OMERO Python language bindings¶

MOVIE: introduction to Blitz Gateway

In addition to the auto-generated Python libraries of the core OMERO Application Programming Interface, we have developed a more user-friendly Python module ‘Blitz Gateway’ that facilitates several aspects of working with the Python API, such as connection handling, object graph traversal and lazy loading.

This page first gives you a large number of code samples to get you started. Below these we describe a bit more about using the Blitz Gateway.

The Python libraries are part of the server build and can be found under OMERO_HOME/lib/python. These include the core omero.model objects and services as well as the Blitz Gateway code (at OMERO_HOME/lib/python/omero/gateway/__init__.py).

To use OmeroPy, you will need to download the libraries (E.g. as part of the server package) and setup your PYTHONPATH to include them:

export OMERO_PREFIX=~/Desktop/OMERO.server-5.0.0-rc1-ice3x-byy       # for example
export PYTHONPATH=$OMERO_PREFIX/lib/python

You will also need Ice libraries 3.3.x or 3.4.x as described in the OMERO.server installation and an OMERO server to connect to, which must be the same major version, i.e. 5.0.x.

All the code examples below can be found at examples/Training/python.

Start by downloading the first example below: examples/Training/python/Connect_To_OMERO.py and edit the USERNAME and PASSWORD variables according to your log-in.

Then you can run the example:

$ python Connect_To_OMERO.py

If all goes well, you should be connected to your OMERO server and see some details of your session printed out.

All the following code examples can be downloaded and run in the same way, and they will use the USERNAME and PASSWORD from the file you just edited. However, you will need to edit some other parameters, usually IDs from Projects, Datasets, Images etc. You can use the OMERO.insight or OMERO.web client to choose suitable data IDs before editing and running the code samples.

Code samples¶

Connect to OMERO¶

# These values will be imported by all the other training scripts.
HOST = 'localhost'
PORT = 4064
USERNAME = 'username'
PASSWORD = 'passwd'

from omero.gateway import BlitzGateway

if __name__ == '__main__':
    """
    NB: This block is only run when calling this file directly
    and not when imported.
    """

# Connect to the Python Blitz Gateway
# =============================================================
# Make a simple connection to OMERO, printing details of the
# connection. See OmeroPy/Gateway for more info
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
connected = conn.connect()

# Check if you are connected.
# =============================================================
if not connected:
    import sys
    sys.stderr.write("Error: Connection not available, please check your user name and password.\n")
    sys.exit(1)

# Using secure connection.
# =============================================================
# By default, once we have logged in, data transfer is not encrypted (faster)
# To use a secure connection, call setSecure(True):

# 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:"
print "   ID:", user.getId()
print "   Username:", user.getName()
print "   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()
# print ctx     # for more info

# Close connection:
# =================================================================
# When you are done, close the session to free up server resources.
conn._closeSession()

Read data¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

Configuration

imageId = 1
datasetId = 2
plateId = -1        # Don't need to set this

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 """%s%s:%s  Name:"%s" (owner=%s)""" % (\
            " " * indent,
            obj.OMERO_CLASS,\
            obj.getId(),\
            obj.getName(),\
            obj.getOwnerOmeName())

List all Projects available to me, and their Datasets and Images:

# The only_owned=True parameter limits the Projects which are returned.
# If the parameter is omitted or the value is False, then all Projects
# visible in the current group are returned.
print "\nList Projects:"
print "=" * 50
my_expId = conn.getUser().getId()
for project in conn.listProjects(my_expId):
    print_obj(project)
    for dataset in project.listChildren():
        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 Image ID:

image = conn.getObject("Image", imageId)
print "\nImage:%s" % imageId
print "=" * 50
print image.getName(), image.getDescription()
# Retrieve information about an image.
print " X:", image.getSizeX()
print " Y:", image.getSizeY()
print " Z:", image.getSizeZ()
print " C:", image.getSizeC()
print " T:", image.getSizeT()
# render the first timepoint, mid Z section
z = image.getSizeZ() / 2
t = 0
renderedImage = image.renderImage(z, t)
#renderedImage.show()               # popup (use for debug only)
#renderedImage.save("test.jpg")     # save in the current folder

