mstm-gui.py
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#!/usr/bin/python
from mstm_materials import *
from mstm_parameters import *
from mstm_simparser import *
import time
import sys
#PyQt4 libraries
from PyQt4 import QtGui
from PyQt4 import QtCore
from PyQt4 import uic
#Matplotlib libraries
import matplotlib.pyplot as plt
from matplotlib.patches import Patch
from pylab import *
class GuiWindow(QtGui.QMainWindow):
params = ParameterClass('msinput.inp')
def setParams(self):
#update the Gui based on values in the parameters structure
self.ui.spinStartLambda.setValue(self.params.minLambda)
self.ui.spinEndLambda.setValue(self.params.maxLambda)
self.ui.spinNearFieldLambda.setValue(self.params.snapshotLambda)
self.ui.spinNumSamples.setValue(self.params.nSamples)
self.ui.spinNumSpheres.setValue(int(self.params['number_spheres']))
#near field stuff
self.ui.cmbPlaneSlice.setCurrentIndex(int(self.params['near_field_plane_coord']) - 1)
verts = self.params['near_field_plane_vertices']
self.ui.spinNearFieldWidth.setValue(verts[2] - verts[0])
self.ui.spinNearFieldHeight.setValue(verts[3] - verts[1])
self.ui.spinNearFieldSteps.setValue(self.params.nSteps)
fi = QtCore.QFileInfo(self.params.matFilename)
self.ui.txtMaterial.setText(fi.baseName())
#update global parameters for the dimer simulation
self.ui.spinSpacing.setValue(self.params.d)
self.ui.spinRadius.setValue(self.params.a)
def getParams(self):
#get the parameters from the GUI and store them in the params structure
self.params.minLambda = self.ui.spinStartLambda.value()
self.params.maxLambda = self.ui.spinEndLambda.value()
self.params.snapshotLambda = self.ui.spinNearFieldLambda.value()
self.params.nSamples = self.ui.spinNumSamples.value()
self.params['number_spheres'] = self.ui.spinNumSpheres.value()
#incident light properties
if self.ui.chkRandomOrientation.isChecked():
self.params['fixed_or_random_orientation'] = 1
else:
self.params['fixed_or_random_orientation'] = 0
self.params['incident_azimuth_angle_deg'] = self.ui.spinAlpha.value()
self.params['incident_polar_angle_deg'] = self.ui.spinBeta.value()
self.params['polarization_angle_deg'] = self.ui.spinGamma.value()
self.params.showOutput = self.ui.chkShowOutput.isChecked()
self.params.inWater = self.ui.chkInWater.isChecked()
#near field
if self.ui.chkNearField.isChecked():
self.params['calculate_near_field'] = 1
else:
self.params['calculate_near_field'] = 0
self.params['near_field_plane_coord'] = self.ui.cmbPlaneSlice.currentIndex() + 1
width = (self.ui.spinNearFieldWidth.value()/2)
height = (self.ui.spinNearFieldHeight.value()/2)
self.params['near_field_plane_vertices'] = [-width, -height, width, height]
dx = self.ui.spinNearFieldWidth.value() / (self.ui.spinNearFieldSteps.value() - 1)
self.params['spacial_step_size'] = dx
#global parameters for dimers
self.params.d = self.ui.spinSpacing.value()
self.params.a = self.ui.spinRadius.value()
#get the spheres from the table
nSpheres = self.ui.tblSpheres.rowCount()
print("Row count: " + str(nSpheres))
print("Orientatino: " + str(self.params['fixed_or_random_orientation']))
self.params.sphereList = []
for s in range(nSpheres):
a = float(self.ui.tblSpheres.item(s, 0).text())
x = float(self.ui.tblSpheres.item(s, 1).text())
y = float(self.ui.tblSpheres.item(s, 2).text())
z = float(self.ui.tblSpheres.item(s, 3).text())
self.params.addSphere(a, x, y, z)
return self.params
def simulate(self):
self.results = RunSimulation(True)
#plot results of interest
wl = self.results['lambda']
#for a fixed orientation
if int(self.params['fixed_or_random_orientation']) == 0:
unpol = self.results['extinction_unpolarized']
para = self.results['extinction_parallel']
perp = self.results['extinction_perpendicular']
plt.plot(wl, unpol, 'r-', label='unpolarized')
plt.plot(wl, para, 'g-', label='parallel')
plt.plot(wl, perp, 'b-', label='perpendicular')
else:
total = self.results['extinction_total']
plt.plot(wl, total, 'r-', label='extinction')
#plot the near field maximum values if available
if self.params['calculate_near_field']:
maxima = self.results.maxNearField
print(len(wl))
print(len(maxima))
plt.plot(wl, maxima)
plt.legend(loc = 'upper left')
plt.ylabel('Extinction')
plt.xlabel('Wavelength (um)')
plt.show()
def func3(self, x,y):
return (1- x/2 + x**5 + y**3)*exp(-x**2-y**2)
def snapshot(self):
self.results = RunSimulation(False)
if self.params['calculate_near_field']:
E = array(self.results.gridNearField)
pcolor(E, cmap=cm.RdBu)
colorbar()
#compute the maximum field magnitude in the plane
print("Maximum enhancement: " + str(abs(E).max()))
#get the scattering amplitude matrix
print(self.results.scatAmpMatrix[0])
show()
def saveresults(self):
fileName = QtGui.QFileDialog.getSaveFileName(w, 'Save Spectral Results', '', 'DAT data files (*.dat)')
if fileName:
self.results.saveFile(fileName)
def loadmaterial(self):
fileName = QtGui.QFileDialog.getOpenFileName(w, 'Load Material Refractive Index', '', 'TXT data files (*.txt)')
if fileName:
self.params.matFilename = fileName
fi = QtCore.QFileInfo(fileName)
self.ui.txtMaterial.setText(fi.baseName())
def spherenum(self, i):
self.ui.tblSpheres.setRowCount(i)
print(i)
def updatedimers(self):
d = self.ui.spinSpacing.value()
a = self.ui.spinRadius.value()
self.ui.tblSpheres.setItem(0, 0, QtGui.QTableWidgetItem(str(a)))
self.ui.tblSpheres.setItem(0, 1, QtGui.QTableWidgetItem(str(-(d/2.0 + a))))
self.ui.tblSpheres.setItem(0, 2, QtGui.QTableWidgetItem(str(0.0)))
self.ui.tblSpheres.setItem(0, 3, QtGui.QTableWidgetItem(str(0.0)))
self.ui.tblSpheres.setItem(1, 0, QtGui.QTableWidgetItem(str(a)))
self.ui.tblSpheres.setItem(1, 1, QtGui.QTableWidgetItem(str((d/2.0 + a))))
self.ui.tblSpheres.setItem(1, 2, QtGui.QTableWidgetItem(str(0.0)))
self.ui.tblSpheres.setItem(1, 3, QtGui.QTableWidgetItem(str(0.0)))
def __init__(self):
QtGui.QWidget.__init__(self)
#dimer-specific settings
self.params['number_spheres'] = 2
self.params['sphere_position_file'] = ''
#load the UI window
self.ui = uic.loadUi('mstm_guiwindow.ui')
#controls
self.connect(self.ui.btnSimulate, QtCore.SIGNAL("clicked()"), self.simulate)
self.connect(self.ui.btnEvaluateNearField, QtCore.SIGNAL("clicked()"), self.snapshot)
self.connect(self.ui.mnuSaveResults, QtCore.SIGNAL("triggered()"), self.saveresults)
self.connect(self.ui.mnuLoadMaterial, QtCore.SIGNAL("triggered()"), self.loadmaterial)
self.connect(self.ui.spinNumSpheres, QtCore.SIGNAL("valueChanged(int)"), self.spherenum)
self.connect(self.ui.spinRadius, QtCore.SIGNAL("valueChanged(double)"), self.updatedimers)
self.connect(self.ui.spinSpacing, QtCore.SIGNAL("valueChanged(double)"), self.updatedimers)
#update the displayed parameters
self.setParams()
#update the sphere table with the default dimer values
self.updatedimers()
#display the UI
self.ui.show()
class ProgressBar(QtGui.QWidget):
def __init__(self, parent=None, total=20):
super(ProgressBar, self).__init__(parent)
self.name_line = QtGui.QLineEdit()
self.progressbar = QtGui.QProgressBar()
self.progressbar.setMinimum(1)
self.progressbar.setMaximum(total)
main_layout = QtGui.QGridLayout()
main_layout.addWidget(self.progressbar, 0, 0)
self.setLayout(main_layout)
self.setWindowTitle("Progress")
def update_progressbar(self, val):
self.progressbar.setValue(val)
def RunSimulation(spectralSim = True):
#set the parameters based on the UI
parameters = w.getParams()
#load the material
material = MaterialClass(parameters.matFilename)
#add water if necessary
if parameters.inWater:
material.addSolution(1.33)
#for a spectral simulation, set the range and number of samples
if spectralSim:
minLambda = parameters.minLambda
maxLambda = parameters.maxLambda
nSamples = parameters.nSamples
else:
minLambda = parameters.snapshotLambda
maxLambda = parameters.snapshotLambda
nSamples = 1
#store the simulation results
results = SimParserClass(parameters)
#create a progress bar
pbar = ProgressBar(total=nSamples)
pbar.show()
#for each wavelength in the material
for i in range(nSamples):
if i == 0:
l = minLambda
else:
l = minLambda + i*(maxLambda - minLambda)/(nSamples - 1)
#set the computed parameters
m = material[l]
n = m.n
parameters['real_ref_index_scale_factor'] = n.real
parameters['imag_ref_index_scale_factor'] = n.imag
parameters['length_scale_factor'] = (2.0 * 3.14159)/l
#parameters['length_scale_factor'] = 1.0/l
parameters['scattering_plane_angle_deg'] = gamma;
parameters['near_field_output_data'] = 0
#parameters['number_spheres'] = 1
#save the scripted input file
parameters.saveFile(l, 'scriptParams.inp')
#run the binary
from subprocess import call
if parameters.showOutput:
call(["./ms-tmatrix", "scriptParams.inp"])
else:
devnull = open('/dev/null', 'w')
call(["./ms-tmatrix", "scriptParams.inp"], stdout=devnull)
#parse the simulation results
results.parseSimFile(l, 'test.dat')
if parameters['calculate_near_field']:
results.parseNearField('nf-temp.dat')
#get the scattering amplitude matrix
results.calcScatteringAmp()
#update the progress bar
pbar.update_progressbar(i+1)
#return the results
return results;
#incident light directions
alpha = 0
beta = 0
gamma = 0
#results stored for each spectral sample
resultLabels = {'lambda', 'extinction_unpolarized', 'extinction_parallel', 'extinction_perpendicular'}
#create a Qt window
app = QtGui.QApplication(sys.argv)
w = GuiWindow()
sys.exit(app.exec_())