Step by step
- Add directories or files in image chooser view,
- Add peaksearch options,
- Launch peaksearch,
- View 3d peaks output.
- Display 2d peaks on the images.
- Save options in "outputfileName".xml.
Select 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.
Options
Add
peaksearch options. For each sample (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. To be analysed, peaksearch algorithm need contigues files.
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. 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
Launch
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 ( ), 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.
View 3D peaks: peaks_tXXXX.flt
In menu Peaksearch, select open 3D peaks file (.flt).
Two views open on the left pane of the workbench by default: the view with the plot and the view that displays information in a table.
Here, in the picture below, table 3d peaks view have been moved to the right pane of the workbench.
Plot view allows you to load other filtered peaks file ( called column file), :
You can also remove/ keep plots in the hidden options :
- Click on button "Edit", X and Y coordinate are displayed.
- Select dots you want to keep/remove using zoom, and click on buttons keep/remove.
- Don't forget to save changes with on the rigth corner of the view.
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 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".
Then in menu/preferences...peaksearch, browse your file "
yourOptionforMyPeaksearch.xml"
and apply. Next time, when you re-launch your application, your default options
are set in the fields. If you want to restore default peaksearch options, press
button "Restore Defaults" and apply.