Retrieve Screening data:

print "\nList Screens:"
print "=" * 50
for screen in conn.getObjects("Screen"):
    print_obj(screen)
    for plate in screen.listChildren():
        print_obj(plate, 2)
        plateId = plate.getId()

Retrieve Wells and Images within a Plate:

if plateId >= 0:
    print "\nPlate:%s" % plateId
    print "=" * 50
    plate = conn.getObject("Plate", plateId)
    print "\nNumber of fields:", plate.getNumberOfFields()
    print "\nGrid size:", plate.getGridSize()
    print "\nWells in Plate:", plate.getName()
    for well in plate.listChildren():
        index = well.countWellSample()
        print "  Well: ", well.row, well.column, " Fields:", index
        for index in xrange(0, index):
            print "    Image: ", \
                    well.getImage(index).getName(),\
                    well.getImage(index).getId()

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

Groups and permissions¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

Configuration

imageId = 1

We are logged in to our ‘default’ group

group = conn.getGroupFromContext()
print "Current group: ", group.getName()

Each group has defined Permissions set

group_perms = group.getDetails().getPermissions()
perm_string = str(group_perms)
permission_names = {'rw----':'PRIVATE',
    'rwr---':'READ-ONLY',
    'rwra--':'READ-ANNOTATE',
    'rwrw--':'READ-WRITE'}  # Not exposed in 4.4.0 clients
print "Permissions: %s (%s)" % (permission_names[perm_string], perm_string)

By default, any query applies to ALL data that we can access in our Current group.

This will be determined by group permissions. E.g. in Read-Only or Read-Annotate groups, this will include other users’ data See Permissions overview.

projects = conn.listProjects()      # may include other users' data
for p in projects:
    print p.getName(), "Owner: ", p.getDetails().getOwner().getFullName()

image = conn.getObject("Image", imageId)     # Will return None if Image is not in current group
print "Image: ", image

In OMERO-4.4, we added ‘cross-group’ querying, use ‘-1’

conn.SERVICE_OPTS.setOmeroGroup('-1')
image = conn.getObject("Image", imageId)     # Will query across all my groups
print "Image: ", image,
if image is not None:
    print "Group: ", image.getDetails().getGroup().getName(),
    print image.details.group.id.val    # access groupId without loading group

To query only a single group (not necessarily your ‘current’ group)

groupId = image.details.group.id.val
conn.SERVICE_OPTS.setOmeroGroup(groupId)   # This is how we 'switch group' in webclient
projects = conn.listProjects()
image = conn.getObject("Image", imageId)
print "Image: ", image,

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

Raw data access¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

Configuration

imageId = 27544

Retrieve a given plane

# Use the pixelswrapper to retrieve the plane as
# a 2D numpy array. See [http://www.scipy.org/Tentative_NumPy_Tutorial]
#
# Numpy array can be used for various analysis routines
#
image = conn.getObject("Image", imageId)
sizeZ = image.getSizeZ()
sizeC = image.getSizeC()
sizeT = image.getSizeT()
z, t, c = 0, 0, 0                     # first plane of the image
pixels = image.getPrimaryPixels()
plane = pixels.getPlane(z, c, t)      # get a numpy array.
print "\nPlane at zct: ", z, c, t
print plane
print "shape: ", plane.shape
print "min:", plane.min(), " max:", plane.max(),\
        "pixel type:", plane.dtype.name

Retrieve a given stack

# Get a Z-stack of tiles. Using getTiles or getPlanes (see below) returns
# a generator of data (not all the data in hand) The RawPixelsStore is
# only opened once (not closed after each plane) Alternative is to use
# getPlane() or getTile() multiple times - slightly slower.
c, t = 0, 0                 # First channel and timepoint
tile = (50, 50, 10, 10)     # x, y, width, height of tile

# list of [ (0,0,0,(x,y,w,h)), (1,0,0,(x,y,w,h)), (2,0,0,(x,y,w,h))....etc... ]
zctList = [(z, c, t, tile) for z in range(sizeZ)]
print "\nZ stack of tiles:"
planes = pixels.getTiles(zctList)
for i, p in enumerate(planes):
    print "Tile:", zctList[i], " min:", p.min(),\
            " max:", p.max(), " sum:", p.sum()

