Note
This documentation is for the new OMERO 5.3 version. See the latest OMERO 5.2.x version or the previous versions page to find documentation for the OMERO version you are using if you have not upgraded yet.
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 gives you a large number of code samples to get you started. Then we describe a bit more about Blitz Gateway documentation.
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-5.3.3-ice3x-byy # for example export PYTHONPATH=$PYTHONPATH:$OMERO_PREFIX/lib/python
You will also need Ice libraries as described in the OMERO.server installation overview and an OMERO server to connect to, which must be the same major version, i.e. .x.
All the code examples below can be found at examples/Training/python.
If you want to run the examples, you will need to download and configure them to connect to your own server e.g. HOST = "localhost". You can edit HOST, PORT, USERNAME and PASSWORD in the Parse_OMERO_Properties.py file and these values will be imported into the other scripts.
Then you can run the scripts:
$ 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. Some scripts will also need editing of 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.
conn = BlitzGateway(USERNAME, PASSWORD, host=HOST, port=PORT)
conn.connect()
# 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)
# 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()
# List the group owners and other members
owners, members = group.groupSummary()
print " Group owners:"
for o in owners:
print " ID: %s %s Name: %s" % (
o.getId(), o.getOmeName(), o.getFullName())
print " Group members:"
for m in members:
print " ID: %s %s Name: %s" % (
m.getId(), m.getOmeName(), m.getFullName())
print "Owner of:"
for g in conn.listOwnedGroups():
print " ID: ", g.getName(), " Name:", g.getId()
# Added in OMERO 5.0
print "Admins:"
for exp in conn.getAdministrators():
print " ID: %s %s Name: %s" % (
exp.getId(), exp.getOmeName(), exp.getFullName())
# The 'context' of our current session
ctx = conn.getEventContext()
# print ctx # for more info
# When you are done, close the session to free up server resources.
conn.close()
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())
# 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.
my_exp_id = conn.getUser().getId()
default_group_id = conn.getEventContext().groupId
for project in conn.getObjects("Project", opts={'owner': my_exp_id,
'group': default_group_id,
'order_by': 'lower(obj.name)',
'limit': 5, 'offset': 0}):
print_obj(project)
# We can get Datasets with listChildren, since we have the Project already.
# Or conn.getObjects("Dataset", opts={'project', id}) if we have Project ID
for dataset in project.listChildren():
print_obj(dataset, 2)
for image in dataset.listChildren():
print_obj(image, 4)
# We can use the 'orphaned' filter to find Datasets, Images
# or Plates that are not in any parent container
print "\nList orphaned Datasets: \n", "=" * 50
datasets = conn.getObjects("Dataset", opts={'orphaned': True})
for dataset in datasets:
print_obj(dataset)
# We can filter Images by their parent Dataset
# We can also filter Datasets by 'project', Plates by 'screen',
# Wells by 'plate'
print "\nImages in Dataset:", datasetId, "\n", "=" * 50
for image in conn.getObjects('Image', opts={'dataset': datasetId}):
print_obj(image)
# Pixels and Channels will be loaded automatically as needed
image = conn.getObject("Image", imageId)
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()
# List Channels (loads the Rendering settings to get channel colors)
for channel in image.getChannels():
print 'Channel:', channel.getLabel(),
print 'Color:', channel.getColor().getRGB()
print 'Lookup table:', channel.getLut()
print 'Is reverse intensity?', channel.isReverseIntensity()
# render the first timepoint, mid Z section
z = image.getSizeZ() / 2
t = 0
rendered_image = image.renderImage(z, t)
# rendered_image.show() # popup (use for debug only)
# rendered_image.save("test.jpg") # save in the current folder
size_x = image.getPixelSizeX() # e.g. 0.132
print " Pixel Size X:", sizeX
# Units support, new in OMERO 5.1.0
size_x_obj = image.getPixelSizeX(units=True)
print " Pixel Size X:", size_x_obj.getValue(), "(%s)" % size_x_obj.getSymbol()
# To get the size with different units, e.g. Angstroms
size_x_ang = image.getPixelSizeX(units="ANGSTROM")
print " Pixel Size X:", size_x_ang.getValue(), "(%s)" % size_x_ang.getSymbol()
for screen in conn.getObjects("Screen"):
print_obj(screen)
for plate in screen.listChildren():
print_obj(plate, 2)
plateId = plate.getId()
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()
group = conn.getGroupFromContext()
print "Current group: ", group.getName()
group_perms = group.getDetails().getPermissions()
perm_string = str(group_perms)
permission_names = {
'rw----': 'PRIVATE',
'rwr---': 'READ-ONLY',
'rwra--': 'READ-ANNOTATE',
'rwrw--': 'READ-WRITE'}
print "Permissions: %s (%s)" % (permission_names[perm_string], perm_string)
This will be determined by group permissions e.g. in Read-Only or Read-Annotate groups, this will include other users’ data - see Groups and permissions system.
