OmeTiffWrapper: OmeTiffWrapper Class
In vitessce/vitessce-htmlwidget: Create Interactive Single-cell Visualizations with the 'Vitessce' JavaScript Library
OmeTiffWrapper R Documentation
OmeTiffWrapper Class
Description
Class representing an OME-TIFF file in a Vitessce dataset.
Details
OME-TIFF object wrapper class
Super class
vitessceR::AbstractWrapper -> OmeTiffWrapper
Public fields
img_pathA local filepath to an OME-TIFF file.
img_urlA remote URL of an OME-TIFF file.
nameThe display name for this OME-TIFF within Vitessce.
transformation_matrixA column-major ordered matrix for transforming
this image (see http://www.opengl-tutorial.org/beginners-tutorials/tutorial-3-matrices/#homogeneous-coordinates for more information).
is_bitmaskWhether or not this image is a bitmask.
is_remoteWhether or not this image is remote.
Methods
Public methods
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Inherited methods
vitessceR::AbstractWrapper$auto_view_config()vitessceR::AbstractWrapper$get_file_defs()vitessceR::AbstractWrapper$get_local_dir_route()vitessceR::AbstractWrapper$get_local_dir_url()vitessceR::AbstractWrapper$get_local_file_route()vitessceR::AbstractWrapper$get_local_file_url()vitessceR::AbstractWrapper$get_out_dir()vitessceR::AbstractWrapper$get_out_dir_route()vitessceR::AbstractWrapper$get_route_str()vitessceR::AbstractWrapper$get_routes()vitessceR::AbstractWrapper$get_url()vitessceR::AbstractWrapper$get_url_simple()
Method new()
Create a wrapper around multiple image objects.
Usage
OmeTiffWrapper$new(
img_path = NA,
img_url = NA,
name = "",
transformation_matrix = NA,
is_bitmask = FALSE,
...
)
Arguments
img_pathA local filepath to an OME-TIFF file.
img_urlA remote URL of an OME-TIFF file.
nameThe display name for this OME-TIFF within Vitessce.
transformation_matrixA column-major ordered matrix for transforming
this image (see http://www.opengl-tutorial.org/beginners-tutorials/tutorial-3-matrices/#homogeneous-coordinates for more information).
is_bitmaskWhether or not this image is a bitmask.
...Parameters inherited from AbstractWrapper.
use_physical_size_scalingWhether or not to scale the image based on the physical size metadata stored in the file.
Returns
A new OmeTiffWrapper object.
Method convert_and_save()
Create the web server routes and file definition creators.
Usage
OmeTiffWrapper$convert_and_save(dataset_uid, obj_i, base_dir = NA)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Method make_raster_routes()
Create a list representing the server routes.
Usage
OmeTiffWrapper$make_raster_routes(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A list of server route objects.
Method make_image_def()
Create an object representing a single image in a raster.json list of images.
Usage
OmeTiffWrapper$make_image_def(dataset_uid, obj_i, base_url)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
base_urlThe base URL for the server.
Returns
A list that can be converted to JSON.
Method make_raster_file_def_creator()
Make the file definition creator function for the raster data type.
Usage
OmeTiffWrapper$make_raster_file_def_creator(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A file definition creator function which takes a base_url parameter.
Method create_image_json()
Usage
OmeTiffWrapper$create_image_json(img_url, offsets_url = NA)
Method get_img_url()
Usage
OmeTiffWrapper$get_img_url(base_url = "", dataset_uid = "", obj_i = "")
Method clone()
The objects of this class are cloneable with this method.
Usage
OmeTiffWrapper$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
vitessce/vitessce-htmlwidget documentation built on Oct. 12, 2024, 11:46 p.m.
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| OmeTiffWrapper | R Documentation |
OmeTiffWrapper Class
Description
Class representing an OME-TIFF file in a Vitessce dataset.
Details
OME-TIFF object wrapper class
Super class
vitessceR::AbstractWrapper -> OmeTiffWrapper
Public fields
img_pathA local filepath to an OME-TIFF file.
img_urlA remote URL of an OME-TIFF file.
nameThe display name for this OME-TIFF within Vitessce.
transformation_matrixA column-major ordered matrix for transforming this image (see http://www.opengl-tutorial.org/beginners-tutorials/tutorial-3-matrices/#homogeneous-coordinates for more information).
is_bitmaskWhether or not this image is a bitmask.
is_remoteWhether or not this image is remote.
Methods
Public methods
Inherited methods
vitessceR::AbstractWrapper$auto_view_config()vitessceR::AbstractWrapper$get_file_defs()vitessceR::AbstractWrapper$get_local_dir_route()vitessceR::AbstractWrapper$get_local_dir_url()vitessceR::AbstractWrapper$get_local_file_route()vitessceR::AbstractWrapper$get_local_file_url()vitessceR::AbstractWrapper$get_out_dir()vitessceR::AbstractWrapper$get_out_dir_route()vitessceR::AbstractWrapper$get_route_str()vitessceR::AbstractWrapper$get_routes()vitessceR::AbstractWrapper$get_url()vitessceR::AbstractWrapper$get_url_simple()
Method new()
Create a wrapper around multiple image objects.
Usage
OmeTiffWrapper$new( img_path = NA, img_url = NA, name = "", transformation_matrix = NA, is_bitmask = FALSE, ... )
Arguments
img_pathA local filepath to an OME-TIFF file.
img_urlA remote URL of an OME-TIFF file.
nameThe display name for this OME-TIFF within Vitessce.
transformation_matrixA column-major ordered matrix for transforming this image (see http://www.opengl-tutorial.org/beginners-tutorials/tutorial-3-matrices/#homogeneous-coordinates for more information).
is_bitmaskWhether or not this image is a bitmask.
...Parameters inherited from
AbstractWrapper.use_physical_size_scalingWhether or not to scale the image based on the physical size metadata stored in the file.
Returns
A new OmeTiffWrapper object.
Method convert_and_save()
Create the web server routes and file definition creators.
Usage
OmeTiffWrapper$convert_and_save(dataset_uid, obj_i, base_dir = NA)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Method make_raster_routes()
Create a list representing the server routes.
Usage
OmeTiffWrapper$make_raster_routes(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A list of server route objects.
Method make_image_def()
Create an object representing a single image in a raster.json list of images.
Usage
OmeTiffWrapper$make_image_def(dataset_uid, obj_i, base_url)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
base_urlThe base URL for the server.
Returns
A list that can be converted to JSON.
Method make_raster_file_def_creator()
Make the file definition creator function for the raster data type.
Usage
OmeTiffWrapper$make_raster_file_def_creator(dataset_uid, obj_i)
Arguments
dataset_uidThe ID for this dataset.
obj_iThe index of this data object within the dataset.
Returns
A file definition creator function which takes a base_url parameter.
Method create_image_json()
Usage
OmeTiffWrapper$create_image_json(img_url, offsets_url = NA)
Method get_img_url()
Usage
OmeTiffWrapper$get_img_url(base_url = "", dataset_uid = "", obj_i = "")
Method clone()
The objects of this class are cloneable with this method.
Usage
OmeTiffWrapper$clone(deep = FALSE)
Arguments
deepWhether to make a deep clone.
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