peak-o-mat documentation

Customising peak-o-mat

«  The modules   ::   Contents   ::   Scripting peak-o-mat  »

Customising peak-o-mat

All customisation data has to be saved in the peak-o-mat configuration folder which is located at $HOME/.peak-o-mat on UNIX-type systems (linux and OSX) or in %UserProfile%\AppData\peak-o-mat on windows (see http://en.wikipedia.org/wiki/Home_directory). Note that the AppData folder (or e.g. ‘Anwendungsdaten’ in german) is usually a hidden folder.

Config file

Upon start peak-o-mat looks for a configuration file config.py. An example config.py file looks like the following:

# if fast_display is True, only fast_max_pts points of all sets but the
# active one are shown
fast_display = False
fast_max_pts = 500

# truncate the data upon import
truncate = False
truncate_max_pts = 2000
truncate_interpolate = False

# set to True if the floating point is ',' (e.g. german windows)
# this affects the data import and export
floating_point_is_comma = False

Adding custom peak shapes

On startup peak-o-mat imports the python module userfunc.py from the configuration folder. Put your own function definitions there according to the following scheme:

import numpy as np
from peak_o_mat import peaksupport as ps

# parbolic background model
ps.add('PAR',
          func='a*x**2+b*x+c',
          ptype='BACKGROUND')

def gauss(x, amp, pos, fwhm):
    return np.amp*np.exp(-(np.pow(x-pos,2)/(fwhm*fwhm/2.0)))

# a gauss peak
ps.add('PEAK',
          func='gauss(x,amp,pos,fwhm)',
          info='a gaussian',
          ptype='PEAK',
          picker=ps.LOPicker)

ps.add() is defined as follows:

def add(self, name, func=None, info='', ptype=None, picker=None):
    name:   uppercase model name, e.g. GA
    info:   an information text describing the model
    func:   the function string
    ptype:  one of 'BACKGROUND','PEAK','EXP','MISC'
    picker: a picker object, e.g. LOPicker, which handles the collection
            of the function's parameters from mouse actions

If you do not specify a picker, the initial guess for that peak must be entered by hand. Common pickers are defined in the file peaksupport.py in the peak-o-mat source distribution.

A more complicated example of a custom peak shape, including a custom picker function is whon in the following:

class GFDPicker(list):
    def __init__(self, component, background_cb):
        list.__init__(self,[(ps.Cmd('mx'),self.pos),(ps.Cmd('mxy'),self.amp_sigma)])
        self.f = component
        self.background_cb = background_cb

    def pos(self, x):
        self.f['pos'].value = x

    def amp_sigma(self, xy):
        x, y = xy
        self.f['sigma'].value = np.abs(x - self.f['pos'].value)
        self.f['amp'].value = -(y - self.background_cb(x, ignore_last=True)) * self.f['sigma'].value * np.sqrt(np.e) * np.sign(x - self.f['pos'].value)

ps.add('GFD',
       func='-amp*(x-pos)/(sigma*sigma)*np.exp(-0.5*(pow((x-pos)/sigma,2)))',
       info='First derivative of a Gaussian',
       ptype='PEAK',
       picker=GFDPicker)

You can add own constants so that they can be used in the model definitions:

from peak_o_mat import symbols

# add gravitation constant
symbols.add_constant('G',6.673e-11)

Installing/Writing Modules

In order to use third-party or own modules move the module’s files to the modules subdirectory whithin the configuration folder. peak-o-mat will load them upon program start. The modules which are distributed with peak-o-mat reside in <site-packages>/peak_o_mat/modules. Those global modules have to be listed in __init__.py at the same location to be activated.

Writing own modules is easy. Use xrced (part of every wxPython installation) to create a GUI and save it as mod_XXX.xrc. The top-level GUI element of each module must be a wx.Panel having the module’s filename as XML ID (in this case mod_XXX). Then add anything you like but remember to keep the overall height of the panel small since the taller the module’s GUI, the fewer space will be availabe for the graphs. If you provide XML IDs for the controls, let the IDs begin with xrc_. This enables you to access the controls by referencing them as self.xrc_xxx in the program. Then create a python source file, named mod_XXX.py, which has the following minimal content:

from peak_o_mat import module

Module(module.Module):
    title = 'this modules title'
    def __init__(self, *args):
        module.Module.__init__(self, __file__, *args)

It is absolutely necessary to call the constructor of module.Module as described above, if not, peak-o-mat will not be able to find the module’s XRC file. However do not add code to the constructor which accesses the GUI, instead define the method:

def init(self):
    ....

and use it like a constructor. When OnInit will be called, the GUI has already been loaded and can be accessed savely, e.g. to set up event bindings. The Module class does not derive from a wx control, however it provides the following instance variables/methods:

self.panel       - reference to the panel
self.controller  - reference to the main controller
self.project     - reference to the project data
self.Bind()      - self.panel.Bind()
self.Unbind()    - self.panel.Unbind()
self.xrc_xxx     - reference to the wx control with
                   the XML ID *xrc_xxx*

See the files template.py/template.xrc in the modules subdir for a working example.

«  The modules   ::   Contents   ::   Scripting peak-o-mat  »