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spectrum_viewer.py
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spectrum_viewer.py
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import sys
import numpy as np
import matplotlib
import matplotlib.pyplot as plt
from PySide import QtCore
from PySide import QtGui
matplotlib.rcParams['backend.qt4']='PySide'
from matplotlib.backends.backend_qt4agg import FigureCanvasQTAgg as FigureCanvas
#project specific items
import analysis
import fit_analysis
class SpectrumViewer(QtGui.QMainWindow):
"""
Viewer for Spectrum Holder
"""
def __init__(self, spectrum_holder, parent=None):
#super(SpectrumViewer, self).__init__()
QtGui.QMainWindow.__init__(self, parent)
self.filename = spectrum_holder.filename
basename = analysis.get_file_basename(spectrum_holder.filename)
self.setWindowTitle('Spectrum Holder for %s'%basename)
self.resize(600,300)
self.spectrum_holder = spectrum_holder
spectrum_box = spectrum_holder.spectrum_box
self.cube_mutex = QtCore.QMutex()
self.inputs()
self.textbox_spectrum_box.setText(spectrum_box)
def inputs(self):
"""populate screen"""
self.main_frame = QtGui.QWidget()
self.table = QtGui.QTableWidget()
self.table.setColumnCount(1)
self.textbox_spectrum_box = QtGui.QTextEdit()
self.textbox_spectrum_box.textChanged.connect(self.update_spectrum_box)
self.button_empty_spectrum_box = QtGui.QPushButton("&Empty Spectrum Box")
self.button_empty_spectrum_box.clicked.connect(self.empty_spectrum_box)
self.label_cube_fitted = QtGui.QLabel("Cube Box Empty")
self.button_display_peak_amplitudes = QtGui.QPushButton("&Display Peak Amplitudes")
self.button_display_peak_amplitudes.clicked.connect(self.display_peak_amplitudes)
self.button_display_peak_m = QtGui.QPushButton("&Display Peak M")
self.button_display_peak_m.clicked.connect(self.display_peak_m)
self.button_display_peak_mu = QtGui.QPushButton("&Display Peak Mu")
self.button_display_peak_mu.clicked.connect(self.display_peak_mu)
self.button_display_peak_sigma = QtGui.QPushButton("&Display Peak Sigmas")
self.button_display_peak_sigma.clicked.connect(self.display_peak_sigma)
self.button_display_cube_residuals = QtGui.QPushButton("&Display Cube Residuals")
self.button_display_cube_residuals.clicked.connect(self.display_cube_residuals)
self.button_save_cube = QtGui.QPushButton("&Save Cube")
self.button_save_cube.clicked.connect(self.save_cube)
grid = QtGui.QGridLayout()
grid.setSpacing(10)
grid.addWidget(self.textbox_spectrum_box,0,0)
grid.addWidget(self.button_empty_spectrum_box,1,0)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.label_cube_fitted)
vbox.addWidget(self.button_display_peak_amplitudes)
vbox.addWidget(self.button_display_peak_mu)
vbox.addWidget(self.button_display_peak_sigma)
vbox.addWidget(self.button_display_peak_m)
vbox.addWidget(self.button_display_cube_residuals)
vbox.addWidget(self.button_save_cube)
grid.addLayout(vbox,0,1)
self.main_frame.setLayout(grid)
self.setCentralWidget(self.main_frame)
def cube_warning(self):
"""popup warning when cube is not fitted yet"""
msg = """
Cube not fitted yet. Fit a cube to display.
"""
QtGui.QMessageBox.about(self, "Spectrum Holder Message", msg.strip())
def display_window(self):
self.show()
def display_peak_amplitudes(self):
"""popup window with all peak amplitudes"""
if not self.spectrum_holder.cube_fitted:
self.cube_warning()
return
self.window_amplitude = QtGui.QWidget()
self.window_amplitude.setWindowTitle("Peak Amplitudes")
self.window_amplitude.fig = plt.figure(figsize=(8.0, 6.0))
self.window_amplitude.canvas = FigureCanvas(self.window_amplitude.fig)
self.window_amplitude.canvas.setParent(self.window_amplitude)
image_cube = self.spectrum_holder.amplitudes
self.plot_peaks(image_cube, self.spectrum_holder.peak_count)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.window_amplitude.canvas)
self.window_amplitude.setLayout(vbox)
self.window_amplitude.show()
def display_peak_m(self):
"""popup window with all peak m's"""
if not self.spectrum_holder.cube_fitted:
self.cube_warning()
return
self.window_m = QtGui.QWidget()
self.window_m.setWindowTitle("Peak M's")
self.window_m.fig = plt.figure(figsize=(8.0, 6.0))
self.window_m.canvas = FigureCanvas(self.window_m.fig)
self.window_m.canvas.setParent(self.window_m)
image_cube = self.spectrum_holder.m
self.plot_peaks(image_cube, self.spectrum_holder.peak_count)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.window_m.canvas)
self.window_m.setLayout(vbox)
self.window_m.show()
def display_peak_mu(self):
"""popup window with all peak mu's"""
if not self.spectrum_holder.cube_fitted:
self.cube_warning()
return
self.window_mu = QtGui.QWidget()
self.window_mu.setWindowTitle("Peak Mu's")
self.window_mu.fig = plt.figure(figsize=(8.0, 6.0))
self.window_mu.canvas = FigureCanvas(self.window_mu.fig)
self.window_mu.canvas.setParent(self.window_mu)
image_cube = self.spectrum_holder.mu
self.plot_peaks(image_cube, self.spectrum_holder.peak_count)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.window_mu.canvas)
self.window_mu.setLayout(vbox)
self.window_mu.show()
def display_peak_sigma(self):
"""popup window with all peak sigmas"""
if not self.spectrum_holder.cube_fitted:
self.cube_warning()
return
self.window_sigma = QtGui.QWidget()
self.window_sigma.setWindowTitle("Peak Sigmas")
self.window_sigma.fig = plt.figure(figsize=(8.0, 6.0))
self.window_sigma.canvas = FigureCanvas(self.window_sigma.fig)
self.window_sigma.canvas.setParent(self.window_sigma)
image_cube = self.spectrum_holder.sigma
self.plot_peaks(image_cube, self.spectrum_holder.peak_count)
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.window_sigma.canvas)
self.window_sigma.setLayout(vbox)
self.window_sigma.show()
def display_cube_residuals(self):
"""popup window with integrated residuals"""
if not self.spectrum_holder.cube_fitted:
self.cube_warning()
return
self.window_residuals = QtGui.QWidget()
self.window_residuals.setWindowTitle("Peak Residuals")
self.window_residuals.fig = plt.figure(figsize=(8.0, 6.0))
self.window_residuals.canvas = FigureCanvas(self.window_residuals.fig)
self.window_residuals.canvas.setParent(self.window_residuals)
plt.subplot()
plt.imshow(self.spectrum_holder.cube_residuals, interpolation='nearest')
plt.colorbar()
vbox = QtGui.QVBoxLayout()
vbox.addWidget(self.window_residuals.canvas)
self.window_residuals.setLayout(vbox)
self.window_residuals.show()
def empty_spectrum_box(self):
if not self.textbox_spectrum_box.isReadOnly():
self.textbox_spectrum_box.clear()
def hide_window(self):
self.hide()
def plot_peaks(self, image_cube, peak_count):
for peak_number in np.arange(peak_count):
axes = plt.subplot(1, peak_count, peak_number)
axes.set_title("Peak Number %s"%str(peak_number+1))
image = fit_analysis.get_image_from_cube(image_cube, peak_number)
plt.imshow(image, interpolation='nearest')
plt.colorbar()
def save_cube(self):
self.spectrum_holder.save_cube()
def update_spectrum_box(self):
self.spectrum_holder.spectrum_box = self.textbox_spectrum_box.toPlainText()
#main function to start up program
def main(spectrum_holder):
app = QtGui.QApplication.instance()
if app is None:
app = QtGui.QApplication(sys.argv)
form = SpectrumViewer(spectrum_holder)
form.show()
app.exec_()
return form
else:
form = SpectrumViewer(spectrum_holder)
form.show()
app.exec_()
return form
#holder function to start up program from interactive terminal
def holder(filename, dimension1, dimension2):
#matplotlib.rcParams['mathtext.fontset'] = 'stixsans'
app = QtCore.QCoreApplication.instance()
app.form = SpectrumViewer(filename, dimension1, dimension2)
#QApplication.setStyle(QStyleFactory.create('Plastique'))
#QApplication.setPalette(QApplication.style().standardPalette())
#app.form.show()
#app.exec_()
return app.form