def setup2nd_385_test():
fw = FitWidget.instance
pw = PlotWidget.instance
_path = r"C:\Users\dominik\Documents\RealTimeSync\Projects\2020-Bilirubin - 2nd half\UV-VIS\QY\new setup final\385 nm"
# _path = r"C:\Users\Dominik\Documents\MUNI\Organic Photochemistry\RealTimeSync\Projects\2020-Bilirubin - 2nd half\UV-VIS\QY\Test 2ZE new setup\better one"
fnames = [
'2Z high conc 01/2Z high conc 01.txt',
'2E high conc 01/2E high conc 01.txt'
]
paths = []
for fname in fnames:
paths.append(os.path.join(_path, fname))
au = AugmentedMatrix(len(paths), 1)
for i in range(len(paths)):
au.load_matrix(i, 0, paths[i])
# au[i, 0].reduce(t_dim=2)
# au[1, 0].crop_data(t1=3000)
m = au.get_aug_LFP_matrix()
pw.plot_matrix(m)
SVDWidget.instance.set_data(m)
fw.matrix = m
fw._au = au
Console.push_variables({'matrix': m})
return au
def setup_test():
fw = FitWidget.instance
pw = PlotWidget.instance
paths = []
path_reactors = r"C:\Users\Dominik\Documents\MUNI\Organic Photochemistry\Projects\Python scripts\Photoreaction kinetics"
paths.append(path_reactors + r"\Z_cut355.txt")
paths.append(path_reactors + r"\E_cut355.txt")
paths.append(path_reactors + r"\Z_cut470.txt")
au = AugmentedMatrix(len(paths), 1)
for i in range(len(paths)):
au.load_matrix(i, 0, paths[i])
au[i, 0].reduce(t_dim=2)
m = au.get_aug_LFP_matrix()
pw.plot_matrix(m)
fw.matrix = m
fw._au = au
Console.push_variables({'matrix': m})
return au
def setup2nd():
fw = FitWidget.instance
pw = PlotWidget.instance
_path = r"C:\Users\dominik\Documents\RealTimeSync\Projects\2020-Bilirubin - 2nd half\UV-VIS\QY\Test 2ZE"
# _path = r"C:\Users\dominik\Documents\RealTimeSync\Projects\2020-Bilirubin - 2nd half\UV-VIS\QY\Test 2ZE"
fnames = ['low conc 1Z.txt', 'high conc 1E.txt']
paths = []
for fname in fnames:
paths.append(os.path.join(_path, fname))
au = AugmentedMatrix(len(paths), 1)
for i in range(len(paths)):
au.load_matrix(i, 0, paths[i])
# au[i, 0].reduce(t_dim=2)
# au[1, 0].crop_data(t1=3000)
m = au.get_aug_LFP_matrix()
pw.plot_matrix(m)
SVDWidget.instance.set_data(m)
fw.matrix = m
fw._au = au
Console.push_variables({'matrix': m})
return au
def settup_baseline_test():
fw = FitWidget.instance
pw = PlotWidget.instance
_path = r"C:\Users\dominik\Documents\GitHub Repositories\Jupyter-Tutorials\Photoreaction kinetics"
fnames = ['D_test.txt', 'D_baseline_test.txt']
paths = []
for fname in fnames:
paths.append(os.path.join(_path, fname))
au = AugmentedMatrix(len(paths), 1)
for i in range(len(paths)):
au.load_matrix(i, 0, paths[i])
# au[i, 0].reduce(t_dim=2)
# au[1, 0].crop_data(t1=3000)
m = au.get_aug_LFP_matrix()
pw.plot_matrix(m)
SVDWidget.instance.set_data(m)
fw.matrix = m
fw._au = au
Console.push_variables({'matrix': m})
return au
def setup4():
fw = FitWidget.instance
pw = PlotWidget.instance
# path = r"C:\Users\Dominik\Documents\MUNI\Organic Photochemistry\Projects\2019-Bilirubin project\UV-VIS\QY measurement\Photodiode\new setup"
paths = []
path_reactors = r"C:\Users\dominik\Documents\Projects\Bilirubin\UV-Vis data\Kinetics Z degassed"
paths.append(path_reactors + r"\355 nm (both modules)\cut.txt")
paths.append(path_reactors + r"\355 nm (both modules)\cut.txt")
paths.append(path_reactors + r"\405 nm (both modules)\cut.txt")
