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guitest.py
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guitest.py
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#!/usr/bin/env python
# -*- coding: utf-8 -*-
"""
Created on Sat Jan 2 15:48:20 2016
TODO: read_chn reads the .chn file header correctly. The number of channels
can now be accessed and used instead of being set manually. This is not
done yet though.
TODO: The find_peak function does not find all peaks. Find better way to
determine what is a peak.
TODO: Implement peakfitting and background subtraction from peaks.
Idea for end guesser.
I want to create the functionality that given peak areas, efficiency curve
and connectivity to DB, get a fairly good guess what kind of nuclide and thus
also the activity.
@author: Oscar Tegmyr
oscar.tegmyr@gmail.com
"""
import sys
from PyQt4 import QtGui, QtCore
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
from matplotlib.figure import Figure
import matplotlib.pyplot as plt
import spectrum_analysis as sa
import fit_peak
import read_chn
import numpy as np
# ==== parameters, these will be stored in a separate file ===
color_hist = 'b'
color_bg_hist = 'r'
filled_hist = False
filled_bg_hist = False
spectrum_cal_slope = 1
spectrum_cal_offset = 0
bg_cal_slope = 1
bg_cal_offset = 0
# ================
def load_spec(fname):
spec_obj = read_chn.gamma_data(fname)
spec_array = spec_obj.hist_array
spec_time = spec_obj.real_time
spec_array_step = np.append(0,spec_array)
x = np.arange(len(spec_array))
x_step = np.arange(len(spec_array)+1)-0.5
en = x*spec_obj.en_slope + spec_obj.en_zero_inter + x**2*spec_obj.en_quad
en_step = x_step*spec_obj.en_slope + spec_obj.en_zero_inter + x_step**2*spec_obj.en_quad
return spec_array, spec_array_step, en, en_step, spec_time
class MyMplCanvas(FigureCanvas):
#Ultimately, this is a QWidget (as well as a FigureCanvasAgg, etc.).
def __init__(self, parent=None, width=20, height=4, dpi=100):
fig = Figure(figsize=(width, height), dpi=dpi)
self.axes = fig.add_subplot(111)
# We want the axes cleared every time plot() is called
self.axes.hold(False)
self.compute_initial_figure()
FigureCanvas.__init__(self, fig)
self.setParent(parent)
FigureCanvas.setSizePolicy(self,
QtGui.QSizePolicy.Expanding,
QtGui.QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def compute_initial_figure(self):
pass
class MyStaticMplCanvas(MyMplCanvas):
def compute_initial_figure(self):
self.axes.plot()
class ApplicationWindow(QtGui.QMainWindow):
def __init__(self):
QtGui.QMainWindow.__init__(self)
self.setAttribute(QtCore.Qt.WA_DeleteOnClose)
#=== Menubar ===
self.setup_menu_bar()
# Setup actions!
peak_find_action = QtGui.QAction('Find Peaks',self)
peak_find_action.setShortcut('Ctrl+f')
peak_find_action.triggered.connect(self.find_roi)
zoom_out_action = QtGui.QAction('Zoom Out',self)
zoom_out_action.triggered.connect(self.zoom_out)
zoom_action = QtGui.QAction('Zoom',self)
zoom_action.setShortcut('z')
zoom_action.triggered.connect(self.activate_zoom)
toggle_lin_log_action = QtGui.QAction('Log',self)
toggle_lin_log_action.triggered.connect(self.logarithmic)
self.toolbar = self.addToolBar('Find peak')
self.toolbar.addAction(peak_find_action)
self.toolbar.addAction(zoom_out_action)
self.toolbar.addAction(zoom_action)
self.toolbar.addAction(toggle_lin_log_action)
self.main_widget = QtGui.QWidget(self)
l = QtGui.QHBoxLayout(self.main_widget)
self.sc = MyStaticMplCanvas(self.main_widget, width=100, height=6, dpi=100)
self.slider = QtGui.QSlider(self.main_widget)
l.addWidget(self.sc)
l.addWidget(self.slider)
self.main_widget.setFocus()
self.setCentralWidget(self.main_widget)
self.ymax = 5000
self.x_limits=[0,8192]
self.y_limits=[0.1,]
