Exemplo n.º 1
0
def xnat_pull(projectid, subjectid, experimentid, storagepath):
    """ Pull the complete set of files from a XNAT project, subject and experiment id """

    absstoragepath = op.abspath(storagepath)

    # we define the unique experimental id based on the user input
    # see push for more comments
    #        subj_id = '%s_%s' % (projectid, subjectid)
    #        exp_id = '%s_%s' % (subj_id, experimentid)
    subj_id = '%s' % subjectid
    exp_id = '%s_%s' % (projectid, experimentid)

    experiment_uri = '/projects/%s/subjects/%s/experiments/%s' % (
        projectid, subj_id, exp_id)
    metacml_uri = '%s/resources/meta/files/meta.cml' % experiment_uri

    # download meta.cml
    metacmlpath = op.join(absstoragepath, 'meta.cml')
    meta_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
    xnat_interface.select(meta_uri).get(metacmlpath)

    # parse meta.cml
    f = open(metacmlpath, 'rb')
    remote_connectome = cf.parseString(f.read())
    f.close()
    if DEBUG_msg:
        print "Remote connectome", remote_connectome.to_xml()

    # loop over objects and download them to pyxnat cache / or path
    for ele in remote_connectome.get_all():
        if DEBUG_msg:
            print("Downloading connectome object")
            ele.print_summary()

        cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
            experiment_uri, '%s_%s' % (exp_id, ele.__class__.__name__),
            quote_for_xnat(ele.name) + ele.get_file_ending())

        # download file
        # does file folder exist?
        eleobjfolderfname = op.join(absstoragepath, ele.get_unique_relpath())

        if not op.exists(op.split(eleobjfolderfname)[0]):
            os.makedirs(op.split(eleobjfolderfname)[0])

        xnat_interface.select(cobj_uri).get(eleobjfolderfname)

    # update current connectome container
    print("=============")
    print("You can load the pulled connectome file with:")
    print("import cfflib as cf; mycon = cf.load('%s')" %
          op.join(absstoragepath, 'meta.cml'))
    print("=============")

    return True
Exemplo n.º 2
0
Arquivo: util.py Projeto: LTS5/cfflib
def xnat_pull( projectid, subjectid, experimentid, storagepath):
    """ Pull the complete set of files from a XNAT project, subject and experiment id """

    absstoragepath = op.abspath(storagepath)

    # we define the unique experimental id based on the user input
    # see push for more comments
#        subj_id = '%s_%s' % (projectid, subjectid)
#        exp_id = '%s_%s' % (subj_id, experimentid)
    subj_id = '%s' % subjectid
    exp_id = '%s_%s' % (projectid, experimentid)

    experiment_uri = '/projects/%s/subjects/%s/experiments/%s' % (projectid, subj_id, exp_id)
    metacml_uri = '%s/resources/meta/files/meta.cml' % experiment_uri

    # download meta.cml
    metacmlpath = op.join(absstoragepath, 'meta.cml')
    meta_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
    xnat_interface.select(meta_uri).get(metacmlpath)

    # parse meta.cml
    f = open(metacmlpath, 'rb')
    remote_connectome = cf.parseString(f.read())
    f.close()
    if DEBUG_msg:
        print "Remote connectome", remote_connectome.to_xml()

    # loop over objects and download them to pyxnat cache / or path
    for ele in remote_connectome.get_all():
        if DEBUG_msg:
            print("Downloading connectome object")
            ele.print_summary()

        cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
                experiment_uri,
                '%s_%s' % (exp_id, ele.__class__.__name__),
                quote_for_xnat(ele.name) + ele.get_file_ending()
                )

        # download file
        # does file folder exist?
        eleobjfolderfname = op.join(absstoragepath, ele.get_unique_relpath())

        if not op.exists(op.split(eleobjfolderfname)[0]):
            os.makedirs( op.split(eleobjfolderfname)[0] )

        xnat_interface.select(cobj_uri).get(eleobjfolderfname)

    # update current connectome container
    print("=============")
    print("You can load the pulled connectome file with:")
    print("import cfflib as cf; mycon = cf.load('%s')" % op.join(absstoragepath, 'meta.cml'))
    print("=============")

    return True
Exemplo n.º 3
0
def _load_from_meta_cml(filename):
    """ Load connectome file from a meta.cml file. """
    
    with open(filename, 'r') as metacml:
        metastr = metacml.read()
        
    connectome = cf.parseString(metastr)
    # update references
    connectome._update_parent_reference()
    connectome.iszip = False
    connectome.fname = op.abspath(filename)
    # check if names are unique!
    connectome.check_names_unique()
    
    return connectome
Exemplo n.º 4
0
def _load_from_cff(filename, *args, **kwargs):
    """ Load connectome file given filename
    
        Returns
        -------
        connectome : ``Connectome``
                Connectome Instance
                
    """
    
    # XXX: take care to have allowZip64 = True (but not supported by unix zip/unzip, same for ubuntu?) ?
    _zipfile = ZipFile(filename, 'a', ZIP_DEFLATED)
    try:
        metadata_string = _zipfile.read('meta.cml')
    except: # XXX: what is the correct exception for read error?
        raise RuntimeError('Can not extract meta.cml from connectome file.')
    
