Liberalize reg suffixes #36
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- Use the labels registered image suffix when finding the labels image during edge detection, allowing users to customize the selected labels image while continuing to fall back to the main annotation image - Allows users to not use any labels image by not supplying the `path_atlas_dir` argument and by setting the registered labels image suffix to an empty string
The registered "atlas" (intensity) image takes precedence over the main intensity image, but this main image will still be loaded even if the registered atlas image is set. This loading allows any metadata from the main image to be loaded, but loading the main image could also trigger an image import or load unintended metadata. As a simplification, skip loading the main image if a registered intensity image is specified.
Registered image suffixes have been assumed to be appended to the main image path. These suffixes are also currently the only way to load images as labels or borders. Occasionally, users may wish to load a labels image that is not registered to the main image, which the registered suffixes does not currently support. As a way to specify a non-registered path while still using the registered suffixes to load certain file types such as labels, load "registered suffixes" given as absolute paths directly, without modifying the path.
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MagellanMapper uses "registered image suffixes" for two main purposes:
atlasVolumefor the atlas intensity image registered to a sample image,annotationfor the registered atlas labels image)atlastype for the intensity image andannotationtype for the labels imageThese suffixes are accessed through the
--reg_suffixescommand-line flag or the "Intensity" and "Labels" selection controls in the "Registered Images" section of the GUI. Registered images are identified by a base image path to which these suffixes are appended. Filenames given in the GUI are deconstructed if possible to these base and suffix components, and starting in v1.4, the same occurs for files given by command-line.Occasionally, users may wish to load a labels image not registered to the main image, which the registered suffixes does not support. As a way to specify a non-registered path while still using the registered suffixes to load certain file types such as labels, this PR allows registered suffixes to be given as absolute paths and loaded directly, without modifying the path.
Also, an image loaded as a registered "atlas" (intensity) image takes precedence over the main intensity image, but this main image will still be loaded even if the registered atlas image is set. This loading allows any metadata from the main image to be loaded, but loading the main image could also trigger an image import or load unintended metadata. As a simplification, this PR skips loading the main image if a registered intensity image is specified.
Many of the atlas-related functions have assumed that certain registered suffixes are used, but we are slowly making these suffixes customizable through the CLI flag. This PR adds supports for this customization in the edge detection task.