESULTS
                        upload_converted_images(dicom_files, dcm_dir, scan_obj,
                                                need_to_zip)

                    # clean tmp folder
                    XnatUtils.clean_directory(OPTIONS.directory)
                else:
                    print "    - ERROR : no proper DICOM files \
found from the resource on XNAT. "

        else:
            print "    - ERROR : issue with resource DICOM: \

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
    li_scans = [scan for scan in li_scans
                if scan['type'] == '1946_PET_NAC_DYNAMIC_0_60MIN']

    row = list()
    for scan in li_scans:
        if scan['session_label'] not in li_sessions:
            msg = 'Download scan number %s for session %s'
            print msg % (scan['ID'], scan['session_label'])
            # data_dir = os.path.join(args.directory, scan['subject_label'],
            #                        scan['session_label'], 'scans',
            #                        '1946_PET_NAC_DYNAMIC_0_60MIN')
            data_dir = os.path.join(args.directory, scan['session_label'])
            if os.path.exists(data_dir):
                print ' --> Folder present. Already downloaded?'
            else:
                scan_obj = XnatUtils.get_full_object(XNAT, scan)
                res_obj = scan_obj.resource('DICOM')
                if not res_obj.exists():
                    print ' Error: No DICOM Resources found for scan.'
                else:
                    if len(res_obj.files().get()) > 0:
                        print ' 1) start download...'
                        os.makedirs(data_dir)
                        dl_files = XnatUtils.download_files_from_obj(data_dir,
                                                                     res_obj)
                        print ' 2) Files downloaded'
                    else:
                        os.makedirs(data_dir)
                        curl = CCMD.format(path=data_dir,
                                           host=HOST,
                                           project='1946',

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
__purpose__ = "Renaming attrs for xnat object"
__version__ = '1.0.0'
__modifications__ = '11 September 2015 - Original write'


if __name__ == '__main__':
    host = os.environ['XNAT_HOST']
    user = os.environ['XNAT_USER']
    pwd = os.environ['XNAT_PASS']
    subject_type = False
    session_type = True
    xnat = XnatUtils.get_interface(host=host, user=user, pwd=pwd)

    if subject_type:
        for subject in XnatUtils.list_subjects(xnat, projectid='INNOVATE'):
            subj_obj = XnatUtils.get_full_object(xnat, subject)
            if subj_obj.exists():
                labels = subject['label'].split('-')
                if subject['label'].startswith('INN_'):
                    sub = subject['label'].replace('_', '-')
                    labels = sub.split('-')
                if len(labels) < 2:
                    print 'stop - wrong label'
                    continue
                if labels[1].isdigit():
                    print 'stop - already good label'
                    continue
                if '_' in labels[2]:
                    fin = '_'+'_'.join(labels[2].split('_')[1:])
                    labels[2] = labels[2].split('_')[0]
                else:

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
                    'Olin': 5,
                    'Pitt': 0,
                    'SBL': 0,
                    'SDSU': 0,
                    'Stanford': 0,
                    'Trinity': 0,
                    'UCLA': 0,
                    'UM': 0,
                    'USM': 0,
                    'Yale': 5}

    XNAT = XnatUtils.get_interface()
    SCANS = XnatUtils.list_project_scans(XNAT, 'ABIDE')
    for SCAN in SCANS:
        if SCAN_TYPE in SCAN['type']:

            OBJECT = XnatUtils.get_full_object(XNAT, SCAN)
            dropvols_num = get_num_dropvols(SCAN['session_label'])
            sys.stdout.write('Setting dropvols to {dropvols} and slorder '
                             'to {slorder} for scan id {scanid} for '
                             'session {session}\n'.format(dropvols=dropvols_num,
                                                          slorder='[]',
                                                          scanid=SCAN['ID'],
                                                          session=SCAN['session_label']))

            OBJECT.attrs.set('xnat:mrScanData/parameters/addParam[name=dropvols]/addField', str(dropvols_num))
            OBJECT.attrs.set('xnat:mrScanData/parameters/addParam[name=slorder]/addField', '[]')
    XNAT.disconnect()

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
        print 'INFO: connection to xnat <%s>:' % (HOST)
        XNAT = XnatUtils.get_interface(host=ARGS.host, user=ARGS.username,
                                       pwd=PWD)
        li_assessors = XnatUtils.list_project_assessors(XNAT, ARGS.project)
        li_assessors = XnatUtils.filter_list_dicts_regex(
                                li_assessors, 'proctype',
                                ['GIF_Parcellation_v2'])
        li_assessors = XnatUtils.filter_list_dicts_regex(
                                li_assessors, 'procstatus',
                                ['COMPLETE'])
        li_assessors = filter(lambda x: 'WHOLEBRAIN' not in x['resources'],
                              li_assessors)
        li_assessors = sorted(li_assessors, key=lambda k: k['session_label'])
        start = False
        for assessor in li_assessors:
            if ARGS.session:
                if assessor['session_label'] == ARGS.session:
                    start = True
            else:
                start = True
            if start:
                print '\n<-- Assessor: %s -->' % assessor['label']
                assessor_obj = XnatUtils.get_full_object(XNAT, assessor)
                brain = generate_bmask_whole(assessor_obj, assessor,
                                             ARGS.tmpdir)
                XnatUtils.upload_file_to_obj(
                    brain, assessor_obj.resource('WHOLEBRAIN'), removeall=True)

    finally:
        XNAT.disconnect()

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import get_full_object [as 别名]
    XNAT = XnatUtils.get_interface()
    ASSESSORS = XnatUtils.list_project_assessors(XNAT, 'WOODWARD_TCP')

    if len(sys.argv) != 4:
        print len(sys.argv)
        sys.stderr.write('ERROR: args must be <ASSESSOR_LABEL> <STATUS> <COMMENTS>')
        sys.exit()
    MY_ASSESSOR = sys.argv[1]
    STATUS = sys.argv[2]
    COMMENTS = sys.argv[3]
    if STATUS not in XNAT_STATUS_LIST:
        sys.stderr.write('ERROR: Status "%s" not in known list: %s\n'
                         %(STATUS, ','.join(XNAT_STATUS_LIST)))

    for ASSESSOR in ASSESSORS:
        if ASSESSOR['label'] == MY_ASSESSOR:
            print "Setting QC of assessor %s to %s" % (MY_ASSESSOR,
                                                       STATUS)
            OBJECT = XnatUtils.get_full_object(XNAT, ASSESSOR)
            if not MY_ASSESSOR.endswith('-x-FS'):
                OBJECT.attrs.set('proc:genProcData/validation/status', STATUS)
                OBJECT.attrs.set('proc:genProcData/validation/notes', COMMENTS)
            else:
                OBJECT.attrs.set('fs:fsData/validation/status', STATUS)
                OBJECT.attrs.set('fs:fsData/validation/notes', COMMENTS)

    XNAT.disconnect()