projects = conn.listProjects() # may include other users' data
for p in projects:
print p.getName(), "Owner: ", p.getDetails().getOwner().getFullName()
# Will return None if Image is not in current group
image = conn.getObject("Image", imageId)
print "Image: ", image
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.getDetails().getGroup().getId() # access groupId without loading group
group_id = image.getDetails().getGroup().getId()
# This is how we 'switch group' in webclient
conn.SERVICE_OPTS.setOmeroGroup(group_id)
projects = conn.listProjects()
image = conn.getObject("Image", imageId)
print "Image: ", image,
# Use the pixelswrapper to retrieve the plane as
# a 2D numpy array see [https://github.com/scipy/scipy]
#
# Numpy array can be used for various analysis routines
#
image = conn.getObject("Image", imageId)
size_z = image.getSizeZ()
size_c = image.getSizeC()
size_t = 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
# 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))... ]
zct_list = [(iz, c, t, tile) for iz in range(size_z)]
print "\nZ stack of tiles:"
planes = pixels.getTiles(zct_list)
for i, p in enumerate(planes):
print "Tile:", zct_list[i], " min:", p.min(),\
" max:", p.max(), " sum:", p.sum()
zct_list = []
for z in range(size_z / 2, size_z): # get the top half of the Z-stack
for c in range(size_c): # all channels
for t in range(size_t): # all time-points
zct_list.append((z, c, t))
print "\nHyper stack of planes:"
planes = pixels.getPlanes(zct_list)
for i, p in enumerate(planes):
print "plane zct:", zct_list[i], " min:", p.min(), " max:", p.max()
dataset_obj = omero.model.DatasetI()
dataset_obj.setName(rstring("New Dataset"))
dataset_obj = conn.getUpdateService().saveAndReturnObject(dataset_obj)
dataset_id = dataset_obj.getId().getValue()
print "New dataset, Id:", dataset_id
project = conn.getObject("Project", projectId)
link = omero.model.ProjectDatasetLinkI()
link.setParent(omero.model.ProjectI(project.getId(), False))
link.setChild(dataset_obj)
conn.getUpdateService().saveObject(link)
tag_ann = omero.gateway.TagAnnotationWrapper(conn)
tag_ann.setValue("New Tag")
tag_ann.save()
project = conn.getObject("Project", projectId)
project.linkAnnotation(tag_ann)
key_value_data = [["Drug Name", "Monastrol"], ["Concentration", "5 mg/ml"]]
map_ann = omero.gateway.MapAnnotationWrapper(conn)
# Use 'client' namespace to allow editing in Insight & web
namespace = omero.constants.metadata.NSCLIENTMAPANNOTATION
map_ann.setNs(namespace)
map_ann.setValue(key_value_data)
map_ann.save()
project = conn.getObject("Project", projectId)
# NB: only link a client map annotation to a single object
project.linkAnnotation(map_ann)
print conn.countAnnotations('Project', [projectId])
for ann in project.listAnnotations():
print ann.getId(), ann.OMERO_TYPE,
print " added by ", ann.link.getDetails().getOwner().getOmeName()
if ann.OMERO_TYPE == omero.model.TagAnnotationI:
print "Tag value:", ann.getTextValue()
dataset = conn.getObject("Dataset", dataset_id)
# Specify a local file e.g. could be result of some analysis
file_to_upload = "README.txt" # This file should already exist
with open(file_to_upload, 'w') as f:
f.write('annotation test')
