GUI

The main window is divided into 3 main parts :

  1. Image chooser : This viewallows user to select directories/files for peaksearch,
  2. Peaksearch View (options view): This is the option view,
  3. Console, this console displays output message.

On the top we find Menu bar with actions followed by the coolbar to launch peaksearch (same action launcher in options view).

  • Menu File/
    • Exit : Close Peaksearch window
  • Menu Edit/
  • Menu Help/
    • About: opens about peaksearch dialog box
    • Help contents: opens this on line help

Status bar at the bottom of the framework displays running jobs

Views

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.

NAMEDESCRIPTIONMOVABLEDETACHABLECLOSABLE
IMAGE CHOOSER VIEWSelect images as input stem for peaksearch. Belongs to peaksearch perspectiveYesNoNo
CONSOLE VIEWDisplays Fable GUI output message. Belongs to peaksearch perspectiveYesYesNo
OPTIONS VIEWOptions for peaksearch. Built with an xml options file for peaksearch.py. Belongs to peaksearch perspectiveYesYesNo
2D PEAK VIEWPeaksearch output. Peaks.spt by default. Contains 2d peaks for each treshold ; Opened from menu Peaksearch/Open 2D peaks file(.spt) YesYesYes
3D PEAK VIEWPeaksearch 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)YesYes Yes

Image chooser view


This view allows you to select directories and files for you data analysis. This view contains 4 parts :
  1. Buttons to add directories or files on the right corner of the view : once you have select a directory or a file, table is filled with a new directory on the left side and lists files.

    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.

  2. Header keys: Once you have loaded a file and/or a directory, this list contains all header key of the active file. You can display its value by adding it in the table : click on add (or double click on the selected key.
    To remove a key added in the table, select the column and click on remove button.(). This button is not active for the two firsts column (# and name).
  3. File name filer: apply or remove a filter on an active directory in the table to display only files with the string.
  4. Table ; this table is divided into two parts :

This group contains sample on which peaksearch is going to be applied. This group is divided into 2 parts:

Header keys

This list is loaded with keys found in the header of first file loaded.

Table

  1. Sample pane: left side
  2. files pane: right side

Remove buttons

These buttons are available under the table.
These buttons allow you to remove a sample from the list of the selected samples for the left button, or to remove one or more selected files in the file list for right button remove. No directory or files are removed from your disk.

The same functionalities are available by selecting an item in table and right clicking : a menu appears with 'remove item'.

Peaksearch View (options view)

Add peaksearch options here.

Fields

When user drag the mouse over the fields, a tooltip text appears. From Sample chooser to Options view, you can use drag and drop to help in adding a stem with the (complicated) file name.
Table bellow describes text fields from fable GUI point of view.
There is no link between fields type described in table and peaksearch options types.
Column variable means values passed to peaksearch options vary for each sample, whereas others are common for all samples loaded in sample chooser view.

NAMEOPTION (python side)DESCRIPTIONVARIABLEREQUIREDFIELD TYPE
Stem-n, --namestem=StemAttempt stem for peaksearch. By default, the stem of first file loaded in the current sample (see sample chooser) is set by default.YesYesAlphanumeric
Format-F, --format=.edfFile format for peaksearchYesYesAlphanumeric
First-f, --first=0First file to process for the selected sampleYesYesNumeric
Last-l, --last=LastLast file to process for the selected sampleYesYesNumeric
Outfile-o, --outfile=Peaks.spt2D peaks output file name. One output per selected sample/directoryYesYesAlphanumeric
nDigits YesNoNumeric
DarkFile-d, --darkfile=imageBrowse a file to subtract dark. Program available in peaksearch. No control is done to check image size in the GUINoNoFile
DarkFileOffset-D, --darfileoffset=100Constant to subtract from dark to avoid overflows, default=100 NoNoDecimal
SplineFile-s, --spline=/data/opid11/inhouse/Frelon2K/spatial2k.spline Browse a file to make spline on samples files.NoNoFile
Perfect image-p, --perfect_image=NIgnore spline Y|N, default=N NoNoBoolean
Flood-O, --floodBrowse a file to make a flood on samples files. Program available in peaksearch. No control is done to check image size in the GUINoNoFile
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
NoYesFloats, separated by ','
OmegaFromHeader''''NoNoBoolean
OmegaOverride'' '' NoNoBoolean
Step-S, --step=OmegaStepStep size in Omega when you have no header info NoNoDecimal
Start--start=OMEGA Start position in Omega when you have no header info NoNoNoDecimal


Console


Console prints out messages : Like all fable console, you can use tool bar option to clean, resize, lock scroll ....you console. (see fable user interface)

Preferences


Preferences are available from menu Edit/preferences. Setting preferences allows you to find your peaksearch options each time you relauch the graphical user interface.

Peaksearch

For peaksearch, we are using an xml files that allows:

Fabio files

This preferences allows you to set the files type you want to load in image chooser.
By default all files extension fabio may read are listed in the table.

Use :