Python XnatUtils.list_project_scans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 list_project_scans [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 list_project_scans [as 别名]
    if pixel_array2.dtype != np.uint16:
        pixel_array2 = pixel_array2.astype(np.uint16)
        print pixel_array2.max()
        print pixel_array2.min()

    ds.PixelData = pixel_array2.tostring()
    # Save the image
    ds.save_as(filename)

if __name__ == '__main__':
    args = parse_args()

    # Scans on XNAT:
    try:
        xnat = XnatUtils.get_interface()
        li_scans = XnatUtils.list_project_scans(xnat, args.project)
        # Filter:
        if args.sessions:
            li_scans = XnatUtils.filter_list_dicts_regex(
                           li_scans, 'session_label', args.sessions.split(','))
        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,

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import list_project_scans [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 list_project_scans [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 list_project_scans [as 别名]
                      help="Directory where the json files are stored.",
                      required=True)
    argp.add_argument('-c', dest='csv',
                      help="Csv file containing the subject that where already\
                            downloaded.",
                      required=True)
    return argp.parse_args()

if __name__ == '__main__':
    args = parse_args()
    row_excel = read_csv(args.csv, header=['subject', 'session'])
    li_sessions = [row['session'].strip() for row in row_excel]

    XNAT = XnatUtils.get_interface(host=HOST)

    li_scans = XnatUtils.list_project_scans(XNAT, '1946')
    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:

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import list_project_scans [as 别名]
                    'MaxMun': 0,
                    'NYU': 5,
                    'OHSU': 0,
                    '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 list_project_scans [as 别名]
    if not os.path.isfile(file_not_zipped):
        sys.stderr.write('ERROR: could not find file %s to gzip' % file_not_zipped)
    else:
        file_name_out = '%s.gz' % file_not_zipped
        content = open(file_not_zipped, 'rb')
        content = content.read()
        fout = gzip.open(file_name_out, 'wb')
        fout.write(content)
        fout.close()
        os.remove(file_not_zipped)
    return file_name_out


if __name__ == '__main__':
    XNAT = XnatUtils.get_interface()
    SCANS = XnatUtils.list_project_scans(XNAT, 'SMITH_DOD')
    FID = open('/tmp/SMITH_DOD.csv', 'w')
    NEEDS_UPLOAD = False
    TMP_DIR_LIST = list()

    for SCAN in SCANS:
        NEED_PAR = False
        NEED_REC = True
        sys.stdout.write('Checking scan %s in session %s\n' % (SCAN['ID'], SCAN['session_label']))
        if 'DICOM' not in SCAN['resources'] and 'secondary' in SCAN['resources'] and SCAN['ID'] not in KNOWN_IGNORE_LIST \
                and 'superpacs' not in SCAN['type'].lower():
            sys.stdout.write(' -DICOM not found. Checking to see if PAR and REC do\n')
            if 'PAR' not in SCAN['resources']:
                sys.stdout.write('  -PAR not found. Marked for upload\n')
                NEED_PAR = True
            if 'REC' not in SCAN['resources']:

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import list_project_scans [as 别名]
__author__ = "damons"
__purpose__ = "set the scan quality of a scan on xnat"

from dax import XnatUtils
import sys

if __name__ == "__main__":

    XNAT = XnatUtils.get_interface()
    SCANS = XnatUtils.list_project_scans(XNAT, "WOODWARD_TCP")

    if len(sys.argv) != 4:
        print len(sys.argv)
        sys.stderr.write("ERROR: args must be <SESSION> <SCAN_ID> <STATUS>")
        sys.exit(1)
    MY_SESSION = sys.argv[1]
    MY_SCAN = sys.argv[2]
    STATUS = sys.argv[3]

    for SCAN in SCANS:
        if SCAN["session_label"] == MY_SESSION and SCAN["ID"] == MY_SCAN:
            print "Setting QC of scan %s in session %s to %s" % (MY_SCAN, MY_SESSION, STATUS)
            OBJECT = XnatUtils.get_full_object(XNAT, SCAN)
            OBJECT.attrs.set("quality", STATUS)

    XNAT.disconnect()

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import list_project_scans [as 别名]
from dax import XnatUtils
import os


if __name__ == "__main__":
    # Variables:
    project = 'DIAN'
    types = {'': 'PhoenixZIPReport'}

    with XnatUtils.get_interface(host=os.environ['DPUK']) as xnat:
        scans = XnatUtils.list_project_scans(xnat, project)
        scans = XnatUtils.filter_list_dicts_regex(scans, 'type', types.keys())
        for scan in sorted(scans, key=lambda k: k['session_label']):
            print "%s - %s - %s - %s" % (scan["session_label"],
                                         scan["ID"],
                                         scan["type"],
                                         scan["series_description"])
            scan_obj = XnatUtils.get_full_object(xnat, scan)
            scan_obj.attrs.set('type', types[scan['type']])
            print('   new type: {}'.format(types[scan['type']]))

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import list_project_scans [as 别名]
__author__ = 'damons'

from dax import XnatUtils

if __name__ == '__main__':
    XNAT = XnatUtils.get_interface()
    SCANS = XnatUtils.list_project_scans(XNAT,'PHOTON')
    print "There are %s scans in the PHOTON project" % str(len(SCANS))
    count = 0
    for SCAN in SCANS:
        if 'SNAPSHOTS' in SCAN['resources']:
            count +=1
    print "There are %s scans in the PHOTON project with SNAPSHOTS" % str(count)
    print "There are %s scans in the PHOTON project WITHOUT SNAPSHOTS" % str((len(SCANS) - count))
    XNAT.disconnect()

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import list_project_scans [as 别名]
import os
import sys
from dax import XnatUtils


SCAN = 'T2 Axial'
HOST = 'https://prostate-xnat.cs.ucl.ac.uk'
PROJECT = 'PICTURE'
RESOURCE = 'OsiriX'
OLD_FILE = 'mantonelli_Unnamed.rois_series'
NEW_FILE = 'Mrishta_Unnamed.rois_series'
TMP_DIR = '/Users/byvernault/data/temp_roi_upgrade/'

with XnatUtils.get_interface(host=HOST) as xnat:

    li_scans = XnatUtils.list_project_scans(xnat, PROJECT)
    li_scans = XnatUtils.filter_list_dicts_regex(li_scans, 'type', SCAN)
    li_scans = filter(lambda x: RESOURCE in x['resources'], li_scans)
    sys.stdout.write('Renaming file %s to %s for scan type %s\n'
                     % (OLD_FILE, NEW_FILE, SCAN))

    for scan in li_scans:
        sys.stdout.write(' - scan: %s / %s ...\n'
                         % (scan['session_label'], scan['ID']))
        scan_obj = XnatUtils.get_full_object(xnat, scan)
        res_obj = scan_obj.resource(RESOURCE)
        files = None
        if res_obj.exists() and OLD_FILE in res_obj.files().get()[:]:

            # fpath = XnatUtils.download_file_from_obj(TMP_DIR, res_obj,
            #                                          fname=OLD_FILE)