def write_twk_jcpds(self):
if not self.model.jcpds_exist():
return
idx_checked = [
s.row() for s in
self.widget.tableWidget_JCPDS.selectionModel().selectedRows()
]
if idx_checked == []:
QtWidgets.QMessageBox.warning(
self.widget, "Warning",
"Highlight the name of JCPDS to write twk jcpds.")
return
if idx_checked.__len__() != 1:
QtWidgets.QMessageBox.warning(
self.widget, "Warning",
"Only one JCPDS card can be written at a time.")
return
# get filename to write
path, __ = os.path.split(self.model.get_base_ptn_filename())
suggested_filen = os.path.join(
path, self.model.jcpds_lst[idx_checked[0]].name + '-twk.jcpds')
filen_twk_jcpds = dialog_savefile(self.widget, suggested_filen)
if filen_twk_jcpds == '':
return
# make comments
comments = "modified from " + \
self.model.jcpds_lst[idx_checked[0]].file + \
", twk for " + \
self.model.base_ptn.fname
self.model.jcpds_lst[idx_checked[0]].write_to_twk_jcpds(
filen_twk_jcpds, comments=comments)
def save_bgsubchi(self):
"""
Save bg subtractd pattern to a chi file
"""
if not self.model.base_ptn_exist():
return
filen_chi_t = self.model.make_filename('bgsub.chi')
filen_chi = dialog_savefile(self.widget, filen_chi_t)
if str(filen_chi) == '':
return
x, y = self.model.base_ptn.get_bgsub()
preheader_line0 = \
'2-theta # BG ROI: {0: .5e}, {1: .5e} \n'.format(
self.widget.doubleSpinBox_Background_ROI_min.value(),
self.widget.doubleSpinBox_Background_ROI_max.value())
preheader_line1 = \
'2-theta # BG Params: {0: d}, {1: d}, {2: d} \n'.format(
self.widget.spinBox_BGParam0.value(),
self.widget.spinBox_BGParam1.value(),
self.widget.spinBox_BGParam2.value())
preheader_line2 = '\n'
writechi(filen_chi,
x,
y,
preheader=preheader_line0 + preheader_line1 + preheader_line2)
def integrate_to_1d(self):
azi_list = self._read_azilist()
if azi_list is None:
QtWidgets.QMessageBox.warning(self.widget, 'Warning',
'No azimuthal ranges in the queue.')
return None
# self.produce_cake()
self.cakemake_ctrl.read_settings()
tth = []
intensity = []
mid_angle = self.widget.spinBox_AziShift.value()
for azi_i in azi_list:
azi_conv = []
if mid_angle <= 180:
azi_conv.append(azi_i[2] - mid_angle)
azi_conv.append(azi_i[4] - mid_angle)
else:
azi_conv.append(azi_i[2] + 360 - mid_angle)
azi_conv.append(azi_i[4] + 360 - mid_angle)
azi_real = []
for azi_conv_i in azi_conv:
if azi_conv_i < -180:
azi_real.append(360 + azi_conv_i)
elif azi_conv_i > 180:
azi_real.append(azi_conv_i - 360)
else:
azi_real.append(azi_conv_i)
tth_i, intensity_i = self.model.diff_img.integrate_to_1d(
azimuth_range=(azi_real[0], azi_real[1]))
tth.append(tth_i)
intensity.append(intensity_i)
intensity_merged = np.zeros_like(intensity[0])
for tth_i, intensity_i in zip(tth, intensity):
if not np.array_equal(tth_i, tth[0]):
QtWidgets.QMessageBox.warning(self.widget, 'Warning',
'Error occured. No output.')
