Python XnatUtils.upload_file_to_obj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 upload_file_to_obj [as 别名]
    def upload_converted_images(self, dcm_dir, scan_obj, scan_info):
        """upload the images after checking them."""
        # Local variables
        nifti_list = []
        bval_fpath = ''
        bvec_fpath = ''

        # G et the bvec/bval files and NIFTI from the folder:
        for fpath in glob.glob(os.path.join(dcm_dir, '*')):
            if os.path.isfile(fpath):
                if fpath.lower().endswith('.bval'):
                    bval_fpath = fpath
                if fpath.lower().endswith('.bvec'):
                    bvec_fpath = fpath
                if fpath.lower().endswith('.nii.gz'):
                    nifti_list.append(fpath)
                if fpath.lower().endswith('.nii'):
                    os.system('gzip ' + fpath)
                    nifti_list.append(fpath + '.gz')

        # Check NIFTI:
        good_to_upload = self.check_outputs(scan_info, nifti_list,
                                            bval_fpath, bvec_fpath)
        # Upload files:
        if good_to_upload:
            if os.path.isfile(bval_fpath) and os.path.isfile(bvec_fpath):
                # BVAL/BVEC
                XnatUtils.upload_file_to_obj(bval_fpath,
                                             scan_obj.resource('BVAL'),
                                             remove=True)
                XnatUtils.upload_file_to_obj(bvec_fpath,
                                             scan_obj.resource('BVEC'),
                                             remove=True)
                # keep the NII with the same name than the BVAL/BVEC
                nifti_list = filter(lambda x: x[:-7] == bval_fpath[:-5],
                                    nifti_list)
                XnatUtils.upload_files_to_obj(nifti_list,
                                              scan_obj.resource('NIFTI'),
                                              remove=True)
            else:
                # NII
                XnatUtils.upload_files_to_obj(nifti_list,
                                              scan_obj.resource('NIFTI'),
                                              remove=True)

            # more than one NIFTI uploaded
            if len(nifti_list) > 1:
                LOGGER.warn('''dcm2nii -- %s -- more than one NIFTI upload'''
                            % scan_info['scan_id'])
                self.log_warning_error('more than one NIFTI upload', scan_info)

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import upload_file_to_obj [as 别名]
def upload_path(resource_obj, resource_label, fpath, force=False,
                delete=False, extract=False):
    """
    Upload path to XNAT: either a file or folder
    :param resource_obj: pyxnat resource obj
    :param resource_label: label of the resource
    :param force: force the upload if file exists
    :param delete: delete the resource and all files before uploading
    :param extract: extract the files if it's a zip
    :return: None
    """
    _format_f = '     - File %s: uploading file...'
    _format_p = '     - Folder %s: uploading folder...'
    isfile, fpath = is_file(fpath)
    if isfile:
        print(_format_f % (os.path.basename(fpath)))
        XnatUtils.upload_file_to_obj(
            fpath, resource_obj, remove=force, removeall=delete)
    else:
        print(_format_p % (os.path.basename(fpath)))
        XnatUtils.upload_folder_to_obj(
            fpath, resource_obj, resource_label,
            remove=force, removeall=delete, extract=extract)

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import upload_file_to_obj [as 别名]
def upload_converted_images(dicom_files, dcm_dir, scan_obj, need_to_zip):
    """Upload the images after checking them.

    :param dicom_files: list of dicoms files to zip
    :param dcm_dir: directory containing the dicoms
    :param scan_obj: scan pyxnat object from XNAT
    """
    # Local variables
    nifti_list = []
    bval_fpath = ''
    bvec_fpath = ''

    # Get the bvec/bval files and NIFTI from the folder:
    for fpath in glob.glob(os.path.join(dcm_dir, '*')):
        if os.path.isfile(fpath):
            if fpath.lower().endswith('.bval'):
                bval_fpath = fpath
            if fpath.lower().endswith('.bvec'):
                bvec_fpath = fpath
            if fpath.lower().endswith('.nii.gz'):
                nifti_list.append(fpath)
            if fpath.lower().endswith('.nii'):
                os.system('gzip '+fpath)
                nifti_list.append(fpath+'.gz')

    # Check NIFTI:
    good_to_upload = check_outputs(nifti_list, bval_fpath, bvec_fpath)
    # Upload files:
    if good_to_upload:
        if os.path.isfile(bval_fpath) and os.path.isfile(bvec_fpath):
            # BVAL/BVEC
            XnatUtils.upload_file_to_obj(bval_fpath,
                                         scan_obj.resource('BVAL'),
                                         remove=True)
            XnatUtils.upload_file_to_obj(bvec_fpath,
                                         scan_obj.resource('BVEC'),
                                         remove=True)
            # keep the NII with the same name than the BVAL/BVEC
            nifti_list = filter(lambda x: x[:-7] == bval_fpath[:-5],
                                nifti_list)
            XnatUtils.upload_files_to_obj(nifti_list,
                                          scan_obj.resource('NIFTI'),
                                          remove=True)
        else:
            # NII
            XnatUtils.upload_files_to_obj(nifti_list,
                                          scan_obj.resource('NIFTI'),
                                          remove=True)

        # ZIP the DICOM if more than one
        if need_to_zip and OPTIONS.zip_dicoms:
            # Remove the files created before zipping:
            for nii_file in nifti_list:
                os.remove(nii_file)
            if os.path.isfile(bval_fpath) and os.path.isfile(bvec_fpath):
                os.remove(bval_fpath)
                os.remove(bvec_fpath)
            print '   --> more than one dicom file, zipping dicoms.'
            fzip = 'dicoms.zip'
            initdir = os.getcwd()
            # Zip all the files in the directory
            os.chdir(dcm_dir)
            os.system('zip -r %s * > /dev/null' % fzip)
            # return to the initial directory:
            os.chdir(initdir)
            _fzip = os.path.join(dcm_dir, fzip)
            # upload
            if os.path.exists():
                print '   --> uploading zip dicoms'
                scan_obj.resource('DICOM').delete()
                size_file = int(os.stat(_fzip).st_size) / (1024 * 1024)
                if size_file >= LIMIT_SIZE:
                    msg = 'Big DICOM resource.'
                    print(msg)
                scan_obj.resource('DICOM').put_zip(_fzip, overwrite=True,
                                                   extract=False)

        # more than one NIFTI uploaded
        if len(nifti_list) > 1:
            print "    - warning: more than one NIFTI upload"

# 需要导入模块: from dax import XnatUtils [as 别名]
# 或者: from dax.XnatUtils import upload_file_to_obj [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()