    # create connectome instance
    connectome = cf.parseString(metadata_string)
    
    # update references
    connectome._update_parent_reference()
    
    # add additional attributes
    connectome.src = filename
    
    # it is from the zip file
    connectome.iszip = True
    # if it is a zip file, we can assume that the src paths are given relatively
    
    connectome._zipfile = _zipfile
    
    # check if all referenced container elements exist in the archive
    connectome.check_file_in_cff()
    
    # check if names are unique!
    connectome.check_names_unique()
    
    return connectome
Exemplo n.º 5
0
def xnat_push(connectome_obj,
              projectid,
              subjectid,
              experimentid,
              overwrite=False):
    """ Push all the connectome objects to the remote XNAT server.

    Parameters
    ----------
    connectome_obj : connectome object
        The connectome object you want to push
    projectid : string
        The id of the project, has to be unique across an XNAT server
    subjectid : string
        The id of the subject
    experimentid : string
        The id of the experiment
    overwrite : boolean
        Overwrite remote version of the connectome object with
        the connectome object contained in the local connectome container

    """
    def _push_metacml(experiment_uri):
        _, fname = tempfile.mkstemp()
        f = open(fname, 'wb')
        f.write(connectome_obj.to_xml())
        f.close()

        # finally update remote meta.cml
        meta_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
        xnat_interface.select(meta_uri).insert(fname, experiments = 'xnat:imageSessionData', \
                    use_label=True)

    if xnat_interface is None:
        raise Exception(
            'You need to setup the XNAT connection first with set_xnat_connection'
        )

    # we define the unique experimental id based on the user input
    # user do not expect this composed identifiers, so we directly use
    # the given parameters to construct the path
    # originally, we thought that this is required because there have to be
    # unique subject identifiers across the whole XNAT instance
    # we seems not to be required anymore
    # subj_id = '%s_%s' % (projectid, subjectid)
    # exp_id = '%s_%s' % (subj_id, experimentid)
    subj_id = '%s' % subjectid
    exp_id = '%s_%s' % (projectid, experimentid)

    experiment_uri = '/projects/%s/subjects/%s/experiments/%s' % (
        projectid, subj_id, exp_id)
    metacml_uri = '%s/resources/meta/files/meta.cml' % experiment_uri

    # does the experiment exists
    if xnat_interface.select(metacml_uri).exists():
        # it exists
        # compare it to the local object
        remote_metacml = open(xnat_interface.select(metacml_uri).get(), 'rb')

        remote_connectome = cf.parseString(remote_metacml.read())

        # loop over local connectome objects and check if the exists remotely
        all_local_cobj = connectome_obj.get_all()

        # connectome objects we need to add to the remote metacml
        push_objects = []

        for ele in all_local_cobj:
            if DEBUG_msg:
                print "Working on element %s" % ele.name
            if (ele in remote_connectome.get_all() and overwrite) or \
                not ele in remote_connectome.get_all():
                if DEBUG_msg:
                    print "We push element %s" % ele.name
                    print "Element in remote? " + str(
                        ele in remote_connectome.get_all())

                # push connectome object to remote
                cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
                    experiment_uri, '%s_%s' % (exp_id, ele.__class__.__name__),
                    quote_for_xnat(ele.name) + ele.get_file_ending())
                if DEBUG_msg:
                    print "uri", cobj_uri
                # insert data file to xnat
                xnat_interface.select(cobj_uri).insert(ele.get_abs_path(), experiments = 'xnat:imageSessionData', \
                    assessors = 'xnat:imageAssessorData', use_label=True)
                # add element for updating metacml later on the remote
                push_objects.append(ele)

            else:
                # we do not push
                if DEBUG_msg:
                    print "We do nothing with element %s (already on remote and no overwrite)" % ele.name

        # synchronize meta_cml
        # we need to retrieve the remote connectome objects and add it to the
        # local if they no not yet exists
        for el in remote_connectome.get_all():
            if not el in connectome_obj.get_all():
                connectome_obj.add_connectome_object(el)

        #for el in push_objects:
        # add all push_objects to remote meta_cml
        #   remote_connectome.add_connectome_object(el)

        # update cmetadata (overwriting remote with local)
        remote_connectome.connectome_meta = connectome_obj.connectome_meta

        _push_metacml(experiment_uri)

        if DEBUG_msg:
            print "Current local connectome container", connectome_obj.to_xml()
            print "Current remote connectome container", remote_connectome.to_xml(
            )
            print "Current push objects", push_objects

    else:
        # create meta.cml

        # loop over local connectome objects and check if the exists remotely
        all_local_cobj = connectome_obj.get_all()

        for ele in all_local_cobj:
            print "We push element %s" % ele.name

            # push connectome object to remote
            cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
                experiment_uri, '%s_%s' %
                (exp_id, ele.__class__.__name__), quote_for_xnat(ele.name))
            # insert data file to xnat
            xnat_interface.select(cobj_uri).insert(ele.get_abs_path(), experiments = 'xnat:imageSessionData', \
                    assessors = 'xnat:imageAssessorData', use_label=True)

        # push the current connectome object to remote
        _push_metacml(experiment_uri)
Exemplo n.º 6
0
Arquivo: util.py Projeto: LTS5/cfflib
def xnat_push(connectome_obj, projectid, subjectid, experimentid, overwrite = False):
    """ Push all the connectome objects to the remote XNAT server.

