OmeTiffWrapper Class

Class representing an OME-TIFF file in a Vitessce dataset.

Details

OME-TIFF object wrapper class

Super class

vitessceR::AbstractWrapper -> OmeTiffWrapper

Public fields

img_path

A local filepath to an OME-TIFF file.

img_url

A remote URL of an OME-TIFF file.

name

The display name for this OME-TIFF within Vitessce.

transformation_matrix

A 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_bitmask

Whether or not this image is a bitmask.

is_remote

Whether or not this image is remote.

Methods

Public methods

• OmeTiffWrapper$new()

• OmeTiffWrapper$convert_and_save()

• OmeTiffWrapper$make_raster_routes()

• OmeTiffWrapper$make_image_def()

• OmeTiffWrapper$make_raster_file_def_creator()

• OmeTiffWrapper$create_image_json()

• OmeTiffWrapper$get_img_url()

• OmeTiffWrapper$clone()

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_path

A local filepath to an OME-TIFF file.

img_url

A remote URL of an OME-TIFF file.

name

The display name for this OME-TIFF within Vitessce.

transformation_matrix

A 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_bitmask

Whether or not this image is a bitmask.

...

Parameters inherited from AbstractWrapper.

use_physical_size_scaling

Whether 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_uid

The ID for this dataset.

obj_i

The 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_uid

The ID for this dataset.

obj_i

The 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_uid

The ID for this dataset.

obj_i

The index of this data object within the dataset.

base_url

The 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_uid

The ID for this dataset.

obj_i

The 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

deep

Whether to make a deep clone.