コード例 #1
0
def connect_to_omero(user, password, host, port=4064):
    conn = BlitzGateway(user, password, host=host, port=port)
    print conn.connect()
    user = conn.getUser()
    print "Current user:"******"   ID:", user.getId()
    print "   Username:"******"   Full Name:", user.getFullName()
    print "Member of:"
    for g in conn.getGroupsMemberOf():
        print "   ID:", g.getName(), " Name:", g.getId()
    group = conn.getGroupFromContext()
    print "Current group: ", group.getName()
    return conn
コード例 #2
0
def connect_to_omero(user, password, host, port=4064):
    conn = BlitzGateway(user, password, host=host, port=port)
    print conn.connect()
    user = conn.getUser()
    print "Current user:"******"   ID:", user.getId()
    print "   Username:"******"   Full Name:", user.getFullName()
    print "Member of:"
    for g in conn.getGroupsMemberOf():
        print "   ID:", g.getName(), " Name:", g.getId()
    group = conn.getGroupFromContext()
    print "Current group: ", group.getName()
    return conn
コード例 #3
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    def create_containers(self, project_name, dataset_name):
        """
        Creates containers with names provided if they don't exist already.
        Returns Project ID and Dataset ID.
        """
        conn = BlitzGateway(self.USER,
                            self.PASSWORD,
                            host=self.HOST,
                            port=self.PORT)
        connected = conn.connect()
        if not connected:
            sys.stderr.write("Server connection error")
            sys.exit(1)

        for g in conn.getGroupsMemberOf():
            if g.getName() == self.GROUP:
                break

        conn.SERVICE_OPTS.setOmeroGroup(g.getId())
        params = omero.sys.Parameters()

        p = conn.getObject("Project",
                           attributes={'name': project_name},
                           params=params)
        d = None
        if p is None:
            p = self.create_project(conn, project_name)
            d = self.create_dataset(conn, dataset_name)
            self.link_dataset(conn, p, d)
        else:
            print "Using existing Project", project_name
            for c in p.listChildren():
                if c.getName() == dataset_name:
                    d = c
                    break

            if d is None:
                d = self.create_dataset(conn, dataset_name)
                self.link_dataset(conn, p, d)
            else:
                print "Using existing Dataset", dataset_name

        conn.seppuku()

        return p.getId(), d.getId()
コード例 #4
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    def group_exists(self, user, group):
        if not self.user_exists(user):
            return False
        else:
            if group in self.known_users[user]:
                print "in Group:", group
                return True
        try:
            try:
                conn = BlitzGateway(user, "ome", host='localhost')
                conn.connect()
                groups = conn.getGroupsMemberOf()
            except:
                return False

            if group in [g.name for g in groups]:
                print "in Group:", group
                self.known_users[user].append(group)
                return True
            else:
                print "is not in Group:", group, "- ignoring."
                return False
        finally:
            conn.seppuku()
コード例 #5
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    # conn.setSecure(True)         # <--------- Uncomment this


    # Current session details
    # =============================================================
    # By default, you will have logged into your 'current' group in OMERO. This
    # can be changed by switching group in the OMERO.insight or OMERO.web clients.

    user = conn.getUser()
    print "Current user:"******"   ID:", user.getId()
    print "   Username:"******"   Full Name:", user.getFullName()

    print "Member of:"
    for g in conn.getGroupsMemberOf():
        print "   ID:", g.getName(), " Name:", g.getId()
    group = conn.getGroupFromContext()
    print "Current group: ", group.getName()

    print "Other Members of current group:"
    for exp in conn.listColleagues():
        print "   ID:", exp.getId(), exp.getOmeName(), " Name:", exp.getFullName()

    print "Owner of:"
    for g in conn.listOwnedGroups():
        print "   ID:", g.getName(), " Name:", g.getId()

    # New in OMERO 5
    print "Admins:"
    for exp in conn.getAdministrators():
コード例 #6
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    # conn.setSecure(True)         # <--------- Uncomment this

    # Current session details
    # =============================================================
    # By default, you will have logged into your 'current' group in OMERO. This
    # can be changed by switching group in the OMERO insight or web clients.