    Parameters
    ----------
    connectome_obj : connectome object
        The connectome object you want to push
    projectid : string
        The id of the project, has to be unique across an XNAT server
    subjectid : string
        The id of the subject
    experimentid : string
        The id of the experiment
    overwrite : boolean
        Overwrite remote version of the connectome object with
        the connectome object contained in the local connectome container

    """
    def _push_metacml(experiment_uri):
        _, fname = tempfile.mkstemp()
        f=open(fname, 'wb')
        f.write(connectome_obj.to_xml())
        f.close()

        # finally update remote meta.cml
        meta_uri = '%s/resources/meta/files/meta.cml' % experiment_uri
        xnat_interface.select(meta_uri).insert(fname, experiments = 'xnat:imageSessionData', \
                    use_label=True)


    if xnat_interface is None:
        raise Exception('You need to setup the XNAT connection first with set_xnat_connection')

    # we define the unique experimental id based on the user input
    # user do not expect this composed identifiers, so we directly use
    # the given parameters to construct the path
    # originally, we thought that this is required because there have to be
    # unique subject identifiers across the whole XNAT instance
    # we seems not to be required anymore
    # subj_id = '%s_%s' % (projectid, subjectid)
    # exp_id = '%s_%s' % (subj_id, experimentid)
    subj_id = '%s' % subjectid
    exp_id = '%s_%s' % (projectid, experimentid)

    experiment_uri = '/projects/%s/subjects/%s/experiments/%s' % (projectid, subj_id, exp_id)
    metacml_uri = '%s/resources/meta/files/meta.cml' % experiment_uri

    # does the experiment exists
    if xnat_interface.select(metacml_uri).exists():
        # it exists
        # compare it to the local object
        remote_metacml = open(xnat_interface.select(metacml_uri).get(), 'rb')

        remote_connectome = cf.parseString(remote_metacml.read())

        # loop over local connectome objects and check if the exists remotely
        all_local_cobj = connectome_obj.get_all()

        # connectome objects we need to add to the remote metacml
        push_objects = []

        for ele in all_local_cobj:
            if DEBUG_msg:
                print "Working on element %s" % ele.name
            if (ele in remote_connectome.get_all() and overwrite) or \
                not ele in remote_connectome.get_all():
                if DEBUG_msg:
                    print "We push element %s" % ele.name
                    print "Element in remote? " + str(ele in remote_connectome.get_all())

                # push connectome object to remote
                cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
                    experiment_uri,
                    '%s_%s' % (exp_id, ele.__class__.__name__),
                    quote_for_xnat(ele.name) + ele.get_file_ending()
                    )
                if DEBUG_msg:
                    print "uri", cobj_uri
                # insert data file to xnat
                xnat_interface.select(cobj_uri).insert(ele.get_abs_path(), experiments = 'xnat:imageSessionData', \
                    assessors = 'xnat:imageAssessorData', use_label=True)
                # add element for updating metacml later on the remote
                push_objects.append(ele)

            else:
                # we do not push
                if DEBUG_msg:
                    print "We do nothing with element %s (already on remote and no overwrite)" % ele.name


        # synchronize meta_cml
        # we need to retrieve the remote connectome objects and add it to the
        # local if they no not yet exists
        for el in remote_connectome.get_all():
            if not el in connectome_obj.get_all():
                connectome_obj.add_connectome_object(el)

        #for el in push_objects:
            # add all push_objects to remote meta_cml
         #   remote_connectome.add_connectome_object(el)

        # update cmetadata (overwriting remote with local)
        remote_connectome.connectome_meta = connectome_obj.connectome_meta

        _push_metacml(experiment_uri)

        if DEBUG_msg:
            print "Current local connectome container", connectome_obj.to_xml()
            print "Current remote connectome container", remote_connectome.to_xml()
            print "Current push objects", push_objects

    else:
        # create meta.cml

        # loop over local connectome objects and check if the exists remotely
        all_local_cobj = connectome_obj.get_all()

        for ele in all_local_cobj:
            print "We push element %s" % ele.name

            # push connectome object to remote
            cobj_uri = '%s/assessors/%s/out/resources/data/files/%s' % (
                experiment_uri,
                '%s_%s' % (exp_id, ele.__class__.__name__),
                quote_for_xnat(ele.name)
                )
            # insert data file to xnat
            xnat_interface.select(cobj_uri).insert(ele.get_abs_path(), experiments = 'xnat:imageSessionData', \
                    assessors = 'xnat:imageAssessorData', use_label=True)

        # push the current connectome object to remote
        _push_metacml(experiment_uri)