Retrieve a given hypercube

zctList = []
for z in range(sizeZ / 2, sizeZ):     # get the top half of the Z-stack
    for c in range(sizeC):          # all channels
        for t in range(sizeT):      # all time-points
            zctList.append((z, c, t))
print "\nHyper stack of planes:"
planes = pixels.getPlanes(zctList)
for i, p in enumerate(planes):
    print "plane zct:", zctList[i], " min:", p.min(), " max:", p.max()

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

Write data¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

Configuration

projectId = 2
#Specify a local file. E.g. could be result of some analysis
fileToUpload = "README.txt"   # This file should already exist

Create a new Dataset

datasetObj = omero.model.DatasetI()
datasetObj.setName(rstring("New Dataset"))
datasetObj = conn.getUpdateService().saveAndReturnObject(datasetObj)
datasetId = datasetObj.getId().getValue()
print "New dataset, Id:", datasetId

Link to Project

project = conn.getObject("Project", projectId)
if project is None:
    import sys
    sys.stderr.write("Error: Object does not exist.\n")
    sys.exit(1)
link = omero.model.ProjectDatasetLinkI()
link.setParent(omero.model.ProjectI(project.getId(), False))
link.setChild(datasetObj)
conn.getUpdateService().saveObject(link)

How to create a file annotation and link to a Dataset

dataset = conn.getObject("Dataset", datasetId)
# create the original file and file annotation (uploads the file etc.)
namespace = "imperial.training.demo"
print "\nCreating an OriginalFile and FileAnnotation"
fileAnn = conn.createFileAnnfromLocalFile(fileToUpload, mimetype="text/plain", ns=namespace, desc=None)
print "Attaching FileAnnotation to Dataset: ", "File ID:", fileAnn.getId(), ",", fileAnn.getFile().getName(), "Size:", fileAnn.getFile().getSize()
dataset.linkAnnotation(fileAnn)     # link it to dataset.

Download a file annotation linked to a Dataset

# make a location to download the file. "download" folder.
path = os.path.join(os.path.dirname(__file__), "download")
if not os.path.exists(path):
    os.makedirs(path)

# Go through all the annotations on the Dataset. Download any file annotations we find.
print "\nAnnotations on Dataset:", dataset.getName()
for ann in dataset.listAnnotations():
    if isinstance(ann, omero.gateway.FileAnnotationWrapper):
        print "File ID:", ann.getFile().getId(), ann.getFile().getName(), "Size:", ann.getFile().getSize()

file_path = os.path.join(path, ann.getFile().getName())

f = open(str(file_path), 'w')
print "\nDownloading file to", file_path, "..."
try:
    for chunk in ann.getFileInChunks():
        f.write(chunk)
finally:
    f.close()
    print "File downloaded!"

Load all the file annotations with a given namespace

nsToInclude = [namespace]
nsToExclude = []
metadataService = conn.getMetadataService()
annotations = metadataService.loadSpecifiedAnnotations('omero.model.FileAnnotation', nsToInclude, nsToExclude, None)
for ann in annotations:
    print ann.getId().getValue(), ann.file.name.val

Get first annotation with specified namespace

ann = dataset.getAnnotation(namespace)
print "Found Annotation with namespace: ", ann.getNs()

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

OMERO tables¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

Configuration

datasetId = 33

Create a name for the Original File (should be unique)

from random import random
tablename = "TablesDemo:%s" % str(random())

col1 = omero.grid.LongColumn('Uid', 'testLong', [])
col2 = omero.grid.StringColumn('MyStringColumnInit', '', 64, [])

columns = [col1, col2]

Create and initialize a new table.

repositoryId = 1
table = conn.c.sf.sharedResources().newTable(repositoryId, tablename)
table.initialize(columns)

Add data to the table.

ids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10]
strings = ["one", "two", "three", "four", "five",\
           "six", "seven", "eight", "nine", "ten"]
data1 = omero.grid.LongColumn('Uid', 'test Long', ids)
data2 = omero.grid.StringColumn('MyStringColumn', '', 64, strings)
data = [data1, data2]
table.addData(data)
table.close()           # when we are done, close.

