else:
yoffset_guess = ydata[-1]
#find width at half height as estimate of sigma
if sigma_guess is None:
variance = numpy.dot(
numpy.abs(ydata), (xdata - mean_guess)**
2) / numpy.abs(ydata).sum() # Fast and numerically precise
sigma_guess = math.sqrt(variance)
#put guess params into an array ready for fitting
p0 = numpy.array([amplitude_guess, mean_guess, sigma_guess, yoffset_guess])
#define the gaussian function and associated error function
fitfunc = lambda p, x: p[0] * scipy.exp(-(x - p[1])**2 /
(2.0 * p[2]**2)) + p[3]
errfunc = lambda p, x, y: fitfunc(p, x) - y
# do the fitting
p1, success = scipy.optimize.leastsq(errfunc, p0, args=(xdata, ydata))
if success not in (1, 2, 3, 4):
raise RuntimeError, "Could not fit Gaussian to data."
fit_y_data = [fitfunc(p1, i) for i in xdata]
return xdata, fit_y_data, GaussianParameters(*p1)
plugins.register(Fitting())
from avoplot.plugins import register from UVVIS_plugin import UVVISPlugin #register the spectrum plotting plugin tester register(UVVISPlugin())
from avoplot.plugins import register from fitting import Fitting #register the fitting plugin register(Fitting())
from avoplot.plugins import register from fitting import Fitting #register the fitting plugin register(Fitting())
if mean_guess > data_midpoint:
yoffset_guess = ydata[0]
else:
yoffset_guess = ydata[-1]
#find width at half height as estimate of sigma
if sigma_guess is None:
variance = numpy.dot(numpy.abs(ydata), (xdata-mean_guess)**2)/numpy.abs(ydata).sum() # Fast and numerically precise
sigma_guess = math.sqrt(variance)
#put guess params into an array ready for fitting
p0 = numpy.array([amplitude_guess, mean_guess, sigma_guess, yoffset_guess])
#define the gaussian function and associated error function
fitfunc = lambda p, x: p[0]*scipy.exp(-(x-p[1])**2/(2.0*p[2]**2)) + p[3]
errfunc = lambda p, x, y: fitfunc(p,x)-y
# do the fitting
p1, success = scipy.optimize.leastsq(errfunc, p0, args=(xdata,ydata))
if success not in (1,2,3,4):
raise RuntimeError, "Could not fit Gaussian to data."
fit_y_data = [fitfunc(p1, i) for i in xdata]
return xdata, fit_y_data, GaussianParameters(*p1)
plugins.register(Fitting())
maxValue=30, style=wx.SL_LABELS)
#add the slider to the control panel's sizer
self.Add(self.slider, 0,
wx.ALL | wx.EXPAND | wx.ALIGN_CENTER_HORIZONTAL, border=10)
#register an event handler for slider change events
wx.EVT_COMMAND_SCROLL(self, self.slider.GetId(), self.on_slider_change)
def on_slider_change(self, evnt):
"""
Event handler for frequency slider change events.
"""
#change the frequency of the sine wave data accordingly
f = self.slider.GetValue()
x_data = numpy.linspace(0, 7, 2000)
y_data = numpy.sin(x_data * f)
#change the data in the series object
self.series.set_xy_data(xdata=x_data, ydata=y_data)
#draw our changes on the display
self.series.update()
#register the plugin with AvoPlot
plugins.register(AdvExamplePlugin())
# def __init__(self, parent, filename):
# self.wavenumber, self.absorbance = load_ftir_file(filename)
# print classify_spectrum(self.wavenumber, self.absorbance)
# PlotPanelBase.__init__(self,parent, os.path.basename(filename))
# self.control_panel = FTIRFittingPanel(self, classify_spectrum(self.wavenumber, self.absorbance))
# self.h_sizer.Insert(0,self.control_panel, flag=wx.ALIGN_LEFT)
#
# self.create_plot()
#
#
# def fit_h2o(self, evnt):
# try:
# wx.BeginBusyCursor()
# bkgd = fit_h2o_peak(self.wavenumber, self.absorbance, self.axes, plot_fit=True)
# peak_height = calc_h2o_peak_height(self.wavenumber, self.absorbance, bkgd)
# self.control_panel.set_peak_height(peak_height)
#
# self.canvas.draw()
# self.canvas.gui_repaint()
# finally:
# wx.EndBusyCursor()
#
# def create_plot(self):
# self.axes.plot(self.wavenumber, self.absorbance)
# self.axes.set_xlim((self.axes.get_xlim()[1],self.axes.get_xlim()[0]))
# self.axes.set_xlabel("Wavenumber")
# self.axes.set_ylabel("Absorbance")
plugins.register(UVVISPlugin())