# create the original file and file annotation (uploads the file etc.)
namespace = "imperial.training.demo"
print "\nCreating an OriginalFile and FileAnnotation"
file_ann = conn.createFileAnnfromLocalFile(
file_to_upload, mimetype="text/plain", ns=namespace, desc=None)
print "Attaching FileAnnotation to Dataset: ", "File ID:", file_ann.getId(), \
",", file_ann.getFile().getName(), "Size:", file_ann.getFile().getSize()
dataset.linkAnnotation(file_ann) # link it to 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())
with open(str(file_path), 'w') as f:
print "\nDownloading file to", file_path, "..."
for chunk in ann.getFileInChunks():
f.write(chunk)
print "File downloaded!"
ns_to_include = [namespace]
ns_to_exclude = []
metadataService = conn.getMetadataService()
annotations = metadataService.loadSpecifiedAnnotations(
'omero.model.FileAnnotation', ns_to_include, ns_to_exclude, None)
for ann in annotations:
print ann.getId().getValue(), ann.getFile().getName().getValue()
ann = dataset.getAnnotation(namespace)
print "Found Annotation with namespace: ", ann.getNs()
from random import random
table_name = "TablesDemo:%s" % str(random())
col1 = omero.grid.LongColumn('Uid', 'testLong', [])
col2 = omero.grid.StringColumn('MyStringColumnInit', '', 64, [])
columns = [col1, col2]
resources = conn.c.sf.sharedResources()
repository_id = resources.repositories().descriptions[0].getId().getValue()
table = resources.newTable(repository_id, table_name)
table.initialize(columns)
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.
orig_file = table.getOriginalFile()
orig_file_id = orig_file.id.val
# ...so you can attach this data to an object e.g. Dataset
file_ann = omero.model.FileAnnotationI()
# use unloaded OriginalFileI
file_ann.setFile(omero.model.OriginalFileI(orig_file_id, False))
file_ann = conn.getUpdateService().saveAndReturnObject(file_ann)
link = omero.model.DatasetAnnotationLinkI()
link.setParent(omero.model.DatasetI(datasetId, False))
link.setChild(omero.model.FileAnnotationI(file_ann.getId().getValue(), False))
conn.getUpdateService().saveAndReturnObject(link)
See also
open_table = resources.openTable(orig_file)
print "Table Columns:"
for col in open_table.getHeaders():
print " ", col.name
rowCount = open_table.getNumberOfRows()
print "Row count:", rowCount
row_numbers = [3, 5, 7]
print "\nGet All Data for rows: ", row_numbers
data = open_table.readCoordinates(range(rowCount))
for col in data.columns:
print "Data for Column: ", col.name
for v in col.values:
print " ", v
col_numbers = [1]
start = 3
stop = 7
print "\nGet Data for cols: ", col_numbers,\
" and between rows: ", start, "-", stop
data = open_table.read(col_numbers, start, stop)
for col in data.columns:
print "Data for Column: ", col.name
for v in col.values:
print " ", v
query_rows = open_table.getWhereList(
"(Uid > 2) & (Uid <= 8)", variables={}, start=0, stop=rowCount, step=0)
data = open_table.readCoordinates(query_rows)
for col in data.columns:
print "Query Results for Column: ", col.name
for v in col.values:
print " ", v
open_table.close() # we're done
orig_table_file = conn.getObject(
"OriginalFile", attributes={'name': table_name}) # if name is unique
saved_table = resources.openTable(orig_table_file._obj)
print "Opened table with row-count:", saved_table.getNumberOfRows()
saved_table.close()
updateService = conn.getUpdateService()
