Select the desired parameters then click the Set button
") + self.modellist.setToolTip( + "Select the desired parameters then click the Set button
") self.pushButton_14 = QtWidgets.QPushButton(self.modeltab) self.pushButton_14.setGeometry(QtCore.QRect(240, 150, 80, 22)) self.pushButton_14.setObjectName("pushButton_14") @@ -625,7 +736,8 @@ def setupUi(self, Neuroptimus): self.dd_type.addItem("External") self.dd_type.currentIndexChanged.connect(self.sim_plat) self.dd_type.setToolTip("Simulator type") - self.lineEdit_folder2 = QtWidgets.QLineEdit(self.modeltab) #mod files line edit, next to check box + self.lineEdit_folder2 = QtWidgets.QLineEdit( + self.modeltab) # mod files line edit, next to check box self.lineEdit_folder2.setGeometry(QtCore.QRect(10, 150, 221, 22)) self.lineEdit_folder2.setObjectName("lineEdit_folder2") self.sim_path = QtWidgets.QLineEdit(self.modeltab) @@ -644,9 +756,7 @@ def setupUi(self, Neuroptimus): self.remover.setObjectName("remover") self.remover.setEnabled(False) - - - #model name label + # model name label self.model_name_label = QtWidgets.QLabel(self.modeltab) self.model_name_label.setGeometry(QtCore.QRect(10, 10, 300, 16)) font.setWeight(50) @@ -654,19 +764,17 @@ def setupUi(self, Neuroptimus): self.model_name_label.setObjectName("model_name_label") self.model_name_label.setText("Model Name") - #model name input + # model name input self.model_name_input = QtWidgets.QLineEdit(self.modeltab) self.model_name_input.setGeometry(QtCore.QRect(10, 30, 221, 22)) self.model_name_input.setObjectName("model_name_input") - #text placeholder + # text placeholder # self.model_name_input.setPlaceholderText("(for HippoUnit)") - self.hippoUnit_only_widgets.append(self.model_name_label) self.hippoUnit_only_widgets.append(self.model_name_input) - - #Simulator label + # Simulator label self.simulator_label = QtWidgets.QLabel(self.modeltab) self.simulator_label.setGeometry(QtCore.QRect(10, 10, 300, 16)) font.setWeight(50) @@ -674,52 +782,44 @@ def setupUi(self, Neuroptimus): self.simulator_label.setObjectName("simulator_label") self.simulator_label.setText("Simulator") - #Simulator input - - - - - + # Simulator input self.layout = QtWidgets.QGridLayout(self.modeltab) - - #1st row + + # 1st row # Modelname label , input self.layout.addWidget(self.model_name_label, 0, 0, 1, 1) self.layout.addWidget(self.model_name_input, 0, 1, 1, 4) - - - #2nd row - #simualtor label , dd_type + # 2nd row + # simualtor label , dd_type self.layout.addWidget(self.simulator_label, 1, 0, 1, 1) - self.layout.addWidget(self.dd_type, 1, 1, 1, 4) #Simulator Drop Down - + self.layout.addWidget(self.dd_type, 1, 1, 1, 4) # Simulator Drop Down - #3rd row + # 3rd row # label_24 , lineEdit_file2 , pushButton_15 , pushButton_13 - self.layout.addWidget(self.label_24, 2, 0, 1, 1) # label Model file - self.layout.addWidget(self.lineEdit_file2, 2, 1, 1, 3) #line edit hoc file - self.layout.addWidget(self.pushButton_15, 2, 4, 1, 1) # browse model file (non-hidden) - self.layout.addWidget(self.pushButton_13, 2, 5, 2, 1) # load model file - - #4th row + self.layout.addWidget(self.label_24, 2, 0, 1, 1) # label Model file + self.layout.addWidget(self.lineEdit_file2, 2, 1, 1, + 3) # line edit hoc file + # browse model file (non-hidden) + self.layout.addWidget(self.pushButton_15, 2, 4, 1, 1) + self.layout.addWidget(self.pushButton_13, 2, 5, 2, + 1) # load model file + + # 4th row # label_23 , load_mods_checkbox , lineEdit_folder2 , pushButton_14 hbox_load_mod = QtWidgets.QHBoxLayout() # Add the checkbox and label to the layout - hbox_load_mod.addWidget(self.load_mods_checkbox, 0, QtCore.Qt.AlignLeft) + hbox_load_mod.addWidget(self.load_mods_checkbox, 0, + QtCore.Qt.AlignLeft) hbox_load_mod.addWidget(self.label_23, 1, QtCore.Qt.AlignLeft) # Set the horizontal stretch factor of the checkbox to 0 and the label to 1 hbox_load_mod.setStretch(0, 0) hbox_load_mod.setStretch(1, 1) self.layout.addLayout(hbox_load_mod, 3, 0, 1, 2) - - - - self.layout.addWidget(self.lineEdit_folder2, 3, 2, 1, 2) self.layout.addWidget(self.pushButton_14, 3, 4, 1, 1) @@ -729,16 +829,17 @@ def setupUi(self, Neuroptimus): font.setPointSize(12) self.param_table_label.setFont(font) self.param_table_label.setObjectName("param_table_label") - self.param_table_label.setText("Selection of parameters to be optimized") - - self.pushButton_16.setMinimumSize(QtCore.QSize(0, 40)) + self.param_table_label.setText( + "Selection of parameters to be optimized") + self.pushButton_16.setMinimumSize(QtCore.QSize(0, 40)) self.layout.addWidget(QHLine(), 4, 0, 1, 6) # Add horizontal line self.layout.addWidget(self.param_table_label, 5, 0, 1, 6) self.layout.addWidget(self.modellist, 6, 0, 10, 3) - self.layout.addWidget(self.pushButton_16, 6, 3, 2, 2) #define function + self.layout.addWidget(self.pushButton_16, 6, 3, 2, + 2) # define function self.layout.addWidget(self.sim_param, 5, 2, 1, 1) self.layout.addWidget(self.setter, 16, 0, 1, 1) self.layout.addWidget(self.remover, 16, 1, 1, 1) @@ -746,17 +847,16 @@ def setupUi(self, Neuroptimus): self.modeltab.setLayout(self.layout) self.tabwidget.addTab(self.modeltab, "Model Tab") - + for widget in self.modeltab.findChildren(QtWidgets.QPushButton): - widget.setSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) + widget.setSizePolicy(QtWidgets.QSizePolicy.Fixed, + QtWidgets.QSizePolicy.Fixed) - #editing self.pushButton_13 to have double vertical size + # editing self.pushButton_13 to have double vertical size self.pushButton_13.setMinimumSize(QtCore.QSize(0, 40)) self.pushButton_13.setMaximumSize(QtCore.QSize(16777215, 80)) - - - #sim tab 3 + # sim tab 3 self.tabwidget.addTab(self.modeltab, "") self.simtab = QtWidgets.QWidget() self.simtab.setObjectName("simtab") @@ -864,10 +964,6 @@ def setupUi(self, Neuroptimus): font.setWeight(50) self.label_55.setFont(font) self.label_55.setObjectName("label_55") - - - - # Create a new QGridLayout layout self.settings_tab_grid = QtWidgets.QGridLayout(self.simtab) @@ -875,17 +971,18 @@ def setupUi(self, Neuroptimus): # Create a group box for the stimulus protocol widgets self.stim_group = QtWidgets.QGroupBox("Stimulus Mode") stim_layout = QtWidgets.QVBoxLayout() - stim_layout.addWidget(self.label_55) #stim protocol + stim_layout.addWidget(self.label_55) # stim protocol stim_layout.addWidget(self.stimprot) - stim_layout.addWidget(self.label_49) #stim type - stim_layout.addWidget(self.stimulus_type) - stim_layout.addWidget(self.base_dir_controll9) #amplitude(s) push button + stim_layout.addWidget(self.label_49) # stim type + stim_layout.addWidget(self.stimulus_type) + # amplitude(s) push button + stim_layout.addWidget(self.base_dir_controll9) self.stim_group.setLayout(stim_layout) # Add the stimulus protocol group box to the self.settings_tab_grid layout self.settings_tab_grid.addWidget(self.stim_group, 0, 0, 5, 1) - #hide stim_group but keep its place in the grid + # hide stim_group but keep its place in the grid # stim_group.hide() # Create a group box for the delay and duration widgets @@ -940,17 +1037,19 @@ def setupUi(self, Neuroptimus): # Add the simulation group box to the self.settings_tab_grid layout self.settings_tab_grid.addWidget(self.sim_group, 0, 2, 6, 1) - ## container for the groups that are only used for Neuroptimus - self.neuroptimus_settings_widgets = [self.stim_group, self.time_group, self.pos_group, self.rec_group, self.sim_group] - - - - + # container for the groups that are only used for Neuroptimus + self.neuroptimus_settings_widgets = [ + self.stim_group, + self.time_group, + self.pos_group, + self.rec_group, + self.sim_group, + ] # container for the widgets that are only used for HippoUnit self.hippounit_settings_widgets = [] - #HippoUnit: output directory + # HippoUnit: output directory self.output_dir_label = QtWidgets.QLabel(self.simtab) self.output_dir_label.setGeometry(QtCore.QRect(10, 30, 300, 16)) font.setWeight(50) @@ -958,48 +1057,42 @@ def setupUi(self, Neuroptimus): self.output_dir_label.setObjectName("output_dir_label") self.output_dir_label.setText("HippoUnit Output Directory") - - self.output_dir_input = QtWidgets.QLineEdit(self.simtab) self.output_dir_input.setGeometry(QtCore.QRect(10, 50, 221, 22)) self.output_dir_input.setObjectName("output_dir_input") - #add browse button next to the output input + # add browse button next to the output input