paths.append(path_reactors + r"\450 nm (one module)\cut.txt")
paths.append(path_reactors + r"\470 nm (one module)\cut.txt")
paths.append(path_reactors +
r"\490 nm, then switched 355 nm (both modules)\cut490.txt")
paths.append(path_reactors +
r"\490 nm, then switched 355 nm (both modules)\cut355.txt")
au = AugmentedMatrix(len(paths), 1)
for i in range(len(paths)):
au.load_matrix(i, 0, paths[i])
au[i, 0].reduce(t_dim=2)
m = au.get_aug_LFP_matrix()
pw.plot_matrix(m)
fw.matrix = m
fw._au = au
Console.push_variables({'matrix': m})
return au
def change_to_fitted_data(self):
fw = FitWidget.instance
pw = PlotWidget.instance
for i in range(self.r):
C = self._C_indiv(i)
self[i, 0].Y = C @ self.ST_aug
self.construct_aug_matrix(True)
m = self.get_aug_LFP_matrix()
pw.plot_matrix(m)
fw.matrix = m
fw._au = self
Console.push_variables({'matrix': m})
def update_model_par_count(self, update_after_fit=False):
"""Updates text boxes from current model params and 'adds' or removes fields if necessary."""
params_count = self.current_model.params.__len__()
if not update_after_fit:
species_count = self.current_model.n
cb_fill_list = ['Unknown (MCR-ALS)'] + [
self.current_model.species_names[i]
for i in range(species_count)
]
for i in range(self.max_species):
cur_idx = self.C_conc_profile_list[i].currentIndex()
self.C_conc_profile_list[i].clear()
self.C_conc_profile_list[i].addItems(cb_fill_list)
self.C_conc_profile_list[i].setCurrentIndex(
cur_idx if cur_idx >= 0 else 0)
for i in range(self.max_params):
visible = params_count > i
self.params_list[i].setVisible(visible)
self.lower_bound_list[i].setVisible(visible)
self.value_list[i].setVisible(visible)
self.upper_bound_list[i].setVisible(visible)
self.fixed_list[i].setVisible(visible)
self.error_list[i].setVisible(visible)
values_errors = np.zeros((params_count, 2), dtype=np.float32)
for i, p in enumerate(self.current_model.params.values()):
self.params_list[i].setText(p.name)
self.lower_bound_list[i].setText(f'{p.min:.3g}')
self.upper_bound_list[i].setText(f'{p.max:.3g}')
self.value_list[i].setText(f'{p.value:.6g}')
self.fixed_list[i].setChecked(not p.vary)
self.error_list[i].setText(
f'{p.stderr:.2g}' if p.stderr is not None else '')
values_errors[i, 0] = p.value
values_errors[i, 1] = p.stderr if p.stderr is not None else 0
if self.fitter.minimizer is not None and update_after_fit:
self.fit_result = FitResult(self.fitter.last_result,
self.fitter.minimizer, values_errors,
self.current_model)
Console.push_variables({'fit': self.fit_result})
def setup_matrix(self, matrix, *args, **kwargs):
if matrix is None or not isinstance(matrix, (LFP_matrix, str)):
raise ValueError(
f"matrix cannot be None or have to be type of {type(LFP_matrix)}"
)
if isinstance(matrix, str):
matrix = lfp_parser.parse_file(matrix)
self.matrix = matrix
self.plot_widget.plot_matrix(self.matrix, **kwargs)
self.SVD_widget.set_data(self.matrix)
Console.push_variables({'matrix': self.matrix})
self.fit_widget.matrix = self.matrix
self.fit_widget.init_matrices()
tail = os.path.split(matrix.filename)[1]
name_of_file = os.path.splitext(tail)[0] # without extension
self.setWindowTitle(name_of_file + ' - Transient Spectra Analyzer')
def setup2(t1=1000):