# We are using the core Python API and omero.model objects here, since ROIs
# are not yet supported in the Python Blitz Gateway.
#
# First we load our image and pick some parameters for shapes
x = 50
y = 200
width = 100
height = 50
image = conn.getObject("Image", imageId)
z = image.getSizeZ() / 2
t = 0
# We have a helper function for creating an ROI and linking it to new shapes
def create_roi(img, shapes):
# create an ROI, link it to Image
roi = omero.model.RoiI()
# use the omero.model.ImageI that underlies the 'image' wrapper
roi.setImage(img._obj)
for shape in shapes:
roi.addShape(shape)
# Save the ROI (saves any linked shapes too)
return updateService.saveAndReturnObject(roi)
# Another helper for generating the color integers for shapes
def rgba_to_int(red, green, blue, alpha=255):
""" Return the color as an Integer in RGBA encoding """
r = red << 24
g = green << 16
b = blue << 8
a = alpha
rgba_int = r+g+b+a
if (rgba_int > (2**31-1)): # convert to signed 32-bit int
rgba_int = rgba_int - 2**32
return rgba_int
# create a rectangle shape (added to ROI below)
print ("Adding a rectangle at theZ: %s, theT: %s, X: %s, Y: %s, width: %s,"
" height: %s" % (z, t, x, y, width, height))
rect = omero.model.RectangleI()
rect.x = rdouble(x)
rect.y = rdouble(y)
rect.width = rdouble(width)
rect.height = rdouble(height)
rect.theZ = rint(z)
rect.theT = rint(t)
rect.textValue = rstring("test-Rectangle")
rect.fillColor = rint(rgba_to_int(255, 255, 255, 255))
rect.strokeColor = rint(rgba_to_int(255, 255, 0, 255))
# create an Ellipse shape (added to ROI below)
ellipse = omero.model.EllipseI()
ellipse.x = rdouble(y)
ellipse.y = rdouble(x)
ellipse.radiusX = rdouble(width)
ellipse.radiusY = rdouble(height)
ellipse.theZ = rint(z)
ellipse.theT = rint(t)
ellipse.textValue = rstring("test-Ellipse")
# Create an ROI containing 2 shapes on same plane
# NB: OMERO.insight client doesn't support display
# of multiple shapes on a single plane.
# Therefore the ellipse is removed later (see below)
create_roi(image, [rect, ellipse])
# create an ROI with single line shape
line = omero.model.LineI()
line.x1 = rdouble(x)
line.x2 = rdouble(x+width)
line.y1 = rdouble(y)
line.y2 = rdouble(y+height)
line.theZ = rint(z)
line.theT = rint(t)
line.textValue = rstring("test-Line")
create_roi(image, [line])
def create_mask(mask_bytes, bytes_per_pixel=1):
if bytes_per_pixel == 2:
divider = 16.0
format_string = "H" # Unsigned short
byte_factor = 0.5
elif bytes_per_pixel == 1:
divider = 8.0
format_string = "B" # Unsigned char
byte_factor = 1
else:
message = "Format %s not supported"
raise ValueError(message)
steps = math.ceil(len(mask_bytes) / divider)
mask = []
for i in range(long(steps)):
binary = mask_bytes[
i * int(divider):i * int(divider) + int(divider)]
format = str(int(byte_factor * len(binary))) + format_string
binary = struct.unpack(format, binary)
s = ""
for bit in binary:
s += str(bit)
mask.append(int(s, 2))
return bytearray(mask)
mask_x = 50
mask_y = 50
mask_h = 100
mask_w = 100
# Create [0, 1] mask
mask_array = numpy.fromfunction(
lambda x, y: (x * y) % 2, (mask_w, mask_h))
# Set correct number of bytes per value
mask_array = mask_array.astype(numpy.uint8)
# Convert the mask to bytes
mask_array = mask_array.tostring()
# Pack the bytes to a bit mask
mask_packed = create_mask(mask_array, 1)
# Define mask's fill color
mask_color = ColorHolder()
mask_color.setRed(255)
mask_color.setBlue(0)
mask_color.setGreen(0)
mask_color.setAlpha(100)
# create an ROI with a single mask
mask = omero.model.MaskI()
