def do_define_2theta_fwhm_function(self):
"""
pop out a dialog for user to input the 2theta-FWHM formula
:return:
"""
formula = guiutility.get_value_from_dialog(
parent=self,
title='Input 2theta-FWHM function',
details='Example: y = 4.0 * x**2 - 1.2 * x + 1./x]=\n'
'where y is FWHM and x is 2theta',
label_name='Equation: ')
if formula is None:
# return if user cancels operation
return
print('[DB...BAT] User input 2theta formula: {}'.format(formula))
state, error_message = self._controller.check_2theta_fwhm_formula(
formula)
if not state:
guiutility.show_message(self,
message=error_message,
message_type='error')
return
return
def do_retrieve_fwhm(self):
"""
Get FWHM from integrated 'STRONG' peaks according to 2theta value
:return:
"""
row_number = self.ui.tableView_summary.rowCount()
error_messages = ''
for row_index in range(row_number):
# check whether FWHM value is set up
fwhm_i = self.ui.tableView_summary.get_fwhm(row_index)
if fwhm_i is not None and fwhm_i > 1.E-10:
continue
# use interpolation to curve
two_theta = self.ui.tableView_summary.get_two_theta(row_index)
try:
gauss_sigma = self._controller.calculate_peak_integration_sigma(
two_theta)
scan_number = self.ui.tableView_summary.get_scan_number(
row_index)
pt_number = 1
roi_name = self.ui.tableView_summary.get_region_of_interest_name(
row_index)
self.ui.tableView_summary.set_gaussian_sigma(
row_index, gauss_sigma)
self._controller.set_single_measure_peak_width(
self._exp_number,
scan_number,
pt_number,
roi_name,
gauss_sigma,
is_fhwm=False)
except RuntimeError as err:
# error!
error_messages += 'Unable to calculate sigma of row {0} due to {1}\n'.format(
row_index, err)
continue
# END-IF-ELSE
# show error message if necessary
if len(error_messages) > 0:
guiutility.show_message(self, error_messages)
def do_integrate_detector_counts(self):
"""
sum over the (selected) scan's detector counts by ROI
:return:
"""
# get ROI
roi_name = str(self.ui.comboBox_roiList.currentText())
if roi_name is None or roi_name == '':
guiutility.show_message(
'A region-of-interest must be chosen in order to integrate detector counts.'
)
return
# integration direction and fit
direction = str(
self.ui.comboBox_integrateDirection.currentText()).lower()
fit_gaussian = self.ui.checkBox_fitPeaks.isChecked()
num_rows = self.ui.tableView_summary.rowCount()
print('[DB...BAT] Number of rows = {}'.format(num_rows))
scan_number_list = list()
for row_number in range(num_rows):
# integrate counts on detector
scan_number = self.ui.tableView_summary.get_scan_number(row_number)
scan_number_list.append(scan_number)
# END-FOR
print('[DB...BAT] Scan numbers: {}'.format(scan_number_list))
peak_height_dict = self._controller.integrate_single_pt_scans_detectors_counts(
self._exp_number, scan_number_list, roi_name, direction,
fit_gaussian)
# set the value to the row to table
for row_number in range(self.ui.tableView_summary.rowCount()):
scan_number = self.ui.tableView_summary.get_scan_number(row_number)
pt_number = 1
peak_height = peak_height_dict[scan_number]
self.ui.tableView_summary.set_peak_height(scan_number, pt_number,
peak_height, roi_name)
# END-FOR (row_number)
return
def do_export_to_movie(self):
"""
export the complete list of single-pt experiment to a movie
:return:
"""
# find out the directory to save the PNG files for making a move
movie_dir = self._controller.get_working_directory()
roi_name = str(self.ui.comboBox_roiList.currentText())
direction = str(
self.ui.comboBox_integrateDirection.currentText()).lower()
movie_dir = os.path.join(movie_dir,
'{}_{}'.format(roi_name, direction))
os.mkdir(movie_dir)
# go through each line to plot and save the data
num_rows = self.ui.tableView_summary.rowCount()
file_list_str = ''
for i_row in range(num_rows):
# get run number and set to plot
scan_number = self.ui.tableView_summary.get_scan_number(i_row)
self.ui.lineEdit_Scan.setText('{}'.format(scan_number))
png_file_name = os.path.join(
movie_dir,
'Scan{0:04d}_ROI{1}_{2}.png'.format(scan_number, roi_name,
direction))
self.do_plot_integrated_pt(show_plot=False,
save_plot_to=png_file_name)
file_list_str += '{}\n'.format(png_file_name)
# END-IF
# write out
png_list_file = open(os.path.join(movie_dir, 'MoviePNGList.txt'), 'w')
png_list_file.write(file_list_str)
png_list_file.close()
# prompt how to make a movie
command_linux = 'ffmpeg -framerate 8 -pattern_type glob -i "*.png" -r 30 test.mp4'
guiutility.show_message(self, command_linux)
return
def menu_load_gauss_sigma_file(self):
