Python BlitzGateway.getObjects方法代码示例

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]
    def create_containers(self, cli, project, dataset):
        """
        Creates containers with names provided if they don't exist already.
        Returns Dataset ID.
        """
        sessionId = cli._event_context.sessionUuid
        conn = BlitzGateway(host='localhost')
        conn.connect(sUuid = sessionId)
        params = omero.sys.Parameters()
        params.theFilter = omero.sys.Filter()
        params.theFilter.ownerId = wrap(conn.getUser().getId())

        d = None
        dsId = None
        if project is not None:
            # We need to find or create a project
            # This is not nice but we really shouldn't be dealing with large numbers of objects here
            plist = list(conn.getObjects("Project", attributes={'name': project}, params=params))
            if len(plist) == 0:
                # Create project and dataset then link
                p = self.create_project(conn, project)
                d = self.create_dataset(conn, dataset)
                dsId = d.id.val
                self.link_dataset(conn, p.id.val, dsId)
            else:
                # Pick the first, it's as good as any
                p = plist[0]
                print "Using existing Project:", project
                # Since Project already exists check children for dataset
                for c in p.listChildren():
                    if c.getName() == dataset:
                        d = c
                        dsId = d.getId()

                # No existing child dataset so create one and link
                if d is None:
                    d = self.create_dataset(conn, dataset)
                    dsId = d.id.val
                    self.link_dataset(conn, p.getId(), dsId)
                else:
                    print "Using existing Dataset:", dataset
        else:
            # There may be more than one dataset with the same name
            # This is not nice but we really shouldn't be dealing with large numbers of objects here
            dlist = list(conn.getObjects("Dataset", attributes={'name': dataset}, params=params))
            if len(dlist) != 0:
                # We want one without a parent, the first will do
                for c in dlist:
                    if len(c.listParents()) == 0:
                        d = c
                        dsId = d.getId()
            if d is None:
                dsId = self.create_dataset(conn, dataset).id.val
            else:
                print "Using existing Dataset:", dataset

        return dsId

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]
def processImages(client, scriptParams):
    message = ''

    # for params with default values, we can get the value directly
    dataType = scriptParams['Data_Type']
    ids = scriptParams['IDs']

    # Get the datasets
    conn = BlitzGateway(client_obj = client)
    objects, logMessage = script_utils.getObjects(conn, scriptParams)
    message += logMessage

    if not objects:
        return message

    datasets = conn.getObjects(dataType, ids)

    good, chNames, msg = checkChannels(datasets)
    message += msg
    if not good:
        raise omero.ServerError(
            'Channel check failed, ' +
            'all images must have the same channels: %s' % message)

    return message

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]
    def create_screen(self, cli, screen):
        """
        Creates screen with name provided if it doesn't exist already.
        Returns Screen ID.
        """
        sessionId = cli._event_context.sessionUuid
        conn = BlitzGateway(host='localhost')
        conn.connect(sUuid = sessionId)
        params = omero.sys.Parameters()
        params.theFilter = omero.sys.Filter()
        params.theFilter.ownerId = wrap(conn.getUser().getId())

        slist = list(conn.getObjects("Screen", attributes={'name': screen}, params=params))
        if len(slist) == 0:
            print "Creating Screen:", screen
            s = ScreenI()
            s.name = wrap(screen.encode('ascii','ignore'))
            scrId = conn.getUpdateService().saveAndReturnObject(s).id.val
        else:
            scrId = slist[0].getId()
            print "Using Screen:", screen

        return scrId

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]
        print_obj(dataset, 2)
        for image in dataset.listChildren():
            print_obj(image, 4)


# Retrieve the datasets owned by the user currently logged in
# ===========================================================
# Here we create an omero.sys.ParametersI instance which we
# can use to filter the results that are returned. If we did
# not pass the params argument to getObjects, then all Datasets
# in the current group would be returned.
print "\nList Datasets:"
print "=" * 50
params = omero.sys.ParametersI()
params.exp(conn.getUser().getId())  # only show current user's Datasets
datasets = conn.getObjects("Dataset", params=params)
for dataset in datasets:
    print_obj(dataset)


# Retrieve the images contained in a dataset
# ==========================================
print "\nDataset:%s" % datasetId
print "=" * 50
dataset = conn.getObject("Dataset", datasetId)
print "\nImages in Dataset:", dataset.getName()
for image in dataset.listChildren():
    print_obj(image)


# Retrieve an image by ID

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]


conn = BlitzGateway('root', 'omero', host='localhost')
conn.connect()

conn.SERVICE_OPTS.setOmeroGroup(-1)


# ---- CONFIGURATION ----
TAG_COUNT = 1       # Number of tags each user should use (link)
TAG_TARGETS = ['Project', 'Dataset', 'Image', "Screen", "Plate"]
ROI_COUNT = 3

allUsers = []
for exp in conn.getObjects("Experimenter"):
    n = exp.getName()
    if n not in ["root", "guest"]:
        print n
        allUsers.append(exp)


def addRect(roi, x=10, y=10, w=100, h=50, theZ=0, theT=0, label=None):
    """ create and save a rectangle shape, add it to roi """
    rect = omero.model.RectI()
    rect.x = rdouble(x)
    rect.y = rdouble(y)
    rect.width = rdouble(w)
    rect.height = rdouble(h)
    if theZ is not None:
        rect.theZ = rint(theZ)

