omero.gateway package

Subpackages

• omero.gateway.scripts package
  • Submodules
  • omero.gateway.scripts.dbhelpers module
  • omero.gateway.scripts.testdb_create module
  • Module contents

Submodules

omero.gateway.pytest_fixtures module

omero.gateway.utils module

class omero.gateway.utils.GatewayConfig

Bases: object

Global Gateway configuration:

• IMG_RDEFNS: a namespace for annotations linked on images holding

  the default rendering settings object id.

• IMG_ROPTSNS: a namespace for annotations linked on images holding

  default rendering options that don’t get saved in the rendering settings.

class omero.gateway.utils.ServiceOptsDict(data=None, *args, **kwargs)

Bases: dict

_testItem(item)

clear()

Remove all items from the dictionary.

copy()

Returns a copy of this object.

get(key, default=None)

Return the value for key if key is in the dictionary, else default. If default is not given, it defaults to None, so that this method never raises a KeyError.

getOmeroGroup()

getOmeroShare()

getOmeroUser()

set(key, value)

Set key to value as string.

setOmeroGroup(value=None)

setOmeroShare(value=None)

setOmeroUser(value=None)

omero.gateway.utils.propertiesToDict(m, prefix=None)

Convert omero properties to nested dictionary, skipping common prefix

omero.gateway.utils.toBoolean(val)

Get the boolean value of the provided input.

If the value is a boolean return the value. Otherwise check to see if the value is in [“true”, “yes”, “y”, “t”, “1”] and returns True if value is in the list

Module contents

omero.gateway.AnnotationLinkWrapper

alias of _AnnotationLinkWrapper

class omero.gateway.AnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_AnnotationI class wrapper extends BlitzObjectWrapper.

OMERO_TYPE = None

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“Annotation”) Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

classmethod _register(regklass)

Adds the AnnotationWrapper regklass to class registry

Parameters:regklass (AnnotationWrapper subclass) – The wrapper class, E.g. DoubleAnnotationWrapper

classmethod _wrap(conn=None, obj=None, link=None)

Class method for creating AnnotationWrapper subclasses based on the type of annotation object, using previously registered mapping between OMERO types and wrapper classes

Parameters:

• conn (BlitzGateway) – The BlitzGateway connection
• obj (omero.model.Annotation subclass) – The OMERO annotation object. E.g. omero.model.DoubleAnnotation
• link (E.g. omero.model.DatasetAnnotationLink) – The link for this annotation

Returns:

Wrapped AnnotationWrapper object or None if obj.__class__ not registered

Return type:

AnnotationWrapper subclass

classmethod createAndLink(target, ns, val=None, sameOwner=False)

Class method for creating an instance of this AnnotationWrapper, setting ns and value and linking to the target.

Parameters:

• target (BlitzObjectWrapper subclass) – The object to link annotation to
• ns (String) – Annotation namespace
• val – Value of annotation. E.g Long, Text, Boolean etc.

getNs()

Gets annotation namespace

Returns:Namespace or None Return type:String

getParentLinks(ptype, pids=None)

getValue()

Needs to be implemented by subclasses

registry = {<class 'omero.model.FileAnnotationI'>: <class 'omero.gateway.FileAnnotationWrapper'>, <class 'omero.model.TagAnnotationI'>: <class 'omero.gateway.TagAnnotationWrapper'>, <class 'omero.model.BooleanAnnotationI'>: <class 'omero.gateway.BooleanAnnotationWrapper'>, <class 'omero.model.TermAnnotationI'>: <class 'omero.gateway.TermAnnotationWrapper'>, <class 'omero.model.MapAnnotationI'>: <class 'omero.gateway.MapAnnotationWrapper'>, <class 'omero.model.TimestampAnnotationI'>: <class 'omero.gateway.TimestampAnnotationWrapper'>, <class 'omero.model.XmlAnnotationI'>: <class 'omero.gateway.XmlAnnotationWrapper'>, <class 'omero.model.DoubleAnnotationI'>: <class 'omero.gateway.DoubleAnnotationWrapper'>, <class 'omero.model.LongAnnotationI'>: <class 'omero.gateway.LongAnnotationWrapper'>, <class 'omero.model.CommentAnnotationI'>: <class 'omero.gateway.CommentAnnotationWrapper'>}

setNs(val)

Sets annotation namespace

Parameters:val (String) – Namespace value

setValue(val)

Needs to be implemented by subclasses

omero.gateway.ArcWrapper

alias of _ArcWrapper

omero.gateway.BinningWrapper

alias of _BinningWrapper

omero.gateway.BlitzGateway

alias of _BlitzGateway

class omero.gateway.BlitzObjectWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: object

Object wrapper class which provides various methods for hierarchy traversing, saving, handling permissions etc. This is the ‘abstract’ super class which is subclassed by E.g. _ProjectWrapper, _DatasetWrapper etc. All objects have a reference to the BlitzGateway connection, and therefore all services are available for handling calls on the object wrapper. E.g listChildren() uses queryservice etc.

CHILD_WRAPPER_CLASS = None

LINK_CHILD = 'child'

LINK_CLASS = None

static LINK_PARENT(x)

OMERO_CLASS = None

PARENT_WRAPPER_CLASS = None

_getAnnotationLinks(ns=None)

Checks links are loaded and returns a list of Annotation Links filtered by namespace if specified

Parameters:ns (String) – Namespace Returns:List of Annotation Links on this object Return type:List of Annotation Links

_getChildWrapper()

Returns the wrapper class of children of this object. Checks that this is one of the Wrapper objects in the omero.gateway module Raises NotImplementedError if this is not true or class is not defined (None) This is used internally by the listChildren() and countChildren() methods.

Returns:The child wrapper class. E.g. omero.gateway.DatasetWrapper.__class__ Return type:class

_getParentWrappers()

Returns the wrapper classes of the parent of this object. This is used internally by the listParents() method.

Returns:List of parent wrapper classes. E.g. omero.gateway.DatasetWrapper.__class__ Return type:class

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“Project”). Returns a tuple of (query, clauses, params). Overridden by sub-classes to specify loading of different portions of the graph. Different sub-classes may allow some control over what’s loaded and filtering of the query using various opts arguments. Opts: See different sub-classes for additional opts.

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

_linkAnnotation(ann)

Saves the annotation to DB if needed, setting the permissions manually. Creates the annotation link and saves it, setting permissions manually. TODO: Can’t set permissions manually in 4.2

• Assumes world & group writable

Parameters:ann (AnnotationWrapper) – The annotation object

_linkObject(obj, lnkobjtype)

Saves the object to DB if needed - setting the permissions manually. Creates the object link and saves it, setting permissions manually. TODO: Can’t set permissions manually in 4.2

• Assumes world & group writable

Parameters:obj (BlitzObjectWrapper) – The object to link

_listChildren(ns=None, val=None, params=None)

Lists available child objects.

Return type:generator of Ice client proxy objects for the child nodes Returns:child objects.

_loadAnnotationLinks()

Loads the annotation links and annotations for the object (if not already loaded) and saves them to the object. Also loads file for file annotations.

_moveLink(newParent)

Moves this object from a parent container (first one if there are more than one) to a new parent. TODO: might be more useful if it didn’t assume only 1 parent - option allowed you to specify the oldParent.

Parameters:newParent – The new parent Object Wrapper. Returns:True if moved from parent to parent. False if no parent exists or newParent has mismatching type Return type:Boolean

_unwrapunits(obj, units=None)

Returns the value of the Value + Unit object. If units is true, return the omero model unit object, e.g. omero.model.LengthI e.g. _unwrapunits(obj).getValue() == 10 e.g. _unwrapunits(obj).getUnit() == NANOMETER # unit enum e.g. _unwrapunits(obj).getSymbol() == “nm” If units specifies a valid unit for the type of value, then we convert E.g. _unwrapunits(obj, units=”MICROMETER”).getValue() == 10000

Parameters:

• obj – The Value + Unit object
• default – Default value if obj is None
• units – If true, return (value, unit) tuple

Returns:

Value or omero.model units

canAnnotate()

Determines if the current user can annotate this object: ie create annotation links. The canAnnotate() property is set on the permissions of every object as it is read from the server, based on the current user, event context and group permissions.

Return type:Boolean Returns:True if user can Annotate this object

canChgrp()

Specifies whether the current user can move this object to another group. Web client will only allow this for the data Owner. Admin CAN move other user’s data, but we don’t support this in Web yet.

canChown()

Specifies whether the current user can give this object to another user. Web client does not yet support this.

canDelete()

Determines if the current user can Delete the object

canEdit()

Determines if the current user can Edit (E.g. name, description) link (E.g. Project, Dataset, Image etc) or Delete this object. The canEdit() property is set on the permissions of every object as it is read from the server, based on the current user, event context and group permissions.

Return type:Boolean Returns:True if user can Edit this object Delete, link etc.

canLink()

Determines whether user can create ‘hard’ links (Not annotation links). E.g. Between Project/Dataset/Image etc. Previously (4.4.6 and earlier) we only allowed this for object owners, but now we delegate to what the server will allow.

canOwnerWrite()

Delegates to the connection BlitzGateway.canWrite() method

Return type:Boolean Returns:True if the objects’s permissions allow owner to write

canWrite()

Delegates to the connection BlitzGateway.canWrite() method

Return type:Boolean

countChildren()

Counts available number of child objects.

Returns:The number of child objects available Return type:Long

countChildren_cached()

countChildren, but caching the first result, useful if you need to call this multiple times in a single sequence, but have no way of storing the value between them. It is actually a hack to support django template’s lack of break in for loops

Returns:The number of child objects available Return type:Long

creationEventDate()

Gets event time in timestamp format (yyyy-mm-dd hh:mm:ss.fffffff) when object was created.

Returns:The datetime for object creation Return type:datetime.datetime

findChildByName(name, description=None)

Find the first child object with a matching name, and description if specified.

Parameters:

• name – The name which must match the child name
• description – If specified, child description must match too

Returns:

The wrapped child object

Return type:

BlitzObjectWrapper

getAncestry()

Get a list of Ancestors. First in list is parent of this object. TODO: Assumes getParent() returns a single parent.

Return type:List of BlitzObjectWrapper Returns:List of Ancestor objects

getAnnotation(ns=None)

Gets the first annotation on the object, filtered by ns if specified

Parameters:ns (String) – Namespace Returns:AnnotationWrapper or None

getAnnotationCounts()

Get the annotion counts for the current object

getChildLinks(chids=None)

Get a list of child objects links.

Parameters:chids (Long) – List of children IDs Return type:List of BlitzObjectWrapper Returns:List of child object links

getDate()

Returns the object’s acquisitionDate, or creation date (details.creationEvent.time)

Returns:A datetime.datetime() object Return type:datetime

getDescription()

Gets this object description

Returns:String

getDetails()

Gets the details of the wrapped object

Returns:DetailsWrapper or None if object not loaded Return type:DetailsWrapper

getId()

Gets this object ID

Returns:Long or None

getName()

Gets this object name

Returns:String or None

getOwner()

Gets user who is the owner of this object.

Returns:_ExperimenterWrapper

getOwnerFullName()

Gets full name of the owner of this object.

Returns:String or None

getOwnerOmeName()

Gets omeName of the owner of this object.

Returns:String

getParent(withlinks=False)

List a single parent, if available.

While the model supports many to many relationships between most objects, there are implementations that assume a single project per dataset, a single dataset per image, etc. This is just a shortcut method to return a single parent object.

Parameters:withlinks (Boolean) – if true result will be a tuple of (linkobj, obj) Return type:BlitzObjectWrapper or tuple(BlitzObjectWrapper, BlitzObjectWrapper) Returns:the parent object with or without the link depending on args

getParentLinks(pids=None)

Get a list of parent objects links.

Parameters:pids (Long) – List of parent IDs Return type:List of BlitzObjectWrapper Returns:List of parent object links

isLeaded()

Returns True if the group that this object belongs to is lead by the currently logged-in user

Return type:Boolean Returns:see above

isOwned()

Returns True if the object owner is the same user specified in the connection’s Event Context

Return type:Boolean Returns:True if current user owns this object

isPrivate()

Determines if the object is private

Return type:Boolean Returns:True if the object is not public and not shared and permissions allow user to read.

isPublic()

Determines if the object permissions are world readable, ie permissions.isWorldRead()

Return type:Boolean Returns:see above

isShared()

Determines if the object is sharable between groups (but not public)

Return type:Boolean Returns:True if the object is not public AND the object permissions allow group read.

linkAnnotation(ann, sameOwner=False)

Link the annotation to this object.