"""
load a Gaussian sigma curve for interpolation or matching
:return:
"""
# get the column ascii file name
file_filter = 'Data Files (*.dat);;All Files (*.*)'
twotheta_sigma_file_name = QFileDialog.getOpenFileName(
self, self._working_dir, '2theta Gaussian-Sigma File', file_filter)
if not twotheta_sigma_file_name:
return
if isinstance(twotheta_sigma_file_name, tuple):
twotheta_sigma_file_name = twotheta_sigma_file_name[0]
# set the file to controller
try:
vec_x, vec_y = self._controller.import_2theta_gauss_sigma_file(
twotheta_sigma_file_name)
self.ui.graphicsView_integration1DView.plot_2theta_model(
vec_x, vec_y)
except RuntimeError as run_err:
guiutility.show_message(self, str(run_err))
def do_browse_output_dir(self):
"""
browse the output directory
:return:
"""
# get scan number or numbers
try:
exp_number = self.get_exp_number()
except RuntimeError as run_err:
gui_util.show_message(self, '[ERROR] {0}'.format(run_err))
return
default_dir = os.path.join(
'/HFIR/HB3A/Exp{0}/shared/'.format(exp_number))
# get output directory
output_dir = QFileDialog.getExistingDirectory(
self, 'Outputs for pre-processed scans', default_dir)
if not output_dir:
return
if isinstance(output_dir, tuple):
output_dir = output_dir[0]
self.ui.lineEdit_outputDir.setText(output_dir)
def do_integrate_single_pt(self):
"""
integrate the 2D data inside region of interest along both axis-0 and axis-1 individually.
and the result (as 1D data) will be saved to ascii file.
the X values will be the corresponding pixel index either along axis-0 or axis-1
:return:
"""
# get ROI
roi_name = str(self.ui.comboBox_roiList.currentText())
if roi_name is None or roi_name == '':
guiutility.show_message(
'A region-of-interest must be chosen in order to integrate detector counts.'
)
return
for row_number in range(self.ui.tableView_summary.rowCount()):
# integrate counts on detector
scan_number = self.ui.tableView_summary.get_scan_number(row_number)
pt_number = self.ui.tableView_summary.get_pt_number(row_number)
# calculate peak intensity
ref_fwhm = self.ui.tableView_summary.get_fwhm(row_number)
intensity = self._controller.calculate_intensity_single_pt(
self._exp_number,
scan_number,
pt_number,
roi_name,
ref_fwhm=ref_fwhm,
is_fwhm=False)
# add to table
self.ui.tableView_summary.set_intensity(scan_number, pt_number,
intensity)
# END-FOR
return
def set_calibration_to_reduction_controller(self, exp_number):
"""set user-specified instrument calibrations to the my controller
:param exp_number:
:return:
"""
# set up the experiment number if it is different
if exp_number != self._myController.get_experiment():
self._myController.set_exp_number(exp_number)
self._myController.set_default_detector_sample_distance(0.3750)
self._myController.set_default_pixel_number(256, 256)
# set up the calibration
# wave length
user_wavelength_str = str(
self.ui.lineEdit_infoWavelength.text()).strip()
if len(user_wavelength_str) > 0:
try:
user_wavelength = float(user_wavelength_str)
self._myController.set_user_wave_length(
exp_number, user_wavelength)
except ValueError:
gui_util.show_message(
self,
'[ERROR] User-specified wave length {0} cannot be converted to float.'
''.format(user_wavelength_str))
return
# END-IF
# detector center
user_det_center_str = str(
self.ui.lineEdit_infoDetCenter.text()).strip()
user_det_center_str = user_det_center_str.replace('x', ',')
if len(user_det_center_str) > 0:
try:
det_center = gui_util.parse_integer_list(
user_det_center_str, 2)
except RuntimeError as run_err:
gui_util.show_message(
self, 'Unable to parse detector center {0} due to {1}'
''.format(user_det_center_str, run_err))
return
self._myController.set_detector_center(exp_number, det_center[0],
det_center[1])
# END-IF
# detector sample distance
status, ret_obj = gui_util.parse_float_editors(
[self.ui.lineEdit_infoDetSampleDistance], allow_blank=True)
if not status:
error_message = ret_obj
gui_util.show_message(self, '[ERROR] {0}'.format(error_message))
return
user_det_sample_distance = ret_obj[0]
if user_det_sample_distance is not None:
self._myController.set_detector_sample_distance(
exp_number, user_det_sample_distance)
# detector size
curr_det_size_index = self.ui.comboBox_detSize.currentIndex()
if curr_det_size_index > 2:
gui_util.show_message(
self, 'Detector {0} is not supported by now!'
''.format(str(self.ui.comboBox_detSize.currentText())))
return
det_size = [256, 512][curr_det_size_index]
self._myController.set_detector_geometry(det_size, det_size)