# def setup_toolbar(self):
def setup_menu_bar(self):
self.menuBar = QtGui.QMenuBar()
self.file_menu = QtGui.QMenu('&File', self)
self.settings_menu = QtGui.QMenu('&Settings', self)
self.analysis_menu = QtGui.QMenu('&Analysis', self)
self.help_menu = QtGui.QMenu('&Help', self)
self.menuBar.addMenu(self.file_menu)
self.menuBar.addMenu(self.settings_menu)
self.menuBar.addMenu(self.analysis_menu)
self.menuBar.addMenu(self.help_menu)
self.file_menu.addAction('&Load spectrum', self.file_load_spec)
self.file_menu.addAction('&Export spectrum', self.file_load_spec)
self.analysis_menu.addAction('&Zoom', self.activate_zoom)
self.analysis_menu.addAction('&Find Roi', self.find_roi)
self.analysis_menu.addAction('&Load background spectrum', self.file_load_background)
self.analysis_menu.addAction('&Logartihmic', self.logarithmic)
def file_load_spec(self):
self.file_name = QtGui.QFileDialog.getOpenFileName(self,"Load Spectrum File", "/home","Spectrum Files (*.chn *.bin)");
self.array,self.array_step, self.en, self.en_step, self.spectrum_time = load_spec(self.file_name)
self.x_limits = [0,self.en_step[-1]]
self.y_limits = [0.1, np.max(self.array)*1.2 ]
self.draw_spectrums()
def file_load_background(self):
self.file_name_bg = QtGui.QFileDialog.getOpenFileName(self,"Load Spectrum File", "/home","Spectrum Files (*.chn *.bin)");
self.bg_spec, self.bg_time = load_spec(self.file_name_bg)
self.ymax = np.max(self.bg_spec)
self.draw_spectrums()
def draw_spectrums(self):
if hasattr(self,'bg_spec') and hasattr(self,'array') :
x_bg = np.arange(len(self.bg_spec))
time_factor = self.spectrum_time/float(self.bg_time)
self.sc.axes.step(x_bg,1.2*time_factor*self.bg_spec,c=color_bg_hist)#TODO: Make sure the step setup is okey!
self.sc.axes.hold(True)
print self.bg_time
if hasattr(self,'array') :
self.sc.axes.step(self.en_step,self.array_step,c=color_hist)#TODO: Make sure the step setup is okey!
print self.spectrum_time
self.sc.axes.set_xlim(self.x_limits[0],self.x_limits[1])
self.sc.axes.set_ylim(self.y_limits[0], self.y_limits[1])
self.sc.draw()
def activate_zoom(self):
#TODO: Draw rectangle when zooming
self.cid_click = self.sc.mpl_connect('button_press_event', self.on_click)
self.cid_release = self.sc.mpl_connect('button_release_event', self.on_release)
def on_click(self, click) :
self.sc.zoom_point1 = [click.xdata,click.ydata]
def on_release(self, release):
self.sc.zoom_point2 = [release.xdata,release.ydata]
#Put control for too small values
if np.abs(self.sc.zoom_point2[0]-self.sc.zoom_point1[0]) > 10 and np.abs(self.sc.zoom_point2[1]-self.sc.zoom_point1[1])>10:
self.zoom(np.sort([self.sc.zoom_point2[0],self.sc.zoom_point1[0]]),np.sort([self.sc.zoom_point2[1],self.sc.zoom_point1[1]]))
self.sc.mpl_disconnect(self.cid_click)
self.sc.mpl_disconnect(self.cid_release)
def logarithmic(self):
self.sc.axes.set_yscale('log')
self.sc.draw()
def zoom_out(self):
self.zoom([0,self.en_step[-1]],[0.1, np.max(self.array)*1.2 ])
def zoom(self,xlimits, ylimits):
self.x_limits = xlimits
self.y_limits = ylimits
print self.x_limits
self.draw_spectrums()
def find_roi(self):
#The Second time you activate this the plot disappears
self.rois = sa.peak_finder(self.array)
self.sc.axes.hold()
self.sc.axes.scatter(self.en[self.rois], self.array[self.rois],marker='x',c='r',s=40)
self.draw_spectrums()
def fit_peak(self, en_low, en_high):
rang = np.linspace(en_low,en_high)
plt.figure(3)
plt.scatter(rang,self.array[rang])
plt.ylim(ymin=1)
print fit_peak.fit_the_peak(rang,self.array[rang])
coeff, var_matrix, hist_fit = fit_peak.fit_the_peak(rang,self.array[rang])
plt.plot(rang, hist_fit)
plt.show()
qApp = QtGui.QApplication(sys.argv)
aw = ApplicationWindow()
aw.setWindowTitle('Ortec GUI')
aw.show()
sys.exit(qApp.exec_())