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happy-data-viewer

Used for viewing data that has been converted into a HAPPy folder structure.

  • File

    • Open dir: for opening HAPPy directories
    • Export image: for exporting the currently displayed image
    • Close: closes the application

  • View

    • Normalization: allows entering the command-line of another normalization plugin to change how the fake RGB is being generated.
    • Zoom: allows the setting of the zoom level

  • Window

    • New window: starts a new Viewer process, using the same options that the current one was started with
    • Half width: resizes the window to half of the screen width, useful when comparing two scans horizontally
    • Half height: resizes the window to half of the screen height, useful when comparing two scans vertically

  • Help: These menu items open browser windows with relevant pages.

Screenshots#

Here is an example of a directory containing several samples:

Data Viewer with sample loaded

When available, a mask can be overlaid with the appropriate opacity:

Data Viewer with mask overlaid

Command-line#

usage: happy-data-viewer [-h] [--base_folder BASE_FOLDER] [--sample SAMPLE]
                         [--region REGION] [-r INT] [-g INT] [-b INT] [-o INT]
                         [--listbox_selectbackground LISTBOX_SELECTBACKGROUND]
                         [--listbox_selectforeground LISTBOX_SELECTFOREGROUND]
                         [--normalization PLUGIN] [--zoom PERCENT]
                         [-V {DEBUG,INFO,WARNING,ERROR,CRITICAL}]

Viewer for HAPPy data folder structures.

optional arguments:
  -h, --help            show this help message and exit
  --base_folder BASE_FOLDER
                        Base folder to display (default: None)
  --sample SAMPLE       The sample to load (default: None)
  --region REGION       The region to load (default: None)
  -r INT, --scale_r INT
                        the wave length to use for the red channel (default:
                        None)
  -g INT, --scale_g INT
                        the wave length to use for the green channel (default:
                        None)
  -b INT, --scale_b INT
                        the wave length to use for the blue channel (default:
                        None)
  -o INT, --opacity INT
                        the opacity to use (0-100) (default: None)
  --listbox_selectbackground LISTBOX_SELECTBACKGROUND
                        The background color to use for selected items in
                        listboxes (default: #4a6984)
  --listbox_selectforeground LISTBOX_SELECTFOREGROUND
                        The foreground color to use for selected items in
                        listboxes (default: #ffffff)
  --normalization PLUGIN
                        the normalization plugin and its options to use
                        (default: norm-simple)
  --zoom PERCENT        the initial zoom to use (%) or -1 for automatic fit
                        (default: -1)
  -V {DEBUG,INFO,WARNING,ERROR,CRITICAL}, --logging_level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
                        The logging level to use. (default: WARN)