Get the table as an original file…

orig_file = table.getOriginalFile()
orig_file_id = orig_file.id.val
# ...so you can attach this data to an object. E.g. Dataset
fileAnn = omero.model.FileAnnotationI()
fileAnn.setFile(omero.model.OriginalFileI(orig_file_id, False))     # use unloaded OriginalFileI
fileAnn = conn.getUpdateService().saveAndReturnObject(fileAnn)
link = omero.model.DatasetAnnotationLinkI()
link.setParent(omero.model.DatasetI(datasetId, False))
link.setChild(omero.model.FileAnnotationI(fileAnn.id.val, False))
conn.getUpdateService().saveAndReturnObject(link)

Table API

See also

javadoc

openTable = conn.c.sf.sharedResources().openTable(orig_file)

print "Table Columns:"
for col in openTable.getHeaders():
    print "   ", col.name

rowCount = openTable.getNumberOfRows()
print "Row count:", rowCount

Get data from every column of the specified rows

rowNumbers = [3, 5, 7]
print "\nGet All Data for rows: ", rowNumbers
data = openTable.readCoordinates(range(rowCount))
for col in data.columns:
    print "Data for Column: ", col.name
    for v in col.values:
        print "   ", v

Get data from specified columns of specified rows

colNumbers = [1]
start = 3
stop = 7
print "\nGet Data for cols: ", colNumbers,\
        " and between rows: ", start, "-", stop

data = openTable.read(colNumbers, start, stop)
for col in data.columns:
    print "Data for Column: ", col.name
    for v in col.values:
        print "   ", v

Query the table for rows where the ‘Uid’ is in a particular range

queryRows = openTable.getWhereList("(Uid > 2) & (Uid <= 8)",\
        variables={}, start=0, stop=rowCount, step=0)
data = openTable.readCoordinates(queryRows)
for col in data.columns:
    print "Query Results for Column: ", col.name
    for v in col.values:
        print "   ", v
openTable.close()           # we're done

In future, to get the table back from Original File

orig_table_file = conn.getObject("OriginalFile", attributes={'name': tablename})    # if name is unique
savedTable = conn.c.sf.sharedResources().openTable(orig_table_file._obj)
print "Opened table with row-count:", savedTable.getNumberOfRows()

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

ROIs¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
updateService = conn.getUpdateService()

Configuration

imageId = 27544

Create ROI.

# We are using the core Python API and omero.model objects here, since ROIs are
# not yet supported in the Python Blitz Gateway.
#
# In this example, we create an ROI with a rectangular shape and attach it to an
# image.
x = 50
y = 200
width = 100
height = 50
image = conn.getObject("Image", imageId)
theZ = image.getSizeZ() / 2
theT = 0
print "Adding a rectangle at theZ: %s, theT: %s, X: %s, Y: %s, width: %s, height: %s" % \
        (theZ, theT, x, y, width, height)

# create an ROI, link it to Image
roi = omero.model.RoiI()
roi.setImage(image._obj)    # use the omero.model.ImageI that underlies the 'image' wrapper

# create a rectangle shape and add to ROI
rect = omero.model.RectI()
rect.x = rdouble(x)
rect.y = rdouble(y)
rect.width = rdouble(width)
rect.height = rdouble(height)
rect.theZ = rint(theZ)
rect.theT = rint(theT)
rect.textValue = rstring("test-Rectangle")
roi.addShape(rect)

# create an Ellipse shape and add to ROI
ellipse = omero.model.EllipseI()
ellipse.cx = rdouble(y)
ellipse.cy = rdouble(x)
ellipse.rx = rdouble(width)
ellipse.ry = rdouble(height)
ellipse.theZ = rint(theZ)
ellipse.theT = rint(theT)
ellipse.textValue = rstring("test-Ellipse")
roi.addShape(ellipse)

# Save the ROI (saves any linked shapes too)
r = updateService.saveAndReturnObject(roi)

Retrieve ROIs linked to an Image.

