In the Graphical user interface, peaksearch can be processed on one directory or more. If you want to process more than one directory, you must add directories in Image Navigator. Or you can search peaks by setting the stem with the correct file path in the field stem. Warning : if you have already files/directories loaded in the Image Navigator, these files are taken in account only. You can' t do the second option if you have files in the navigator.

Step by step

  1. Add directories or files in image chooser view, or set stem of the files to process directly in peaksearch option view with the correct path,
  2. Add peaksearch options,
  3. Launch peaksearch,
  4. View 3d peaks output.
  5. Display 2d peaks on the images.
  6. Save options in "outputfileName".xml.

1. Which stem?

As mentionned previously, you can either search peaks on several directories, or only on one directory (one stem). The second option is like launching peaksearch with a command line.

Peak search on several directories

In image chooser view, click on "Add directory..." and select a directory containing files.
Files are loaded in the table (right pane) with their corresponding stem on the left pane.
Only files with extension set in menu "preferences.../ fabio" are loaded ;

You can add several directories to launch peaksearch WITH THE SAME options for all of them EXCEPT for the stem, file format first and last which vary for each sample(see section fields in user interface)

If python modules are correctly installed, header keys of image files are set in the list 'Header keys'.
To get header key values of you samples, select a key in the list and press button.
A new column with the key values is displayed in the table.
You can sort ascendant/descendant columns : click on column header you want to sort (desc by default).

To remove a column added (you can not remove the two firsts column #, name ( is disabled if you try)), select the column header, and click on , now not disabled.

Peak search on one stem

Load the files/directory to peaksearch in the navigator, or remove all the directories in the navigator and goes to step 2.

2. Options

Use imageViewer plot to see which files belongs too which scan (one run) if you have several scans in you directory, otherwhise its non sens.
To be analyzed, peaksearch algorithm need contigues files.

Case 1 : Several directories

For each scan (select one sample after another in sample chooser view), set a stem, the first file of the scan, and the last file of the scan. The other options are common for all directories.
Other fields are common to each sample of sample chooser view. To fill your fields, for example stem, you can drag and drop an item from the table in sample chooser to text field

Case 2 : One scan

You have no images in image navigator. Set the stem as you would have done in the command line.
Stem option: Example
You want to search peaks on files filestem_00.img to filestem_99.img.
Current image file directory is : ~home/usr/user1/data Fable application runs in ~home/usr/user1/ Stem should be set with the full path or relative to fable current directory. You can set stem like the followinf two examples, if fable is not running in current image directory (no workspace directory):
  1. ~home/usr/user1/data/filestem
  2. ./data/filestem

3. Launch yellow arrow

If all options are right (required fields, values are correct), launch peaksearch. If you can't, an error message is displayed in the console view. When peaksearch is running (red square ), you can view python program output in a java console (see screen shot).

Once peaksearch has finished, you can open the results files filtered peaks file (.flt) and 2peaks file (.spt) from the menu peaksearch.

4. Output files

One Peaksearch produces two types of output files in the output directory :
Output directory is stem current directory : flt and spt files are generated in images files directory. To create these output file in a different directory, set the path of the directory to outfile name (can be relative to file directory).
Outfile option: Example
Current image file directory is : ~home/usr/user1/data You have a sub directory in data directory : TotalCryst where you want to have your peaks_t###.flt and peaks.spt output file. In field outfile, set one of these two path in outfile:
  1. ./TotalCryst/peaks
  2. ~home/usr/user1/data/TotalCryst/peaks

Display 3D peaks (peaks_tXXXX.flt) : Open 3D peaks editor

In menu Peaksearch, select open 3D peaks file (.flt). Two editors open on the left pane of the workbench by default: one plots data and the other displays data in a sort table. See screenshot below.

These editors allow you to remove/ keep plots in the plot with options "Plot editor", or with a right click in the other editor to display a popup menu :

You can save changes with button save column file in the toolbar if the editor is active, or select File/save. You can "Save as" too.

View 2D peaks: peaks.spt

This view presents peaksearch output file in a grid with file names on the left side and selected file peaks on the right. When you select a file, imageviewer displays the image and its peaks in red squares (increase or decrease their default size of 3 if you want in the image view). By default, all the peaks of the selected file are displayed (all checked). You can hide one or several peaks displayed in the image by unchecking action (available with rigth click too...). Selected peaks in the grid are colored in green.

Note: Select gray scale on imageView if you want to view peaks (red/green squares) found by peaksearch.

Save your peaksearch options

When you open peaksearch, default options are set in text fields. But you can save you own.
Options are saved in an xml file :
Select menu Edit/save options. And save "yourOptionforMyPeaksearch.xml".
To load this file and options saved, select Menu Peaksearch/Options ....load options, or click on available in the toolbar of "Options view".

Preferences

To use options values for several analysis, you can set the files in the preferences so that you options will be set in options view when you launch application again.
in menu/preferences...peaksearch, browse your file "yourOptionforMyPeaksearch.xml" and apply.
If you want to restore default peaksearch options, press button "Restore Defaults" and apply available in Peaksearch preferences preferences.