#Copyright (C) Nial Peters 2013 # #This file is part of AvoPlot. # #AvoPlot is free software: you can redistribute it and/or modify #it under the terms of the GNU General Public License as published by #the Free Software Foundation, either version 3 of the License, or #(at your option) any later version. # #AvoPlot is distributed in the hope that it will be useful, #but WITHOUT ANY WARRANTY; without even the implied warranty of #MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #GNU General Public License for more details. # #You should have received a copy of the GNU General Public License #along with AvoPlot. If not, see <http://www.gnu.org/licenses/>. from avoplot.plugins import register from txt_file_loader import TextFilePlugin register(TextFilePlugin())
# Copyright (C) Nial Peters 2013 # # This file is part of AvoPlot. # # AvoPlot is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation, either version 3 of the License, or # (at your option) any later version. # # AvoPlot is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with AvoPlot. If not, see <http://www.gnu.org/licenses/>. from avoplot.plugins import register from txt_file_loader import TextFilePlugin register(TextFilePlugin())
from avoplot.plugins import register from UVVIS_plugin import UVVISPlugin #register the spectrum plotting plugin tester register(UVVISPlugin())
# def __init__(self, parent, filename):
# self.wavenumber, self.absorbance = load_ftir_file(filename)
# print classify_spectrum(self.wavenumber, self.absorbance)
# PlotPanelBase.__init__(self,parent, os.path.basename(filename))
# self.control_panel = FTIRFittingPanel(self, classify_spectrum(self.wavenumber, self.absorbance))
# self.h_sizer.Insert(0,self.control_panel, flag=wx.ALIGN_LEFT)
#
# self.create_plot()
#
#
# def fit_h2o(self, evnt):
# try:
# wx.BeginBusyCursor()
# bkgd = fit_h2o_peak(self.wavenumber, self.absorbance, self.axes, plot_fit=True)
# peak_height = calc_h2o_peak_height(self.wavenumber, self.absorbance, bkgd)
# self.control_panel.set_peak_height(peak_height)
#
# self.canvas.draw()
# self.canvas.gui_repaint()
# finally:
# wx.EndBusyCursor()
#
# def create_plot(self):
# self.axes.plot(self.wavenumber, self.absorbance)
# self.axes.set_xlim((self.axes.get_xlim()[1],self.axes.get_xlim()[0]))
# self.axes.set_xlabel("Wavenumber")
# self.axes.set_ylabel("Absorbance")
plugins.register(UVVISPlugin())
from avoplot.plugins import register from ftir_spectrum import FTIRPlugin #register the spectrum plotting plugin register(FTIRPlugin())
#change the data in the series object
self.series.set_xy_data(xdata=res[:,0], ydata=res[:,1])
#draw our changes on the display
self.series.update()
class ProsailPlugin(plugins.AvoPlotPluginSimple):
def __init__(self):
super(ProsailPlugin, self).__init__("PyProSAIL",
ProSAILSeries)
self.set_menu_entry(['Optical RS','PyProSAIL'],
"Plot outputs from the PyProSAIL vegetation reflectance model")
def plot_into_subplot(self, subplot):
res = pyprosail.run(1.5, 40, 8, 0, 0.1, 0.009, 1, 3, 0.01, 30, 0, 10, 0, pyprosail.Planophile)
data_series = ProSAILSeries("ProSAIL Output", xdata=res[:,0],
ydata=res[:,1])
subplot.add_data_series(data_series)
return True
plugins.register(ProsailPlugin())
from avoplot.plugins import register from ftir_spectrum import FTIRPlugin #register the spectrum plotting plugin register(FTIRPlugin())
# def __init__(self, parent, filename):
# self.wavenumber, self.absorbance = load_ftir_file(filename)
# print classify_spectrum(self.wavenumber, self.absorbance)
# PlotPanelBase.__init__(self,parent, os.path.basename(filename))
# self.control_panel = FTIRFittingPanel(self, classify_spectrum(self.wavenumber, self.absorbance))
# self.h_sizer.Insert(0,self.control_panel, flag=wx.ALIGN_LEFT)
#
# self.create_plot()
#
#
# def fit_h2o(self, evnt):
# try:
# wx.BeginBusyCursor()
# bkgd = fit_h2o_peak(self.wavenumber, self.absorbance, self.axes, plot_fit=True)
# peak_height = calc_h2o_peak_height(self.wavenumber, self.absorbance, bkgd)
# self.control_panel.set_peak_height(peak_height)
#
# self.canvas.draw()
# self.canvas.gui_repaint()
# finally:
# wx.EndBusyCursor()
#
# def create_plot(self):
# self.axes.plot(self.wavenumber, self.absorbance)
# self.axes.set_xlim((self.axes.get_xlim()[1],self.axes.get_xlim()[0]))
# self.axes.set_xlabel("Wavenumber")
# self.axes.set_ylabel("Absorbance")
plugins.register(FTIRPlugin())
