The main window is divided into 3 main parts :
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On the top we find Menu bar with actions followed by the coolbar to launch peaksearch (same action launcher in options view). |
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Status bar at the bottom of the framework displays running jobs |
To move views, set mouse focus on the title of the view, press left button on the mouse and move the view as you want in the main layout or outside.
NAME | DESCRIPTION | MOVABLE | DETACHABLE | CLOSABLE |
IMAGE CHOOSER VIEW | Select images as input stem for peaksearch. Belongs to peaksearch perspective | Yes | No | No |
CONSOLE VIEW | Displays Fable GUI output message. Belongs to peaksearch perspective | Yes | Yes | No |
OPTIONS VIEW | Options for peaksearch. Built with an xml options file for peaksearch.py. Belongs to peaksearch perspective | Yes | Yes | No |
2D PEAK VIEW | Peaksearch output. Peaks.spt by default. Contains 2d peaks for each treshold ; Opened from menu Peaksearch/Open 2D peaks file(.spt) | Yes | Yes | Yes |
3D PEAK VIEW | Peaksearch output, Peaks_tvalue.flt by default. One filtered file per treshold; opened in the end of peaksearch or from menu Peaksearch/Open 3D peaks file(.flt) | Yes | Yes | Yes |
Files loaded have the same extension as set in Fabio files preferences. For example, if you have set only "tif" as file extension, only tiff files are loaded in the table.
This group contains sample on which peaksearch is going to be applied. This group is divided into 2 parts:
The same functionalities are available by selecting an item in table and right clicking : a menu appears with 'remove item'.
NAME | OPTION (python side) | DESCRIPTION | VARIABLE | REQUIRED | FIELD TYPE | |
Stem | -n, --namestem=Stem | Attempt stem for peaksearch. By default, the stem of first file loaded in the current sample (see sample chooser) is set by default. | Yes | Yes | Alphanumeric | |
Format | -F, --format=.edf | File format for peaksearch | Yes | Yes | Alphanumeric | |
First | -f, --first=0 | First file to process for the selected sample | Yes | Yes | Numeric | |
Last | -l, --last=Last | Last file to process for the selected sample | Yes | Yes | Numeric | |
Outfile | -o, --outfile=Peaks.spt | 2D peaks output file name. One output per selected sample/directory | Yes | Yes | Alphanumeric | |
nDigits | --ndigits=NDIGITS | Number of digits in file numbering | Yes | No | Numeric | |
DarkFile | -d, --darkfile=image | Browse a file to subtract dark. Program available in peaksearch. No control is done to check image size in the GUI | No | No | File | |
DarkFileOffset | -D, --darfileoffset=100 | Constant to subtract from dark to avoid overflows, default=100 | No | No | Decimal | |
SplineFile | -s, --spline=/data/opid11/inhouse/Frelon2K/spatial2k.spline | Browse a file to make spline on samples files. | No | No | File | |
Perfect image | -p, --perfect_image=N | Ignore spline Y|N, default=N | No | No | Boolean | |
Flood | -O, --flood | Browse a file to make a flood on samples files. Program available in peaksearch. No control is done to check image size in the GUI | No | No | File | |
Tresholds | -t, --tresholds=[500, 2000] | In text fields, seperate treshold values with a ','. You can use fable-imageviewer to get treshold values for your images | No | Yes | Floats, separated by ',' | |
OmegaFromHeader | --OmegaFromHeader | Read Omega values from headers | No | No | Boolean | |
OmegaOverRide | --OmegaOverRide | Override Omega values from headers | No | No | Boolean | |
Step | -S, --step=OmegaStep | Step size in Omega when you have no header info | No | No | Decimal | |
Start | --start=OMEGA | Start position in Omega when you have no header info | No | No | No | Decimal |
Use :