roiService = conn.getRoiService()
result = roiService.findByImage(imageId, None)
for roi in result.rois:
    print "ROI:  ID:", roi.getId().getValue()
    for s in roi.copyShapes():
        shape = {}
        shape['id'] = s.getId().getValue()
        shape['theT'] = s.getTheT().getValue()
        shape['theZ'] = s.getTheZ().getValue()
        if s.getTextValue():
            shape['textValue'] = s.getTextValue().getValue()
        if type(s) == omero.model.RectI:
            shape['type'] = 'Rectangle'
            shape['x'] = s.getX().getValue()
            shape['y'] = s.getY().getValue()
            shape['width'] = s.getWidth().getValue()
            shape['height'] = s.getHeight().getValue()
        elif type(s) == omero.model.EllipseI:
            shape['type'] = 'Ellipse'
            shape['cx'] = s.getCx().getValue()
            shape['cy'] = s.getCy().getValue()
            shape['rx'] = s.getRx().getValue()
            shape['ry'] = s.getRy().getValue()
        elif type(s) == omero.model.PointI:
            shape['type'] = 'Point'
            shape['cx'] = s.getCx().getValue()
            shape['cy'] = s.getCy().getValue()
        elif type(s) == omero.model.LineI:
            shape['type'] = 'Line'
            shape['x1'] = s.getX1().getValue()
            shape['x2'] = s.getX2().getValue()
            shape['y1'] = s.getY1().getValue()
            shape['y2'] = s.getY2().getValue()
        elif type(s) in (omero.model.MaskI, omero.model.LabelI, omero.model.PolygonI):
            print type(s), " Not supported by this code"
        # Do some processing here, or just print:
        print "   Shape:",
        for key, value in shape.items():
            print "  ", key, value,
        print ""

Remove shape from ROI

result = roiService.findByImage(imageId, None)
for roi in result.rois:
    for s in roi.copyShapes():
        # Find and remove the Shape we added above
        if s.getTextValue() and s.getTextValue().getValue() == "test-Ellipse":
            print "Removing Shape from ROI..."
            roi.removeShape(s)
            roi = updateService.saveAndReturnObject(roi)

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

Delete data¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

Configuration

projectId = 507        # NB: This will be deleted!

Load the Project

project = conn.getObject("Project", projectId)
if project is None:
    import sys
    sys.stderr.write("Error: Object does not exist.\n")
    sys.exit(1)

print "\nProject:", project.getName()

Delete Project

# You can delete a number of objects of the same type at the same
# time. In this case 'Project'. Use deleteChildren=True if you are
# deleting a Project and you want to delete Datasets and Images.
obj_ids = [projectId]
deleteChildren = False
handle = conn.deleteObjects("Project", obj_ids,\
        deleteAnns=True, deleteChildren=deleteChildren)

Retrieve callback and wait until delete completes

# This is not necessary for the Delete to complete. Can be used
# if you want to know when delete is finished or if there were any errors
cb = omero.callbacks.CmdCallbackI(conn.c, handle)
print "Deleting, please wait."
while not cb.block(500):
    print "."
err = isinstance(cb.getResponse(), omero.cmd.ERR)
print "Error?", err
if err:
    print cb.getResponse()
cb.close(True)      # close handle too

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

Render Images¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

Configuration

imageId = 27544

Get thumbnail

# Thumbnail is created using the current rendering settings on the image
image = conn.getObject("Image", imageId)
img_data = image.getThumbnail()
renderedThumb = Image.open(StringIO(img_data))
#renderedThumb.show()           # shows a pop-up
renderedThumb.save("thumbnail.jpg")

Get current settings

print "Channel rendering settings:"
for ch in image.getChannels():
    print "Name: ", ch.getLabel()   # if no name, get emission wavelength or index
    print "  Color:", ch.getColor().getHtml()
    print "  Active:", ch.isActive()
    print "  Levels:", ch.getWindowStart(), "-", ch.getWindowEnd()
print "isGreyscaleRenderingModel:", image.isGreyscaleRenderingModel()

