OMERO Python language bindings
==============================
:snapshot:`MOVIE: introduction to Blitz Gateway
<movies/omero-4-3/mov/BlitzGatewayIntro-4.3.mov>`
In addition to the auto-generated Python libraries of the core |OmeroApi|,
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 gives you a large number of code samples to get you
started. Then we describe a bit more about :doc:`PythonBlitzGateway`.
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 :envvar:`PYTHONPATH` to include them:
.. parsed-literal::
export OMERO_PREFIX=~/Desktop/|OMEROserver| # for example
export PYTHONPATH=$PYTHONPATH:$OMERO_PREFIX/lib/python
.. |OMEROserver| replace:: OMERO.server-|release|-ice3x-byy
You will also need Ice libraries as described in the
:doc:`/sysadmins/unix/server-installation` and an OMERO server to connect to,
which must be the same major version, i.e. |version|.x.
All the code examples below can be found at
:sourcedir:`examples/Training/python`.
Start by downloading the first example below:
:source:`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()
::
# New in OMERO 5
print "Admins:"
for exp in conn.getAdministrators():
print " ID:", exp.getId(), exp.getOmeName(), " Name:", exp.getFullName()
::
# 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
:doc:`/sysadmins/server-permissions`.
::
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()
.. _python_omero_tables_code_samples:
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** (also see the
:javadoc:`Table javadocs <slice2html/omero/grid/Table.html>`)
::
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()
Filesets - New in OMERO 5
^^^^^^^^^^^^^^^^^^^^^^^^^
- **Create a connection**
::
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
- **Configuration**
::
imageId = 101
- **Get the 'Fileset' for an Image**
::
# A Fileset is a collection of the original files imported to
# create an image or set of images in OMERO.
image = conn.getObject("Image", imageId)
fileset = image.getFileset() # will be None for pre-FS images
fsId = fileset.getId()
# List all images that are in this fileset
for fsImage in fileset.copyImages():
print fsImage.getId(), fsImage.getName()
# List original imported files
for origFile in fileset.listFiles():
name = origFile.getName()
path = origFile.getPath()
print path, name
- **Get Original Imported Files directly from the image**
::
# this will include pre-FS data IF images were archived on import
print image.countImportedImageFiles()
# specifically count Fileset files
fileCount = image.countFilesetFiles()
# list files
if fileCount > 0:
for origFile in image.getImportedImageFiles():
name = origFile.getName()
path = origFile.getPath()
print path, name
- **Can get the Fileset using conn.getObject()**
::
fileset = conn.getObject("Fileset", fsId)
- **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 :doc:`/developers/scripts/user-guide`.