return None
intensity_merged += intensity_i
n_azi = azi_list.__len__()
first_azi = azi_list[0]
intensity_output = intensity_merged
ext = "{0:d}_{1:d}_{2:d}.chi".format(n_azi, int(first_azi[2]),
int(first_azi[4]))
filen_chi_t = self.model.make_filename(ext)
filen_chi = dialog_savefile(self.widget, filen_chi_t)
if str(filen_chi) == '':
return None
azi_text = '# azi. angles: '
for azi_i in azi_list:
azi_text += "({0:.5e}, {1:.5e})".format(azi_i[2], azi_i[4])
preheader_line0 = azi_text + ' \n'
preheader_line1 = '2-theta\n'
preheader_line2 = '\n'
writechi(filen_chi,
tth[0],
intensity_output,
preheader=preheader_line0 + preheader_line1 + preheader_line2)
return filen_chi
def export_to_xls(self):
"""
Export ucfitlist to an excel file
"""
if not self.model.ucfit_exist():
return
new_filen_xls = self.model.make_filename('ucfit.xls')
filen_xls = dialog_savefile(self.widget, new_filen_xls)
if str(filen_xls) == '':
return
xls_ucfitlist(filen_xls, self.model.ucfit_lst)
def _save_cake_marker_file(self):
azi_list = self._read_azilist()
if azi_list is None:
return
ext = "cake.marker"
filen_t = self.model.make_filename(ext)
filen = dialog_savefile(self.widget, filen_t)
if str(filen) == '':
return
with open(filen, "w") as f:
for s in azi_list:
f.write(s[0] + ',' + str(s[1]) + ',' + str(s[2]) + ',' +
str(s[3]) + ',' + str(s[4]) + '\n')
def save_xls(self):
"""
Export jlist to an excel file
"""
if not self.model.jcpds_exist():
return
filen_xls_t = self.model.make_filename('jlist.xls')
filen_xls = dialog_savefile(self.widget, filen_xls_t)
if str(filen_xls) == '':
return
xls_jlist(filen_xls, self.model.jcpds_lst,
self.widget.doubleSpinBox_Pressure.value(),
self.widget.doubleSpinBox_Temperature.value())
def save_xls(self):
"""
Export jlist to an excel file
"""
if not self.model.jcpds_exist():
return
temp_dir = get_temp_dir(self.model.get_base_ptn_filename())
filen_xls_t = make_filename(self.model.get_base_ptn_filename(),
'jlist.xls',
temp_dir=temp_dir)
filen_xls = dialog_savefile(self.widget, filen_xls_t)
if str(filen_xls) == '':
return
xls_jlist(filen_xls, self.model.jcpds_lst,
self.widget.doubleSpinBox_Pressure.value(),
self.widget.doubleSpinBox_Temperature.value())
def write_jcpds(self):
if self.file_name == '':
QtWidgets.QMessageBox.warning(self.widget, "Warning",
"Input filename is not given.")
return
path, filen, ext = breakdown_filename(self.file_name)
if ext == '.cif':
stamp = '-cif-jt'
else:
stamp = '-jt'
filen_default = os.path.join(path, filen + stamp + '.jcpds')
filen = dialog_savefile(self.widget, filen_default)
if filen == '':
return
comment = str(self.widget.lineEdit_Comment.text())
int_min = self.widget.doubleSpinBox_MinDsp.value()
dsp_min = self.widget.doubleSpinBox_MinInt.value()
self.read_jcpds_values()
textoutput = self.model.write_to_file(filen, comments = comment, \
int_min = int_min, dsp_min=dsp_min, \
calculate_1bar_table = True)
def write_dioptas_jcpds(self):
QtWidgets.QMessageBox.warning(self.widget, "Warning",
"This function is not yet supported.")
return
if self.file_name == '':
QtWidgets.QMessageBox.warning(self.widget, "Warning",
"Input filename is not given.")
return
path, filen, ext = breakdown_filename(self.file_name)
stamp = '-dioptas-jt'
filen_default = os.path.join(path, filen + stamp + '.jcpds')
filen = dialog_savefile(self.widget, filen_default)
if filen == '':
return
self.model.comments = str(self.widget.lineEdit_Comment.text())
int_min = self.widget.doubleSpinBox_MinDsp.value()
dsp_min = self.widget.doubleSpinBox_MinInt.value()
self.read_jcpds_values()
self.model.write_to_dioptas_jcpds(filen, int_min=int_min, \
dsp_min=dsp_min)
def save_cake_format_file(self):
# make filename
ext = "cakeformat"
filen_t = self.model.make_filename(ext)
print('please be here')
filen = dialog_savefile(self.widget, filen_t)
if str(filen) == '':
return
# save cake related Values
names = ['azi_shift', 'int_max', 'min_bar', 'max_bar', 'scale_bar']
values = [
self.widget.spinBox_AziShift.value(),
self.widget.spinBox_MaxCakeScale.value(),
self.widget.horizontalSlider_VMin.value(),
self.widget.horizontalSlider_VMax.value(),
self.widget.horizontalSlider_MaxScaleBars.value()
]
with open(filen, "w") as f:
for n, v in zip(names, values):
f.write(n + ' : ' + str(v) + '\n')
def perform_ucfit(self):
# get jcpds data in df. use display to choose data points
if self.model.section_lst == []:
QtWidgets.QMessageBox.warning(
self.widget, "Warning",
"No peak fitting result exist for this file.")
return
if self.phase == None:
QtWidgets.QMessageBox.warning(
self.widget, "Warning", "No phase has been chosen for fitting")
return
data_by_phase_df = self._get_all_peakfit_results_df()
data_to_fit_df = data_by_phase_df[self.phase].loc[data_by_phase_df[
self.phase]['display'] == True]
# number of data point check
n_data_points = len(data_to_fit_df.index)
if n_data_points < 2:
QtWidgets.QMessageBox.warning(self.widget, "Warning",
"You need at least 2 data points.")
return
# perform ucfit
text_output = self.phase + '\n\n'
text_output += 'Fitted unit cell parameters \n'
text_output += 'Crystal system = ' + \
self.widget.comboBox_Symmetry.currentText() + '\n'
wavelength = self.model.get_base_ptn_wavelength()
if self.widget.comboBox_Symmetry.currentText() == 'cubic':
a, s_a, v, s_v, res_lin, res_nlin = fit_cubic_cell(data_to_fit_df,
wavelength,
verbose=False)
cell_params = [a, a, a]
text_output += "a = {0:.5f} +/- {1:.5f} \n".format(a, s_a)
text_output += "V = {0:.5f} +/- {1:.5f} \n\n".format(v, s_v)
elif self.widget.comboBox_Symmetry.currentText() == 'tetragonal':
if n_data_points < 3:
QtWidgets.QMessageBox.warning(
self.widget, "Warning",
"You need at least 3 data points for tetragonal.")
return
a, s_a, c, s_c, v, s_v, res_lin, res_nlin = \
fit_tetragonal_cell(data_to_fit_df, wavelength,
verbose=False)
cell_params = [a, a, c]
text_output += "a = {0:.5f} +/- {1:.5f} \n".format(a, s_a)
text_output += "c = {0:.5f} +/- {1:.5f} \n".format(c, s_c)
text_output += "V = {0:.5f} +/- {1:.5f} \n\n".format(v, s_v)
elif self.widget.comboBox_Symmetry.currentText() == 'hexagonal':
if n_data_points < 3:
QtWidgets.QMessageBox.warning(
self.widget, "Warning",
"You need at least 3 data points for hexagonal.")
return
a, s_a, c, s_c, v, s_v, res_lin, res_nlin = \
fit_hexagonal_cell(data_to_fit_df, wavelength,
verbose=False)
cell_params = [a, a, c]
text_output += "a = {0:.5f} +/- {1:.5f} \n".format(a, s_a)
text_output += "c = {0:.5f} +/- {1:.5f} \n".format(c, s_c)
text_output += "V = {0:.5f} +/- {1:.5f} \n\n".format(v, s_v)
elif self.widget.comboBox_Symmetry.currentText() == 'orthorhombic':
if n_data_points < 4:
QtWidgets.QMessageBox.warning(
self.widget, "Warning",
"You need at least 4 data points for orthorhombic.")
return
a, s_a, b, s_b, c, s_c, v, s_v, res_lin, res_nlin = \
fit_orthorhombic_cell(data_to_fit_df, wavelength,
verbose=False)
cell_params = [a, b, c]
text_output += "a = {0:.5f} +/- {1:.5f} \n".format(a, s_a)
text_output += "b = {0:.5f} +/- {1:.5f} \n".format(b, s_b)
text_output += "c = {0:.5f} +/- {1:.5f} \n".format(c, s_c)
text_output += "V = {0:.5f} +/- {1:.5f} \n\n".format(v, s_v)
# output results
output_df = make_output_table(res_lin, res_nlin, data_to_fit_df)
text_output += 'Output table\n'
text_output += output_df[[
'h', 'k', 'l', 'twoth', 'dsp', 'twoth residue'
]].to_string()
text_output += '\n\nHat: influence for the fit result. \n'
text_output += ' 1 ~ large influence, 0 ~ no influence.\n'
text_output += output_df[['h', 'k', 'l', 'twoth', 'dsp',
'hat']].to_string()
text_output += '\n\nRstudent: how much the parameter would change' + \
' if deleted.\n'
text_output += output_df[['h', 'k', 'l', 'twoth', 'dsp',
'Rstudent']].to_string()
text_output += '\n\ndfFits: deletion diagnostic giving' + \
' the change in\n'
text_output += ' the predicted value twotheta.\n'
text_output += ' upon deletion of the data point as a ' + \
'multiple of\n'
text_output += ' the standard deviation for 1/d-spacing^2.\n'
text_output += output_df[['h', 'k', 'l', 'twoth', 'dsp',
'dfFits']].to_string()
text_output += '\n\ndfBetas: normalized residual\n'
text_output += output_df[['h', 'k', 'l', 'twoth', 'dsp',
'dfBetas']].to_string()
text_output += '\n\nNon-linear fit statistics \n'
text_output += lmfit.fit_report(res_nlin)
self.widget.plainTextEdit_UCFitOutput.setPlainText(text_output)
# save jcpds and save output file automatically.
# ask for filename. at the moment, simply overwrite
temp_dir = get_temp_dir(self.model.get_base_ptn_filename())
ext = "ucfit.jcpds"
#filen_t = self.model.make_filename(ext)
filen_t = make_filename(self.template_jcpds.file,
ext,
temp_dir=temp_dir)
filen_j = dialog_savefile(self.widget, filen_t)
if str(filen_j) == '':
return
self._write_to_jcpds(filen_j, cell_params)
# write to a textfile
ext = "ucfit.output"
#filen_t = self.model.make_filename(ext)
filen_t = make_filename(self.template_jcpds.file,
ext,
temp_dir=temp_dir)
filen_o = dialog_savefile(self.widget, filen_t)
if str(filen_o) == '':
return
with open(filen_o, "w") as f:
f.write(text_output)