mask.setTheC(rint(0))
mask.setTheZ(rint(0))
mask.setTheT(rint(0))
mask.setX(rdouble(mask_x))
mask.setY(rdouble(mask_y))
mask.setWidth(rdouble(mask_w))
mask.setHeight(rdouble(mask_h))
mask.setFillColor(rint(mask_color.getInt()))
mask.setTextValue(rstring("test-Mask"))
mask.setBytes(mask_packed)
create_roi(image, [mask])
# create an ROI with single point shape
point = omero.model.PointI()
point.x = rdouble(x)
point.y = rdouble(y)
point.theZ = rint(z)
point.theT = rint(t)
point.textValue = rstring("test-Point")
create_roi(image, [point])
# create an ROI with a single polygon, setting colors and lineWidth
polygon = omero.model.PolygonI()
polygon.theZ = rint(z)
polygon.theT = rint(t)
polygon.fillColor = rint(rgba_to_int(255, 0, 255, 50))
polygon.strokeColor = rint(rgba_to_int(255, 255, 0))
polygon.strokeWidth = omero.model.LengthI(10, UnitsLength.PIXEL)
points = "10,20, 50,150, 200,200, 250,75"
polygon.points = rstring(points)
create_roi(image, [polygon])
roi_service = conn.getRoiService()
result = roi_service.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.RectangleI:
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['x'] = s.getX().getValue()
shape['y'] = s.getY().getValue()
shape['radiusX'] = s.getRadiusX().getValue()
shape['radiusY'] = s.getRadiusY().getValue()
elif type(s) == omero.model.PointI:
shape['type'] = 'Point'
shape['x'] = s.getX().getValue()
shape['y'] = s.getY().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) == omero.model.MaskI:
shape['type'] = 'Mask'
shape['x'] = s.getX().getValue()
shape['y'] = s.getY().getValue()
shape['width'] = s.getWidth().getValue()
shape['height'] = s.getHeight().getValue()
elif type(s) in (
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 ""
result = roi_service.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)
# 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 = [project_id]
delete_children = False
conn.deleteObjects(
"Project", obj_ids, deleteAnns=True,
deleteChildren=delete_children, wait=True)
# 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
handle = conn.deleteObjects("Project", [project_id])
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
# Thumbnail is created using the current rendering settings on the image
image = conn.getObject("Image", imageId)
img_data = image.getThumbnail()
rendered_thumb = Image.open(StringIO(img_data))
# renderedThumb.show() # shows a pop-up
rendered_thumb.save("thumbnail.jpg")
print "Channel rendering settings:"
for ch in image.getChannels():
# if no name, get emission wavelength or index
print "Name: ", ch.getLabel()
print " Color:", ch.getColor().getHtml()
print " Active:", ch.isActive()
print " Levels:", ch.getWindowStart(), "-", ch.getWindowEnd()
print "isGreyscaleRenderingModel:", image.isGreyscaleRenderingModel()
print "Default Z/T positions:"
print " Z = %s, T = %s" % (image.getDefaultZ(), image.getDefaultT())
print "Rendering Defs on Image:"
for rdef in image.getAllRenderingDefs():
img_data = image.getThumbnail(rdefId=rdef['id'])
print " ID: %s (owner: %s %s)" % (
rdef['id'], rdef['owner']['firstName'], rdef['owner']['lastName'])
image.setGreyscaleRenderingModel()
size_c = image.getSizeC()
z = image.getSizeZ() / 2
t = 0
for c in range(1, size_c + 1): # Channel index starts at 1
channels = [c] # Turn on a single channel at a time
image.setActiveChannels(channels)
rendered_image = image.renderImage(z, t)
# renderedImage.show() # popup (use for debug only)
rendered_image.save("channel%s.jpg" % c) # save in the current folder