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]
class TableConnection(object):
    """
    A basic client-side wrapper for OMERO.tables which handles opening
    and closing tables.
    """

    def __init__(self, user = None, passwd = None, host = 'localhost',
                 client = None, tableName = None, tableId = None):
        """
        Create a new table handler, either by specifying user and passwd or by
        providing a client object (for scripts)
        @param user Username
        @param passwd Password
        @param host The server hostname
        @param client Client object with an active session
        @param tableName The name of the table file
        @param tableId The OriginalFile ID of the table file
        """
        if not client:
            client = omero.client(host)
            sess = client.createSession(user, passwd)
            client.enableKeepAlive(60)
        else:
             sess = client.getSession()

        self.conn = BlitzGateway(client_obj = client)

        self.res = sess.sharedResources()
        if (not self.res.areTablesEnabled()):
            raise TableConnectionError('OMERO.tables not enabled')

        repos = self.res.repositories()
        self.rid = repos.descriptions[0].id.val

        self.tableName = tableName
        self.tableId = tableId
        self.table = None

    def __enter__(self):
        print 'Entering Connection'
        return self

    def __exit__(self, type, value, traceback):
        print 'Exiting Connection'
        self.close()

    def close(self):
        print 'Closing Connection'
        try:
            self.closeTable()
        finally:
            self.conn._closeSession()


    def openTable(self, tableId = None, tableName = None):
        """
        Opens an existing table by ID or name.
        If there are multiple tables with the same name this throws an error
        (should really use an annotation to keep track of this).
        If tableId is supplied it will be used in preference to tableName
        @param tableName The name of the table file
        @param tableId The OriginalFile ID of the table file
        @return handle to the table
        """
        if not tableId and not tableName:
            tableId = self.tableId
            tableName = self.tableName

        if not tableId:
            if not tableName:
                tableName = self.tableName
            attrs = {'name': tableName}
            ofiles = list(
                self.conn.getObjects("OriginalFile", attributes = attrs))
            if len(ofiles) > 1:
                raise TableConnectionError(
                    'Multiple tables with name:%s found' % tableName)
            if not ofiles:
                raise TableConnectionError(
                    'No table found with name:%s' % tableName)
            ofile = ofiles[0]
        else:
            attrs = {'id': long(tableId)}
            if tableName:
                attrs['name'] = tableName
            ofile = self.conn.getObject("OriginalFile", attributes = attrs)

        if not ofile:
            raise TableConnectionError('No table found with name:%s id:%s' %
                                       (tableName, tableId))

        if self.tableId == ofile.getId():
            print 'Using existing connection to table name:%s id:%d' % \
                (tableName, tableId)
        else:
            self.closeTable()
            self.table = self.res.openTable(ofile._obj)
            self.tableId = ofile.getId()
            print 'Opened table name:%s id:%d' % (tableName, self.tableId)

#.........这里部分代码省略.........

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]
def print_obj(obj, indent=0):
    """
    Helper method to display info about OMERO objects.
    Not all objects will have a "name" or owner field.
    """
    print >> sys.stderr, """%s%s:%s  Name:"%s" (owner=%s)""" % (\
            " " * indent,
            obj.OMERO_CLASS,\
            obj.getId(),\
            obj.getName(),\
            obj.getOwnerOmeName())

conn.SERVICE_OPTS.setOmeroGroup('-1')

# Retrieve a list of all projects owned by user:
# =================================================================
print "\nList Projects:"
print "=" * 50
for project in conn.getObjects("Project"):
    print_obj(project)
    for dataset in project.listChildren():
        print_obj(dataset, 2)
        datasetId = dataset.getId()

# Close connection:
# =================================================================
# When you're done, close the session to free up server resources.

conn._closeSession()

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]

# Create Tags
# =================================================================
object_array = list()
for i in xrange(3):
    tag = omero.model.TagAnnotationI()
    tag.setTextValue(rstring(tag_name))
    tag.setDescription(rstring("%s %i" % (tag_name, i)))
    object_array.append(tag)
conn.getUpdateService().saveArray(object_array)


# Find the datasets by name.
# =================================================================
datasets = conn.getObjects("Dataset", attributes={'name': dataset_name})
print "\nList Datasets:"
for d in datasets:
    print "ID:", d.getId(), "Name:", d.getName()


# Find the tag by textValue
# =================================================================
Tags = conn.getObjects("TagAnnotation", attributes={'textValue': tag_name})
print "\nList Tags:"
for t in Tags:
    print "ID:", t.getId(), "Text:", t.getTextValue(), "Desc:", t.getDescription()


# Close connection:
# =================================================================

# 需要导入模块: from omero.gateway import BlitzGateway [as 别名]
# 或者: from omero.gateway.BlitzGateway import getObjects [as 别名]
    Helper method to display info about OMERO objects.
    Not all objects will have a "name" or owner field.
    """
#    print >> sys.stderr, """%s%s:%s  Name:"%s" (owner=%s)""" % (\
#            " " * indent,
#            obj.OMERO_CLASS,\
#            obj.getId(),\
#            obj.getName(),\
#            obj.getOwnerOmeName())


# Retrieve Screening data:
# =================================================================
conn.SERVICE_OPTS.setOmeroGroup('-1') ### Set the group to search within. -1 for all groups.
print "ScreenID,Screen Name,PlateID,Plate Name,Image,ImageID" 
for screen in conn.getObjects("Screen"):
    print_obj(screen)
    for plate in screen.listChildren():
        print_obj(plate, 5)
        plateId = plate.getId()
        for well in plate.listChildren():
            index = well.countWellSample()
            for index in xrange(0, index):
                print ",".join(map(str, [\
                    screen.getId(),\
                    screen.getName(),\
                    plateId, '"' + \
                    plate.getName(),\
                    well.getImage(index).getName() + '"',\
                    well.getImage(index).getId()]))