    user = conn.getUser()
    print "Current user:"******"   ID:", user.getId()
    print "   Username:"******"   Full Name:", user.getFullName()

    print "Member of:"
    for g in conn.getGroupsMemberOf():
        print "   ID:", g.getName(), " Name:", g.getId()
    group = conn.getGroupFromContext()
    print "Current group: ", group.getName()

    print "Other Members of current group:"
    for exp in conn.listColleagues():
        print "   ID:", exp.getId(), exp.getOmeName(
        ), " Name:", exp.getFullName()

    print "Owner of:"
    for g in conn.listOwnedGroups():
        print "   ID:", g.getName(), " Name:", g.getId()

    # The 'context' of our current session
    ctx = conn.getEventContext()
コード例 #7
0
ファイル: iomero.py プロジェクト: graemeball/omero_scripts
class Omg(object):
    """
    OMERO gateway that wraps Blitz gateway and CLI, intended for
    scripting and interactive work.

    Attributes
    ----------
    conn : Blitz gateway connection

    """

    def __init__(self, conn=None, user=None, passwd=None,
                 server=SERVER, port=PORT, skey=None):
        """
        Requires active Blitz connection OR username plus password or sesskey
        """
        if conn is None and (user is None or (passwd is None and skey is None)):
            raise ValueError("Bad parameters," + self.__init__.__doc__)
        if conn is not None:
            if conn.isConnected():
                self.conn = conn
            else:
                raise ValueError("Cannot initialize with closed connection!")
        else:
            if passwd is not None:
                self.conn = BlitzGateway(user, passwd, host=server, port=port)
                self.conn.connect()
            else:
                self.conn = BlitzGateway(user, host=server, port=port)
                self.conn.connect(skey)
        if self.conn.isConnected():
            self._server = self.conn.host
            self._port = self.conn.port
            self._user = self.conn.getUser().getName()
            self._key = self.conn.getSession().getUuid().getValue()
            print("Connected to {0} (port {1}) as {2}, session key={3}".format(
                  self._server, self._port, self._user, self._key))
        else:
            print("Failed to open connection :-(")

    def ls(self):
        """
        Print groups, then projects/datasets/images for current group.
        """
        print("Groups for {0}:-".format(self.conn.getUser().getName()))
        for gid, gname in self._ls_groups():
            print("  {0} ({1})".format(gname, str(gid)))
        curr_grp = self.conn.getGroupFromContext()
        gid, gname = curr_grp.getId(), curr_grp.getName()
        print("\nData for current group, {0} ({1}):-".format(gname, gid))
        for pid, pname in self._ls_projects():
            print("  Project: {0} ({1})".format(pname, str(pid)))
            for did, dname in self._ls_datasets(pid):
                print("    Dataset: {0} ({1})".format(dname, str(did)))
                for iid, iname in self._ls_images(did):
                    print("      Image: {0} ({1})".format(iname, str(iid)))
        # TODO, list orphaned Datasets and Images

    def _ls_groups(self):
        """list groups (id, name) this session is a member of"""
        groups = self.conn.getGroupsMemberOf()
        return [(group.getId(), group.getName()) for group in groups]

    def _ls_projects(self):
        """list projects (id, name) in the current session group"""
        projs = self.conn.listProjects(self.conn.getUserId())
        return [(proj.getId(), proj.getName()) for proj in projs]

    def _ls_datasets(self, proj_id):
        """list datasets (id, name) within the project id given"""
        dsets = self.conn.getObject("Project", proj_id).listChildren()
        return [(dset.getId(), dset.getName()) for dset in dsets]

    def _ls_images(self, dset_id):
        """list images (id, name) within the dataset id given"""
        imgs = self.conn.getObject("Dataset", dset_id).listChildren()
        return [(img.getId(), img.getName()) for img in imgs]

    def chgrp(self, group_id):
        """
        Change group for this session to the group_id given.
        """
        self.conn.setGroupForSession(group_id)