image.setColorRenderingModel()
channels = [1, 2, 3]
color_list = ['F00', None, 'FFFF00'] # do not change color of 2nd channel
image.setActiveChannels(channels, colors=color_list)
# max intensity projection 'intmean' for mean-intensity
image.setProjection('intmax')
rendered_image = image.renderImage(z, t) # z and t are ignored for projections
# renderedImage.show()
rendered_image.save("all_channels.jpg")
image.setProjection('normal') # turn off projection
channels = [1, 2]
range_list = [[100.0, 120.2], [None, None]]
image.setActiveChannels(channels, windows=range_list)
# Set default Z and T. These will be used as defaults for further rendering
image.setDefaultZ(0)
image.setDefaultT(0)
# default compression is 0.9
rendered_image = image.renderImage(z=None, t=None, compression=0.5)
rendered_image.show()
rendered_image.save("two_channels.jpg")
image.saveDefaults()
image.resetDefaults(save=True)
# 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
import omero
size_x, size_y, size_z, size_c, size_t = 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 plane_gen():
"""generator will yield planes"""
for p in planes:
yield p
desc = "Image created from a hard-coded arrays"
i = conn.createImageFromNumpySeq(
plane_gen(), "numpy image", size_z, size_c, size_t, description=desc,
dataset=None)
print 'Created new Image:%s Name:"%s"' % (i.getId(), i.getName())
Lengths are specified by value and a unit enumeration Here we set the pixel size X and Y to be 9.8 Angstroms
from omero.model.enums import UnitsLength
# Re-load the image to avoid update conflicts
i = conn.getObject("Image", i.getId())
u = omero.model.LengthI(9.8, UnitsLength.ANGSTROM)
p = i.getPrimaryPixels()._obj
p.setPhysicalSizeX(u)
p.setPhysicalSizeY(u)
conn.getUpdateService().saveObject(p)
# 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.
zct_list = []
image = conn.getObject('Image', imageId)
size_z, size_c, size_t = image.getSizeZ(), image.getSizeC(), image.getSizeT()
dataset = image.getParent()
pixels = image.getPrimaryPixels()
new_size_c = 1
def plane_gen():
"""
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(size_z): # all Z sections
# Illustrative purposes only, since we only have 1 channel
for c in range(new_size_c):
for t in range(size_t): # 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"
# average of 2 channels
new_plane = (channel0 + channel1) / 2
print "newPlane for z,t:", z, t, new_plane.dtype, \
new_plane.min(), new_plane.max()
yield new_plane
desc = ("Image created from Image ID: %s by averaging Channel 1 and Channel 2"
% imageId)
i = conn.createImageFromNumpySeq(
plane_gen(), "new image", size_z, new_size_c, size_t, description=desc,
dataset=dataset)
# 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
fs_id = fileset.getId()
# List all images that are in this fileset
for fs_image in fileset.copyImages():
print fs_image.getId(), fs_image.getName()
# List original imported files
for orig_file in fileset.listFiles():
name = orig_file.getName()
path = orig_file.getPath()
print path, name
# this will include pre-FS data IF images were archived on import
print image.countImportedImageFiles()
# specifically count Fileset files
file_count = image.countFilesetFiles()
# list files
if file_count > 0:
for orig_file in image.getImportedImageFiles():
name = orig_file.getName()
path = orig_file.getPath()
print path, name
fileset = conn.getObject("Fileset", fs_id)
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.