def export_cube(filename, data, data_view):
"""
export the entire cube to an excel file in the original file's
folder.
format is xdata, spectrum etc.
"""
display_ev = copy.copy(data_view.display_ev)
no_ext_filename, ext = os.path.splitext(filename)
out_filename = no_ext_filename + '.csv'
rows, columns, slices = np.shape(data.ycube[...])
spectra_count = 0
for i in np.arange(rows):
for j in np.arange(columns):
xdata = analysis.xdata_calc2(data.xdata,
data.xdata_info['data_type'],
display_ev)
ydata = analysis.ydata_calc2(data.ycube[i, j, :], data.xdata,
data.xdata_info['data_type'],
display_ev)
if spectra_count == 0:
out = np.c_[xdata, ydata]
spectra_count = 1
else:
out = np.c_[out, xdata, ydata]
print np.shape(out)
np.savetxt(str(out_filename), out, delimiter=",", fmt="%10.5f")
def convert_ev_cube_process(self, hdf5_file, wavelength_xdata, dimension1,
dimension2):
"""
makes an ev cube from wavelength cube and puts it into original file
"""
locker = QtCore.QMutexLocker(self.convert_mutex)
ev_xdata = 1240/wavelength_xdata
ev_step = ev_xdata[1]-ev_xdata[0]
rebinned_ev_xdata = np.arange(start=ev_xdata[0], stop=ev_xdata[-1],
step=ev_step)
ev_list_size, = np.shape(rebinned_ev_xdata)
ev_cube = hdf5_file.create_dataset('Experiments/__unnamed__/ev_data',
(dimension1,
dimension2, ev_list_size))
hdf5_file.create_dataset('Experiments/__unnamed__/ev_xdata',
data=rebinned_ev_xdata)
for i in np.arange(dimension1):
for j in np.arange(dimension2):
if self.stop_convert:
return
ydata = hdf5_file["Experiments/__unnamed__/data"][i,j,:]
ev_ydata = analysis.ydata_calc2(input_ydata=ydata,
input_xdata=wavelength_xdata,
dtype='wavelength',
display_ev=True)
rebinned_ev_ydata = self.rebin_ev_ydata(ev_ydata,ev_xdata,
rebinned_ev_xdata)
ev_cube[i,j,:] = rebinned_ev_ydata
current_spectrum = i*dimension2 + j
self.update_progress(current_spectrum)
self.progress_window.close()
def export_cube(filename, data, data_view):
"""
export the entire cube to an excel file in the original file's
folder.
format is xdata, spectrum etc.
"""
display_ev = copy.copy(data_view.display_ev)
no_ext_filename, ext = os.path.splitext(filename)
out_filename = no_ext_filename + '.csv'
rows, columns, slices = np.shape(data.ycube[...])
spectra_count = 0
for i in np.arange(rows):
for j in np.arange(columns):
xdata = analysis.xdata_calc2(data.xdata,
data.xdata_info['data_type'],
display_ev)
ydata = analysis.ydata_calc2(data.ycube[i,j,:],
data.xdata,
data.xdata_info['data_type'],
display_ev)
if spectra_count == 0:
out = np.c_[xdata, ydata]
spectra_count = 1
else:
out = np.c_[out, xdata, ydata]
print np.shape(out)
np.savetxt(str(out_filename), out, delimiter=",", fmt="%10.5f")
def fit_cube_process(self):
locker = QtCore.QMutexLocker(self.spectrum_holder.cube_mutex)
self.spectrum_holder.notify_cube_fitting()
self.spectrum_viewer.textbox_spectrum_box.setReadOnly(True)
(rows,columns,slices) = np.shape(self.data.ycube[...])
#self.progress_bar = self.fit_cube_progress_bar(rows*columns)
value = 0
self.stop_fit = False
row_count=0
for i in np.arange(rows):
column_count = 0
for j in np.arange(columns):
peak_holder = DataHolder()
ydata = analysis.ydata_calc2(input_ydata=self.data.ycube[i,j,:],
input_xdata = self.data.xdata,
dtype=self.data.xdata_info['data_type'],
display_ev = self.display_ev)
ydata = np.float64(ydata)
peak_holder.load_from_mf1_cube(self.xdata[:],
ydata,
j,
i)
spectrum = peak_holder.get_spectrum(0)
if row_count == 0:
self.fit_from_spectrum_holder(spectrum)
row_count = 1
column_count = 1
elif column_count == 0:
index = i*(columns-1)
self.fit_from_cube_peaks(spectrum, index)
column_count = 1
else:
index = -1
self.fit_from_cube_peaks(spectrum, index)
peak_list = []
for peak in spectrum.peaks.peak_list:
peak_list.append(peak.get_spec())
self.spectrum_holder.cube_peaks.append(peak_list)
norm_int_res = self.get_normalized_integrated_residuals(spectrum)
self.spectrum_holder.cube_residuals.append(norm_int_res)
if self.stop_fit is True:
return
value += 1
self.update_progress(value)
self.progress_window.close()
self.spectrum_holder.notify_cube_fitted()
self.spectrum_viewer.textbox_spectrum_box.setReadOnly(False)
self.spectrum_viewer.label_cube_fitted.setText("Cube Box Loaded")