    def get(self, im_id, get_att=True):
        """
        Download the specified image as an OME-TIFF to current directory,
        with attachments also downloaded to folder: img_path + '_attachments'
        Return : path to downloaded image
        """
        img = self.conn.getObject("Image", oid=im_id)
        img_name = self._unique_name(img.getName(), im_id)
        img_path = os.path.join(os.getcwd(), img_name)
        img_file = open(str(img_path + ".ome.tiff"), "wb")
        fsize, blockgen = img.exportOmeTiff(bufsize=65536)
        for block in blockgen:
            img_file.write(block)
        img_file.close()
        fa_type = omero.model.FileAnnotationI
        attachments = [ann for ann in img.listAnnotations()
                       if ann.OMERO_TYPE == fa_type]
        if get_att and len(attachments) > 0:
            att_dir = img_path + "_attachments"
            os.mkdir(att_dir)

            def download_attachment(att, att_dir):
                """download OMERO file annotation to att_dir"""
                att_file = open(os.path.join(att_dir, att.getFileName()), "wb")
                for att_chunk in att.getFileInChunks():
                    att_file.write(att_chunk)
                att_file.close()

            for att in attachments:
                download_attachment(att, att_dir)
        return img_path

    def _unique_name(self, img_name, im_id):
        """Make unique name combining a file basename & OMERO Image id"""
        path_and_base, ext = os.path.splitext(img_name)
        base = os.path.basename(path_and_base)  # name in OMERO can has path
        return "{0}_{1}".format(base, str(im_id))

    def dget(self, dataset_id):
        """
        Download an entire OMERO Dataset to the current directory.
        """
        downloads = []
        wdir = os.getcwd()
        dset_name = self.conn.getObject("Dataset", dataset_id).getName()
        dset_path = os.path.join(wdir, dset_name + "_D" + str(dataset_id))
        os.mkdir(dset_path)
        os.chdir(dset_path)
        for img_id, img_name in self._ls_images(dataset_id):
            downloads.append(self.get(img_id))
        os.chdir(wdir)
        return downloads

    def pget(self, project_id):
        """
        Download an entire OMERO Project to the current directory.
        """
        downloads = []
        wdir = os.getcwd()
        proj_name = self.conn.getObject("Project", project_id).getName()
        proj_path = os.path.join(wdir, proj_name + "_P" + str(project_id))
        os.mkdir(proj_path)
        os.chdir(proj_path)
        for dset_id, dset_name in self._ls_datasets(project_id):
            downloads.extend(self.dget(dset_id))
        os.chdir(wdir)
        return downloads

    def put(self, filename, name=None, dataset=None):
        """
        Import filename using OMERO CLI, optionally with a specified name
        to a specified dataset (dataset_id).
        Return : OMERO image Id
        """
        cli = omero.cli.CLI()
        cli.loadplugins()
        import_args = ["import"]
        import_args.extend(["-s", str(self._server)])
        import_args.extend(["-k", str(self._key)])
        if dataset is not None:
            import_args.extend(["-d", str(dataset)])
        if name is not None:
            import_args.extend(["-n", str(name)])
        clio = "cli.out"
        clie = "cli.err"
        import_args.extend(["---errs=" + clie, "---file=" + clio, "--"])
        import_args.append(filename)
        cli.invoke(import_args, strict=True)
        pix_id = int(open(clio, 'r').read().rstrip())
        im_id = self.conn.getQueryService().get("Pixels", pix_id).image.id.val
        os.remove(clio)
        os.remove(clie)
        return im_id

    def describe(self, im_id, description):
        """
        Append to image description.
        """
        img = self.conn.getObject("Image", oid=im_id)
        old_description = img.getDescription() or ""
        img.setDescription(old_description + "\n" + description)
        img.save()

    def attach(self, im_id, attachments):
        """
        Attach a list of files to an image.
        """
        img = self.conn.getObject("Image", oid=im_id)
        for attachment in attachments.split():
            fann = self.conn.createFileAnnfromLocalFile(attachment)
            img.linkAnnotation(fann)
        img.save()