self.output_dir_browse = QtWidgets.QPushButton(self.simtab) self.output_dir_browse.setGeometry(QtCore.QRect(240, 50, 80, 22)) self.output_dir_browse.setObjectName("output_dir_browse") self.output_dir_browse.setText("Browse") - #connect the browse button to the browsse function to get the output directory + # connect the browse button to the browsse function to get the output directory self.output_dir_browse.clicked.connect(self.set_hippounit_output_dir) - - - #add output_dir_input and output_dir_browse to horizental group box + # add output_dir_input and output_dir_browse to horizental group box self.output_dir_group = QtWidgets.QGroupBox("") output_dir_layout = QtWidgets.QHBoxLayout() output_dir_layout.addWidget(self.output_dir_input) output_dir_layout.addWidget(self.output_dir_browse) self.output_dir_group.setLayout(output_dir_layout) - - #add output_dir_label to the hippounit_settings_widgets list - + # add output_dir_label to the hippounit_settings_widgets list self.hippounit_settings_widgets.append(self.output_dir_label) # self.hippounit_settings_widgets.append(self.output_dir_input) - #add output_dir_browse to the hippounit_settings_widgets list + # add output_dir_browse to the hippounit_settings_widgets list # self.hippounit_settings_widgets.append(self.output_dir_browse) self.hippounit_settings_widgets.append(self.output_dir_group) - - #HippoUnit: template name + # HippoUnit: template name self.template_name_label = QtWidgets.QLabel(self.simtab) self.template_name_label.setGeometry(QtCore.QRect(10, 70, 300, 16)) font.setWeight(50) self.template_name_label.setFont(font) self.template_name_label.setObjectName("template_name_label") - self.template_name_label.setText("Template Name (leave empty if no template is used)") + self.template_name_label.setText( + "Template Name (leave empty if no template is used)") self.template_name_input = QtWidgets.QLineEdit(self.simtab) self.template_name_input.setGeometry(QtCore.QRect(10, 90, 221, 22)) @@ -1008,7 +1101,7 @@ def setupUi(self, Neuroptimus): self.hippounit_settings_widgets.append(self.template_name_label) self.hippounit_settings_widgets.append(self.template_name_input) - #HippoUnit: v_init + # HippoUnit: v_init self.v_init_label = QtWidgets.QLabel(self.simtab) self.v_init_label.setGeometry(QtCore.QRect(10, 110, 300, 16)) font.setWeight(50) @@ -1023,7 +1116,7 @@ def setupUi(self, Neuroptimus): self.hippounit_settings_widgets.append(self.v_init_label) self.hippounit_settings_widgets.append(self.v_init_input) - #HippoUnit: celsius + # HippoUnit: celsius self.celsius_label = QtWidgets.QLabel(self.simtab) self.celsius_label.setGeometry(QtCore.QRect(10, 150, 300, 16)) font.setWeight(50) @@ -1038,7 +1131,7 @@ def setupUi(self, Neuroptimus): self.hippounit_settings_widgets.append(self.celsius_label) self.hippounit_settings_widgets.append(self.celsius_input) - #HippoUnit: soma + # HippoUnit: soma self.soma_label = QtWidgets.QLabel(self.simtab) self.soma_label.setGeometry(QtCore.QRect(10, 190, 300, 16)) @@ -1054,8 +1147,7 @@ def setupUi(self, Neuroptimus): self.hippounit_settings_widgets.append(self.soma_label) self.hippounit_settings_widgets.append(self.soma_input) - - #creat a groub box for the hippounit settings + # creat a groub box for the hippounit settings self.hippounit_group = QtWidgets.QGroupBox("HippoUnit Settings") self.hippounit_group.setEnabled(False) hippounit_layout = QtWidgets.QVBoxLayout() @@ -1063,26 +1155,32 @@ def setupUi(self, Neuroptimus): hippounit_layout.addWidget(widget) self.hippounit_group.setLayout(hippounit_layout) - #add the hippounit group box to the self.settings_tab_grid layout + # add the hippounit group box to the self.settings_tab_grid layout self.settings_tab_grid.addWidget(self.hippounit_group, 6, 1, 7, 1) self.hippounit_group.hide() - #add these group boxes except hippounit_group to a list - self.simtab_neuroptimus_group_boxes = [self.stim_group, self.time_group, self.pos_group, self.rec_group, self.sim_group] - + # add these group boxes except hippounit_group to a list + self.simtab_neuroptimus_group_boxes = [ + self.stim_group, + self.time_group, + self.pos_group, + self.rec_group, + self.sim_group, + ] for widget in self.simtab.findChildren(QtWidgets.QPushButton): - widget.setSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) + widget.setSizePolicy(QtWidgets.QSizePolicy.Fixed, + QtWidgets.QSizePolicy.Fixed) - #setting groupbox titles only to bold centered + # setting groupbox titles only to bold centered for widget in self.simtab.findChildren(QtWidgets.QGroupBox): widget.setAlignment(QtCore.Qt.AlignCenter) widget.setStyleSheet("QGroupBox {font-weight: bold;}") # Set the layout of the widget to the new QGridLayout self.simtab.setLayout(self.settings_tab_grid) - - #fit tab 4 + + # fit tab 4 self.tabwidget.addTab(self.simtab, "") self.fittab = QtWidgets.QWidget() self.fittab.setObjectName("fittab") @@ -1127,35 +1225,32 @@ def setupUi(self, Neuroptimus): self.fittab_help_icon.setAlignment(QtCore.Qt.AlignCenter) self.fittab_help = QtWidgets.QLabel("",self.fittab) self.fittab_help.setGeometry(350, 260, 30, 30)""" - self.pushButton_normalize.setToolTip("Rescale the active fitness weights sum to 1
") - self.fitlist.setToolTip("Fitness functions with 0 weights considered inactive
") - self.core=Core.coreModul() - + self.pushButton_normalize.setToolTip( + "Rescale the active fitness weights sum to 1
") + self.fitlist.setToolTip( + "Fitness functions with 0 weights considered inactive
") + self.core = Core.coreModul() + self.fit_tab_grid = QtWidgets.QGridLayout(self.fittab) self.fit_tab_grid.addWidget(self.pushButton_normalize, 0, 2, 1, 1) self.fit_tab_grid.addWidget(self.fitlist, 1, 0, 5, 7) - #make the table widget stretch to fill the available space + # make the table widget stretch to fill the available space # self.fit_tab_grid.setColumnStretch(0, 1) # self.fit_tab_grid.setRowStretch(0, 1) # self.fitlist.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents) - #decrease size of 2nd column to be small + # decrease size of 2nd column to be small # self.fit_tab_grid.setColumnMinimumWidth(0, 200) - - - #stretch first column to fill text - + # stretch first column to fill text # Create a new QGroupBox for the spike detection parameters # self.spike_group_box = QtWidgets.QGroupBox("Spike Detection Parameters") - #make the group panel flat - + # make the group panel flat - #set the font to be bold for the group box title + # set the font to be bold for the group box title # self.spike_group_box.setStyleSheet("QGroupBox { font-weight: bold; }") - # # Create a new QGridLayout for the spike detection group box # spike_group_layout = QtWidgets.QVBoxLayout(self.spike_group_box) @@ -1165,37 +1260,39 @@ def setupUi(self, Neuroptimus): # spike_group_layout.addWidget(self.label_70) # spike_group_layout.addWidget(self.spike_window) - - # self.fit_tab_grid.addWidget(self.spike_group_box, 1, 3, 2, 4) - # Set the layout of the spike detection group box # self.spike_group_box.setLayout(spike_group_layout) - - #HippoUnit: Test specific settings + # HippoUnit: Test specific settings # #Create a table with 3 columns and a label above the table HippoUnit Test-Specific Settings - self.hippounit_test_specific_settings_label = QtWidgets.QLabel(self.fittab) - self.hippounit_test_specific_settings_label.setGeometry(QtCore.QRect(330, 260, 300, 16)) + self.hippounit_test_specific_settings_label = QtWidgets.QLabel( + self.fittab) + self.hippounit_test_specific_settings_label.setGeometry( + QtCore.QRect(330, 260, 300, 16)) self.hippounit_test_specific_settings_label.setFont(font) - self.hippounit_test_specific_settings_label.setObjectName("test_specific_settings_label") - self.hippounit_test_specific_settings_label.setText("Fitness function settings") - + self.hippounit_test_specific_settings_label.setObjectName( + "test_specific_settings_label") + self.hippounit_test_specific_settings_label.setText( + "Fitness function settings") # #add the label and the table to the self.fit_tab_grid layout - self.fit_tab_grid.addWidget(self.hippounit_test_specific_settings_label, 7, 0, 1, 7) + self.fit_tab_grid.addWidget( + self.hippounit_test_specific_settings_label, 7, 0, 1, 7) # #stretch the table to fill the available space self.fit_tab_grid.setColumnStretch(5, 2) self.fit_tab_grid.setRowStretch(5, 1) - - #create new table under it + # create new table under it self.test_specific_settings_table = QtWidgets.QTableWidget(self.fittab) - self.test_specific_settings_table.setObjectName("hippounit_test_sections_names_table") + self.test_specific_settings_table.setObjectName( + "hippounit_test_sections_names_table") self.test_specific_settings_table.setColumnCount(2) - self.test_specific_settings_table.setHorizontalHeaderLabels(["Property", "Value"]) - self.test_specific_settings_table.