Render each channel as a separate greyscale image

image.setGreyscaleRenderingModel()
sizeC = image.getSizeC()
z = image.getSizeZ() / 2
t = 0
for c in range(1, sizeC + 1):       # Channel index starts at 1
    channels = [c]                  # Turn on a single channel at a time
    image.setActiveChannels(channels)
    renderedImage = image.renderImage(z, t)
    #renderedImage.show()                        # popup (use for debug only)
    renderedImage.save("channel%s.jpg" % c)     # save in the current folder

Turn 3 channels on, setting their colours

image.setColorRenderingModel()
channels = [1, 2, 3]
colorList = ['F00', None, 'FFFF00']         # do not change colour of 2nd channel
image.setActiveChannels(channels, colors=colorList)
image.setProjection('intmax')               # max intensity projection 'intmean' for mean-intensity
renderedImage = image.renderImage(z, t)     # z and t are ignored for projections
#renderedImage.show()
renderedImage.save("all_channels.jpg")
image.setProjection('normal')               # turn off projection

Turn 2 channels on, setting levels of the first one

channels = [1, 2]
rangeList = [[100.0, 120.2], [None, None]]
image.setActiveChannels(channels, windows=rangeList)
renderedImage = image.renderImage(z, t, compression=0.5)    # default compression is 0.9
#renderedImage.show()
renderedImage.save("two_channels.jpg")

Save the current rendering settings

image.saveDefaults()

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

Create Image¶

Create a connection

conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()

Configuration

imageId = 27544     # This image must have at least 2 channels

Create an image from scratch

# This example demonstrates the usage of the convenience method
# createImageFromNumpySeq() Here we create a multi-dimensional image from a
# hard-coded array of data.
from numpy import array, int8
sizeX, sizeY, sizeZ, sizeC, sizeT = 5, 4, 1, 2, 1
plane1 = array([[0, 1, 2, 3, 4], [5, 6, 7, 8, 9], [0, 1, 2, 3, 4], [5, 6, 7, 8, 9]], dtype=int8)
plane2 = array([[5, 6, 7, 8, 9], [0, 1, 2, 3, 4], [5, 6, 7, 8, 9], [0, 1, 2, 3, 4]], dtype=int8)
planes = [plane1, plane2]

def planeGen():
    """generator will yield planes"""
    for p in planes:
        yield p

desc = "Image created from a hard-coded arrays"
i = conn.createImageFromNumpySeq(planeGen(), "numpy image",\
        sizeZ, sizeC, sizeT, description=desc, dataset=None)

Create an Image from an existing image

# We are going to create a new image by passing the method a 'generator' of 2D
# planes This will come from an existing image, by taking the average of 2 channels.
zctList = []
image = conn.getObject('Image', imageId)
sizeZ, sizeC, sizeT = image.getSizeZ(), image.getSizeC(), image.getSizeT()
dataset = image.getParent()
pixels = image.getPrimaryPixels()
newSizeC = 1

def planeGen():
    """
    set up a generator of 2D numpy arrays.

The createImage method below expects planes in the order specified here (for
z.. for c.. for t..)
"""
for z in range(sizeZ):              # all Z sections
    for c in range(newSizeC):       # Illustrative purposes only, since we only have 1 channel
        for t in range(sizeT):      # all time-points
            channel0 = pixels.getPlane(z, 0, t)
            channel1 = pixels.getPlane(z, 1, t)
            # Here we can manipulate the data in many different ways. As an example we are doing "average"
            newPlane = (channel0 + channel1) / 2    # average of 2 channels
            print "newPlane for z,t:", z, t, newPlane.dtype, newPlane.min(), newPlane.max()
            yield newPlane

desc = "Image created from Image ID: %s by averaging Channel 1 and Channel 2" % imageId
i = conn.createImageFromNumpySeq(planeGen(), "new image",\
        sizeZ, newSizeC, sizeT, description=desc, dataset=dataset)

Close connection:

# When you are done, close the session to free up server resources.
conn._closeSession()

Python OMERO.scripts¶

It is relatively straightforward to take the code samples above and re-use them in OMERO.scripts. This allows the code to be run on the OMERO server and called from either the OMERO.insight client or OMERO.web by any users of the server. See OMERO.scripts user guide.

Blitz Gateway documentation¶

The epydoc-generated documentation of methods provided by OMERO Gateway is available showing wrapper classes.

Specifically, the API for the ‘conn’ connection wrapper created above is here.

When working with OMERO model objects (omero.model.Image etc) the Gateway will wrap these objects in classes such as omero.gateway.ImageWrapper to handle object loading and hierarchy traversal. For example:

>>> for p in conn.listProjects():         # Initially we just load Projects
...     print p.getName()
...     for dataset in p.listChildren():      # lazy-loading of Datasets here
...             print "  ", dataset.getName()
...
TestProject
   Aurora-B
tiff stacks
   newTimeStack
   test
siRNAi
   CENP
   live-cell
   survivin

Access to the OMERO API services¶

If you need access to API methods that are not provided by the gateway library, you can get hold of the OMERO Application Programming Interface.

Note

These services will always work with omero.model objects and not the gateway wrapper objects.

The gateway handles creation and reuse of the API services, so that new ones are not created unnecessarily. Services can be accessed using the methods of the underlying Service Factory with the Gateway handling reuse as needed. Stateless services (those retrieved with get… methods E.g. getQueryService) are always reused for each call, E.g. blitzon.getQueryService() whereas stateful services E.g. createRenderingEngine may be created each time.

Not all methods of the service factory are currently supported in the gateway. You can get an idea of the currently supported services by looking at the source code under the _createProxies method.

Example: ContainerService can load Projects and Datasets in a single call to server (no lazy loading)

cs = conn.getContainerService()
projects = cs.loadContainerHierarchy("Project", None, None)
for p in projects:                # omero.model.ProjectI
    print p.getName().getValue()     # need to 'unwrap' rstring
    for d in p.linkedDatasetList():
        print d.getName().getValue()

Stateful services, reconnection, error handling etc¶

The Blitz gateway was designed for use in the OMERO.web framework framework and it is not expected that stateful services will be maintained on the client for significant time. There is various error-handling functionality in the Blitz gateway that will close existing services and recreate them in order to maintain a working connection. If this happens then any stateful services that you have on the client-side will become stale. We will attempt to document this a little better in due course, but our general advice is to create, use and close the stateful services in the shortest practicable time.

Overwriting and extending omero.gateway classes¶

When working with omero.gateway or wrapper classes such as omero.gateway.ImageWrapper you might want to add your own functionality or customize an existing one. NB: Note the call to omero.gateway.refreshWrappers() to ensure that your subclasses are returned by calls to getObjects() For example:

class MyBlitzGateway (omero.gateway.BlitzGateway):

    def __init__ (self, *args, **kwargs):
        super(MyBlitzGateway, self).__init__(*args, **kwargs)

        ...do something, e.g. add new field...
        self.new_field = 'foo'

    def connect (self, *args, **kwargs):

        rv = super(MyBlitzGateway, self).connect(*args,**kwargs)
        if rv:
            ...do something, e.g. modify new field...
            self.new_field = 'bla'

        return rv

omero.gateway.BlitzGateway = MyBlitzGateway

class MyBlitzObjectWrapper (object):

    annotation_counter = None

    def countAnnotations (self):
        """
        Count on annotations linked to the object and set the value
        on the custom field 'annotation_counter'.

        @return     Counter
        """

        if self.annotation_counter is not None:
            return self.annotation_counter
        else:
            container = self._conn.getContainerService()
            m = container.getCollectionCount(self._obj.__class__.__name__, type(self._obj).ANNOTATIONLINKS, [self._oid], None)
            if m[self._oid] > 0:
                self.annotation_counter = m[self._oid]
                return self.annotation_counter
            else:
                return None

class ImageWrapper (MyBlitzObjectWrapper, omero.gateway.ImageWrapper):
    """
    omero_model_ImageI class wrapper overwrite omero.gateway.ImageWrapper
    and extends MyBlitzObjectWrapper.
    """

    def __prepare__ (self, **kwargs):
        if kwargs.has_key('annotation_counter'):
            self.annotation_counter = kwargs['annotation_counter']

omero.gateway.ImageWrapper = ImageWrapper

# IMPORTANT to update the map of wrappers for 'Image' etc. returned by getObjects("Image")
omero.gateway.refreshWrappers()

This page provides some background information on the OMERO Python client ‘gateway’ (omero.gateway module) and describes work to improve the API, beginning with the OMERO 4.3 release.

The Blitz Gateway is a Python client-side library that facilitates working with the OMERO API, handling connection to the server, loading of data objects and providing convenience methods to access the data. It was originally designed as part of the OMERO.web framework framework, to provide connection and data retrieval services to various web clients. However, we have now decided to encourage its use for all access to the OMERO Python API.

Wrapper objects¶

The Gateway consists of a number of wrapper objects:

Connection wrapper¶

The BlitzGateway class (see API of development code) is a wrapper for the OMERO client and session objects. It provides various methods for connecting to the OMERO server, querying the status or context of the current connection and as a starting point for retrieving data objects from OMERO.

from omero.gateway import *

conn = BlitzGateway("username", "password", host="localhost", port=4064)
conn.connect()

for p in conn.listProjects():
    print p.name

Model object wrappers¶

OMERO model objects, E.g. omero.model.Project, omero.model.Pixels etc (see full list) are code-generated and mapped to the OMERO database schema. They are language agnostic and their data is in the form of omero.rtypes as described: about model objects).

import omero
from omero.model import *
from omero.rtypes import rstring
p = omero.model.ProjectI()
p.name = rstring("My Project")   # attributes are all rtypes
print p.getName().getValue()     # getValue() to unwrap the rtype
print p.name.val                 # short-hand

To facilitate work in Python, particularly in web page templates, these Python model objects are wrapped in Blitz Object Wrappers. This hides the use of rtypes.

import omero
from omero.model import *
from omero.rtypes import rstring
p = omero.model.ProjectI()
p.setName(rstring("Omero Model Project"))   # attributes are all rtypes
print p.getName().getValue()                # getValue() to unwrap the rtype
print p.name.val                            # short-hand

from omero.gateway import *
project = ProjectWrapper(obj=p)             # wrap the model.object
project.setName("Project Wrapper")          # Don't need to use rtypes
print project.getName()
print project.name

print project._obj                  # access the wrapped object with ._obj

These wrappers also have a reference to the BlitzGateway connection wrapper, so they can make calls to the server and load more data when needed (lazy loading).

E.g.

# connect as above
for p in conn.listProjects():
    print p.name
    for dataset in p.listChildren():   # lazy loading of datasets, wrapped in DatasetWrapper
        print "Dataset", d.name

Wrapper coverage¶

The OMERO data model has a large number of objects, not all of which are used by the OMERO.web framework framework. For this reason, the Blitz gateway (which was originally built for OMERO.web framework) has not yet been extended to wrap every omero.model object with a specific Blitz Object Wrapper. The current list of object wrappers can be found in the omero.gateway module API. As more functionality is provided by the Blitz Gateway, the coverage of object wrappers will increase accordingly.

OMERO

Page Contents

Previous topic

Next topic

This Page

OMERO Python language bindings¶

Code samples¶

Connect to OMERO¶

Read data¶

Groups and permissions¶

Raw data access¶

Write data¶

OMERO tables¶

ROIs¶

Delete data¶

Render Images¶

Create Image¶

Python OMERO.scripts¶

Blitz Gateway documentation¶

Access to the OMERO API services¶

Stateful services, reconnection, error handling etc¶

Overwriting and extending omero.gateway classes¶

Wrapper objects¶

Connection wrapper¶

Model object wrappers¶

Wrapper coverage¶

Navigation

OMERO

Page Contents

Previous topic

Next topic

Quick search

This Page

OMERO Python language bindings¶

Code samples¶

Connect to OMERO¶

Read data¶

Groups and permissions¶

Raw data access¶

Write data¶

OMERO tables¶

ROIs¶

Delete data¶

Render Images¶

Create Image¶

Python OMERO.scripts¶

Blitz Gateway documentation¶

Access to the OMERO API services¶

Stateful services, reconnection, error handling etc¶

Overwriting and extending omero.gateway classes¶

Wrapper objects¶

Connection wrapper¶

Model object wrappers¶

Wrapper coverage¶

Navigation