    # TODO: ls_tags() and tag() methods?

    def mkp(self, project_name, description=None):
        """
        Make new OMERO project in current group, returning the new project Id.
        """
        # see: omero/lib/python/omeroweb/webclient/controller/container.py
        proj = omero.model.ProjectI()
        proj.name = omero.rtypes.rstring(str(project_name))
        if description is not None and description != "":
            proj.description = omero.rtypes.rstring(str(description))
        return self._save_and_return_id(proj)

    def mkd(self, dataset_name, project_id=None, description=None):
        """
        Make new OMERO dataset, returning the new dataset Id.
        """
        dset = omero.model.DatasetI()
        dset.name = omero.rtypes.rstring(str(dataset_name))
        if description is not None and description != "":
            dset.description = omero.rtypes.rstring(str(description))
        if project_id is not None:
            l_proj_dset = omero.model.ProjectDatasetLinkI()
            proj = self.conn.getObject("Project", project_id)
            l_proj_dset.setParent(proj._obj)
            l_proj_dset.setChild(dset)
            dset.addProjectDatasetLink(l_proj_dset)
        return self._save_and_return_id(dset)

    def _save_and_return_id(self, obj):
        """Save new omero object and return id assgined to it"""
        # see: OmeroWebGateway.saveAndReturnId
        # in: lib/python/omeroweb/webclient/webclient_gateway.py
        u_s = self.conn.getUpdateService()
        res = u_s.saveAndReturnObject(obj, self.conn.SERVICE_OPTS)
        res.unload()
        return res.id.val

    def im(self, im_id):
        """
        Return an Im object for the image id specified.
        """
        img = self.conn.getObject("Image", im_id)
        # build pixel np.ndarray
        nx, ny = img.getSizeX(), img.getSizeY()
        nz, nt, nc = img.getSizeZ(), img.getSizeT(), img.getSizeC()
        planes = [(z, c, t) for c in range(nc)
                  for t in range(nt)
                  for z in range(nz)]
        pix_gen = img.getPrimaryPixels().getPlanes(planes)
        pix = np.array([i for i in pix_gen]).reshape((nc, nt, nz, ny, nx))
        # initialize Im using pix and extracted metadata
        meta = self._extract_meta(img, im_id)
        return Im(pix=pix, meta=meta)

    def _extract_meta(self, img, im_id):
        """Extract metadata attributes from OMERO Blitz gateway Image"""
        meta = {}
        meta['name'] = self._unique_name(img.getName(), im_id)
        meta['description'] = img.getDescription()

        def _extract_ch_info(ch):
            """extract core metadata for for channel, return as dict"""
            ch_info = {'label': ch.getLabel()}
            ch_info['ex_wave'] = ch.getExcitationWave()
            ch_info['em_wave'] = ch.getEmissionWave()
            ch_info['color'] = ch.getColor().getRGB()
            return ch_info

        meta['channels'] = [_extract_ch_info(ch) for ch in img.getChannels()]
        meta['pixel_size'] = {'x': img.getPixelSizeX(),
                              'y': img.getPixelSizeY(),
                              'z': img.getPixelSizeZ(),
                              'units': "um"}
        tag_type = omero.model.TagAnnotationI
        tags = [ann for ann in img.listAnnotations()
                if ann.OMERO_TYPE == tag_type]
        meta['tags'] = {tag.getValue() + " (" + str(tag.getId()) + ")":
                        tag.getDescription() for tag in tags}
        fa_type = omero.model.FileAnnotationI
        attachments = [ann for ann in img.listAnnotations()
                       if ann.OMERO_TYPE == fa_type]
        meta['attachments'] = [att.getFileName() + " (" + str(att.getId()) +
                               ")" for att in attachments]
        user_id = self.conn.getUser().getName() + " (" + \
            str(self.conn.getUser().getId()) + ") @" + self.conn.host
        meta_ext = {}
        meta_ext['user_id'] = user_id
        meta['meta_ext'] = meta_ext
        # TODO: ROIs, display settings?
        # objective: Image.loadOriginalMetadata()[1][find 'Lens ID Number'][1],
        return meta