Parameters:

• ann (AnnotationWrapper) – The Annotation object
• sameOwner (Boolean) – If True, try to make sure that the link is created by the object owner

Returns:

The annotation

Return type:

AnnotationWrapper

listAnnotations(ns=None)

List annotations in the ns namespace, linked to this object

Returns:Generator yielding AnnotationWrapper Return type:AnnotationWrapper generator

listChildren(ns=None, val=None, params=None)

Lists available child objects.

Return type:generator of BlitzObjectWrapper objs Returns:child objects.

listOrphanedAnnotations(eid=None, ns=None, anntype=None, addedByMe=True)

Retrieve all Annotations not linked to the given Project, Dataset, Image, Screen, Plate, Well ID controlled by the security system.

Parameters:

• o_type (String) – type of Object
• oid (Long) – Object ID

Returns:

Generator yielding Tags

Return type:

AnnotationWrapper generator

listParents(withlinks=False)

Lists available parent objects.

Parameters:withlinks (Boolean) – if true each yielded result will be a tuple of (linkobj, obj) Return type:list of BlitzObjectWrapper or tuple(BlitzObjectWrapper, BlitzObjectWrapper) Returns:the parent objects, with or without the links depending on args

removeAnnotations(ns)

Uses the delete service to delete annotations, with a specified ns, and their links on the object and any other objects. Will raise a omero.LockTimeout if the annotation removal has not finished in 5 seconds.

Parameters:ns (String) – Namespace

save()

Uses the updateService to save the wrapped object.

Return type:None

saveAs(details)

Save this object, keeping the object owner the same as the one on provided details If the current user is an admin but is NOT the owner specified in ‘details’, then create a new connection for that owner, clone the current object under that connection and save. Otherwise, simply save.

Parameters:details (DetailsWrapper) – The Details specifying owner to save to Returns:None

setDescription(value)

Sets the description of the object

Parameters:value (String) – New description

setName(value)

Sets the name of the object

Parameters:value (String) – New name

simpleMarshal(xtra=None, parents=False)

Creates a dict representation of this object. E.g. for Image:

{'description': '', 'author': 'Will Moore', 'date': 1286332557.0,
'type': 'Image', 'id': 3841L, 'name': 'cb_4_w500_t03_z01.tif'}

Parameters:

• xtra (Dict) – A dict of extra keys to include. E.g. ‘childCount’
• parents (Boolean) – If True, include a list of ancestors (in simpleMarshal form) as ‘parents’

Returns:

A dict representation of this object

Return type:

Dict

unlinkAnnotations(ns)

Submits request to unlink annotations, with specified ns

Parameters:ns (String) – Namespace

updateEventDate()

Gets event time in timestamp format (yyyy-mm-dd hh:mm:ss.fffffff) when object was updated.

Returns:The datetime for object update Return type:datetime.datetime

class omero.gateway.BooleanAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper

omero_model_BooleanAnnotationI class wrapper extends AnnotationWrapper.

OMERO_TYPE

alias of BooleanAnnotationI

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“BooleanAnnotation”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

getValue()

Gets boolean value

Returns:Value Return type:Boolean

setValue(val)

Sets boolean value

Parameters:val (Boolean) – Value

omero.gateway.ChannelWrapper

alias of _ChannelWrapper

class omero.gateway.ColorHolder(colorname=None)

Bases: object

Stores color internally as (R,G,B,A) and allows setting and getting in multiple formats

_color = {'blue': 0, 'alpha': 255, 'green': 0, 'red': 0}

classmethod fromRGBA(r, g, b, a)

Class method for creating a ColorHolder from r,g,b,a values

Parameters:

• r (int) – red 0 - 255
• g (int) – green 0 - 255
• b (int) – blue 0 - 255
• a (int) – alpha 0 - 255

Returns:

new Color object

Return type:

ColorHolder

getAlpha()

Gets the Alpha component

Returns:alpha Return type:int

getBlue()

Gets the Blue component

Returns:blue Return type:int

getCss()

Gets the css string: rgba(r,g,b,a)

Returns:css color Return type:String

getGreen()

Gets the Green component

Returns:green Return type:int

getHtml()

Gets the html usable color. Dumps the alpha information. E.g. ‘FF0000’

Returns:html color Return type:String

getInt()

Returns the color as an Integer

Returns:Integer Return type:int

getRGB()

Gets the (r,g,b) as a tuple.

Returns:Tuple of (r,g,b) values Return type:tuple of ints

getRed()

Gets the Red component

Returns:red Return type:int

setAlpha(val)

Set alpha, as int 0..255.

Parameters:val – value of alpha.

setBlue(val)

Set Blue, as int 0..255

Parameters:val (Int) – value of Blue.

setGreen(val)

Set green, as int 0..255

Parameters:val (Int) – value of Green.

setRed(val)

Set red, as int 0..255

Parameters:val (Int) – value of Red.

class omero.gateway.CommentAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper

omero_model_CommentAnnotationI class wrapper extends AnnotationWrapper.

OMERO_TYPE

alias of CommentAnnotationI

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“CommentAnnotation”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

getValue()

Gets the value of the Comment

Returns:Value Type:String

setValue(val)

Sets comment text value

Parameters:val (String) – Value

omero.gateway.DatasetWrapper

alias of _DatasetWrapper

class omero.gateway.DetailsWrapper(*args, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_DetailsI class wrapper extends BlitzObjectWrapper.

getGroup()

Returns the Group that these details refer to

Returns:Group Return type:ExperimenterGroupWrapper

getOwner()

Returns the Owner of the object that these details apply to

Returns:Owner Return type:ExperimenterWrapper

omero.gateway.DetectorSettingsWrapper

alias of _DetectorSettingsWrapper

omero.gateway.DetectorWrapper

alias of _DetectorWrapper

omero.gateway.DichroicWrapper

alias of _DichroicWrapper

class omero.gateway.DoubleAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper

omero_model_DoubleAnnotationI class wrapper extends AnnotationWrapper.

OMERO_TYPE

alias of DoubleAnnotationI

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“DoubleAnnotation”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

getValue()

Gets the value of the Double Annotation

Returns:Value Type:Double

setValue(val)

Sets Double annotation value

Parameters:val (Double) – Value

omero.gateway.EnumerationWrapper

alias of _EnumerationWrapper

omero.gateway.ExperimenterGroupWrapper

alias of _ExperimenterGroupWrapper

omero.gateway.ExperimenterWrapper

alias of _ExperimenterWrapper

omero.gateway.FilamentWrapper

alias of _FilamentWrapper

class omero.gateway.FileAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper, omero.gateway.OmeroRestrictionWrapper

omero_model_FileAnnotationI class wrapper extends AnnotationWrapper.

OMERO_TYPE

alias of FileAnnotationI

_attrs = ('file|OriginalFileWrapper',)

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“FileAnnotation”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

getFile()

Returns an OriginalFileWrapper for the file. Wrapper object will load the file if it isn’t already loaded. File is cached to prevent repeated loading of the file.

getFileInChunks(buf=2621440)

Returns a generator yielding chunks of the file data.

Returns:Data from file in chunks Return type:Generator

getFileName()

Gets the file name

Returns:File name Return type:String

getFileSize()

Looks up the size of the file in bytes

Returns:File size (bytes) Return type:Long

getValue()

Not implemented

isOriginalMetadata()

Checks if this file annotation is an ‘original_metadata’ file

Returns:True if namespace and file name follow metadata convention Return type:Boolean

setDescription(val)

setFile(originalfile)

setValue(val)

Not implemented

omero.gateway.FilesetWrapper

alias of _FilesetWrapper

omero.gateway.FilterSetWrapper

alias of _FilterSetWrapper

omero.gateway.FilterWrapper

alias of _FilterWrapper

omero.gateway.ImageStageLabelWrapper

alias of _ImageStageLabelWrapper

omero.gateway.ImageWrapper

alias of _ImageWrapper

omero.gateway.ImagingEnviromentWrapper

alias of _ImagingEnviromentWrapper

omero.gateway.ImagingEnvironmentWrapper

alias of _ImagingEnvironmentWrapper

omero.gateway.InstrumentWrapper

alias of _InstrumentWrapper

omero.gateway.LaserWrapper

alias of _LaserWrapper

omero.gateway.LightEmittingDiodeWrapper

alias of _LightEmittingDiodeWrapper

omero.gateway.LightPathWrapper

alias of _LightPathWrapper

omero.gateway.LightSettingsWrapper

alias of _LightSettingsWrapper

omero.gateway.LightSourceWrapper(conn, obj, **kwargs)

Creates wrapper instances for omero.model light source objects

Parameters:

• conn – BlitzGateway connection
• obj – omero.model object

Returns:

_LightSourceWrapper subclass

omero.gateway.LogicalChannelWrapper

alias of _LogicalChannelWrapper

class omero.gateway.LongAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper

omero_model_LongAnnotationI class wrapper extends AnnotationWrapper.

OMERO_TYPE

alias of LongAnnotationI

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“LongAnnotation”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

getValue()

Gets the value of the Long annotation

Returns:Value Type:Long

setValue(val)

Sets long annotation value

Parameters:val (Long) – Value

class omero.gateway.MapAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper

omero_model_MapAnnotationI class wrapper.

OMERO_TYPE

alias of MapAnnotationI

getValue()

Gets the value of the Map Annotation as a list of (key, value) tuples.

Returns:List of tuples Type:String

setValue(val)

Sets value of the Map Annotation where val is a list of (key, value) tuples or [key, value] lists.

Parameters:val (String) – List of tuples

omero.gateway.MicroscopeWrapper

alias of _MicroscopeWrapper

class omero.gateway.NoProxies

Bases: object

A dummy placeholder to indicate that proxies haven’t been created

values()

omero.gateway.OTFWrapper

alias of _OTFWrapper

omero.gateway.ObjectiveSettingsWrapper

alias of _ObjectiveSettingsWrapper

omero.gateway.ObjectiveWrapper

alias of _ObjectiveWrapper

class omero.gateway.OmeroGatewaySafeCallWrapper(proxyObjectWrapper, attr, f)

Bases: object

Function or method wrapper that handles certain types of server side exceptions and debugging of errors.

debug(exc_class, args, kwargs)

handle_exception(e, *args, **kwargs)

Exception handler that is expected to be overridden by sub-classes. The expected behaviour is either to handle a type of exception and return the server side result or to raise the already thrown exception. The calling context is an except block and the original *args and **kwargs from the wrapped function or method are provided to allow re-execution of the original.

Parameters:e (Exception) – The exception that has already been raised.

class omero.gateway.OmeroRestrictionWrapper

Bases: object

canDownload()

Determines if the current user can Download raw data linked to this object. The canDownload() property is set on objects: Image, Plate and FileAnnotation as it is read from the server, based on the current user, event context and group permissions.

Return type:Boolean Returns:True if user can download.

omero.gateway.OriginalFileWrapper

alias of _OriginalFileWrapper

omero.gateway.PixelsWrapper

alias of _PixelsWrapper

omero.gateway.PlaneInfoWrapper

alias of _PlaneInfoWrapper

omero.gateway.PlateAcquisitionWrapper

alias of _PlateAcquisitionWrapper

omero.gateway.PlateWrapper

alias of _PlateWrapper

omero.gateway.ProjectWrapper

alias of _ProjectWrapper

class omero.gateway.ProxyObjectWrapper(conn, func_str, cast_to=None, service_name=None)

Bases: object

Wrapper for services. E.g. Admin Service, Delete Service etc. Maintains reference to connection. Handles creation of service when requested.

_connect(forcejoin=False)

Returns True if connected. If connection OK, wrapped service is also created.

Parameters:forcejoin (Boolean) – if True forces the connection to only succeed if we can rejoin the current sessionid Returns:True if connection OK Return type:Boolean

_getObj()

Returns the wrapped service. If it is None, service is created.