fw = FitWidget.instance
pw = PlotWidget.instance
path = r"C:\Users\Dominik\Documents\MUNI\Organic Photochemistry\Projects\2019-Bilirubin project\UV-VIS\Irradiation kinetics\for MCR\Kinetics Z"
paths = []
paths.append(path + r"\355 nm MeOH aerated 2 LED modules\cut.txt")
paths.append(path + r"\375 nm MeOH aerated 2 LED modules\cut.txt")
paths.append(
r'C:\Users\Dominik\Documents\MUNI\Organic Photochemistry\Projects\2019-Bilirubin project\UV-VIS\QY measurement\Z start\365 nm LED irr, pinhole 3\kin.txt'
)
# paths.append(path + r"\375 nm MeOH aerated\cut.txt")
paths.append(path + r"\400 nm MeOH aerated\cut.txt")
paths.append(path + r"\450 nm MeOH aerated\cut.txt")
paths.append(path + r"\490 nm MeOH aerated\cut.txt")
# paths.append(path + r"\01_1000 uL MeOH\1000 uL bc cut.txt")
au = AugmentedMatrix(len(paths), 1)
for i in range(len(paths)):
au.load_matrix(i, 0, paths[i])
au[i, 0].crop_data(0, t1)
# au[0, 0].crop_data(0, t1)
# au[1, 0].crop_data(0, t1)
# au[2, 0].crop_data(0, t1)
m = au.get_aug_LFP_matrix()
pw.plot_matrix(m)
fw.matrix = m
fw._au = au
Console.push_variables({'matrix': m})
return au
def setup3_half():
fw = FitWidget.instance
pw = PlotWidget.instance
path = r"C:\Users\Dominik\Documents\MUNI\Organic Photochemistry\Projects\2019-Bilirubin project\UV-VIS\QY measurement\Photodiode\new setup"
# path = r"C:\Users\dominik\Documents\Projects\Bilirubin\new setup"
paths = []
# paths.append(path + r"\Z 330 nm\cut.txt")
# paths.append(path + r"\E 330 nm\cut.txt")
#
# paths.append(path + r"\Z 375 nm\cut.txt")
#
# paths.append(path + r"\Z 400 nm\cut.txt")
# paths.append(path + r"\E 400 nm\cut.txt")
#
# paths.append(path + r"\Z 450 nm\cut.txt")
#
# paths.append(path + r"\Z 480 nm\cut.txt")
# paths.append(path + r"\E 480 nm\cut.txt")
paths.append(path + r"\Z 350p\cut.txt")
paths.append(path + r"\E 350p\cut.txt")
paths.append(path + r"\Z 410p\cut.txt")
paths.append(path + r"\E 410p\cut.txt")
paths.append(path + r"\Z 500p\cut.txt")
paths.append(path + r"\E 500p\cut.txt")
path += r"\reactor LEDs"
#
paths.append(path + r"\Z 355\cut.txt")
paths.append(path + r"\Z 400\cut.txt")
# paths.append(path + r"\450 nm (one module)\cut.txt")
# paths.append(path + r"\470 nm (one module)\cut.txt")
# paths.append(path + r"\Z 490\cut.txt")
#
paths.append(path + r"\HL 355\cut.txt")
paths.append(path + r"\HL 400\cut.txt")
au = AugmentedMatrix(len(paths), 1)
for i in range(len(paths)):
au.load_matrix(i, 0, paths[i])
# au[i, 0].reduce(t_dim=2)
au[-4, 0].crop_data(t1=3000)
au[-3, 0].crop_data(t1=3000)
m = au.get_aug_LFP_matrix()
m.wavelengths += 230
pw.plot_matrix(m)
fw.matrix = m
fw._au = au
Console.push_variables({'matrix': m})
return au
def setup3():
fw = FitWidget.instance
pw = PlotWidget.instance
path = r"C:\Users\Dominik\Documents\MUNI\Organic Photochemistry\Projects\2019-Bilirubin project\UV-VIS\QY measurement\Photodiode\new setup"
# path = r"C:\Users\dominik\Documents\Projects\Bilirubin\UV-Vis data"
paths = []
paths.append(path + r"\Z 330 nm\cut.txt")
paths.append(path + r"\E 330 nm\cut.txt")
paths.append(path + r"\Z 375 nm\cut.txt")
paths.append(path + r"\Z 400 nm\cut.txt")
paths.append(path + r"\E 400 nm\cut.txt")
paths.append(path + r"\Z 450 nm\cut.txt")
paths.append(path + r"\Z 480 nm\cut.txt")
paths.append(path + r"\E 480 nm\cut.txt")
# path_reactors = r"C:\Users\dominik\Documents\Projects\Bilirubin\UV-Vis data\Kinetics Z degassed"
path += r"\reactor LEDs"
path_reactors = r"C:\Users\Dominik\Documents\MUNI\Organic Photochemistry\Projects\2019-Bilirubin project\UV-VIS\Irradiation kinetics\for MCR\Kinetics Z degassed"
# #
# #
# # paths.append(path_reactors + r"\355 nm (both modules)\cut.txt")
# # paths.append(path_reactors + r"\375 nm (both modules)\cut.txt")
# # paths.append(path_reactors + r"\405 nm (both modules)\cut.txt")
# # paths.append(path_reactors + r"\450 nm (one module)\cut.txt")
# # paths.append(path_reactors + r"\470 nm (one module)\cut.txt")
# #
# # paths.append(path_reactors + r"\490 nm, then switched 355 nm (both modules)\cut490.txt")
# # paths.append(path_reactors + r"\490 nm, then switched 355 nm (both modules)\cut355.txt")
paths.append(path + r"\Z 355\cut.txt")
paths.append(path + r"\Z 400\cut.txt")
paths.append(path_reactors + r"\450 nm (one module)\cut.txt")
paths.append(path_reactors + r"\470 nm (one module)\cut.txt")
paths.append(path + r"\Z 490\cut.txt")
#
paths.append(path + r"\HL 355\cut.txt")
paths.append(path + r"\HL 400\cut.txt")
# paths.append(path_reactors + r"\450 nm (one module)\cut.txt")
# paths.append(path_reactors + r"\470 nm (one module)\cut.txt")
au = AugmentedMatrix(len(paths), 1)
for i in range(len(paths)):
au.load_matrix(i, 0, paths[i])
# au[i, 0].reduce(t_dim=2)
au[-7, 0].crop_data(t1=3000)
m = au.get_aug_LFP_matrix()
m.wavelengths += 230
pw.plot_matrix(m)
fw.matrix = m
fw._au = au
Console.push_variables({'matrix': m})
return au
def __init__(self, parent=None):
super(fMain, self).__init__(parent)
self.setWindowTitle("Transient Spectra Analyzer")
self.resize(1800, 1000)
self.console = Console(self)
self.matrix = None # object of LFP matrix
self.addDockWidget(Qt.RightDockWidgetArea, self.console)
# fixing the resize bug https://stackoverflow.com/questions/48119969/qdockwidget-splitter-jumps-when-qmainwindow-resized
# self.resizeDocks([self.dockTreeWidget], [270], Qt.Horizontal)
self.resizeDocks([self.console], [200], Qt.Horizontal)
# self.setCorner(Qt.BottomLeftCorner, Qt.LeftDockWidgetArea)
self.coor_label = QLabel() # coordinates
self.plot_widget = PlotWidget(
set_coordinate_func=self.coor_label.setText, parent=self)
self.SVD_widget = SVDWidget(self)
self.fit_widget = FitWidget(None, self)
self.tabWidget = QtWidgets.QTabWidget(self)
self.tabWidget.addTab(self.plot_widget, "Data")
self.tabWidget.addTab(self.SVD_widget, "SVD + EFA")
self.tabWidget.addTab(self.fit_widget, "Fit")
self.tabWidget.currentChanged.connect(self.tabChanged)
self.setCentralWidget(self.tabWidget)
self.createStatusBar()
self.logger = Logger(self.console.show_message,
self.statusBar().showMessage)
sys.stdout = Transcript()
self.user_namespace = UserNamespace(self)
self.setMenuBar(MenuBar(self))
Settings.load()
self.update_recent_files()
Console.push_variables({'main_widget': self})
Console.execute_command(
"from LFP_matrix import LFP_matrix\nimport fitmodels as m\n"
"import matplotlib.pyplot as plt\nfrom Widgets.fit_widget import FitWidget\n"
"import augmentedmatrix")
Console.push_variables({'pw': self.plot_widget})