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.Stretch) + self.test_specific_settings_table.setHorizontalHeaderLabels( + ["Property", "Value"]) + self.test_specific_settings_table.horizontalHeader( + ).setSectionResizeMode(QtWidgets.QHeaderView.Stretch) self.test_specific_settings_table.verticalHeader().setVisible(False) self.test_specific_settings_table.setRowCount(6) self.test_specific_settings_table.setAlternatingRowColors(False) @@ -1203,79 +1300,77 @@ def setupUi(self, Neuroptimus): self.test_specific_settings_table.setShowGrid(True) self.test_specific_settings_table.setWordWrap(True) self.test_specific_settings_table.setCornerButtonEnabled(True) - self.test_specific_settings_table.horizontalHeader().setStretchLastSection(True) - #column size resizeable with dragging the column border - self.test_specific_settings_table.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.Interactive) - self.test_specific_settings_table.horizontalHeader().setStretchLastSection(True) - self.test_specific_settings_table.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.Stretch) - self.test_specific_settings_table.horizontalHeader().setSectionResizeMode(0, QtWidgets.QHeaderView.ResizeToContents) - - - - #add it to the self.fit_tab_grid layout - self.fit_tab_grid.addWidget(self.test_specific_settings_table, 8, 0, 2, 7) - #stretch it to fill the available space + self.test_specific_settings_table.horizontalHeader( + ).setStretchLastSection(True) + # column size resizeable with dragging the column border + self.test_specific_settings_table.horizontalHeader( + ).setSectionResizeMode(QtWidgets.QHeaderView.Interactive) + self.test_specific_settings_table.horizontalHeader( + ).setStretchLastSection(True) + self.test_specific_settings_table.horizontalHeader( + ).setSectionResizeMode(QtWidgets.QHeaderView.Stretch) + self.test_specific_settings_table.horizontalHeader( + ).setSectionResizeMode(0, QtWidgets.QHeaderView.ResizeToContents) + + # add it to the self.fit_tab_grid layout + self.fit_tab_grid.addWidget(self.test_specific_settings_table, 8, 0, 2, + 7) + # stretch it to fill the available space # self.fit_tab_grid.setColumnStretch(5, 2) # self.fit_tab_grid.setRowStretch(5, 1) # row 0 Spike detection threshold self.test_specific_settings_table.insertRow(0) - self.test_specific_settings_table.setItem(0, 0, QtWidgets.QTableWidgetItem("Spike detection threshold (mV) ")) - self.test_specific_settings_table.setItem(0, 1, QtWidgets.QTableWidgetItem("0")) - self.test_specific_settings_table.item(0, 0).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.setItem( + 0, 0, + QtWidgets.QTableWidgetItem("Spike detection threshold (mV) ")) + self.test_specific_settings_table.setItem( + 0, 1, QtWidgets.QTableWidgetItem("0")) + self.test_specific_settings_table.item(0, 0).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(0, 0).setForeground(BLACK) # row 1 Spike Window (ms) self.test_specific_settings_table.insertRow(1) - self.test_specific_settings_table.setItem(1, 0, QtWidgets.QTableWidgetItem("Spike Window (ms)")) - self.test_specific_settings_table.setItem(1, 1, QtWidgets.QTableWidgetItem("1.0")) - self.test_specific_settings_table.item(1, 0).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.setItem( + 1, 0, QtWidgets.QTableWidgetItem("Spike Window (ms)")) + self.test_specific_settings_table.setItem( + 1, 1, QtWidgets.QTableWidgetItem("1.0")) + self.test_specific_settings_table.item(1, 0).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(1, 0).setForeground(BLACK) - - - + # appending these components to hippounit_test_specific_settings_widgets + self.hippounit_settings_widgets.append( + self.hippounit_test_specific_settings_label) - #appending these components to hippounit_test_specific_settings_widgets - self.hippounit_settings_widgets.append(self.hippounit_test_specific_settings_label) - - self.hippounit_settings_widgets.append(self.test_specific_settings_table) + self.hippounit_settings_widgets.append( + self.test_specific_settings_table) + self.hippounit_test_specific_settings_label.setAlignment( + QtCore.Qt.AlignCenter) + self.hippounit_test_specific_settings_label.setStyleSheet( + "QGroupBox {font-weight: bold;}") + self.test_specific_settings_table.horizontalHeader( + ).setSectionResizeMode(QtWidgets.QHeaderView.Interactive) + self.test_specific_settings_table.horizontalHeader( + ).setStretchLastSection(True) + self.test_specific_settings_table.horizontalHeader( + ).setSectionResizeMode(QtWidgets.QHeaderView.Stretch) + self.test_specific_settings_table.horizontalHeader( + ).setSectionResizeMode(0, QtWidgets.QHeaderView.ResizeToContents) - self.hippounit_test_specific_settings_label.setAlignment(QtCore.Qt.AlignCenter) - self.hippounit_test_specific_settings_label.setStyleSheet("QGroupBox {font-weight: bold;}") - - - self.test_specific_settings_table.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.Interactive) - self.test_specific_settings_table.horizontalHeader().setStretchLastSection(True) - self.test_specific_settings_table.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.Stretch) - self.test_specific_settings_table.horizontalHeader().setSectionResizeMode(0, QtWidgets.QHeaderView.ResizeToContents) - - #block signals of the table to prevent the user from editing it + # block signals of the table to prevent the user from editing it self.fitlist.blockSignals(True) self.prepare_fitnessFunctions_table() self.fitlist.blockSignals(False) - #when a cell value is edited in the table, call fitchanged function + # when a cell value is edited in the table, call fitchanged function # self.fitlist.itemChanged.connect(self.fitchanged) self.fitlist.cellChanged.connect(self.fitchanged) - - - - - - - - - - - self.fittab.setLayout(self.fit_tab_grid) - - - - #run tab 5 + # run tab 5 self.tabwidget.addTab(self.fittab, "") self.runtab = QtWidgets.QWidget() self.runtab.setObjectName("runtab") @@ -1325,10 +1420,12 @@ def setupUi(self, Neuroptimus): self.algolist = QtWidgets.QTableWidget(self.runtab) self.algolist.setGeometry(QtCore.QRect(10, 120, 441, 321)) self.algolist.setObjectName("algolist") - #setting selection model to have always one active selected - self.algolist.setSelectionMode(QtWidgets.QAbstractItemView.SingleSelection) + # setting selection model to have always one active selected + self.algolist.setSelectionMode( + QtWidgets.QAbstractItemView.SingleSelection) self.algorithm_parameter_list = QtWidgets.QTableWidget(self.runtab) - self.algorithm_parameter_list.setGeometry(QtCore.QRect(470, 90, 241, 351)) + self.algorithm_parameter_list.setGeometry( + QtCore.QRect(470, 90, 241, 351)) self.algorithm_parameter_list.setObjectName("algorithm_parameter_list") self.label_60 = QtWidgets.QLabel(self.runtab) self.label_60.setGeometry(QtCore.QRect(470, 70, 200, 16)) @@ -1345,7 +1442,7 @@ def setupUi(self, Neuroptimus): grid = QtWidgets.QGridLayout(self.runtab) - grid.addWidget(self.label_59, 0, 0, 1, 2) #Algorithm label + grid.addWidget(self.label_59, 0, 0, 1, 2) # Algorithm label # group the push buttons in a tight horizontal group button_layout = QtWidgets.QHBoxLayout() @@ -1355,7 +1452,7 @@ def setupUi(self, Neuroptimus): button_layout.addWidget(self.pushButton_Bluepyopt) button_layout.addWidget(self.pushButton_Scipy) - #setting all the labels in the run tab to bold + # setting all the labels in the run tab to bold for widget in self.runtab.findChildren(QtWidgets.QLabel): font = QtGui.QFont() font.setFamily("Ubuntu") @@ -1363,52 +1460,54 @@ def setupUi(self, Neuroptimus): font.setBold(True) widget.setFont(font) - - # Creating and configuring the progress bar self.progressBar = QProgressBar(self.runtab) - self.progressBar.setGeometry(QtCore.QRect(10, 500, 441, 23)) - self.progressBar.setMinimum(0) # Set the minimum value of the progress bar - self.progressBar.setMaximum(100) # Set the maximum value of the progress bar - self.progressBar.setValue(0) # Set the