Returns:The wrapped service Return type:omero.api.ServiceInterface subclass

_ping()

For some reason, it seems that keepAlive doesn’t, so every so often I need to recreate the objects. Calls serviceFactory.keepAlive(service). If this returns false, attempt to create service.

Returns:True if no exception thrown Return type:Boolean

_resyncConn(conn)

Reset refs to connection and session factory. Resets session creation function. Attempts to reload the wrapped service - if already created (doesn’t create service)

Parameters:conn (BlitzGateway) – Connection

clone()

Creates and returns a new ProxyObjectWrapper with the same connection and service creation method name as this one.

Returns:Cloned service wrapper Return type:ProxyObjectWrapper

close(*args, **kwargs)

Closes the underlying service, so next call to the proxy will create a new instance of it.

taint()

Sets the tainted flag to True

untaint()

Sets the tainted flag to False

omero.gateway.RoiWrapper

alias of _RoiWrapper

omero.gateway.SafeCallWrapper

alias of OmeroGatewaySafeCallWrapper

omero.gateway.ScreenWrapper

alias of _ScreenWrapper

omero.gateway.ShapeWrapper

alias of _ShapeWrapper

class omero.gateway.TagAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper

omero_model_BooleanAnnotationI class wrapper extends AnnotationWrapper.

OMERO_TYPE

alias of TagAnnotationI

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“TagAnnotation”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

countTagsInTagset()

getValue()

Gets the value of the Tag

Returns:Value Type:String

listParents(withlinks=True)

We override the listParents() to look for ‘Tag-Group’ Tags on this Tag

listTagsInTagset()

setValue(val)

Sets Tag value

Parameters:val (String) – Tag text value

class omero.gateway.TermAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper

omero_model_TermAnnotationI class wrapper extends AnnotationWrapper.

only in 4.2+

OMERO_TYPE

alias of TermAnnotationI

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“TermAnnotation”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

getValue()

Gets the value of the Term

Returns:Value Type:String

setValue(val)

Sets term value

Parameters:val (String) – Value

class omero.gateway.TimestampAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.AnnotationWrapper

omero_model_TimestampAnnotationI class wrapper extends AnnotationWrapper.

OMERO_TYPE

alias of TimestampAnnotationI

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“TimestampAnnotation”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

getValue()

Returns a datetime object of the timestamp in seconds

Returns:Timestamp value Return type:datetime.datetime

setValue(val)

Sets the timestamp value

Parameters:val (datetime.datetime OR omero.RTime OR Long) – Timestamp value

omero.gateway.TransmittanceRangeWrapper

alias of _TransmittanceRangeWrapper

omero.gateway.WellSampleWrapper

alias of _WellSampleWrapper

omero.gateway.WellWrapper

alias of _WellWrapper

class omero.gateway.XmlAnnotationWrapper(*args, **kwargs)

Bases: omero.gateway.CommentAnnotationWrapper

omero_model_XmlAnnotationI class wrapper extends CommentAnnotationWrapper.

OMERO_TYPE

alias of XmlAnnotationI

class omero.gateway._AnnotationLinkWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_AnnotationLinkI class wrapper extends omero.gateway.BlitzObjectWrapper.

getAnnotation()

getParent()

Gets the parent (Annotated Object) as a BlitzObjectWrapper, but attempts to wrap it in the correct subclass using L{KNOWN_WRAPPERS}, E.g. ImageWrapper

class omero.gateway._ArcWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway._FilamentWrapper

omero_model_ArcI class wrapper extends FilamentWrapper.

OMERO_CLASS = 'Arc'

class omero.gateway._BinningWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_BinningI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Binning'

class omero.gateway._BlitzGateway(username=None, passwd=None, client_obj=None, group=None, clone=False, try_super=False, host=None, port=None, extra_config=None, secure=False, anonymous=True, useragent=None, userip=None)

Bases: object

Connection wrapper. Handles connecting and keeping the session alive, creation of various services, context switching, security privileges etc.

ICE_CONFIG = '/opt/hudson/workspace/OMERO-DEV-release/src/dist/etc/ice.config'

ICE_CONFIG - Defines the path to the Ice configuration

_assert_unregistered(prefix='Service left open!')

Log an ERROR for every stateful service that is open and was registered by this BlitzGateway instance.

Return the number of unclosed services found.

_closeSession()

Close session.

_createProxies()

Creates proxies to the server services. Called on connection or security switch. Doesn’t actually create any services themselves. Created if/when needed. If proxies have been created already, they are resynced and reused.

_createSession()

Creates a new session for the principal given in the constructor. Used during :meth`connect` method

_getSessionId()

_register_service(service_string, stack)

Register the results of traceback.extract_stack() at the time that a service was created.

_resetOmeroClient()

Creates new omero.client object using self.host or self.ice_config (if host is None) Also tries to setAgent for the client

_unregister_service(service_string)

Called on close of a service.

_waitOnCmd(handle, loops=10, ms=500, failonerror=True, failontimeout=False, closehandle=False)

applySettingsToSet(fromid, to_type, toids)

Applies the rendering settings from one image to others. Returns a dict of success { True:[ids], False:[ids] }

Parameters:

• fromid – ID of Image to copy settings from.
• toids – List of Image IDs to apply setting to.
• to_type – toids refers to Images by default, but can refer to Project, Dataset, Image, Plate, Screen, Pixels

buildCountQuery(obj_type, opts=None)

Prepares a ‘projection’ query to count objects.

Based on buildQuery(), we modify the query to only return a count. Modified query does not ‘fetch’ any data or add any other unnecessary objects to query. We return just the query and omero.sys.ParametersI for the query.

Parameters:

• obj_type – Object type, e.g. “Project” see above
• opts – Dict of options for filtering by offset, limit and owner for all objects. Additional opts handled by _getQueryString() e.g. filter Dataset by ‘project’

Returns:

(query, params)

buildQuery(obj_type, ids=None, params=None, attributes=None, opts=None)

Prepares a query for iQuery. Also prepares params and determines appropriate wrapper for result Returns (query, params, wrapper) which can be used with the appropriate query method. Used by getObjects() and getObject() above.

Parameters:

• obj_type (String) – Object type, e.g. “Project” see above
• ids (List of Long) – object IDs
• params – omero.sys.Parameters, can be used for pagination, & filtering by owner. Takes precedence over opts.
• attributes – Dict of key-value pairs to filter results by. Key must be attribute of obj_type. E.g. ‘name’, ‘ns’
• opts – Dict of additional options for filtering or defining extra data to load. offset, limit and owner for all objects. Also ‘order_by’: ‘obj.name’ to order results. Additional opts handled by _getQueryString() e.g. filter Dataset by ‘project’

Returns:

(query, params, wrapper)

canBeAdmin()

Checks if a user is in system group, i.e. can have administration privileges.

Returns:Boolean

canCreate()

Get the read-only status of the server. Warning: This is EXPERIMENTAL API that is subject to change.

Returns:True if the server is wholly in read-write mode, False if the server is wholly in read-only mode, otherwise None

canOwnerWrite(obj)

Returns isUserWrite() from the object’s permissions

Parameters:obj – Given object Returns:True if the objects’s permissions allow owner to write

canWrite(obj)

Checks if a user has write privileges to the given object.

Parameters:obj – Given object Returns:Boolean

chgrpObjects(graph_spec, obj_ids, group_id, container_id=None)

Change the Group for a specified objects using queue.

Parameters:

• graph_spec –

  String to indicate the object type or graph specification. Examples include:

  • ‘Image’
  • ‘Project’ # will move contents too.
  • NB: Also supports ‘/Image’ etc for backwards compatibility.
• obj_ids – IDs for the objects to move.
• group_id – The group to move the data to.

chmodGroup(group_Id, permissions)

Change the permissions of a particular Group. Returns the proxy ‘prx’ handle that can be processed like this: callback = CmdCallbackI(self.gateway.c, prx) callback.loop(20, 500) rsp = prx.getResponse()

clone()

Returns a new instance of this class, with all matching properties. TODO: Add anonymous and userAgent parameters?

Returns:Clone of this connection wrapper Return type:_BlitzGateway

close(hard=True)

Terminates connection with killSession(), where the session is terminated regardless of its connection refcount, or closeSession().

Parameters:hard – If True, use killSession(), otherwise closeSession()

connect(sUuid=None)

Creates or retrieves connection for the given sessionUuid. Returns True if connected.

Parameters:sUuid – omero_model_SessionI Returns:Boolean

containedExperimenters(gid)

Fetch all users contained in this group. The returned users will have all fields filled in and all collections unloaded.

Parameters:gid (Long) – Group ID Returns:Generator of experimenters Return type:ExperimenterWrapper generator

countAnnotations(obj_type, obj_ids=[])

Count the annotions linked to the given objects

Parameters:

• obj_type – The type of the object the annotations are linked to
• obj_ids – List of object ids

Returns:

Dictionary of annotation counts per annotation type

createEnumeration(obj)

Create an enumeration with given object

Parameters:obj (omero.model.IObject) – Object

createExporter()

New instance of non cached Exporter, wrapped in ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

createFileAnnfromLocalFile(localPath, origFilePathAndName=None, mimetype=None, ns=None, desc=None)

Class method to create a FileAnnotationWrapper from a local file. File is uploaded to create an omero.model.OriginalFileI referenced from this File Annotation. Returns a new FileAnnotationWrapper

Parameters:

• conn – Blitz connection
• localPath – Location to find the local file to upload
• origFilePathAndName – Provides the ‘path’ and ‘name’ of the OriginalFile. If None, use localPath
• mimetype – The mimetype of the file. String. E.g. ‘text/plain’
• ns – The namespace of the file.
• desc – A description for the file annotation.

Returns:

New FileAnnotationWrapper

createGroup(name, owner_Ids=None, member_Ids=None, perms=None, description=None, ldap=False)

Creates a new ExperimenterGroup. Must have Admin permissions to call this.

Parameters:

• name – New group name
• owner_Ids – Option to add existing Experimenters as group owners
• member_Ids – Option to add existing Experimenters as group members
• perms – New group permissions. E.g. ‘rw—-‘ (private), ‘rwr—’(read-only), ‘rwrw–’
• description – Group description
• ldap – Group ldap setting

createImageFromNumpySeq(zctPlanes, imageName, sizeZ=1, sizeC=1, sizeT=1, description=None, dataset=None, sourceImageId=None, channelList=None)

Creates a new multi-dimensional image from the sequence of 2D numpy arrays in zctPlanes. zctPlanes should be a generator of numpy 2D arrays of shape (sizeY, sizeX) ordered to iterate through T first, then C then Z. Example usage:

original = conn.getObject("Image", 1)
sizeZ = original.getSizeZ()
sizeC = original.getSizeC()
sizeT = original.getSizeT()
clist = range(sizeC)
zctList = []
for z in range(sizeZ):
    for c in clist:
        for t in range(sizeT):
            zctList.append( (z,c,t) )
def planeGen():
    planes = original.getPrimaryPixels().getPlanes(zctList)
    for p in planes:
        # perform some manipulation on each plane
        yield p
createImageFromNumpySeq(
    planeGen(), imageName, sizeZ=sizeZ, sizeC=sizeC, sizeT=sizeT,
    sourceImageId=1, channelList=clist)

Parameters:

• session – An OMERO service factory or equivalent with getQueryService() etc.
• zctPlanes – A generator of numpy 2D arrays, corresponding to Z-planes of new image.
• imageName – Name of new image
• description – Description for the new image
• dataset – If specified, put the image in this dataset. omero.model.Dataset object
• sourceImageId – If specified, copy this image with metadata, then add pixel data
• channelList – Copies metadata from these channels in source image (if specified). E.g. [0,2]

Returns:

The new OMERO image: omero.model.ImageI

createOriginalFileFromFileObj(fo, path, name, fileSize, mimetype=None, ns=None)

Creates a OriginalFileWrapper from a local file. File is uploaded to create an omero.model.OriginalFileI. Returns a new OriginalFileWrapper

Parameters:

• conn – Blitz connection
• fo – The file object
• path – The file path
• name – The file name
• fileSize – The file size
• mimetype – The mimetype of the file. String. E.g. ‘text/plain’
• ns – Deprecated in 5.4.0. This is ignored

Returns:

New OriginalFileWrapper

createOriginalFileFromLocalFile(localPath, origFilePathAndName=None, mimetype=None, ns=None)

Creates a OriginalFileWrapper from a local file. File is uploaded to create an omero.model.OriginalFileI. Returns a new OriginalFileWrapper

Parameters:

• conn – Blitz connection
• localPath – Location to find the local file to upload
• origFilePathAndName – Provides the ‘path’ and ‘name’ of the OriginalFile. If None, use localPath
• mimetype – The mimetype of the file. String. E.g. ‘text/plain’
• ns – Deprecated in 5.4.0. This is ignored

Returns:

New OriginalFileWrapper

createRawFileStore()

Gets a reference to the raw file store on this connection object or creates a new one if none exists.