Console.push_variables({'fw': self.fit_widget})
Console.push_variables({'sw': self.SVD_widget})
def __init__(self, matrix=None, parent=None):
super(FitWidget, self).__init__(parent)
self.setupUi(self)
FitWidget.instance = self
# reference to matrix in parent - instance of LFP_matrix
self.matrix = matrix
# visible ST and C matrices - used as initial estimates for fitter
self._ST = None
self._C = None
self.D_fit = None
self.fit_result = None
self.plot_chirp = True
self.fitter = Fitter()
self.t_fit = None # task fit
self._au = None # augmented matrix
self.C_matrix_constraints = []
Console.push_variables({'f': self.fitter})
self.fit_plot_layout = FitLayout(None, self)
self.main_layout.addWidget(self.fit_plot_layout)
self.current_model = None
self.classes = []
# get all models from fitmodels, get classes that inherits from Model base class and sort them by name
# and number of species
classes = inspect.getmembers(sys.modules[fitmodels.__name__],
inspect.isclass)
tuples = list(
filter(lambda tup: issubclass(tup[1], fitmodels._Model), classes))
# self.models = sorted(list(map(lambda tup: tup[1], tuples)), key=lambda cls: (cls.name, cls.n))
_classes = list(map(lambda tup: tup[1]._class, tuples))
for cls in _classes:
if cls == '-class-':
continue
if cls not in self.classes:
self.classes.append(cls)
self.classes.sort()
# fill the combo box items with model names
self.cbClass.addItems(self.classes)
self.methods = [ # minimizing algorithms
{
'name': 'Levenberg–Marquardt',
'abbr': 'leastsq'
}, {
'name': 'Trust-Region Reflective method',
'abbr': 'least_squares'
}, {
'name': 'Nelder-Mead, Simplex method',
'abbr': 'nelder'
}, {
'name': 'L-BFGS-B',
'abbr': 'lbfgsb'
}, {
'name': 'Powell',
'abbr': 'powell'
}
]
self.regressors = [
{
'name': 'OLS (Ordinary Least Squares)',
'abbr': 'ols'
},
{
'name': 'Ridge (fast OLS with Tikhonov regularization)',
'abbr': 'ridge'
},
{
'name': 'NNLS (Non-Negative Least Squares)',
'abbr': 'nnls'
},
]
# fill the combo box items with method names
self.cbMethod.addItems(map(lambda m: m['name'], self.methods))
self.cbMethod.setCurrentIndex(1)
self.cbRegressorC.addItems(map(lambda m: m['name'], self.regressors))
self.cbRegressorS.addItems(map(lambda m: m['name'], self.regressors))
self.btnFit.clicked.connect(self.fit)
self.cbClass.currentIndexChanged.connect(self.model_class_changed)
self.cbModel.currentIndexChanged.connect(self.model_changed)
self.sbN.valueChanged.connect(self.sbN_value_changed)
self.sbN.setMaximum(self.max_species)
self.btnC_calc.clicked.connect(self.calc_C)
self.btnST_calc.clicked.connect(self.calc_ST)
self.btnOneIt.clicked.connect(self.one_iter_clicked)
self.btnSimulateModel.clicked.connect(self.simulate_model_clicked)
self.btnSetNMFSol.clicked.connect(self.set_NMF_solution)
def _open_model_sett():
self.update_params()
self.current_model.open_model_settings()
self.update_model_par_count()
self.btnModelSettings.clicked.connect(_open_model_sett)
# soft modeling
self.species_label_list = []
self.S_constrain_list = []
self.ST_fix_list = []
self.C_constrain_list = []
self.C_conc_profile_list = []
self.C_fix_list = []
for i in range(self.max_species):
self.species_label_list.append(QLabel(f'{i + 1}.'))