    def imput(self, im, dataset_id=None):
        """
        Create a new OMERO Image using an Im object, returning new image id.
        """
        # see: omero/lib/python/omero/util/script_utils.py
        # see: omero/lib/python/omeroweb/webclient/webclient_gateway.py
        # see: https://gist.github.com/will-moore/4141708
        if not isinstance(im, Im):
            raise TypeError("first imput argument must be of type Im")
        nc, nt, nz, ny, nx = im.shape
        ch_nums = range(nc)
        q_s = self.conn.getQueryService()
        p_s = self.conn.getPixelsService()
        c_s = self.conn.getContainerService()
        u_s = self.conn.getUpdateService()
        pu_s = self.conn.c.sf.createRawPixelsStore()
        q_ptype = "from PixelsType as p where p.value='{0}'".format(
                  str(im.dtype))
        pixelsType = q_s.findByQuery(q_ptype, None)
        im_id = p_s.createImage(nx, ny, nz, nt, ch_nums, pixelsType,
                    im.name, im.description)
        img_i = c_s.getImages("Image", [im_id.getValue()], None)[0]
        img = self.conn.getObject("Image", im_id.getValue())
        pix_id = img_i.getPrimaryPixels().getId().getValue()
        pu_s.setPixelsId(pix_id, True)
        for c in range(nc):
            for t in range(nt):
                for z in range(nz):
                    plane = im.pix[c, t, z, :, :]
                    script_utils.uploadPlaneByRow(pu_s, plane, z, c, t)
        l_dset_im = omero.model.DatasetImageLinkI()
        dset = self.conn.getObject("Dataset", dataset_id)
        l_dset_im.setParent(dset._obj)
        l_dset_im.setChild(img._obj)
        self._update_meta(im, im_id)
        u_s.saveObject(l_dset_im, self.conn.SERVICE_OPTS)
        return im_id.getValue()

    def _update_meta(self, im, im_id):
        """Set OMERO Image metadata using Im metadata"""
コード例 #8
0
    if theT is not None:
        rect.theT = rint(theT)
    if label is not None:
        rect.textValue = wrap(label)
    rect.setRoi(roi)
    roi.addShape(rect)


# First, we want to make sure that every user has a tag(s) in every group
print "\n---- CREATING TAGS ----\n"
for exp in allUsers:
    username = exp.getOmeName()
    print username
    userConn = BlitzGateway(username, "ome")
    userConn.connect()
    for g in userConn.getGroupsMemberOf():
        if g.getName() == "user":
            continue
        print " ", g.getName()
        userConn.SERVICE_OPTS.setOmeroGroup(g.getId())
        params = omero.sys.Parameters()
        params.theFilter = omero.sys.Filter()
        params.theFilter.ownerId = rlong(exp.getId())
        tags = list( userConn.getObjects("TagAnnotation", params=params) )
        for i in range( TAG_COUNT-len(tags) ):
            t = TagAnnotationI()
            newTagVal = "%s_%s_TEST" % (username, g.getName())
            print "creating TAG:", newTagVal
            t.textValue = wrap(str(newTagVal))
            userConn.getUpdateService().saveObject(t, userConn.SERVICE_OPTS)
        # for t in tags:
コード例 #9
0
    if theT is not None:
        rect.theT = rint(theT)
    if label is not None:
        rect.textValue = wrap(label)
    rect.setRoi(roi)
    roi.addShape(rect)


# First, we want to make sure that every user has a tag(s) in every group
print "\n---- CREATING TAGS ----\n"
for exp in allUsers:
    username = exp.getOmeName()
    print username
    userConn = BlitzGateway(username, "ome")
    userConn.connect()
    for g in userConn.getGroupsMemberOf():
        if g.getName() == "user":
            continue
        print " ", g.getName()
        userConn.SERVICE_OPTS.setOmeroGroup(g.getId())
        params = omero.sys.Parameters()
        params.theFilter = omero.sys.Filter()
        params.theFilter.ownerId = rlong(exp.getId())
        tags = list(userConn.getObjects("TagAnnotation", params=params))
        for i in range(TAG_COUNT - len(tags)):
            t = TagAnnotationI()
            newTagVal = "%s_%s_TEST" % (username, g.getName())
            print "creating TAG:", newTagVal
            t.textValue = wrap(str(newTagVal))
            userConn.getUpdateService().saveObject(t, userConn.SERVICE_OPTS)
        # for t in tags: