omero::api::Gateway
Overview
[ "deprecated:The Gateway service is deprecated. use the native language gateways instead instead.", "ami" ]
interface Gateway extends StatefulServiceInterface
High-level service which provides a single interface for most client
activities. Each stateful Gateway instance internally manages multiple
other stateful instances (RenderingEngine, ThumbnailStore, etc.) significantly
simplyifing usage.
This interface is deprecated.
Operation Index
- getProjects
-
Get the projects, and datasets in the OMERO.Blitz server in the user
account.
- getDatasets
-
Get the datasets in the OMERO.Blitz server with the given ids.
- getDataset
-
Get the dataset in the OMERO.Blitz server with the given id.
- getPixelsFromImage
-
Get the pixels associated with the image, this is normally one pixels per
image, but can be more.
- getImage
-
Get the image with id
@param id see above
@return see above.
- getImages
-
Get the images in the OMERO.Blitz server from the object parentType with
id's in list ids.
- findAllByQuery
-
Run the query passed as a string in the iQuery interface.
- findByQuery
-
Run the query passed as a string in the iQuery interface.
- getPlane
-
Get the raw plane for the pixels pixelsId, this returns a 2d array
representing the plane, it returns doubles but will not lose data.
- getPixels
-
Get the pixels information for an image, this method will also
attach the logical channels, channels, and other metadata in the pixels.
- copyPixelsXYTZ
-
Copy the pixels to a new pixels, this is only the data object
and does not create a pixels object in the RawPixelsStore,
To load data into the plane the uploadPlane(long, int, int, int, DoubleArrayArray)
to add data to the pixels.
- copyPixels
-
Copy the pixels to a new pixels, this is only the data object
and does not create a pixels object in the RawPixelsStore,
To load data into the plane the uploadPlane(long, DoubleArrayArray)
to add data to the pixels.
- copyImage
-
Copy the image and it's attached pixels and
metadata to a new Image and return the id of the new image.
- uploadPlane
-
Upload the plane to the server, on pixels id with channel and the
time, + z section.
- updatePixels
-
Update the pixels object on the server, updating appropriate tables in the
database and returning a new copy of the pixels.
- getPixelTypes
-
Get a list of all the possible pixelsTypes in the server.
- getPixelType
-
Get the pixelsType for type of name type.
- getRenderedImage
-
Render the pixels for the zSection z and timePoint t.
- renderAsPackedIntAsRGBA
-
Render the pixels for the zSection z and timePoint t.
- getRenderedImageMatrix
-
Render the pixels for the zSection z and timePoint t.
- setActive
-
Set the active channels to be on or off in the rendering engine for
the pixels.
- getThumbnail
-
Get the thumbnail of the image.
- getThumbnailSet
-
Get a set of thumbnails, of size X, Y from the list of pixelId's supplied
in the list.
- attachImageToDataset
-
Attach an image to a dataset.
- createImage
-
Create a new Image of X,Y, and zSections+time-points.
- getImageFromDatasetByName
-
Get the images from the dataset with name, this can use wild cards.
- getImageByName
-
Get the list of images with name containing imageName.
- saveObject
-
Save the object to the db .
- saveAndReturnObject
-
Save and return the Object.
- saveArray
-
Save the array.
- saveAndReturnArray
-
Save and return the array.
- deleteObject
-
Delete the object.
- keepAlive
-
Keep service alive.
Operations
Get the projects, and datasets in the OMERO.Blitz server in the user
account.
This operation is deprecated.
Parameters
- ids
-
The ids of the projects from, if null will retrieve all
projects from the users account.
- withLeaves
-
get the projects, images and pixels too.
Return Value
see above.
Exceptions
-
Get the datasets in the OMERO.Blitz server with the given ids.
This operation is deprecated.
Parameters
- ids
-
of the datasets to retrieve, if null get all users datasets.
- withLeaves
-
get the images and pixels too.
Return Value
see above.
Exceptions
-
Get the dataset in the OMERO.Blitz server with the given id.
This operation is deprecated.
Parameters
- id
-
of the dataset to retrieve
- withLeaves
-
get the images and pixels too.
Return Value
see above.
Exceptions
-
Get the pixels associated with the image, this is normally one pixels per
image, but can be more.
This operation is deprecated.
Parameters
-
Return Value
the list of pixels.
Exceptions
-
Get the image with id
This operation is deprecated.
Parameters
- id
-
see above
Return Value
see above.
Exceptions
-
Get the images in the OMERO.Blitz server from the object parentType with
id's in list ids.
This operation is deprecated.
Parameters
- parentType
-
see above.
- ids
-
see above.
Return Value
see above.
Exceptions
-
Run the query passed as a string in the iQuery interface. This method will
return list of objects.
This operation is deprecated.
Parameters
- myQuery
-
string containing the query.
Return Value
the result.
Exceptions
-
Run the query passed as a string in the iQuery interface.
The method expects to return only one result from the query, if more than
one result is to be returned the method will throw an exception.
This operation is deprecated.
Parameters
- myQuery
-
string containing the query.
Return Value
the result.
Exceptions
-
::Ice::ByteSeq getPlane(long pixelsId, int z, int c, int t) throws ServerError
Get the raw plane for the pixels pixelsId, this returns a 2d array
representing the plane, it returns doubles but will not lose data.
This operation is deprecated.
Parameters
- pixelsId
-
id of the pixels to retrieve.
- c
-
the channel of the pixels to retrieve.
- t
-
the time point to retrieve.
- z
-
the z section to retrieve.
Return Value
The raw plane in as byte stream.
Exceptions
-
Get the pixels information for an image, this method will also
attach the logical channels, channels, and other metadata in the pixels.
This operation is deprecated.
Parameters
- pixelsId
-
image id relating to the pixels.
Return Value
see above.
Exceptions
-
long copyPixelsXYTZ(long pixelsID, int x, int y, int t, int z, IntegerList channelList, string methodology) throws ServerError
Copy the pixels to a new pixels, this is only the data object
and does not create a pixels object in the RawPixelsStore,
To load data into the plane the uploadPlane(long, int, int, int, DoubleArrayArray)
to add data to the pixels.
This operation is deprecated.
Parameters
- pixelsID
-
pixels id to copy.
- x
-
width of plane.
- y
-
height of plane.
- t
-
num timepoints
- z
-
num zsections.
- channelList
-
the list of channels to copy, this is the channel index.
- methodology
-
user supplied text, describing the methods that
created the pixels.
Return Value
new id.
Exceptions
-
Copy the pixels to a new pixels, this is only the data object
and does not create a pixels object in the RawPixelsStore,
To load data into the plane the uploadPlane(long, DoubleArrayArray)
to add data to the pixels.
This operation is deprecated.
Parameters
- pixelsID
-
pixels id to copy.
- channelList
-
the list of channels to copy, this is the channel index.
- methodology
-
user supplied text, describing the methods that
created the pixels.
Return Value
new id.
Exceptions
-
long copyImage(long imageId, int x, int y, int t, int z, IntegerList channelList, string imageName) throws ServerError
Copy the image and it's attached pixels and
metadata to a new Image and return the id of the new image. The method
will not copy annotations or attachments.
This operation is deprecated.
Parameters
- imageId
-
image id to copy.
- x
-
width of plane.
- y
-
height of plane.
- t
-
The number of time-points
- z
-
The number of zSections.
- channelList
-
the list of channels to copy, 0-(sizeC-1).
- imageName
-
The image name.
Return Value
new id.
Exceptions
-
void uploadPlane(long pixelsId, int z, int c, int t, ::Ice::ByteSeq data) throws ServerError
Upload the plane to the server, on pixels id with channel and the
time, + z section. the data is the client 2d data values. This will
be converted to the raw server bytes.
This operation is deprecated.
Parameters
- pixelsId
-
pixels id to upload to .
- z
-
z section.
- c
-
channel.
- t
-
time point.
- data
-
plane data.
Exceptions
-
Update the pixels object on the server, updating appropriate tables in the
database and returning a new copy of the pixels.
This operation is deprecated.
Parameters
- object
-
see above.
Return Value
the new updated pixels.
Exceptions
-
Get a list of all the possible pixelsTypes in the server.
This operation is deprecated.
Return Value
see above.
Exceptions
-
Get the pixelsType for type of name type.
This operation is deprecated.
Parameters
- type
-
see above.
Return Value
see above.
Exceptions
-
Render the pixels for the zSection z and timePoint t.
This operation is deprecated.
Parameters
- pixelsId
-
pixels id of the plane to render
- z
-
z section to render
- t
-
timepoint to render
Return Value
The image as a buffered image.
Exceptions
-
Render the pixels for the zSection z and timePoint t.
This operation is deprecated.
Parameters
- pixelsId
-
pixels id of the plane to render
- z
-
z section to render
- t
-
timepoint to render
Return Value
The image as a buffered image.
Exceptions
-
Render the pixels for the zSection z and timePoint t.
This operation is deprecated.
Parameters
- pixelsId
-
pixels id of the plane to render
- z
-
z section to render
- t
-
timepoint to render
Return Value
The image as a 3d array where it represents the image as
xychannel
Exceptions
-
void setActive(long pixelsId, int w, bool active) throws ServerError
Set the active channels to be on or off in the rendering engine for
the pixels.
This operation is deprecated.
Parameters
- pixelsId
-
the pixels id.
- w
-
the channel
- active
-
set active?
Exceptions
-
Get the thumbnail of the image.
This operation is deprecated.
Parameters
- pixelsId
-
for pixelsId
- sizeX
-
size of thumbnail.
- sizeY
-
size of thumbnail.
Return Value
see above.
Exceptions
-
Get a set of thumbnails, of size X, Y from the list of pixelId's supplied
in the list.
This operation is deprecated.
Parameters
- sizeX
-
size of thumbnail.
- sizeY
-
size of thumbnail.
- pixelsIds
-
list of ids.
Return Value
see above.
Exceptions
-
Attach an image to a dataset.
This operation is deprecated.
Parameters
- dataset
-
see above.
- image
-
see above.
Exceptions
-
long createImage(int sizeX, int sizeY, int sizeZ, int sizeT, IntegerList channelList, model::PixelsType pixelsType, string name, string description) throws ServerError
Create a new Image of X,Y, and zSections+time-points. The channelList is
the emission wavelength of the channel and the pixelsType.
This operation is deprecated.
Parameters
- sizeX
-
width of plane.
- sizeY
-
height of plane.
- sizeZ
-
num zSections.
- sizeT
-
num time-points
- channelList
-
the list of channels to copy.
- pixelsType
-
the type of pixels in the image.
- name
-
the image name.
- description
-
the description of the image.
Return Value
new id.
Exceptions
-
Get the images from the dataset with name, this can use wild cards.
This operation is deprecated.
Parameters
- datasetId
-
see above.
- imageName
-
see above.
Return Value
see above.
Exceptions
-
Get the list of images with name containing imageName.
This operation is deprecated.
Parameters
- imageName
-
see above.
Return Value
see above.
Exceptions
-
Save the object to the db .
This operation is deprecated.
Parameters
- obj
-
see above.
Exceptions
-
Save and return the Object.
This operation is deprecated.
Parameters
- obj
-
see above.
Return Value
see above.
Exceptions
-
Save the array.
This operation is deprecated.
Parameters
- graph
-
see above.
Exceptions
-
Save and return the array.
This operation is deprecated.
Parameters
-
The Type to return.
- graph
-
the object
Return Value
see above.
Exceptions
-
Delete the object.
This operation is deprecated.
Parameters
- row
-
the object.(commonly a row in db)
Exceptions
-
Keep service alive.
This operation is deprecated.
Exceptions
-