Returns:omero.gateway.ProxyObjectWrapper

createRawPixelsStore()

Gets a reference to the raw pixels store on this connection object or creates a new one if none exists.

Returns:omero.gateway.ProxyObjectWrapper

createRenderingEngine()

Creates a new rendering engine. This service is special in that it does not get cached inside BlitzGateway so every call to this function returns a new object, avoiding unexpected inherited states.

Returns:omero.gateway.ProxyObjectWrapper

createSearchService()

Gets a reference to the searching service on this connection object or creates a new one if none exists.

Returns:omero.gateway.ProxyObjectWrapper

createServiceOptsDict()

createThumbnailStore()

Gets a reference to the thumbnail store on this connection object or creates a new one if none exists.

Return type:omero.gateway.ProxyObjectWrapper Returns:The proxy wrapper of the thumbnail store

deleteEnumeration(obj)

Deletes an enumeration object

Parameters:obj (omero.model.IObject) – Enumeration object

deleteObject(obj)

Delete a single object.

Parameters:obj (IObject) – Object to delete

deleteObjectDirect(obj)

Directly Delete object (removes row from database). This may fail with various constraint violations if the object is linked to others in the database

Parameters:obj (IObject) – Object to delete

** Deprecated ** Use deleteObject() or deleteObjects().

deleteObjects(graph_spec, obj_ids, deleteAnns=False, deleteChildren=False, dryRun=False, wait=False)

Generic method for deleting using the delete queue. Options allow to delete ‘independent’ Annotations (Tag, Term, File) and to delete child objects.

Parameters:

• graph_spec –

  String to indicate the object type or graph specification. Examples include:

  • ‘Project’
  • ‘Dataset’
  • ‘Image’
  • ‘Screen’
  • ‘Plate’
  • ‘Well’
  • ‘Annotation’
  • ‘OriginalFile’
  • ‘Roi’
  • ‘Image/Pixels/Channel’

  As of OMERO 4.4.0 the correct case is now explicitly required, the use of ‘project’ or ‘dataset’ is no longer supported.

• obj_ids – List of IDs for the objects to delete
• deleteAnns – If true, delete linked Tag, Term and File annotations
• deleteChildren – If true, delete children. E.g. Delete Project AND it’s Datasets & Images.

Returns:

Delete handle

Return type:

omero.api.delete.DeleteHandle

findExperimenters(start='')

Return a generator for all Experimenters whose omeName starts with ‘start’. Experimenters ordered by omeName.

Parameters:start (String) – omeName must start with these letters Returns:Generator of experimenters Return type:ExperimenterWrapper generator

getAdminPrivileges(user_id)

Returns list of Admin Privileges for the specified user.

Returns:List of strings such as [“ModifyUser”, “ModifyGroup”]

getAdminService()

Gets reference to the admin service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getAdministrators()

Returns Experimenters with administration privileges.

Returns:Current Experimenter Returns:Generator of BlitzObjectWrapper subclasses

getAnnotationCounts(objDict={})

Get the annotion counts for the given objects

getAnnotationLinks(parent_type, parent_ids=None, ann_ids=None, ns=None, params=None)

Retrieve Annotation Links by parent_type E.g. “Image”. Not Ordered. Returns generator of AnnotationLinkWrapper If parent_ids is None, all available objects will be returned. i.e. listObjects()

Parameters:

• obj_type (String) – Object type, e.g. “Project” see above
• ids (List of Long) – object IDs

Returns:

Generator yielding wrapped objects.

getArchivedFilesInfo(imageIds)

Gets summary of Original Files that are archived from OMERO 4 imports Returns a dict of files ‘count’ and sum of ‘size’

Parameters:imageIds – Image IDs list Returns:Dict of files ‘count’ and ‘size’

getClientSettings()

Returns all client properties matching omero.client.*

getConfigService()

Gets reference to the config service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getContainerService()

Gets reference to the container service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getCurrentAdminPrivileges()

Returns list of Admin Privileges for the current session.

Returns:List of strings such as [“ModifyUser”, “ModifyGroup”]

getDefaultGroup(eid)

Retrieve the default group for the given user id.

Parameters:eid (Long) – Experimenter ID Returns:The default group for user Return type:ExperimenterGroupWrapper

getDefaultOmeroGroup()

getDefaultOmeroUser()

getDownloadAsMaxSizeSetting()

Returns default max size of images that can be downloaded as jpg, png or tiff, expressed as number of pixels. Default is 144000000 (12k * 12k image)

Returns:Integer

getEnumeration(klass, string)

Get enumeration by class and value

Parameters:

• klass (Class or string) – Class
• string (String) – Enum value

Returns:

Enumeration or None

Return type:

EnumerationWrapper

getEnumerationById(klass, eid)

Get enumeration by class and ID

Parameters:

• klass (Class or string) – Class
• eid (Long) – Enum ID

Returns:

Enumeration or None

Return type:

EnumerationWrapper

getEnumerationEntries(klass)

Get all enumerations by class

Parameters:klass (Class or string) – Class Returns:Generator of Enumerations Return type:EnumerationWrapper generator

getEnumerations()

Gets list of enumeration types

Returns:List of enum types Return type:List of Strings

getEnumerationsWithEntries()

Get enumeration types, with lists of Enum entries

Returns:Dictionary of type: entries Return type:Dict of <string: EnumerationWrapper list >

getEventContext()

Returns omero_System_ice.EventContext. It contains: shareId, sessionId, sessionUuid, userId, userName, groupId, groupName, isAdmin, isReadOnly, eventId, eventType, eventType, memberOfGroups, leaderOfGroups Also saves context to self._ctx

Returns:Event Context from admin service. Return type:omero.sys.EventContext

getFilesetFilesInfo(imageIds)

Gets summary of Original Files that are part of the FS Fileset linked to images Returns a dict of files ‘count’ and sum of ‘size’

Parameters:imageIds – Image IDs list Returns:Dict of files ‘count’ and ‘size’

getFreeSpace()

Returns the free or available space on this file system including nested subdirectories.

Returns:Free space in bytes Return type:Int

getGroupFromContext()

Returns current omero_model_ExperimenterGroupI.

Returns:omero.model.ExperimenterGroupI

getGroupsLeaderOf()

Look up Groups where current user is a leader of.

Returns:Groups that current user leads Return type:ExperimenterGroupWrapper generator

getGroupsMemberOf()

Look up Groups where current user is a member of (except “user” group).

Returns:Current users groups Return type:ExperimenterGroupWrapper generator

getInitialZoomLevel()

Returns default initial zoom level set on the server.

getInterpolateSetting()

Returns default interpolation setting on the server. This is a string but represents a boolean, E.g. ‘true’

Returns:String

getLastError()

Returns error if thrown by _BlitzGateway.connect connect.

Returns:String

getMaxPlaneSize()

Returns the maximum plane size the server will allow for an image to not be considered big i.e. width or height larger than this will trigger image pyramids to be calculated.

This is useful for the client to filter images based on them needing pyramids or not, without the full rendering engine overhead.

Returns:tuple holding (max_plane_width, max_plane_height) as set on the server Return type:Tuple

getMetadataService()

Gets reference to the metadata service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getObject(obj_type, oid=None, params=None, attributes=None, opts=None)

Retrieve single Object by type E.g. “Image” or None if not found. If more than one object found, raises ome.conditions.ApiUsageException See getObjects() for more info.

Parameters:

• obj_type (String) – Object type, e.g. “Project” see above
• ids (List of Long) – object IDs
• params – omero.sys.Parameters, can be used for pagination, filtering etc.
• attributes – Map of key-value pairs to filter results by. Key must be attribute of obj_type. E.g. ‘name’, ‘ns’

Returns:

getObjects(obj_type, ids=None, params=None, attributes=None, respect_order=False, opts=None)

Retrieve Objects by type E.g. “Image” Returns generator of appropriate BlitzObjectWrapper type. E.g. ImageWrapper. If ids is None, all available objects will be returned. i.e. listObjects() Filter objects by attributes. E.g. attributes={‘name’:name}

Parameters:

• obj_type (String) – Object type, e.g. “Project” see above
• ids (List of Long) – object IDs
• params – omero.sys.Parameters, can be used for pagination, & filtering by owner. Takes precedence over opts.
• attributes – Dict of key-value pairs to filter results by. Key must be attribute of obj_type. E.g. ‘name’, ‘ns’
• respect_order – Returned items will be ordered according to the order of ids
• opts – Dict of additional options for filtering or defining extra data to load. offset, limit and owner for all objects. Additional opts handled by _getQueryString() e.g. filter Dataset by ‘project’

Returns:

Generator of BlitzObjectWrapper subclasses

getObjectsByAnnotations(obj_type, annids)

Retrieve objects linked to the given annotation IDs controlled by the security system.

Parameters:annids (Long) – Annotation IDs Returns:Generator yielding Objects Return type:BlitzObjectWrapper generator

getOriginalEnumerations()

Gets original enumerations. Returns a dictionary of enumeration class: list of Enumerations

Returns:Original enums Return type:Dict of <string: EnumerationWrapper list >

getOtherGroups(eid)

Fetch all groups of which the given user is a member. The returned groups will have all fields filled in and all collections unloaded.

Parameters:eid (Long) – Experimenter ID Returns:Generator of groups for user Return type:ExperimenterGroupWrapper generator

getPixelsService()

Gets reference to the pixels service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getProperty(k)

Returns named property of the wrapped omero.client

Returns:named client property

getQueryService()

Gets reference to the query service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getRenderingSettingsService()

Gets reference to the rendering settings service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getRepositoryInfoService()

Gets reference to the repository info service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getRoiLimitSetting()

getRoiService()

Gets ROI service.

Returns:omero.gateway.ProxyObjectWrapper

getScriptService()

Gets script service.

Returns:omero.gateway.ProxyObjectWrapper

getSession()

Returns the existing session, or creates a new one if needed

Returns:The session from session service Return type:omero.model.session

getSessionService()

Gets reference to the session service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getShareService()

Gets reference to the share service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getSharedResources()

Gets reference to the sharedresources from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getThumbnailSet(image_ids, max_size=64)

Retrieves a number of thumbnails for image sets. If the Thumbnails exist in the on-disk cache they will be returned directly, otherwise they will be created, for more details see ome.api.ThumbnailStore.getThumbnailByLongestSideSet

Parameters:

• image_ids – A list of image ids
• max_size – The longest side of the image will be used to calculate the size for the smaller side in order to keep the aspect ratio of the original image.

Returns:

dictionary of strings holding a rendered JPEG of the thumbnails.

getTimelineService()

Gets reference to the timeline service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getTypesService()

Gets reference to the types service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getUpdateService()

Gets reference to the update service from ProxyObjectWrapper.

Returns:omero.gateway.ProxyObjectWrapper

getUser()

Returns current Experimenter.

Returns:Current Experimenter Return type:ExperimenterWrapper

getUserId()

Returns current experimenter id

Returns:Current Experimenter id Return type:long

getWebclientHost()

Returns default initial zoom level set on the server.

groupSummary(gid=None, exclude_self=False)

Returns unsorted lists of ‘leaders’ and ‘members’ of the specified group (default is current group) as a dict with those keys.

Returns:{‘leaders’: list ExperimenterWrapper, ‘colleagues’: list ExperimenterWrapper} Return type:dict

** Deprecated ** Use ExperimenterGroupWrapper.groupSummary().

isAdmin()

Checks if a user has administration privileges.

Returns:Boolean

isAnonymous()

Returns the anonymous flag

Returns:Anonymous Return type:Boolean

isConnected()

Returns last status of connection.

Returns:Boolean

isFullAdmin()

Checks if a user has full administration privileges.

Returns:Boolean

isLeader(gid=None)

Is the current group (or a specified group) led by the current user?

Returns:True if user leads the current group Return type:Boolean

isSecure()

Returns ‘True’ if the underlying omero.clients.BaseClient is connected using SSL

keepAlive()

Keeps service alive. Returns True if connected. If connection was lost, reconnecting. If connection failed, returns False and error is logged.

Returns:True if connection alive. Return type:Boolean

listColleagues()

Look up users who are a member of the current user active group. Returns None if the group is private and isn’t lead by the current user

Returns:Generator of Experimenters or None Return type:ExperimenterWrapper generator

listFileAnnotations(eid=None, toInclude=[], toExclude=[])

Lists FileAnnotations created by users, filtering by namespaces if specified. If NO namespaces are specified, then ‘known’ namespaces are excluded by default, such as original files and companion files etc. File objects are loaded so E.g. file name is available without lazy loading.

Parameters:

• eid – Filter results by this owner Id
• toInclude – Only return annotations with these namespaces. List of strings.
• toExclude – Don’t return annotations with these namespaces. List of strings.

Returns:

Generator of FileAnnotationWrapper - with files loaded.

listGroups()

Look up all experimenters and related groups. Groups are also loaded

Returns:All experimenters Return type:ExperimenterWrapper generator

listOrphanedAnnotations(parent_type, parent_ids, eid=None, ns=None, anntype=None, addedByMe=True)

Retrieve all Annotations not linked to the given parents: Projects, Datasets, Images, Screens, Plates OR Wells etc.

Parameters:

• parent_type – E.g. ‘Dataset’, ‘Image’ etc.
• parent_ids – IDs of the parent.
• eid – Optional filter by Annotation owner
• ns – Filter by annotation namespace
• anntype – Optional specify ‘Text’, ‘Tag’, ‘File’, Long’, ‘Boolean’

Returns:

Generator yielding AnnotationWrappers

Return type:

AnnotationWrapper generator

listOrphans(obj_type, eid=None, params=None, loadPixels=False)

List orphaned Datasets, Images, Plates controlled by the security system, Optionally filter by experimenter ‘eid’

Parameters:

• obj_type – ‘Dataset’, ‘Image’, ‘Plate’
• eid (Long) – experimenter id
• params – omero.sys.ParametersI, can be used for pagination, filtering etc.
• attributes – Map of key-value pairs to filter results by. Key must be attribute of obj_type. E.g. ‘name’, ‘ns’

Returns:

Generator yielding Datasets

Return type:

DatasetWrapper generator

listOwnedGroups()

Looks up owned groups for the logged user.

Returns:Groups owned by current user Return type:ExperimenterGroupWrapper generator

listProjects(eid=None)

List every Project controlled by the security system.

Parameters:eid – Filters Projects by owner ID Return type:ProjectWrapper list

listScreens(eid=None)

List every Screens controlled by the security system.

Parameters:eid – Filters Screens by owner ID Return type:ProjectWrapper list

listStaffs()

Look up users who are members of groups lead by the current user.

Returns:Members of groups lead by current user Return type:ExperimenterWrapper generator

resetEnumerations(klass)

Resets the enumerations by type

Parameters:klass (String) – Type of enum to reset

revertGroupForSession()

Switches the group to the previous group

searchObjects(obj_types, text, created=None, fields=(), batchSize=1000, page=0, searchGroup=None, ownedBy=None, useAcquisitionDate=False, rawQuery=True)

Search objects of type “Project”, “Dataset”, “Image”, “Screen”, “Plate” Returns a list of results

Parameters:

• obj_types – E.g. [“Dataset”, “Image”]
• text – The text to search for
• created – omero.rtime list or tuple (start, stop)
• useAcquisitionDate – if True, then use Image.acquisitionDate rather than import date for queries.

:param rawQuery If True, text is passed directly to byFullText()

without processing. fields is ignored.

Returns:List of Object wrappers. E.g. ImageWrapper

seppuku(softclose=False)

Terminates connection with killSession(). If softclose is False, the session is really terminated disregarding its connection refcount. If softclose is True then the connection refcount is decremented by 1.

Parameters:softclose – Boolean

** Deprecated ** Use close(). Our apologies for any offense caused by this previous method name.

setChannelNames(data_type, ids, nameDict, channelCount=None)

Sets and saves new names for channels of specified Images. If an image has fewer channels than the max channel index in nameDict, then the channel names will not be set for that image.

Parameters:

• data_type – ‘Image’, ‘Dataset’, ‘Plate’
• ids – Image, Dataset or Plate IDs
• nameDict – A dict of index:’name’ ** 1-based ** E.g. {1:”DAPI”, 2:”GFP”}
• channelCount – If specified, only rename images with this number of channels

Returns:

{‘imageCount’:totalImages, ‘updateCount’:updateCount}

setDefaultOmeroGroup(defaultOmeroGroup)

setDefaultOmeroUser(defaultOmeroUser)

setGroupForSession(groupid)

Sets the security context of this connection to the specified group

Parameters:groupid (Long) – The ID of the group to switch to Return type:Boolean Returns:True if the group was switched successfully

setGroupNameForSession(group)

Looks up the group by name, then delegates to setGroupForSession(), returning the result

Parameters:group (String) – Group name Returns:True if group set successfully Return type:Boolean

setIdentity(username, passwd, _internal=False)

Saves the username and password for later use, creating session etc

Parameters:

• username (String) – User name.
• passwd (String) – Password.
• _internal (Boolean) – If False, set _anonymous = False

setSecure(secure=True)

Switches between SSL and insecure (faster) connections to Blitz. The gateway must already be connected.

Parameters:secure (Boolean) – If False, use an insecure connection

setUserId(uid)

Sets current experimenter id

suConn(username, group=None, ttl=60000)

If current user isAdmin, return new connection owned by ‘username’

Parameters:

• username (String) – Username for new connection
• group (String) – If specified, try to log in to this group
• ttl (Int) – Timeout for new session

Returns:

Clone of this connection, with username’s new Session

Return type:

_BlitzGateway or None if not admin or username unknown

timelineListImages(tfrom=None, tto=None, limit=10, only_owned=True)

List images based on their creation times. If both tfrom and tto are None, grab the most recent batch.

Parameters:

• tfrom – milliseconds since the epoch for start date
• tto – milliseconds since the epoch for end date
• limit – maximum number of results
• only_owned – Only owned by the logged user. Boolean.

Returns:

Generator yielding _ImageWrapper

Return type:

ImageWrapper generator

updateAdminPrivileges(exp_id, add=[], remove=[])

Update the experimenter’s Admin Priviledges, adding and removing.

Parameters:

• exp_id – ID of experimenter to update
• add – List of strings
• remove – List of strings

updateEnumerations(new_entries)

Updates enumerations with new entries

Parameters:new_entries (List of omero.model.IObject) – List of objects

class omero.gateway._ChannelWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ChannelI class wrapper extends BlitzObjectWrapper.

BLUE_MAX = 500

BLUE_MIN = 400

COLOR_MAP = ((400, 500, <omero.gateway.ColorHolder object>), (501, 600, <omero.gateway.ColorHolder object>), (601, 700, <omero.gateway.ColorHolder object>))

GREEN_MAX = 600

GREEN_MIN = 501

OMERO_CLASS = 'Channel'

RED_MAX = 700

RED_MIN = 601

getCoefficient()

Returns the channel coefficient

Returns:the channel coefficient Return type:float

getColor()

Returns the rendering settings color of this channel

Returns:Channel color Return type:ColorHolder

getEmissionWave(units=None)

Returns the emission wave or None. If units is true, returns omero.model.LengthI If units specifies a unit e,g, “METER”, we convert.

Returns:Emission wavelength or None Return type:float or omero.model.LengthI

getExcitationWave(units=None)

Returns the excitation wave or None. If units is true, returns omero.model.LengthI If units specifies a unit e,g, “METER”, we convert.

Returns:Excitation wavelength or None Return type:float or omero.model.LengthI

getFamily()

Returns the channel family

Returns:the channel family Return type:String

getLabel()

Returns the logical channel name, emission wave or index. The first that is not null in the described order.

Returns:The logical channel string representation Return type:String

getLogicalChannel()

Returns the logical channel

Returns:Logical Channel Return type:LogicalChannelWrapper

getLut()

Returns the Lookup Table name for the Channel. E.g. “cool.lut” or None if no LUT.

Returns:Lut name. Return type:String

getName()

Returns the logical channel name or None

Returns:The logical channel string representation Return type:String

getWindowEnd()

Returns the rendering settings window-end of this channel

Returns:Window end Return type:double

getWindowMax()

Returns the maximum pixel value of the channel

Returns:Min pixel value Return type:double

getWindowMin()

Returns the minimum pixel value of the channel

Returns:Min pixel value Return type:double

getWindowStart()

Returns the rendering settings window-start of this channel

Returns:Window start Return type:double

isActive()

Returns True if the channel is active (turned on in rendering settings)

Returns:True if Channel is Active Return type:Boolean

isInverted()

Returns True if this channel has ReverseIntensityContext set on it.

Returns:True if ReverseIntensityContext found Return type:Boolean

isReverseIntensity()

Deprecated in 5.4.0. Use isInverted().

save()

Extends the superclass save method to save Pixels. Returns result of saving superclass (TODO: currently this is None)

setWindow(minval, maxval)

setWindowEnd(val)

setWindowStart(val)

class omero.gateway._DatasetWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_DatasetI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = 'ImageWrapper'

LINK_CLASS = 'DatasetImageLink'

OMERO_CLASS = 'Dataset'

PARENT_WRAPPER_CLASS = 'ProjectWrapper'

classmethod _getQueryString(opts=None)

Extend base query to handle filtering of Datasets by Projects. Returns a tuple of (query, clauses, params). Supported opts: ‘project’: <project_id> to filter by Project

‘image’: <image_id> to filter by child Image ‘orphaned’: <bool>. Filter by ‘not in Project’

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

class omero.gateway._DetectorSettingsWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_DetectorSettingsI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'DetectorSettings'

_attrs = ('voltage', 'gain', 'offsetValue', 'readOutRate', 'binning|BinningWrapper', 'detector|DetectorWrapper', 'version')

class omero.gateway._DetectorWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_DetectorI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Detector'

_attrs = ('manufacturer', 'model', 'serialNumber', 'voltage', 'gain', 'offsetValue', 'zoom', 'amplificationGain', '#type;detectorType', 'version')

getDetectorType()

The type of detector (enum value)

Returns:Detector type Return type:EnumerationWrapper

class omero.gateway._DichroicWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_DichroicI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Dichroic'

_attrs = ('manufacturer', 'model', 'lotNumber', 'version')

class omero.gateway._EnumerationWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

getType()

Gets the type (class) of the Enumeration

Returns:The omero class Type:Class

class omero.gateway._ExperimenterGroupWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ExperimenterGroupI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = 'ExperimenterWrapper'

LINK_CLASS = 'GroupExperimenterMap'

OMERO_CLASS = 'ExperimenterGroup'

PARENT_WRAPPER_CLASS = None

classmethod _getQueryString(opts=None)

Returns string for building queries, loading Experimenters for each group. Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

groupSummary(exclude_self=False)

Returns tuple of unsorted lists of ‘leaders’ and ‘members’ of the group.

Returns:(list ExperimenterWrapper, list ExperimenterWrapper) Return type:tuple

class omero.gateway._ExperimenterWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ExperimenterI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = None

LINK_CLASS = 'GroupExperimenterMap'

OMERO_CLASS = 'Experimenter'

PARENT_WRAPPER_CLASS = 'ExperimenterGroupWrapper'

classmethod _getQueryString(opts=None)

Returns string for building queries, loading Experimenters only.

Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

getDescription()

Returns Experimenter’s Full Name

Returns:Full Name or None Return type:String

getFullName()

Gets full name of this experimenter. E.g. ‘William James. Moore’ or ‘William Moore’ if no middle name

Returns:Full Name or None Return type:String

getName()

Returns Experimenter’s omeName

Returns:Name Return type:String

getNameWithInitial()

Returns first initial and Last name. E.g. ‘W. Moore’

Returns:Initial and last name Return type:String

getPreference(key, default='', section=None)

Gets a preference for the experimenter

Parameters:

• key – Preference key
• default – Default value to return
• section – Preferences section

Returns:

Preference value

getPreferences(section=None)

Gets all preferences for section

Parameters:section – Preferences section Returns:Dict of preferences

getRawPreferences()

Returns the experimenter’s preferences annotation contents, as a ConfigParser instance

Returns:See above Return type:ConfigParser

isActive()

Returns true if Experimenter is Active (if they are in any group named ‘user’)

Returns:True if experimenter is Active Return type:Boolean

isAdmin()

Returns true if Experimenter is Admin (if they are in any group named ‘system’)

Returns:True if experimenter is Admin Return type:Boolean

isGuest()

Returns true if Experimenter is Guest (if they are in any group named ‘guest’)

Returns:True if experimenter is Admin Return type:Boolean

is_self()

Returns True if this Experimenter is the current user

setPreference(key, value, section=None)

Sets a preference for the experimenter

Parameters:

• key – Preference key
• value – Value to set
• section – Preferences section - created if needed

setRawPreferences(prefs)

Sets the experimenter’s preferences annotation contents, passed in as a ConfigParser instance

Parameters:prefs (ConfigParser) – ConfigParser of preferences

simpleMarshal(xtra=None, parents=False)

class omero.gateway._FilamentWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway._LightSourceWrapper

omero_model_FilamentI class wrapper extends LightSourceWrapper.

OMERO_CLASS = 'Filament'

class omero.gateway._FilesetWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_FilesetI class wrapper extends BlitzObjectWrapper

OMERO_CLASS = 'Fileset'

classmethod _getQueryString(opts=None)

Used for building queries in generic methods such as getObjects(“Fileset”). Returns a tuple of (query, clauses, params).

Parameters:opts – Dictionary of optional parameters. NB: No options supported for this class. Returns:Tuple of string, list, ParametersI

copyImages()

Returns a list of ImageWrapper linked to this Fileset

listFiles()

Returns a list of OriginalFileWrapper linked to this Fileset via Fileset Entries

class omero.gateway._FilterSetWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_FilterSetI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'FilterSet'

_attrs = ('manufacturer', 'model', 'lotNumber', 'dichroic|DichroicWrapper', 'version')

copyEmissionFilters()

TODO: not implemented

copyExcitationFilters()

TODO: not implemented

class omero.gateway._FilterWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_FilterI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Filter'

_attrs = ('manufacturer', 'model', 'lotNumber', 'filterWheel', '#type;filterType', 'transmittanceRange|TransmittanceRangeWrapper', 'version')

getFilterType()

Gets the Filter type for this filter (enum value)

Returns:Filter type Return type:EnumerationWrapper

class omero.gateway._ImageStageLabelWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_StageLabelI class wrapper extends BlitzObjectWrapper.

class omero.gateway._ImageWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper, omero.gateway.OmeroRestrictionWrapper

omero_model_ImageI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = None

LINE_PLOT_DTYPES = {(1, False, False): 'B', (1, False, True): 'b', (4, True, True): 'f', (2, False, True): 'h', (2, False, False): 'H'}

LINK_CLASS = None

LP_BGCOLOR = 1

LP_FGCOLOR = 2

LP_PALLETE = [0, 0, 0, 0, 0, 0, 255, 255, 255]

LP_TRANSPARENT = 0

OMERO_CLASS = 'Image'

PARENT_WRAPPER_CLASS = ['DatasetWrapper', 'WellSampleWrapper']

PLANEDEF = 0

PROJECTIONS = {'intmax': MAXIMUMINTENSITY, 'intsum': SUMINTENSITY, 'intmean': MEANINTENSITY, 'normal': -1}

_archivedFileCount = None

_closeRE()

_collectRenderOptions()

Returns a map of rendering options not stored in rendering settings.

• ‘p’ : projection
• ‘ia’ : inverted axis (swap Z and T)

Returns:Dict of render options Return type:Dict

_deleteSettings()

_filesetFileCount = None

_getProjectedThumbnail(*args, **kwargs)

classmethod _getQueryString(opts=None)

Extend base query to handle filtering of Images by Datasets. Returns a tuple of (query, clauses, params). Supported opts: ‘dataset’: <dataset_id> to filter by Dataset

‘load_pixels’: <bool> to load Pixel objects ‘load_channels’: <bool> to load Channels and

Logical Channels

‘orphaned’: <bool> Images not in Dataset or WellSample

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

_getRDef()

Return a rendering def ID based on custom logic.

Returns:Rendering definition ID or None if no custom logic has found a rendering definition.

_importedFilesInfo = None

_invertedAxis = False

_loadPixels()

Checks that pixels are loaded

Returns:True if loaded Return type:Boolean

_loadRenderOptions()

Loads rendering options from an Annotation on the Image.

Returns:Dict of rendering options Return type:Dict

_onResetDefaults(rdid)

Called whenever a reset defaults is called by the preparation of the rendering engine or the thumbnail bean.

Parameters:rdid (Long) – Current Rendering Def ID

_pd = None

_pixels = None

_pr = None

_prEnd = None

_prStart = None

_prepareRE(rdid=None)

Prepare the rendering engine with pixels ID and existing or new rendering def.

Returns:The Rendering Engine service Return type:ProxyObjectWrapper

_prepareRenderingEngine(rdid=None)

Checks that the rendering engine is prepared, calling _prepareRE() if needed. Used by the assert_re() method to wrap calls requiring rendering engine

Returns:True if rendering engine is created Return type:Boolean

_prepareTB(_r=False, rdefId=None)

Prepares Thumbnail Store for the image.

Parameters:

• _r (Boolean) – If True, don’t reset default rendering (return None if no rDef exists)
• rdefId (Long) – Rendering def ID to use for rendering thumbnail

Returns:

Thumbnail Store or None

Return type:

ProxyObjectWrapper

_qf = {}

_re = None

_renderSplit_channelLabel(channel)

_rm = {}

_thumbInProgress = False

_wordwrap(width, text, font)

Wraps text into lines that are less than a certain width (when rendered in specified font)

Parameters:

• width (Int) – The max width to wrap text (pixels)
• text (String) – The text to wrap
• font (E.g. PIL ImageFont) – Font to use.

Returns:

List of text lines

Return type:

List of Strings

clearDefaults()

Removes specific color settings from channels

Returns:True if allowed to do this Return type:Boolean

countArchivedFiles()

Returns the number of Original ‘archived’ Files linked to primary pixels.

countFilesetFiles()

Counts the Original Files that are part of the FS Fileset linked to this image

countImportedImageFiles()

Returns a count of the number of Imported Image files (Archived files for pre-FS images) This will only be 0 if the image was imported pre-FS and original files NOT archived

createMovie(*args, **kwargs)

exportOmeTiff(bufsize=0)

Exports the OME-TIFF representation of this image.

Parameters:bufsize (int or tuple) – if 0 return a single string buffer with the whole OME-TIFF if >0 return a tuple holding total size and generator of chunks (string buffers) of bufsize bytes each Returns:OME-TIFF file data Return type:String or (size, data generator)

classmethod fromPixelsId(conn, pid)

Creates a new Image wrapper with the image specified by pixels ID

Parameters:

• conn (BlitzGateway) – The connection
• pid (Long) – Pixels ID

Returns:

New Image wrapper

Return type:

ImageWrapper

getAcquisitionDate()

Returns the acquisition date for the image or None if not set.

Returns:A datetime.datetime() object Return type:datetime

getAllRenderingDefs(eid=-1)

Returns a dict of the rendering settings that exist for this Image Can be filtered by owner using the eid parameter.

Returns:Rdef dict Return type:Dict

getArchivedFiles()

Returns a generator of OriginalFileWrapper corresponding to the archived files linked to primary pixels ** Deprecated ** Use getImportedImageFiles().

getAuthor()

Returns ‘Firstname Lastname’ of image owner

Returns:Image owner Return type:String

getChannelLabels()

Returns a list of the labels for the Channels for this image

getChannels(noRE=False)

Returns a list of Channels, each initialised with rendering engine. If noRE is True, Channels will not have rendering engine enabled. In this case, calling channel.getColor() or getWindowStart() etc will return None.

Returns:Channels Return type:List of ChannelWrapper

getCol(z, t, x, channels=None, range=None)

Grab a horizontal line from the image pixel data, for the specified channels (or active ones)

Parameters:

• z – Z index
• t – T index
• x – X position of column
• channels – map of {index: ChannelWrapper }
• range – height of scale (use image width by default)

Returns:

rv List of lists (one per channel)

getDefaultT(*args, **kwargs)

getDefaultZ(*args, **kwargs)

getFamilies()

Gets a dict of available families.

Returns:Families Return type:Dict

getFileset()

Returns the Fileset linked to this Image. Fileset images, usedFiles and originalFiles are loaded.

getHistogram(*args, **kwargs)

Tries to load pixels, then call function and return the result

getImagingEnvironment()

Gets the Imaging Environment of the Image, or None

Returns:Imaging Environment Return type:ImagingEnvironmentWrapper

getImportedFilesInfo()

Returns a dict of ‘count’ and ‘size’ of the Fileset files (OMERO 5) or the Original Archived files (OMERO 4)

Returns:A dict of ‘count’ and sum ‘size’ of the files.

getImportedImageFilePaths()

Returns a generator of path strings corresponding to the Imported image files that created this image, if available.

getImportedImageFiles()

Returns a generator of OriginalFileWrapper corresponding to the Imported image files that created this image, if available.

getInplaceImport()

If the image was imported using file transfer, return the type of file transfer. One of: ‘ome.formats.importer.transfers.MoveFileTransfer’, ‘ome.formats.importer.transfers.CopyFileTransfer’, ‘ome.formats.importer.transfers.CopyMoveFileTransfer’, ‘ome.formats.importer.transfers.HardlinkFileTransfer’, ‘ome.formats.importer.transfers.SymlinkFileTransfer’

Return type:String or None Returns:Transfer type or None

getInstrument()

Returns the Instrument for this image (or None) making sure the instrument is loaded.

Returns:Instrument (microscope) Return type:InstrumentWrapper

getObjectiveSettings()

Gets the Objective Settings of the Image, or None

Returns:Objective Settings Return type:ObjectiveSettingsWrapper

getPixelLine(z, t, pos, axis, channels=None, range=None)

Grab a horizontal or vertical line from the image pixel data, for the specified channels (or ‘active’ if not specified) and using the specified range (or 1:1 relative to the image size). Axis may be ‘h’ or ‘v’, for horizontal or vertical respectively.

Parameters:

• z – Z index
• t – T index
• pos – X or Y position
• axis – Axis ‘h’ or ‘v’
• channels – map of {index: ChannelWrapper }
• range – height of scale (use image height (or width) by default)

Returns:

rv List of lists (one per channel)

getPixelRange(*args, **kwargs)

Tries to load pixels, then call function and return the result

getPixelSizeX(*args, **kwargs)

Tries to load pixels, then call function and return the result

getPixelSizeY(*args, **kwargs)

Tries to load pixels, then call function and return the result

getPixelSizeZ(*args, **kwargs)

Tries to load pixels, then call function and return the result

getPixelsId(*args, **kwargs)

Tries to load pixels, then call function and return the result

getPixelsType(*args, **kwargs)

Tries to load pixels, then call function and return the result

getPlate()

If the image is in a Plate/Well hierarchy, returns the parent Plate, otherwise None

Returns:Plate Return type:PlateWrapper

getPrimaryPixels(*args, **kwargs)

Tries to load pixels, then call function and return the result

getProject()

Gets the Project that image is in, or None. TODO: Assumes image is in only 1 Project. Why not use getAncestory()[-1] Returns None if Image is in more than one Dataset & Project.

Returns:Project Return type:ProjectWrapper

getProjection()

Returns the current projection option (checking it is valid).

Returns:Projection key. E.g. ‘intmax’ Return type:String

getProjectionRange()

Gets the range used for Z-projection as tuple (proStart, proEnd)

getProjections()

Returns list of available keys for projection. E.g. [‘intmax’, ‘intmean’]

Returns:Projection options Return type:List of strings

getROICount(shapeType=None, filterByCurrentUser=False)

Count number of ROIs associated to an image

Parameters:

• shapeType – Filter by shape type (“Rectangle”,...).
• filterByCurrentUser – Whether or not to filter the count by the currently logged in user.

Returns:

Number of ROIs found for the currently logged in user if filterByCurrentUser is True, otherwise the total number found.

getRenderingDefId(*args, **kwargs)

getRenderingModel(*args, **kwargs)

getRenderingModels()

Gets a list of available rendering models.

Returns:Rendering models Return type:List of BlitzObjectWrapper

getRow(z, t, y, channels=None, range=None)

Grab a horizontal line from the image pixel data, for the specified channels (or active ones)

Parameters:

• z – Z index
• t – T index
• y – Y position of row
• channels – map of {index: ChannelWrapper }
• range – height of scale (use image height by default)

Returns:

rv List of lists (one per channel)

getSizeC(*args, **kwargs)

Tries to load pixels, then call function and return the result

getSizeT(*args, **kwargs)

Tries to load pixels, then call function and return the result

getSizeX(*args, **kwargs)

Tries to load pixels, then call function and return the result

getSizeY(*args, **kwargs)

Tries to load pixels, then call function and return the result

getSizeZ(*args, **kwargs)

Tries to load pixels, then call function and return the result

getStageLabel()

Returns the stage label or None

Returns:Stage label Return type:ImageStageLabelWrapper

getT(*args, **kwargs)

getThumbVersion(*args, **kwargs)

Tries to load pixels, then call function and return the result

getThumbnail(size=(64, 64), z=None, t=None, direct=True, rdefId=None)

Returns a string holding a rendered JPEG of the thumbnail.

Parameters:

• size (tuple or number) – A tuple with one or two ints, or an integer. If a tuple holding a single int, or a single int is passed as param, then that will be used as the longest size on the rendered thumb, and image aspect ratio is kept. If two ints are passed in a tuple, they set the width and height of the rendered thumb.
• z (number) – the Z position to use for rendering the thumbnail. If not provided default is used.
• t (number) – the T position to use for rendering the thumbnail. If not provided default is used.
• direct – If true, force creation of new thumbnail (don’t use cached)
• rdefId – The rendering def to apply to the thumbnail.

Return type:

string or None

Returns:

the rendered JPEG, or None if there was an error.

getZ(*args, **kwargs)

getZoomLevelScaling(*args, **kwargs)

isGreyscaleRenderingModel()

Returns True if the current rendering model is ‘greyscale’

Returns:isGreyscale Return type:Boolean

isInvertedAxis()

Returns the inverted axis flag

Returns:Inverted Axis Return type:Boolean

loadOriginalMetadata(sort=True)

Gets original metadata from the file annotation. Returns the File Annotation, list of Global Metadata, list of Series Metadata in a tuple. Metadata lists are lists of (key, value) tuples.

Parameters:sort – If True, we sort Metadata by key Returns:Tuple (file-annotation, global-metadata, series-metadata) Return type:Tuple (FileAnnotationWrapper, [], [])

loadRenderOptions()

Loads rendering options from an Annotation on the Image and applies them to the Image.

Returns:True! TODO: Always True??

prepareLinePlotCanvas()

Common part of horizontal and vertical line plot rendering.

Returns:(Image, width, height).

renderBirdsEyeView(*args, **kwargs)

renderColLinePlotGif(*args, **kwargs)

renderImage(z, t, compression=0.90000000000000002)

Render the Image, (projected) and compressed. For projection, call setProjection() before renderImage.

Parameters:

• z – Z index
• t – T index
• compression – Image compression level

Returns:

A PIL Image or None

Return type:

PIL Image.

renderJpeg(*args, **kwargs)

renderJpegRegion(*args, **kwargs)

renderRowLinePlotGif(*args, **kwargs)

renderSplitChannel(z, t, compression=0.90000000000000002, border=2)

Prepares a jpeg representation of a 2d grid holding a render of each channel, along with one for all channels at the set Z and T points.

Parameters:

• z – Z index
• t – T index
• compression – Image compression level
• border –

Returns:

value

renderSplitChannelImage(z, t, compression=0.90000000000000002, border=2)

Prepares a PIL Image with a 2d grid holding a render of each channel, along with one for all channels at the set Z and T points.

Parameters:

• z – Z index
• t – T index
• compression – Compression level
• border – space around each panel (int)

Returns:

canvas

Return type:

PIL Image

requiresPixelsPyramid()

Returns True if Image Plane is over the max plane size.

resetDefaults(*args, **kwargs)

resetRDefs()

saveDefaults(*args, **kwargs)

setActiveChannels(*args, **kwargs)

setChannelInverted(*args, **kwargs)

setColorRenderingModel(*args, **kwargs)

setDefaultT(*args, **kwargs)

setDefaultZ(*args, **kwargs)

setGreyscaleRenderingModel(*args, **kwargs)

setInvertedAxis(inverted)

Sets the inverted axis flag

Parameters:inverted (Boolean) – Inverted Axis

setProjection(proj)

Sets the current projection option.

Parameters:proj (String) – Projection Option. E.g. ‘intmax’ or ‘normal’

setProjectionRange(projStart, projEnd)

Sets the range used for Z-projection. Will only be used if E.g. setProjection(‘intmax’) is not ‘normal’

setQuantizationMap(*args, **kwargs)

setQuantizationMaps(*args, **kwargs)

setReverseIntensity(*args, **kwargs)

set_active_channels(*args, **kwargs)

shortname(length=20, hist=5)

Provides a truncated name of the image. E.g. ...catedNameOfTheImage.tiff

Parameters:

• length (Int) – The ideal length to return. If truncated, will be ...length
• hist (Int) – The amount of leeway allowed before truncation (avoid truncating 1 or 2 letters)

Returns:

Truncated ...name

Type:

String

simpleMarshal(xtra=None, parents=False)

Creates a dict representation of the Image, including author and date info.

Parameters:xtra – controls the optional parts of simpleMarshal; - thumbUrlPrefix - allows customizing the thumb URL by either a static string prefix or a callable function that will take a single ImgId int argument and return the customized URL string - tiled - if passed and value evaluates to true, add information on whether this image is tiled on this server. Type:Dict Returns:Dict Return type:Dict

splitChannelDims(border=2)

Returns a dict of layout parameters for generating split channel image. E.g. row count, column count etc. for greyscale and color layouts.

Parameters:border (int) – spacing between panels Returns:Dict of parameters Return type:Dict

class omero.gateway._ImagingEnviromentWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ImagingEnvironmentI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'ImagingEnvironment'

_attrs = ('temperature', 'airPressure', 'humidity', 'co2percent', 'version')

class omero.gateway._ImagingEnvironmentWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ImagingEnvironment class wrapper extends BlitzObjectWrapper.

class omero.gateway._InstrumentWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_InstrumentI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Instrument'

_attrs = ('microscope|MicroscopeWrapper',)

getDetectors()

Gets the Instrument detectors.

Returns:List of Detectors Return type:DetectorWrapper list

getDichroics()

Gets the Instrument Dichroics.

Returns:List of Dichroics Return type:DichroicWrapper list

getFilterSets()

Gets the Instrument FilterSets.

Returns:List of FilterSets Return type:FilterSetWrapper list

getFilters()

Gets the Instrument Filters.

Returns:List of Filters Return type:FilterWrapper list

getLightSources()

Gets the Instrument LightSources.

Returns:List of LightSources Return type:LightSourceWrapper list

getMicroscope()

Returns the microscope component of the Instrument.

Returns:Microscope Return type:omero.model.Microscope

getOTFs()

Gets the Instrument OTFs.

Returns:List of OTFs Return type:OTFWrapper list

getObjectives()

Gets the Instrument Objectives.

Returns:List of Objectives Return type:ObjectiveWrapper list

simpleMarshal()

class omero.gateway._LaserWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway._LightSourceWrapper

omero_model_LaserI class wrapper extends LightSourceWrapper.

OMERO_CLASS = 'Laser'

getLaserMedium()

Gets the laser medium type for this Laser (enum value)

Returns:Laser medium type Return type:EnumerationWrapper

getPump()

Gets the pump (Light Source) for this Laser

Returns:Pump (Light Source) Return type:LightSourceWrapper

class omero.gateway._LightEmittingDiodeWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway._LightSourceWrapper

omero_model_LightEmittingDiodeI class wrapper extends LightSourceWrapper.

OMERO_CLASS = 'LightEmittingDiode'

class omero.gateway._LightPathWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

base Light Source class wrapper, extends BlitzObjectWrapper.

OMERO_CLASS = 'LightPath'

_attrs = ('dichroic|DichroicWrapper', '()emissionFilters|', '()excitationFilters|')

getEmissionFilters()

Returns list of emission FilterWrapper

getExcitationFilters()

Returns list of excitation FilterWrapper. Ordered collections can contain nulls

class omero.gateway._LightSettingsWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

base Light Source class wrapper, extends BlitzObjectWrapper.

OMERO_CLASS = 'LightSettings'

_attrs = ('attenuation', 'wavelength', 'microbeamManipulation', 'version')

getLightSource()

class omero.gateway._LightSourceWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

base Light Source class wrapper, extends BlitzObjectWrapper.

_attrs = ('manufacturer', 'model', 'power', 'serialNumber', '#type;lightSourceType', 'version')

getLightSourceType()

Gets the Light Source type for this light source (enum value)

Returns:Light Source type Return type:EnumerationWrapper

class omero.gateway._LogicalChannelWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_LogicalChannelI class wrapper extends BlitzObjectWrapper. Specifies a number of _attrs for the channel metadata.

_attrs = ('name', 'pinHoleSize', '#illumination', 'contrastMethod', 'excitationWave', 'emissionWave', 'fluor', 'ndFilter', 'otf', 'detectorSettings|DetectorSettingsWrapper', 'lightSourceSettings|LightSettingsWrapper', 'filterSet|FilterSetWrapper', 'samplesPerPixel', '#photometricInterpretation', 'mode', 'pockelCellSetting', '()lightPath|', 'version')

getLightPath()

Make sure we have the channel fully loaded, then return LightPathWrapper

class omero.gateway._MicroscopeWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_MicroscopeI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Microscope'

_attrs = ('manufacturer', 'model', 'serialNumber', '#type;microscopeType', 'version')

getMicroscopeType()

Returns the ‘type’ of microscope this is.

Returns:Microscope type. Return type:EnumerationWrapper

class omero.gateway._OTFWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_OTFI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'OTF'

_attrs = ('sizeX', 'sizeY', 'opticalAxisAveragedpixelsType', 'path', 'filterSet|FilterSetWrapper', 'objective|ObjectiveWrapper', 'version')

class omero.gateway._ObjectiveSettingsWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ObjectiveSettingsI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'ObjectiveSettings'

_attrs = ('correctionCollar', '#medium', 'refractiveIndex', 'objective|ObjectiveWrapper', 'version')

getMedium()

Gets the Medium type that these settings refer to (enum value)

Returns:Medium Return type:EnumerationWrapper

getObjective()

Gets the Objective that these settings refer to

Returns:Objective Return type:ObjectiveWrapper

class omero.gateway._ObjectiveWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ObjectiveI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Objective'

_attrs = ('manufacturer', 'model', 'serialNumber', 'nominalMagnification', 'calibratedMagnification', 'lensNA', '#immersion', '#correction', 'workingDistance', 'iris', 'version')

getCorrection()

The type of Correction for this objective (enum value)

Returns:Correction type, or None Return type:EnumerationWrapper

getImmersion()

The type of immersion for this objective (enum value)

Returns:Immersion type, or None Return type:EnumerationWrapper

getIris()

The type of Iris for this objective (enum value)

Returns:Iris type Return type:EnumerationWrapper

class omero.gateway._OriginalFileAsFileObj(originalfile, buf=2621440)

Bases: object

Based on https://docs.python.org/2/library/stdtypes.html#file-objects

close()

read(n=-1)

seek(n, mode=0)

tell()

class omero.gateway._OriginalFileWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper, omero.gateway.OmeroRestrictionWrapper

omero_model_OriginalFileI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'OriginalFile'

asFileObj(buf=2621440)

Return a read-only file-like object. Caller must call close() on the file object after use. This can be done automatically by using the object as a ContextManager. For example:

with f.asFileObj() as fo:

content = fo.read()

Returns:File-like object wrapping the OriginalFile Return type:File-like object

getFileInChunks(buf=2621440)

Returns a generator yielding chunks of the file data.

Returns:Data from file in chunks Return type:Generator

class omero.gateway._PixelsWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_PixelsI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Pixels'

_prepareRawPixelsStore()

Creates RawPixelsStore and sets the id etc

copyPlaneInfo(theC=None, theT=None, theZ=None)

Loads plane infos and returns sequence of omero.model.PlaneInfo objects wrapped in BlitzObjectWrappers ordered by planeInfo.deltaT. Set of plane infos can be filtered by C, T or Z

Parameters:

• theC (int or None) – Filter plane infos by Channel index
• theT (int or None) – Filter plane infos by Time index
• theZ – Filter plane infos by Z index

Returns:

Generator of PlaneInfo wrapped in BlitzObjectWrappers

getPixelsType()

This simply wraps the omero.model.PixelsType object in a BlitzObjectWrapper. Shouldn’t be needed when this is done automatically.

It has the methods getValue() and getBitSize().

getPlane(theZ=0, theC=0, theT=0)

Gets the specified plane as a 2D numpy array by calling getPlanes() If a range of planes are required, getPlanes() is approximately 30% faster.

getPlanes(zctList)

Returns generator of numpy 2D planes from this set of pixels for a list of Z, C, T indexes.

Parameters:zctList – A list of indexes: [(z,c,t), ]

getTile(theZ=0, theC=0, theT=0, tile=None)

Gets the specified plane as a 2D numpy array by calling getTiles() If a range of tile are required, getTiles() is approximately 30% faster.

getTiles(zctTileList)

Returns generator of numpy 2D planes from this set of pixels for a list of (Z, C, T, tile) where tile is (x, y, width, height) or None if you want the whole plane.

Parameters:zctrList – A list of indexes: [(z,c,t, region), ]

class omero.gateway._PlaneInfoWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_PlaneInfo class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'PlaneInfo'

getDeltaT(units=None)

Gets the PlaneInfo deltaT with units support If units is True, return omero.model.TimeI If units specifies a different unit E.g. “MILLISECOND”, we convert

Parameters:units (True or unit string, e.g. "S") – Option to include units in tuple Returns:DeltaT value or omero.model.TimeI

getExposureTime(units=None)

Gets the PlaneInfo ExposureTime with units support If units is True, return omero.model.TimeI If units specifies a different unit E.g. “MILLISECOND”, we convert

Parameters:units (True or unit string) – Option to include units in tuple Returns:ExposureTime value or omero.model.TimeI

class omero.gateway._PlateAcquisitionWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

OMERO_CLASS = 'PlateAcquisition'

classmethod _getQueryString(opts=None)

Extend base query to handle filtering of PlateAcquisitions by Plate. Returns a tuple of (query, clauses, params). Supported opts: ‘plate’: <plate_id> to filter by Plate

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

getEndTime()

Get the EndTime as a datetime object or None if not set.

getName()

getStartTime()

Get the StartTime as a datetime object or None if not set.

listParents(withlinks=False)

Because PlateAcquisitions are direct children of plates, with no links in between, a special listParents is needed

name

class omero.gateway._PlateWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper, omero.gateway.OmeroRestrictionWrapper

omero_model_PlateI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = 'WellWrapper'

LINK_CLASS = None

OMERO_CLASS = 'Plate'

PARENT_WRAPPER_CLASS = 'ScreenWrapper'

classmethod _getQueryString(opts=None)

Custom query to load Screen with Plate.

Also handles filtering of Plates by Screens. Returns a tuple of (query, clauses, params). Supported opts: ‘screen’: <screen_id> to filter by Screen

‘well’: <well_id> to filter by Well ‘orphaned’: <bool>. Filter by ‘not in Screen’

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

_listChildren(**kwargs)

Lists Wells in this plate, not sorted. Saves wells to _childcache map, where key is (row, column).

Return type:list of omero.model.WellI objects Returns:child objects.

_loadPlateAcquisitions()

countChildren()

countPlateAcquisitions()

exportOmeTiff()

Make sure full project export doesn’t pick up wellsample images TODO: do we want to support this at all?

getColumnLabels()

Returns a list of labels for the columns on this plate. E.g. [1, 2, 3...] or [‘A’, ‘B’, ‘C’...] etc

getGridSize()

Iterates all wells on plate to retrieve grid size as {‘rows’: rSize, ‘columns’:cSize} dict.

Return type:dict of {‘rows’: rSize, ‘columns’:cSize}

getNumberOfFields(*args, **kwargs)

getRowLabels()

Returns a list of labels for the rows on this plate. E.g. [1, 2, 3...] or [‘A’, ‘B’, ‘C’...] etc

getWellGrid(index=0)

Returns a grid of WellWrapper objects, indexed by [row][col].

Return type:2D array of WellWrapper. Empty well positions are None

listPlateAcquisitions()

setGridSizeConstraints(row, col)

Makes sure the grid side count is the exact power of two of row and col arguments, keeping their ratio, that fits the existing well count.

class omero.gateway._ProjectWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ProjectI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = 'DatasetWrapper'

LINK_CLASS = 'ProjectDatasetLink'

OMERO_CLASS = 'Project'

PARENT_WRAPPER_CLASS = None

classmethod _getQueryString(opts=None)

Extend base query to handle filtering of Projects by Datasets. Returns a tuple of (query, clauses, params). Supported opts: ‘dataset’: <dataset_id> to filter by Dataset

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

class omero.gateway._RoiWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ExperimenterI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = 'ShapeWrapper'

OMERO_CLASS = 'Roi'

classmethod _getQueryString(opts=None)

Extend base query to handle loading of Shapes. Returns a tuple of (query, clauses, params). Supported opts: ‘load_shapes’: boolean.

‘image’: <image_id> to filter by Image

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

getImage()

Returns the Image for this ROI.

Returns:The Image Return type:ImageWrapper

class omero.gateway._ScreenWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ScreenI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = 'PlateWrapper'

LINK_CLASS = 'ScreenPlateLink'

OMERO_CLASS = 'Screen'

PARENT_WRAPPER_CLASS = None

classmethod _getQueryString(opts=None)

Extend base query to handle filtering of Screens by Plate. Returns a tuple of (query, clauses, params). Supported opts: ‘plate’: <plate_id> to filter by Plate

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

class omero.gateway._ShapeWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_ShapeI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'Shape'

class omero.gateway._TransmittanceRangeWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_TransmittanceRangeI class wrapper extends BlitzObjectWrapper.

OMERO_CLASS = 'TransmittanceRange'

_attrs = ('cutIn', 'cutOut', 'cutInTolerance', 'cutOutTolerance', 'transmittance', 'version')

class omero.gateway._WellSampleWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper

omero_model_WellSampleI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = 'ImageWrapper'

LINK_CHILD = 'image'

LINK_CLASS = 'WellSample'

static LINK_PARENT(link)

Direct parent is Well. No Link between Well and WellSample.

OMERO_CLASS = 'WellSample'

PARENT_WRAPPER_CLASS = 'WellWrapper'

getImage()

Gets the Image for this well sample.

Returns:The Image Return type:ImageWrapper

getPlateAcquisition()

Gets the PlateAcquisition for this well sample, or None

Returns:The PlateAcquisition Return type:PlateAcquisitionWrapper or None

image()

Gets the Image for this well sample.

Returns:The Image Return type:ImageWrapper

listParents(withlinks=False)

Because wellsamples are direct children of wells, with no links in between, a special listParents is needed

class omero.gateway._WellWrapper(conn=None, obj=None, cache=None, **kwargs)

Bases: omero.gateway.BlitzObjectWrapper, omero.gateway.OmeroRestrictionWrapper

omero_model_WellI class wrapper extends BlitzObjectWrapper.

CHILD_WRAPPER_CLASS = 'WellSampleWrapper'

LINK_CLASS = None

OMERO_CLASS = 'Well'

PARENT_WRAPPER_CLASS = 'PlateWrapper'

classmethod _getQueryString(opts=None)

Extend base query to handle filtering of Wells by Plate. Returns a tuple of (query, clauses, params). Supported opts: ‘plate’: <plate_id> to filter by Plate

‘load_images’: <bool> to load WellSamples and Images ‘load_pixels’: <bool> to load Image Pixels ‘load_channels’: <bool> to load Pixels and Channels

Parameters:opts – Dictionary of optional parameters. Returns:Tuple of string, list, ParametersI

_listChildren(**kwargs)

countWellSample()

Return the number of well samples loaded

Returns:well sample count Return type:Int

getImage(index=None)

Return the image at the specified well sample index. If index is omitted, the currently selected index is used instead (self.index) and if that is not defined, the first one (index 0) is returned.

Parameters:index (integer) – the well sample index Returns:The Image Return type:ImageWrapper

getScreens()

returns the screens that link to plates that link to this well

getWellPos()

Gets the Well’s label according to the row and column naming convention on the Plate. E.g. ‘A1’

getWellSample(index=None)

Return the well sample at the specified index. If index is omitted, the currently selected index is used instead (self.index) and if that is not defined, the first one (index 0) is returned.

Parameters:index (integer) – the well sample index Returns:The Well Sample Return type:WellSampleWrapper

isWellSample()

Return True if well samples exist (loaded)

Returns:True if well samples loaded Return type:Boolean

listParents(withlinks=False)

Because wells are direct children of plates, with no links in between, a special listParents is needed

selectedWellSample()

Return the well sample at the current index (0 if not set)

Returns:The Well Sample wrapper Return type:WellSampleWrapper

simpleMarshal(xtra=None, parents=False)

Marshals the Well ID, label and Plate ID with simple Marshal of the first image in the Well.

omero.gateway._letterGridLabel(i)

Convert number to letter label. E.g. 0 -> ‘A’ and 100 -> ‘CW’

omero.gateway.add_plate_filter(clauses, params, opts)

Helper for adding ‘plate’ to filtering clauses and parameters.

omero.gateway.assert_pixels(func)

Function decorator to make sure that pixels are loaded before call

Parameters:func (Function) – Function Returns:Decorated function Return type:Function

class omero.gateway.assert_re(onPrepareFailureReturnNone=True, ignoreExceptions=None)

Bases: object

Function decorator to make sure that rendering engine is prepared before call. Is configurable by various options.

omero.gateway.fileread(fin, fsize, bufsize)

Reads everything from fin, in chunks of bufsize.

Parameters:

• fin (file) – filelike readable object
• fsize (int) – total number of bytes to read
• fsize – size of each chunk of data read from fin

Return type:

string

Returns:

string buffer holding the contents read from the file

omero.gateway.fileread_gen(fin, fsize, bufsize)

Generator helper function that yields chunks of the file of size fsize.

Parameters:

• fin (file) – filelike readable object
• fsize (int) – total number of bytes to read
• fsize – size of each chunk of data read from fin that gets yielded

Return type:

generator

Returns:

generator of string buffers of size up to bufsize read from fin

omero.gateway.getAnnotationLinkTableName(objecttype)

Get the name of the *AnnotationLink table for the given objecttype

omero.gateway.getChannelsQuery()

Helper for building Query for Images or Wells & Images

omero.gateway.getPixelsQuery(imageName)

Helper for building Query for Images or Wells & Images

omero.gateway.omero_type(val)

Converts rtypes from static factory methods:

• StringType to rstring
• UnicodeType to rstring
• BooleanType to rbool
• IntType to rint
• LongType to rlong

else return the argument itself

Parameters:val – value Return type:omero.rtype Returns:matched RType or value

omero.gateway.refreshWrappers()

this needs to be called by modules that extend the base wrappers

omero.gateway.splitHTMLColor(color)

splits an hex stream of characters into an array of bytes in format (R,G,B,A). - abc -> (0xAA, 0xBB, 0xCC, 0xFF) - abcd -> (0xAA, 0xBB, 0xCC, 0xDD) - abbccd -> (0xAB, 0xBC, 0xCD, 0xFF) - abbccdde -> (0xAB, 0xBC, 0xCD, 0xDE)

Parameters:color – Characters to split. Returns:rgba Return type:list of Ints