self.S_constrain_list.append(ComboBoxCB())
self.ST_fix_list.append(QCheckBox())
self.C_constrain_list.append(ComboBoxCB())
self.C_conc_profile_list.append(QComboBox())
self.C_fix_list.append(QCheckBox())
self.S_constrain_list[i].setSizePolicy(QSizePolicy.Ignored,
QSizePolicy.Preferred)
self.C_constrain_list[i].setSizePolicy(QSizePolicy.Ignored,
QSizePolicy.Preferred)
self.C_conc_profile_list[i].setSizePolicy(QSizePolicy.Ignored,
QSizePolicy.Preferred)
self.S_constrain_list[i].setMinimumSize(1, 1)
self.C_constrain_list[i].setMinimumSize(1, 1)
self.C_conc_profile_list[i].setMinimumSize(1, 1)
# self.species_list[i].setAlignment(Qt.AlignLeft)
# Qt.AlignCenter
self.glSC_setup.addWidget(self.species_label_list[i], i + 1, 0,
Qt.AlignLeft, 1)
self.glSC_setup.addWidget(self.S_constrain_list[i], i + 1, 1,
Qt.AlignLeft, 1)
self.glSC_setup.addWidget(self.ST_fix_list[i], i + 1, 2,
Qt.AlignLeft, 1)
self.glSC_setup.addWidget(self.C_constrain_list[i], i + 1, 4,
Qt.AlignLeft, 1)
self.glSC_setup.addWidget(self.C_conc_profile_list[i], i + 1, 5,
Qt.AlignLeft, 1)
self.glSC_setup.addWidget(self.C_fix_list[i], i + 1, 6,
Qt.AlignLeft, 1)
# kinetic hard modeling
self.params_list = []
self.lower_bound_list = []
self.value_list = []
self.upper_bound_list = []
self.fixed_list = []
self.error_list = []
for i in range(self.max_params):
self.params_list.append(QLabel())
self.lower_bound_list.append(QLineEdit())
self.value_list.append(QLineEdit())
self.upper_bound_list.append(QLineEdit())
self.fixed_list.append(QCheckBox())
self.error_list.append(QLineEdit())
self.glKinetics.addWidget(self.params_list[i], i + 1, 0, 1, 1)
self.glKinetics.addWidget(self.lower_bound_list[i], i + 1, 1, 1, 1)
self.glKinetics.addWidget(self.value_list[i], i + 1, 2, 1, 1)
self.glKinetics.addWidget(self.upper_bound_list[i], i + 1, 3, 1, 1)
self.glKinetics.addWidget(self.fixed_list[i], i + 1, 4, 1, 1)
self.glKinetics.addWidget(self.error_list[i], i + 1, 5, 1, 1)
self.fixed_list[i].stateChanged.connect(self.fixed_checked_changed)
# setup_size_policy(self)
self.cbClass.setCurrentIndex(2)
self.model_class_changed()
self.cbModel.setCurrentIndex(7)
self.model_changed()
self.sbN_value_changed()