Mask Editor GUI is intended to manually create/edit mask of bad pixels and save it as 2-d image and 3-d array shaped as data.

Content

Launch Mask Editor

Mask Editor GUI can be launched in lcls2 software release (>ps-4.6.0) by command

masked

with(out) optional parameters as explained in help

masked -h

masked -h command dump on 2023-10-01

ps-4.6.0 [dubrovin@sdflogin002:~/LCLS/con-lcls2/lcls2]$ masked -h
usage: Usage:
  masked -a <fname-nda.npy> -k <DataSource-kwargs> -d <detector> -g <fname-geometry.txt> [-L <logging-mode>] [...]

Help:
  masked -h

Examples:
  masked  # set all parameters using GUI
  masked -d epix10ka_000001                          # takes geometry from detector DB
  masked -d epix10ka_000001 -k exp=ueddaq02,run=569  # takes geometry from experiment DB
  masked -g /sdf/group/lcls/ds/ana/detector/data2_test/geometry/geo-epix10kaquad-tstx00117.data  # takes geometry from file
  masked -a /sdf/group/lcls/ds/ana/detector/data2_test/misc/epix10kaquad-meclv2518-0101-CeO2-ave.npy  # takes array for image from file
  masked -a /sdf/group/lcls/ds/ana/detector/data2_test/misc/epix10kaquad-meclv2518-0101-CeO2-ave.npy -g /sdf/group/lcls/ds/ana/detector/data2_test/geometry/geo-epix10kaquad-tstx00117.data
  masked -d epix10ka_000001 -a /sdf/group/lcls/ds/ana/detector/data2_test/misc/epix10kaquad-meclv2518-0101-CeO2-ave.npy
  masked -d epix10ka_000001 -k exp=ueddaq02,run=569 -a /sdf/group/lcls/ds/ana/detector/data2_test/misc/epix10kaquad-meclv2518-0101-CeO2-ave.npy

masked - command opens mask editor GUI

positional arguments:
  posargs               list of positional arguments: [<fname-nda.npy>] [<fname-geometry.txt>], default = []

optional arguments:
  -h, --help            show this help message and exit
  -a NDAFNAME, --ndafname NDAFNAME
                        image array file name*.nda, default = Select
  -d DETNAME, --detname DETNAME
                        detector name, default = Select
  -k DSKWARGS, --dskwargs DSKWARGS
                        string of comma-separated (no spaces) simple parameters for DataSource(**kwargs), ex: exp=<expname>,run=<runs>,dir=<xtc-dir>, ..., or <fname.xtc> or
                        files=<fname.xtc> or pythonic dict of generic kwargs, e.g.: "{'exp':'tmoc00318', 'run':[10,11,12], 'dir':'/a/b/c/xtc'}", default = Select
  -g GEOFNAME, --geofname GEOFNAME
                        geometry description constants file name *.txt, *.data, default = Select
  -L LOGMODE, --logmode LOGMODE
                        logging mode, one of CRITICAL, FATAL, ERROR, WARN, WARNING, INFO, DEBUG, NOTSET, default = INFO
  -o DIRREPO, --dirrepo DIRREPO
                        repository for files, default = ./repo-masked
  --ctab CTAB           color table index in range [1,8], default = 3
  --dirmode DIRMODE     directory access mode, default = 0o2775
  --filemode FILEMODE   file access mode, default = 0o664
  --group GROUP         group ownership for all files, default = ps-users
  --savelog             On/Off saving log file, default = 1

Mask Editor GUI main window

Mask Editor main window consists of sub-panels listed in this section with brief description of their functionality.

Image with axes and cursor info panel

Image nested in center of the main window.

Displays assembled image of the detector or stack of panels if geometry constants are not available. Click and drag or scroll mouse on image to translate or zoom-in/out desired part of the image. At mouse release spectrum will be updated. for visible part of the image. The same operation on axis works for appropriate transformation of its dimension, changing aspect ratio.

Spectrum with statistical data

Spectral widget is displayed on the right side of the image.

It shows spectral histogram of the visible part of the image, color bar, two axes, and statistical panel on the top.

Click and drag or scroll mouse on spectrum to select its part projected on color map on image. The same works for vertical axis. Horizontal scale does the same things for histogram scale. At mouse release image will be updated.

Color bar selection

Color bar maps intensity values to color map used on image. There are eight pre-defined color maps currently available.

To change color map - click on color bar and select color map/bar from pop-up window. The color bar and Image will be updated after selection is done.

Logger

Most important info messages are displayed in the logger window located in the bottom part of the main window. By default it has low profile, but can be expanded by mouse using expansion mark on the top boarder of the logger window.

Control panel

Control panel with multiple fields allows to set imaging array and geometry constants from DB or files.

Select DB parameters

After click on the button next to DataSource: label a bunch of sequentially pop-up windows for instrument, experiment, and run number allows to set DB parameters. To terminate selection - click on highlighted-yellow title.

Select detector

After click on the button next to Detector: label pop-up menu window allows to select detector from specified DB

If geometry is available for specified DataSource and Detector the field next to geo DB will be filled out automatically.

If many geometry constants available for specified detector, click on button next to geo DB: label and select desired constants from pop-up menu window.

Select files

Use standard dialog to select I/O files

More fields

Switching button More/Less shows more or less control field between default and advanced modes. It adds fields to load geometry constants from file (button next to label geo:) and array (button next to label array DB:) for image from DB constants.

ROI control buttons

Control buttons for ROI are stacked in menu on the left side of the main window. Their functionality is described below.

Translate and zoom image

Click on Image mode button, then click and drag or scroll mouse for translation or zooming image, respectively. At release mouse button spectrum will be updated for visible part of the image.

Add ROI

Click on Add button and select ROI type from pop-up menu:

Available shapes of ROIs are self-explaining in this pop-up menu.

Adding ROI

Right after selected ROI type click on image to mark ROI control point locations as many times as it is necessary to define particular ROI shape.

Add/Remove PIXEL and PIXGROUP

Right after click on Add button and selection of PIXEL or PIXGROUP ROI, start clicking on desired pixels or click-hold-and-pan. Added pixels will be marked by color. Double click removes appropriate pixel. Input of the PIXGROUP is compleated by the click on Compl.(ete) button.

Button Cancel

Button Cancel cancels adding of non-compleated ROI if it is not too late...

Button Compl.

Button Compl. completes adding of ROI with multi-point definition like PIXGROUP and POLYGON.

Select and Delete ROIs

Currently Select mode is used in combination with Delete in order to preview deleting ROI.

Click on Select button, then on ROIs to select. Selected items will change color.

PIXEL type ROI will be selected one-by-one. PIXGROUP ROI will be selected as whole by a single click.

Invert bad pixel region

Click on button Invert then select ROIs to invert region of good/bad pixels. By default internal region of each ROI is marked as bad pixels. Operation Invert inverts this definition.

Edit mode

Click on Edit button, then on ROIs to edit. Selected for edition ROI changes color and shows control handle. Then, click and pan control handles to translate, resize or rotate ROIs.