This is the default PeakSearch perspective:
The above layout is as it appears on a relatively small notebook. It will be less crowded on a larger screen. You can change this layout in many ways as described in the Workspace section in the Fable help.
The Navigator is to the right. You can organize your projects there. See the Workspace section in the Fable help for more information. The PeakSearch Options View is in the middle. This is where you open and save files, set your parameters, and run. The editor area is to the left, showing a ColFile Editor editing a .flt file. All of the open Fable editors appear in this area, represented by tabs. For more information on managing the editor area see the Workspace section in the Fable help. The Console is at the bottom. This is where the output appears while Peaksearch is running.
To move views, drag the view tab with the mouse and move the view as you want in the workspace. Double clicking the tab will cause the view to occupy the entire workspace. If you right click on the view tab, you will get a context menu showing other options, including detaching the view from the workbench.
You can do much the same with editors, but they must remain in the editor area.
Name | Description |
Image Navigator View | Select images as input for PeakSearch. |
Console view | Displays Fable GUI output messages. Appears in the PeakSearch perspective by default. |
PeakSearch Options View | Options for PeakSearch. Built with an XML options file for peaksearch.py. Appears in the PeakSearch perspective by default. |
PeakSearch SPT View | Peaksearch .spt output. peaks_t<value>.spt by default. Contains 2D peaks for each threshold. Opened from menu Open 2D Peak File (.spt) or from the Open With (Other) context menu in the Navigator. |
ColFile Editor | Peaksearch .flt output, peaks_t<value>.flt by default. Opened from menu Open 3D Peak File (.flt) or by double clicking a .flt file in the Navigator or from the Open With (Other) context menu in the Navigator. |
This view allows you to select directories and files for your data analysis. It contains five parts, described below.
These are the five parts:
Title Bar Buttons and MenuThere are buttons
to add directories or files on the right corner of the view . Once you have selected a directory or a file, the table is filled with directories on the left side and files on the right.
Files loaded have the only those extensions as set in Fabio Files Preferences. For example, if you have set only "tif" as a file extension, only TIFF files are loaded in the table.
Header KeysOnce you have loaded a file and/or a directory, this list contains all header keys in the active file. You can add or remove keys using the buttons to the right. To remove a key from the table, select the item and click on the remove button. This button is not active for the two first items (Typically # and Name).
File Name FilterUse the file name filer to apply or remove a filter on an active directory in the table. This will cause it to display only files containing the filter entered. Use the buttons to the right to apply or stop applying the filter,
TableThe table is divided into two parts :
You can right click on the items on either side to get a context menu with additional choices.
Lower ButtonsThis is the main view for running PeakSearch.
The view title bar includes buttons for loading and saving XML Options Files, for restoring default values, and for running Peaksearch. Note that the XML file includes both values and defaults. The default values are reset when you run, so reset does not necessarily take you back to the original defaults in the file. You can reload the file to do that. In the same way, when you save, the defaults that get saved are the current values.
There is also a drop-down menu with the same actions as the buttons, plus a Help item.
The top part contains two controls that belong to the GUI and not to the Peaksearch Python application. The first is the name of the XML options file. This field will be filled in automatically when you open an XML options file through the various means provided, including via the PeakSearch menu, right clicking a file in the Navigator and then using Open With (Other), or by dragging an XML options file from the Navigator. You can also type in a name and hit enter, or use the Browse button.
The second is the checkbox that determines whether you want to link to the Image Navigator or not, as described in Getting Started.
The remaining controls or fields are options for the Python Peaksearch application. You can get a listing and summary of the available options by selecting PeakSearch | Options | PeakSearch Command-Line Options. This summary comes from the Peaksearch application and is likely to be more up to date than this manual.
When you drag the mouse over most of the text fields, a tool tip text appears. For choice buttons, the tool tip is on the group title for the buttons. You can use drag and drop for most of the text fields.
In most cases you can use forward slashes for directory separators, even on Windows. An example is the Workdir specification in the screen shot above. Note, however, that if you do this with the stem, then on Windows the forward slashes may be mixed with backslashes in the file names in the .spt file.
The table below describes options from the PeakSearch GUI point of view. The Field Type is a property of the PeakSearch GUI and is not necessarily linked to the Peaksearch Python application. Variable means values passed to Peaksearch may vary for each sample, whereas others are common for all samples loaded in the Image Navigator.
NAME | PYTHON OPTION | 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, --darkfileoffset=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, separate threshold values with a ','. You can use the Fable ImageViewer to get threshold 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 |
Workdir | [--w=dir, possibly in the future] | Working directory. Same as doing cd before running Peaksearch. | No | No | Directory | Directory |
The Console prints out messages in different colors for:
Like with all Fable Consoles, you can use the tool bar options to clean, resize, lock scroll, etc. (see Graphical User Interface.)
Preferences are available from Window | Preferences. These allow you to customize your workbench. There are several preferences relevant to PeakSearch.
You can specify the default XML options file. This file contains the options you see when no file or sample has yet been loaded. By default this is an internal file supplied with PeakSearch. It has the defaults from the Peaksearch Python application, as well as the proper configuration for the PeakSearch GUI. You can specify another file that you have saved with the values you normally use. You can revert to the internal file by selecting Reset.
Keep in mind that the XML file also contains the configuration information, so be sure the file you use has been saved correctly from the internal default. In the event that new options have been added since you saved your file, then the defaults from the internal file will be used for those options. When you next save the file, those previously missing options will be in it.
You can also specify in Preferences whether to link with the Image Navigator by default or not. You should set this to your usual mode of operation in order to not have to check the box in the PeakSearch Options View each time.
This preference allows you to set the file extensions you want to load in the Image Navigator. By default most of the file extensions Fabio can read are listed in the table.