initial value of the progress bar + self.progressBar.setGeometry(QtCore.QRect(10, 500, 441, 23)) + # Set the minimum value of the progress bar + self.progressBar.setMinimum(0) + # Set the maximum value of the progress bar + self.progressBar.setMaximum(100) + # Set the initial value of the progress bar + self.progressBar.setValue(0) # show the percentage: - self.progressBar.setFormat('%p%') # Display the percentage completed + self.progressBar.setFormat("%p%") # Display the percentage completed self.progressBar.setAlignment(QtCore.Qt.AlignCenter) # Center the text - self.progressBar.setStyleSheet("QProgressBar {border: 1px solid grey; border-radius: 5px; text-align: center;} QProgressBar::chunk {background-color: #05B8CC; width: 20px;}") - + self.progressBar.setStyleSheet( + "QProgressBar {border: 1px solid grey; border-radius: 5px; text-align: center;} QProgressBar::chunk {background-color: #05B8CC; width: 20px;}" + ) - #making the buttons layout very tight + # making the buttons layout very tight button_layout.setSpacing(0) button_layout.setContentsMargins(0, 0, 0, 0) - + grid.addLayout(button_layout, 1, 0, 1, 2) - - #make the table widget stretch to fill the available space + + # make the table widget stretch to fill the available space self.algolist.horizontalHeader().setStretchLastSection(True) grid.addWidget(self.algolist, 2, 0, 1, 4) - grid.addWidget(self.label_60,0,2,1,1) #Parameters label - grid.addWidget(self.algorithm_parameter_list,1,2,2,4) - self.algorithm_parameter_list.horizontalHeader().setStretchLastSection(True) - - grid.addWidget(self.pushButton_32, 3, 0, 1, 1) #Boundaries - grid.addWidget(self.pushButton_33, 3, 2, 1, 1) #Evaluate - grid.addWidget(self.pushButton_30, 3, 3, 1, 1) #Run - grid.addWidget(self.progressBar, 4, 0, 1, 6) #Progress bar + grid.addWidget(self.label_60, 0, 2, 1, 1) # Parameters label + grid.addWidget(self.algorithm_parameter_list, 1, 2, 2, 4) + self.algorithm_parameter_list.horizontalHeader().setStretchLastSection( + True) - self.pushButton_32.setSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) - self.pushButton_33.setSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) - self.pushButton_30.setSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) + grid.addWidget(self.pushButton_32, 3, 0, 1, 1) # Boundaries + grid.addWidget(self.pushButton_33, 3, 2, 1, 1) # Evaluate + grid.addWidget(self.pushButton_30, 3, 3, 1, 1) # Run + grid.addWidget(self.progressBar, 4, 0, 1, 6) # Progress bar - - + self.pushButton_32.setSizePolicy(QtWidgets.QSizePolicy.Fixed, + QtWidgets.QSizePolicy.Fixed) + self.pushButton_33.setSizePolicy(QtWidgets.QSizePolicy.Fixed, + QtWidgets.QSizePolicy.Fixed) + self.pushButton_30.setSizePolicy(QtWidgets.QSizePolicy.Fixed, + QtWidgets.QSizePolicy.Fixed) self.runtab.setLayout(grid) - - #plot tab 6 + # plot tab 6 font = QtGui.QFont() font.setFamily("Ubuntu") font.setPointSize(11) @@ -1427,41 +1526,31 @@ def setupUi(self, Neuroptimus): self.pushButton_34.setGeometry(QtCore.QRect(30, 400, 121, 22)) self.pushButton_34.setObjectName("pushButton_34") - - - self.results_tab_grid = QtWidgets.QGridLayout(self.results_tab) grid.addWidget(self.label_72, 0, 0, 1, 1) - self.label_72.sizePolicy = QtWidgets.QSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) + self.label_72.sizePolicy = QtWidgets.QSizePolicy( + QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) self.results_tab_grid.addWidget(self.pushButton_34, 2, 0, 1, 2) self.results_tab_grid.addWidget(self.plot_widget, 0, 4, 4, 3) # self.plot_widget.setSizePolicy(QtWidgets.QSizePolicy.MinimumExpanding, QtWidgets.QSizePolicy.Expanding) - - #making pushButton 34 not to stretch and be fixed + # making pushButton 34 not to stretch and be fixed for widget in self.results_tab.findChildren(QtWidgets.QPushButton): - widget.setSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Fixed) + widget.setSizePolicy(QtWidgets.QSizePolicy.Fixed, + QtWidgets.QSizePolicy.Fixed) - - self.results_tab.setLayout(self.results_tab_grid) - - - - - - - #stat tab 7 + # stat tab 7 self.stat_tab = QtWidgets.QWidget() self.stat_tab.setObjectName("stat_tab") self.tabwidget.addTab(self.stat_tab, "") self.pushButton_35 = QtWidgets.QPushButton(self.stat_tab) self.pushButton_35.setGeometry(QtCore.QRect(30, 400, 111, 22)) self.pushButton_35.setObjectName("pushButton_34") - self.pushButton_36 = QtWidgets.QPushButton(self.stat_tab) + self.pushButton_36 = QtWidgets.QPushButton(self.stat_tab) self.pushButton_36.setGeometry(QtCore.QRect(150, 400, 111, 22)) self.pushButton_36.setObjectName("pushButton_34") self.pushButton_37 = QtWidgets.QPushButton(self.stat_tab) @@ -1475,7 +1564,7 @@ def setupUi(self, Neuroptimus): self.errorlist.setGeometry(QtCore.QRect(300, 200, 350, 180)) self.errorlist.setObjectName("errorlist") self.fitstat = QtWidgets.QLabel(self.stat_tab) - self.fitstat.setGeometry(QtCore.QRect(300, 50,200, 24)) + self.fitstat.setGeometry(QtCore.QRect(300, 50, 200, 24)) font = QtGui.QFont() font.setFamily("Ubuntu") font.setPointSize(10) @@ -1483,34 +1572,28 @@ def setupUi(self, Neuroptimus): font.setWeight(50) self.fitstat.setFont(font) self.fitstat.setObjectName("label") - self.fitstat.setText(QtCore.QCoreApplication.translate("Neuroptimus", 'Fitness statistics')) - + self.fitstat.setText( + QtCore.QCoreApplication.translate("Neuroptimus", + "Fitness statistics")) - #grid layout + # grid layout self.statLayout = QtWidgets.QGridLayout(self.stat_tab) # self.statLayout.addWidget(self.label_74, 0, 0, 1, 2) # self.statLayout.addWidget(self.pushButton_35, 2, 0, 1, 2) # self.statLayout.addWidget(self.fitstat, 0, 1, 1, 1) - # self.statLayout.addWidget(self.errorlist, 1, 1, 1, 2) + # self.statLayout.addWidget(self.errorlist, 1, 1, 1, 2) # self.statLayout.addWidget(self.pushButton_37, 2, 1, 1, 1) - - #making pushButtons 37,35 not to stretch and be fixed - self.pushButton_37.setSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Preferred) - self.pushButton_35.setSizePolicy(QtWidgets.QSizePolicy.Fixed, QtWidgets.QSizePolicy.Preferred) - #making all coloumns of the errorlist table widget stretch to fill the available space - self.errorlist.horizontalHeader().setStretchLastSection(True) - - + # making pushButtons 37,35 not to stretch and be fixed + self.pushButton_37.setSizePolicy(QtWidgets.QSizePolicy.Fixed, + QtWidgets.QSizePolicy.Preferred) + self.pushButton_35.setSizePolicy(QtWidgets.QSizePolicy.Fixed, + QtWidgets.QSizePolicy.Preferred) + # making all coloumns of the errorlist table widget stretch to fill the available space + self.errorlist.horizontalHeader().setStretchLastSection(True) self.stat_tab.setLayout(self.statLayout) - - - - - - Neuroptimus.setCentralWidget(self.centralwidget) self.menubar = QtWidgets.QMenuBar(Neuroptimus) self.menubar.setGeometry(QtCore.QRect(0, 0, 771, 19)) @@ -1523,7 +1606,7 @@ def setupUi(self, Neuroptimus): Neuroptimus.setStatusBar(self.statusbar) self.actionunlock = QtWidgets.QAction(Neuroptimus) self.actionunlock.setObjectName("actionunlock") - #for unlock action we place a check box in the menu left + # for unlock action we place a check box in the menu left self.actionunlock.setCheckable(True) self.actionexit = QtWidgets.QAction(Neuroptimus) @@ -1538,7 +1621,6 @@ def setupUi(self, Neuroptimus): self.actionLoadSettings.setObjectName("actionLoadSettings") self.actionLoadSettings.setIcon(QIcon.fromTheme("document-open")) - self.fileMenu.addAction(self.actionSaveSettings) self.fileMenu.addAction(self.actionLoadSettings) self.fileMenu.addAction(self.actionunlock) @@ -1547,25 +1629,23 @@ def setupUi(self, Neuroptimus): self.menubar.addAction(self.fileMenu.menuAction()) self.container = [] - self.temp=[] + self.temp = [] - - self.SW = SecondWindow(self) + self.SW = SecondWindow(self) self.SW.setObjectName("Neuroptimus") self.SW.resize(500, 500) - #Amplitudes window - self.SiW = StimuliWindow(self) + # Amplitudes window + self.SiW = StimuliWindow(self) self.SiW.setObjectName("Neuroptimus") self.SiW.resize(400, 500) - - #Parameters boundaries window - self.BW = BoundaryWindow(self) + # Parameters boundaries window + self.BW = BoundaryWindow(self) - #when actionSaveSettings clicked call function self.save_gui_state + # when actionSaveSettings clicked call function self.save_gui_state self.actionSaveSettings.triggered.connect(self.save_gui_state) - #when actionLoadSettings clicked call function self.load_gui_state + # when actionLoadSettings clicked call function self.load_gui_state self.actionLoadSettings.triggered.connect(self.load_gui_state) self.retranslateUi(Neuroptimus) @@ -1573,112 +1653,171 @@ def setupUi(self, Neuroptimus): self.tabwidget.setCurrentIndex(0) def modify_gui_state_dict(self, key, value_dict): + """ + + :param key: + :param value_dict: + + """ if key in self.gui_elements_state: self.gui_elements_state[key].update(value_dict) else: self.gui_elements_state[key] = value_dict - - def save_gui_state(self): - """ - Save the current state of the GUI to a file. - """ - #get the file name from the user - file_name, _ = QtWidgets.QFileDialog.getSaveFileName(self.centralwidget, "Save File", "", "JSON files (*.json)") + """Save the current state of the GUI to a file.""" + # get the file name from the user + file_name, _ = QtWidgets.QFileDialog.getSaveFileName( + self.centralwidget, "Save File", "", "JSON files (*.json)") if file_name: - #save the state of the GUI to the file + # save the state of the GUI to the file self.serialize_gui_state(file_name) - - def get_deep_attribute(self,obj, attr_path): + def get_deep_attribute(self, obj, attr_path): + """ + + :param obj: + :param attr_path: + + """ try: - attrs = attr_path.split('.') + attrs = attr_path.split(".") for attr in attrs: obj = getattr(obj, attr) return obj except AttributeError: return None - def serialize_gui_state(self,file_name): - """ - Serialize the state of the GUI to a file. + def serialize_gui_state(self, file_name): + """Serialize the state of the GUI to a file. + + :param file_name: + """ - + for component_name in self.gui_elements_state: # self.gui_elements_state[component_name] = {"type": type(getattr(self, component_name)).__name__, "value": self.agnostic_component_getter(getattr(self, component_name)), "enabled": getattr(self, component_name).isEnabled()} if component_name == "SW.plaintext": - self.gui_elements_state[component_name] = {"type": "QPlainTextEdit", "value": self.SW.plaintext.toPlainText()} + self.gui_elements_state[component_name] = { + "type": "QPlainTextEdit", + "value": self.SW.plaintext.toPlainText(), + } elif component_name == "SW.pushButton_46": - self.gui_elements_state[component_name] = {"type": "QPushButton", "value": self.SW.was_loaded} + self.gui_elements_state[component_name] = { + "type": "QPushButton", + "value": self.SW.was_loaded, + } elif component_name == "SiW.stim_table": - self.gui_elements_state[component_name] = {"type": type(self.SiW.stim_table).__name__, "value": self.agnostic_component_getter(self.SiW.stim_table), "enabled": self.SiW.stim_table.isEnabled()} + self.gui_elements_state[component_name] = { + "type": type(self.SiW.stim_table).__name__, + "value": + self.agnostic_component_getter(self.SiW.stim_table), + "enabled": self.SiW.stim_table.isEnabled(), + } elif component_name == "SiW.amplit_edit": - self.gui_elements_state[component_name] = {"type": "QLineEdit", "value": self.SiW.amplit_edit.text()} + self.gui_elements_state[component_name] = { + "type": "QLineEdit", + "value": self.SiW.amplit_edit.text(), + } elif component_name == "SiW.pushButton_create": - self.gui_elements_state[component_name] = {"type": "QPushButton", "value": self.SiW.is_stimuli_created} + self.gui_elements_state[component_name] = { + "type": "QPushButton", + "value": self.SiW.is_stimuli_created, + } elif component_name == "SiW.pushButton_accept": - self.gui_elements_state[component_name] = {"type": "QPushButton", "value": self.SiW.is_stimuli_accepted} + self.gui_elements_state[component_name] = { + "type": "QPushButton", + "value": self.SiW.is_stimuli_accepted, + } elif component_name == "algolist": # self.gui_elements_state[component_name] = {"type": "QTabelWidget", "value": self.agnostic_component_getter(self.algolist), "current_row": self.algolist.currentRow() } table_cells = [] for row in range(self.algolist.rowCount()): - #it is a single column table + # it is a single column table table_cells.append(self.algolist.item(row, 0).text()) - self.gui_elements_state[component_name] = {"type": "QTabelWidget", "value": table_cells, "current_row": self.algolist.currentRow() } + self.gui_elements_state[component_name] = { + "type": "QTabelWidget", + "value": table_cells, + "current_row": self.algolist.currentRow(), + } elif component_name == "fitlist": - #get text of each cell and save it in a list + # get text of each cell and save it in a list table = [] for row in range(self.fitlist.rowCount()): row_values = [] for col in range(self.fitlist.columnCount()): row_values.append(self.fitlist.item(row, col).text()) table.append(row_values) - self.gui_elements_state[component_name] = {"type": "CustomTableWidget", "value": table} - + self.gui_elements_state[component_name] = { + "type": "CustomTableWidget", + "value": table, + } + elif component_name == "algorithm_parameter_list": table = [] - #if not empty save it else save [] + # if not empty save it else save [] if self.algorithm_parameter_list.rowCount() > 0: # iterate over rows and columns if a cell is checkable save it as true or false else save it's text for row in range(self.algorithm_parameter_list.rowCount()): row_values = [] - for col in range(self.algorithm_parameter_list.columnCount()): + for col in range( + self.algorithm_parameter_list.columnCount()): item = self.algorithm_parameter_list.item(row, col) - if (item.flags() & QtCore.Qt.ItemIsUserCheckable) and not self.algorithm_parameter_list.item(row, col).text(): - row_values.append(item.checkState() == QtCore.Qt.Checked) + if (item.flags() & QtCore.Qt.ItemIsUserCheckable + ) and not self.algorithm_parameter_list.item( + row, col).text(): + row_values.append( + item.checkState() == QtCore.Qt.Checked) else: - row_values.append(self.algorithm_parameter_list.item(row, col).text()) + row_values.append( + self.algorithm_parameter_list.item( + row, col).text()) table.append(row_values) - self.gui_elements_state[component_name] = {"type": "QTabelWidget", "value": table} - + self.gui_elements_state[component_name] = { + "type": "QTabelWidget", + "value": table, + } + elif component_name == "BW.boundary_table": if self.BW.boundary_table.rowCount() > 0: - self.gui_elements_state[component_name] = {"type": type(self.BW.boundary_table).__name__, "value": self.agnostic_component_getter(self.BW.boundary_table), "enabled": self.BW.boundary_table.isEnabled()} + self.gui_elements_state[component_name] = { + "type": + type(self.BW.boundary_table).__name__, + "value": + self.agnostic_component_getter(self.BW.boundary_table), + "enabled": + self.BW.boundary_table.isEnabled(), + } else: - self.gui_elements_state[component_name] = {"type": type(getattr(self, component_name)).__name__, "value": self.agnostic_component_getter(getattr(self, component_name)), "enabled": getattr(self, component_name).isEnabled()} + self.gui_elements_state[component_name] = { + "type": + type(getattr(self, component_name)).__name__, + "value": + self.agnostic_component_getter( + getattr(self, component_name)), + "enabled": + getattr(self, component_name).isEnabled(), + } # self.gui_elements_state["input_tree"] = {"type": "QTreeWidget", "value": self.input_tree.currentItem().text(0)} verbose(self.gui_elements_state) - #save to json - file_name= f"{file_name}.json" if not file_name.endswith(".json") else file_name + # save to json + file_name = (f"{file_name}.json" + if not file_name.endswith(".json") else file_name) with open(file_name, "w") as file: json.dump(self.gui_elements_state, file, indent=4) - - def load_gui_state(self): - """ - Load the state of the GUI from a file. - """ - #open file dialog to get the file name - file_name, _ = QtWidgets.QFileDialog.getOpenFileName(self.centralwidget, "Open File", "", "") - verbose("loading gui state from: ",file_name) + """Load the state of the GUI from a file.""" + # open file dialog to get the file name + file_name, _ = QtWidgets.QFileDialog.getOpenFileName( + self.centralwidget, "Open File", "", "") + verbose("loading gui state from: ", file_name) if file_name: with open(file_name, "r") as file: loaded_ui_element = json.load(file) @@ -1698,198 +1837,234 @@ def load_gui_state(self): if loadedValue["value"]: self.SiW.pushButton_create.click() elif component_name == "SiW.stim_table": - self.agnostic_component_setter(self.SiW.stim_table, loadedValue) + self.agnostic_component_setter(self.SiW.stim_table, + loadedValue) elif component_name == "SiW.pushButton_accept": if loadedValue["value"]: self.SiW.pushButton_accept.click() elif component_name == "fitlist": - table = loadedValue["value"] # [[],[]] + table = loadedValue["value"] # [[],[]] if table: for row in range(len(table)): - for col in range(1,len(table[row])): + for col in range(1, len(table[row])): verbose(table[row][1]) - #first filling the rows + # first filling the rows self.fitlist.blockSignals(True) # self.fitlist.setItem(row, col, QtWidgets.QTableWidgetItem(table[row][col])) - self.fitlist.item(row,col).setText(table[row][col]) - self.fitlist.blockSignals(False) #then fill the table with the rest of the values except the weight - for col in range(1,len(table[0])): + self.fitlist.item(row, + col).setText(table[row][col]) + # then fill the table with the rest of the values except the weight + self.fitlist.blockSignals(False) + for col in range(1, len(table[0])): for row in range(len(table)): - #then fill the - self.fitlist.setSelectionBehavior(QtWidgets.QTableView.SelectRows) + # then fill the + self.fitlist.setSelectionBehavior( + QtWidgets.QTableView.SelectRows) self.fitlist.selectRow(row) # self.fitlist.setItem(row, col, QtWidgets.QTableWidgetItem(table[row][col])) - self.fitlist.item(row,col).setText(table[row][col]) + self.fitlist.item(row, + col).setText(table[row][col]) self.fitchanged() elif component_name == "test_specific_settings_table": - #update cells value in the table from the loaded table + # update cells value in the table from the loaded table table = loadedValue["value"] if table: for row in range(len(table)): - for column in range(0,len(table[0])): - self.test_specific_settings_table.item(row, column).setText(table[row][column]) + for column in range(0, len(table[0])): + self.test_specific_settings_table.item( + row, column).setText(table[row][column]) elif component_name == "algolist": selected_row = loadedValue["current_row"] table_cells = loadedValue["value"] - #disable signals to prevent the table from emitting signals + # disable signals to prevent the table from emitting signals self.algolist.blockSignals(True) # self.agnostic_component_setter(self.algolist, loadedValue) - #clear rows first + # clear rows first self.algolist.setRowCount(0) for row in range(len(table_cells)): self.algolist.insertRow(row) - self.algolist.setItem(row, 0, QtWidgets.QTableWidgetItem(table_cells[row])) + self.algolist.setItem( + row, 0, + QtWidgets.QTableWidgetItem(table_cells[row])) self.algolist.blockSignals(False) - self.algolist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) + self.algolist.setSelectionBehavior( + QtWidgets.QAbstractItemView.SelectRows) - #select as double click + # select as double click self.algolist.selectRow(selected_row) self.algoselect() - - + elif component_name == "algorithm_parameter_list": table = loadedValue["value"] if table: - #iterate over rows and cols + # iterate over rows and cols for row in range(len(table)): - for col in range(1,len(table[0])): - #if the cell is checkable set it's check state else set it's text - if isinstance(table[row][col],bool): - state = QtCore.Qt.Checked if table[row][col] else QtCore.Qt.Unchecked - self.algorithm_parameter_list.item(row, col).setCheckState(state) + for col in range(1, len(table[0])): + # if the cell is checkable set it's check state else set it's text + if isinstance(table[row][col], bool): + state = (QtCore.Qt.Checked + if table[row][col] else + QtCore.Qt.Unchecked) + self.algorithm_parameter_list.item( + row, col).setCheckState(state) else: - self.algorithm_parameter_list.item(row, col).setText(table[row][col]) + self.algorithm_parameter_list.item( + row, col).setText(table[row][col]) - elif component_name == "BW.boundary_table": self.boundarywindow() - self.agnostic_component_setter(self.BW.boundary_table, loadedValue) - #clicking self.BW.Setbutton + self.agnostic_component_setter(self.BW.boundary_table, + loadedValue) + # clicking self.BW.Setbutton self.BW.Setbutton.click() self.BW.close() - + else: - self.agnostic_component_setter(getattr(self,component_name), loadedValue) + self.agnostic_component_setter( + getattr(self, component_name), loadedValue) + def agnostic_component_setter(self, component, metadata: dict): + """Set the value of a component regardless of its type. + :param component: + :param metadata: dict: - def agnostic_component_setter(self,component, metadata:dict): - """ - Set the value of a component regardless of its type. """ value = metadata["value"] - if isinstance(component,QtWidgets.QComboBox): + if isinstance(component, QtWidgets.QComboBox): component.setCurrentText(value) - elif isinstance(component,QtWidgets.QLineEdit): + elif isinstance(component, QtWidgets.QLineEdit): component.setText(value) - elif isinstance(component,QtWidgets.QCheckBox): + elif isinstance(component, QtWidgets.QCheckBox): component.setChecked(value) - elif isinstance(component,QtWidgets.QTreeWidget): + elif isinstance(component, QtWidgets.QTreeWidget): component.setCurrentItem(value) - elif isinstance(component,QtWidgets.QPushButton): + elif isinstance(component, QtWidgets.QPushButton): if value is True: - #click the button to raise the subsequent events + # click the button to raise the subsequent events component.setEnabled(True) component.click() - elif isinstance(component,QtWidgets.QTableWidget): + elif isinstance(component, QtWidgets.QTableWidget): # return - #iterate over the rows and columns of the table widget and set the values + # iterate over the rows and columns of the table widget and set the values if value: for row in range(component.rowCount()): for col in range(component.columnCount()): - component.setItem(row, col, QtWidgets.QTableWidgetItem(value[row][col])) + component.setItem( + row, col, + QtWidgets.QTableWidgetItem(value[row][col])) # component.item(row,col).setText(text = value[row][col]) elif isinstance(component, TableSelections): if value: - table_widget_to_set = getattr(self,component.get_table_widget()) + table_widget_to_set = getattr(self, + component.get_table_widget()) rows_to_select = value - #select all the rows in the table widget at once - table = table_widget_to_set + # select all the rows in the table widget at once + table = table_widget_to_set # Set the selection mode to allow multiple selections - table_widget_to_set.setSelectionMode(QTableWidget.MultiSelection) + table_widget_to_set.setSelectionMode( + QTableWidget.MultiSelection) # Set the selection behavior to select entire rows - table_widget_to_set.setSelectionBehavior(QTableWidget.SelectRows) + table_widget_to_set.setSelectionBehavior( + QTableWidget.SelectRows) for row in rows_to_select: table_widget_to_set.selectRow(row) - #reset the multi selection mode to single selection - table_widget_to_set.setSelectionMode(QTableWidget.ContiguousSelection) - + # reset the multi selection mode to single selection + table_widget_to_set.setSelectionMode( + QTableWidget.ContiguousSelection) + + def agnostic_component_getter(self, component: QtWidgets.QWidget): + """Get the value of a component regardless of its type. + + :param component: QtWidgets.QWidget: - def agnostic_component_getter(self,component: QtWidgets.QWidget): - """ - Get the value of a component regardless of its type. """ - if isinstance(component,QtWidgets.QComboBox): + if isinstance(component, QtWidgets.QComboBox): return component.currentText() - elif isinstance(component,QtWidgets.QLineEdit): + elif isinstance(component, QtWidgets.QLineEdit): return component.text() - elif isinstance(component,QtWidgets.QCheckBox): + elif isinstance(component, QtWidgets.QCheckBox): return component.isChecked() - elif isinstance(component,QtWidgets.QTreeWidget): + elif isinstance(component, QtWidgets.QTreeWidget): return component.currentItem() - elif isinstance(component,QtWidgets.QPushButton): - return self.gui_elements_state[component.objectName()].get("value", False) + elif isinstance(component, QtWidgets.QPushButton): + return self.gui_elements_state[component.objectName()].get( + "value", False) - elif isinstance(component,QtWidgets.QTableWidget): - #print component anme + elif isinstance(component, QtWidgets.QTableWidget): + # print component anme # print(component.objectName()) - #iterate over the rows and columns of the table widget and get the values - return [[component.item(row, col).text() for col in range(component.columnCount())] for row in range(component.rowCount())] + # iterate over the rows and columns of the table widget and get the values + return [[ + component.item(row, col).text() + for col in range(component.columnCount()) + ] for row in range(component.rowCount())] elif isinstance(component, TableSelections): return component.get_selected_rows_indices() - - def retranslateUi(self, Neuroptimus): - """ - Set PyQT widgets behaviors and implements functions. + """Set PyQT widgets behaviors and implements functions. + + :param Neuroptimus: + """ _translate = QtCore.QCoreApplication.translate Neuroptimus.setWindowTitle(_translate("Neuroptimus", "Neuroptimus")) - #self.tabwidget.currentChanged.connect(self.onChange) - #modeltab 2 disappearing + # self.tabwidget.currentChanged.connect(self.onChange) + # modeltab 2 disappearing self.actionunlock.triggered.connect(self.toggleTabLock) - + self.actionexit.triggered.connect(QApplication.quit) - self.tabwidget.setTabText(self.tabwidget.indexOf(self.filetab), _translate("Neuroptimus", "Target data")) - self.label_23.setText(_translate("Neuroptimus", "Load mod files from:")) + self.tabwidget.setTabText( + self.tabwidget.indexOf(self.filetab), + _translate("Neuroptimus", "Target data"), + ) + self.label_23.setText(_translate("Neuroptimus", + "Load mod files from:")) self.label_24.setText(_translate("Neuroptimus", "Model file")) self.lineEdit_folder2.setEnabled(False) self.pushButton_14.setEnabled(False) self.load_mods_checkbox.clicked.connect(self.disable_mod_path) self.pushButton_13.setText(_translate("Neuroptimus", "Load")) self.pushButton_13.clicked.connect(self.Load2) - self.pushButton_12.setText(_translate("Neuroptimus", "Load python file")) + self.pushButton_12.setText( + _translate("Neuroptimus", "Load python file")) self.pushButton_12.clicked.connect(self.Loadpython) self.pushButton_12.hide() - self.pushButton_14.setText(_translate("Neuroptimus", "Browse...")) + self.pushButton_14.setText(_translate("Neuroptimus", "Browse...")) self.pushButton_14.clicked.connect(self.openFolderNameDialog2) self.pushButton_15.setText(_translate("Neuroptimus", "Browse...")) self.pushButton_15.clicked.connect(self.openFileNameDialog2) - self.pushButton_16.setText(_translate("Neuroptimus", "Define parameter mapping")) + self.pushButton_16.setText( + _translate("Neuroptimus", "Define parameter mapping")) self.pushButton_16.clicked.connect(self.UF) self.label_26.setText(_translate("Neuroptimus", "Command")) self.label_26.hide() - self.label_27.setText(_translate("Neuroptimus", "Number of parameters")) + self.label_27.setText(_translate("Neuroptimus", + "Number of parameters")) self.label_27.hide() self.setter.setText(_translate("Neuroptimus", "Set")) self.setter.clicked.connect(self.Set) self.remover.setText(_translate("Neuroptimus", "Remove")) self.remover.clicked.connect(self.Remove) self.modellist.setColumnCount(4) - self.modellist.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents) - self.modellist.setHorizontalHeaderLabels(("Section;Segment;Mechanism;Parameter").split(";")) - #self.modellist.resizeColumnsToContents() + self.modellist.setSizeAdjustPolicy( + QtWidgets.QAbstractScrollArea.AdjustToContents) + self.modellist.setHorizontalHeaderLabels( + ("Section;Segment;Mechanism;Parameter").split(";")) + # self.modellist.resizeColumnsToContents() self.modellist.horizontalHeader().setStretchLastSection(True) - self.modellist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) - self.modellist.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) - + self.modellist.setSelectionBehavior( + QtWidgets.QAbstractItemView.SelectRows) + self.modellist.setEditTriggers( + QtWidgets.QAbstractItemView.NoEditTriggers) + self.input_tree.setWidgetResizable(True) font = QtGui.QFont() font.setFamily("Ubuntu") @@ -1900,11 +2075,11 @@ def retranslateUi(self, Neuroptimus): self.input_label.setObjectName("label") self.input_tree.setWidget(self.input_label) - - #filetab 1 + # filetab 1 self.datfileName = "" self.label_3.setText(_translate("Neuroptimus", "Base directory")) - self.label_4.setText(_translate("Neuroptimus", "Length of traces (ms)")) + self.label_4.setText(_translate("Neuroptimus", + "Length of traces (ms)")) self.label_5.setText(_translate("Neuroptimus", "Number of traces")) self.label_7.setText(_translate("Neuroptimus", "Units")) self.pushButton_3.setText(_translate("Neuroptimus", "Load data")) @@ -1913,26 +2088,30 @@ def retranslateUi(self, Neuroptimus): self.label_2.setText(_translate("Neuroptimus", "Data file")) self.base_dir_controll.setText(_translate("Neuroptimus", "Browse...")) self.base_dir_controll.clicked.connect(self.openFolderNameDialog) - self.label_6.setText(_translate("Neuroptimus", "Sampling frequency (Hz)")) - self.type_selector.setItemText(0, _translate("Neuroptimus", "Voltage trace")) - self.type_selector.setItemText(1, _translate("Neuroptimus", "Current trace")) - self.type_selector.setItemText(2, _translate("Neuroptimus", "Features")) - if is_hippounit_installed(): - self.type_selector.setItemText(3, _translate("Neuroptimus", "HippoUnit")) + self.label_6.setText( + _translate("Neuroptimus", "Sampling frequency (Hz)")) + self.type_selector.setItemText( + 0, _translate("Neuroptimus", "Voltage trace")) + self.type_selector.setItemText( + 1, _translate("Neuroptimus", "Current trace")) + self.type_selector.setItemText(2, _translate("Neuroptimus", + "Features")) + if is_hippounit_installed(): + self.type_selector.setItemText( + 3, _translate("Neuroptimus", "HippoUnit")) else: - self.type_selector.setItemText(3, _translate("Neuroptimus", "HippoUnit (not installed)")) - #remove last item + self.type_selector.setItemText( + 3, _translate("Neuroptimus", "HippoUnit (not installed)")) + # remove last item self.type_selector.removeItem(3) # self.type_selector.setItemText(4, _translate("Neuroptimus", "Other")) - - - self.type_selector.currentTextChanged.connect(self.type_change) - #if current tab changed to second tab, then call the function + # if current tab changed to second tab, then call the function self.tabwidget.currentChanged.connect(self.tabchange) - self.input_file_controll.setText(_translate("Neuroptimus", "Browse...")) + self.input_file_controll.setText(_translate("Neuroptimus", + "Browse...")) self.input_file_controll.clicked.connect(self.openFileNameDialog) self.time_checker.setText(_translate("Neuroptimus", "Contains time")) self.time_checker.toggled.connect(self.time_calc) @@ -1941,97 +2120,104 @@ def retranslateUi(self, Neuroptimus): self.dropdown.setItemText(2, _translate("Neuroptimus", "V")) self.dropdown.setCurrentIndex(1) - self.tvoltage=None - self.tcurrent=None - self.tspike_t=None - self.tother=None - self.tfeatures=None - - #Input data plot - self.figure = plt.figure(figsize=(4,2.5), dpi=80) + self.tvoltage = None + self.tcurrent = None + self.tspike_t = None + self.tother = None + self.tfeatures = None + + # Input data plot + self.figure = plt.figure(figsize=(4, 2.5), dpi=80) self.canvas = FigureCanvas(self.figure) self.canvas.setParent(self.widget) # self.canvas.setSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding) - - #add to horizontal layout + + # add to horizontal layout self.hbox = QtWidgets.QHBoxLayout(self.widget) self.hbox.addWidget(self.canvas) self.widget.setLayout(self.hbox) - - - # plot = MyWidget(parent=self.widget) # self.figure = plot.figure # self.canvas = plot.canvas - #enable this later - self.loaded_input_types=[self.tvoltage , - self.tcurrent , -# self.tspike_t , -# self.tother, - self.tfeatures] + # enable this later + self.loaded_input_types = [ + self.tvoltage, + self.tcurrent, + # self.tspike_t , + # self.tother, + self.tfeatures, + ] # self.core=Core.coreModul() - - #optiontab 3 - self.tabwidget.setTabText(self.tabwidget.indexOf(self.modeltab), _translate("Neuroptimus", "Model")) + + # optiontab 3 + self.tabwidget.setTabText(self.tabwidget.indexOf(self.modeltab), + _translate("Neuroptimus", "Model")) self.label_44.setText(_translate("Neuroptimus", "Delay (ms)")) - self.label_66.setText(_translate("Neuroptimus", "Initial voltage (mV)")) + self.label_66.setText(_translate("Neuroptimus", + "Initial voltage (mV)")) self.label_67.setText(_translate("Neuroptimus", "tstop (ms)")) self.label_45.setText(_translate("Neuroptimus", "Section")) self.label_46.setText(_translate("Neuroptimus", "Duration (ms)")) - self.base_dir_controll9.setText(_translate("Neuroptimus", "Amplitude(s)")) + self.base_dir_controll9.setText( + _translate("Neuroptimus", "Amplitude(s)")) self.base_dir_controll9.clicked.connect(self.amplitudes_fun) self.label_48.setText(_translate("Neuroptimus", "Section")) self.label_49.setText(_translate("Neuroptimus", "Stimulus Type")) self.label_68.setText(_translate("Neuroptimus", "Time step")) - self.label_51.setText(_translate("Neuroptimus", "Position inside section")) + self.label_51.setText( + _translate("Neuroptimus", "Position inside section")) self.label_52.setText(_translate("Neuroptimus", "Parameter to record")) - self.label_55.setText(_translate("Neuroptimus", "Stimulation protocol")) - self.label_71.setText(_translate("Neuroptimus", "Position inside section")) + self.label_55.setText(_translate("Neuroptimus", + "Stimulation protocol")) + self.label_71.setText( + _translate("Neuroptimus", "Position inside section")) self.lineEdit_pos.setText("0.5") self.lineEdit_posins.setText("0.5") self.lineEdit_initv.setText("-65") self.lineEdit_dt.setText("0.05") - - self.stimprot.addItems(["IClamp","VClamp"]) - self.stimulus_type.addItems(["Step Protocol","Custom Waveform"]) + + self.stimprot.addItems(["IClamp", "VClamp"]) + self.stimulus_type.addItems(["Step Protocol", "Custom Waveform"]) self.stimulus_type.currentIndexChanged.connect(self.typeChange) - self.param_to_record.addItems(["v","i"]) - #self.stimprot.setItemText(0, _translate("Neuroptimus", "IClamp")) - #self.stimprot.setItemText(1, _translate("Neuroptimus", "VClamp")) + self.param_to_record.addItems(["v", "i"]) + # self.stimprot.setItemText(0, _translate("Neuroptimus", "IClamp")) + # self.stimprot.setItemText(1, _translate("Neuroptimus", "VClamp")) # self.container = [] # self.temp=[] - - #fittab 4 - self.tabwidget.setTabText(self.tabwidget.indexOf(self.simtab), _translate("Neuroptimus", "Settings")) + # fittab 4 + self.tabwidget.setTabText(self.tabwidget.indexOf(self.simtab), + _translate("Neuroptimus", "Settings")) self.fitlist.setColumnCount(2) - #self.fitlist.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents) - #self.flist.setHorizontalHeaderLabels(("Section;Segment;Mechanism;Parameter").split(";")) + # self.fitlist.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents) + # self.flist.setHorizontalHeaderLabels(("Section;Segment;Mechanism;Parameter").split(";")) self.fitlist.resizeColumnsToContents() - - #self.fitlist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) - self.fitlist.setHorizontalHeaderLabels(["Fitness functions","Weights"]) - #self.fitlist.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) - self.fitlist.setColumnWidth(0,200) - self.fitlist.setColumnWidth(1,80) - self.fitlist.setSelectionMode(QtWidgets.QAbstractItemView.SingleSelection) - #self.fitlist.itemSelectionChanged.connect(self.fitselect) - #self.fitlist.cellClicked.connect(self.fitselect) + + # self.fitlist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) + self.fitlist.setHorizontalHeaderLabels( + ["Fitness functions", "Weights"]) + # self.fitlist.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) + self.fitlist.setColumnWidth(0, 200) + self.fitlist.setColumnWidth(1, 80) + self.fitlist.setSelectionMode( + QtWidgets.QAbstractItemView.SingleSelection) + # self.fitlist.itemSelectionChanged.connect(self.fitselect) + # self.fitlist.cellClicked.connect(self.fitselect) # self.fitlist.horizontalHeader().setStretchLastSection(True) # self.label_69.setText(_translate("Neuroptimus", "Spike detection tresh. (mV)")) # self.label_70.setText(_translate("Neuroptimus", "Spike window (ms)")) self.pushButton_normalize.clicked.connect(self.Fit_normalize) # self.HippoTests_parameter_location_in_table = {"TrunkSecList_name":3 , "ObliqueSecList_name":4 , "TuftSecList_name":5, "num_of_dend_locations":6} - - - #self.fittab_help.clicked.connect(self.help_popup_fit) - #runtab 5 - self.tabwidget.setTabText(self.tabwidget.indexOf(self.fittab), _translate("Neuroptimus", "Fitness")) + # self.fittab_help.clicked.connect(self.help_popup_fit) + + # runtab 5 + self.tabwidget.setTabText(self.tabwidget.indexOf(self.fittab), + _translate("Neuroptimus", "Fitness")) self.pushButton_30.setText(_translate("Neuroptimus", "Run")) self.pushButton_30.clicked.connect(self.startFittingThread) - # self.pushButton_30.clicked.connect(self.runsim) + # self.pushButton_30.clicked.connect(self.runsim) # self.pushButton_31.setText(_translate("Neuroptimus", "Starting points")) # self.pushButton_31.clicked.connect(self.startingpoints) # self.pushButton_31.setEnabled(False) @@ -2042,148 +2228,232 @@ def retranslateUi(self, Neuroptimus): self.pushButton_32.clicked.connect(self.boundarywindow) self.label_59.setText(_translate("Neuroptimus", "Algorithms")) self.label_60.setText(_translate("Neuroptimus", "Parameters")) - self.tabwidget.setTabText(self.tabwidget.indexOf(self.runtab), _translate("Neuroptimus", "Run")) - + self.tabwidget.setTabText(self.tabwidget.indexOf(self.runtab), + _translate("Neuroptimus", "Run")) + self.pushButton_Recom.setText(_translate("Neuroptimus", "Recommended")) - self.pushButton_Recom.clicked.connect(partial(self.packageselect,"Recommended")) + self.pushButton_Recom.clicked.connect( + partial(self.packageselect, "Recommended")) self.pushButton_Inspyred.setText(_translate("Neuroptimus", "Inspyred")) - self.pushButton_Inspyred.clicked.connect(partial(self.packageselect,"Inspyred")) + self.pushButton_Inspyred.clicked.connect( + partial(self.packageselect, "Inspyred")) self.pushButton_Pygmo.setText(_translate("Neuroptimus", "Pygmo")) - self.pushButton_Pygmo.clicked.connect(partial(self.packageselect,"Pygmo")) - self.pushButton_Bluepyopt.setText(_translate("Neuroptimus", "Bluepyopt")) - self.pushButton_Bluepyopt.clicked.connect(partial(self.packageselect,"Bluepyopt")) + self.pushButton_Pygmo.clicked.connect( + partial(self.packageselect, "Pygmo")) + self.pushButton_Bluepyopt.setText( + _translate("Neuroptimus", "Bluepyopt")) + self.pushButton_Bluepyopt.clicked.connect( + partial(self.packageselect, "Bluepyopt")) self.pushButton_Scipy.setText(_translate("Neuroptimus", "Scipy")) - self.pushButton_Scipy.clicked.connect(partial(self.packageselect,"Scipy")) + self.pushButton_Scipy.clicked.connect( + partial(self.packageselect, "Scipy")) self.algolist.setColumnCount(2) - self.algolist.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) + self.algolist.setEditTriggers( + QtWidgets.QAbstractItemView.NoEditTriggers) self.algolist.clicked.connect(self.algoselect) - self.algolist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) - self.algolist.setColumnWidth(0,440) - self.algolist.setHorizontalHeaderLabels(['Algorithms']) + self.algolist.setSelectionBehavior( + QtWidgets.QAbstractItemView.SelectRows) + self.algolist.setColumnWidth(0, 440) + self.algolist.setHorizontalHeaderLabels(["Algorithms"]) self.algorithm_parameter_list.setColumnCount(2) - self.algorithm_parameter_list.horizontalHeader().setStretchLastSection(True) - self.algorithm_parameter_list.setHorizontalHeaderLabels(["Option","Value"]) + self.algorithm_parameter_list.horizontalHeader().setStretchLastSection( + True) + self.algorithm_parameter_list.setHorizontalHeaderLabels( + ["Option", "Value"]) self.seed = [] - self.resolution=0 - self.Recom=["Classical Evolution Strategy (CES) - Inspyred","Covariance Matrix Adaptation ES (CMAES) - Cmaes", "Covariance Matrix Adaptation ES (CMAES) - Pygmo", - "Particle Swarm (PSO) - Inspyred","Particle Swarm Gen (PSOG) - Pygmo","Indicator Based (IBEA) - Bluepyopt","L-BFGS-B - Scipy","Random Search"] - self.Inspyred=["Classical Evolution Strategy (CES) - Inspyred","Particle Swarm (PSO) - Inspyred", - "Differential Evolution (DE) - Inspyred", - "Nondominated Sorted GA (NSGA2) - Inspyred","Pareto Archived ES (PAES) - Inspyred", - "Simulated Annealing (SA) - Inspyred"] - self.Scipy=["Basinhopping (BH) - Scipy","Nelder-Mead (NM) - Scipy","L-BFGS-B - Scipy"] - self.Bluepyopt=["Nondominated Sorted GA (NSGA2) - Bluepyopt","Indicator Based (IBEA) - Bluepyopt"] - self.Pygmo=["Particle Swarm Gen (PSOG) - Pygmo","Nondominated Sorted Particle Swarm (NSPSO) - Pygmo", - "Nondominated Sorted GA (NSGA2) - Pygmo","Differential Evolution (DE) - Pygmo", - "Extended Ant Colony (GACO) - Pygmo","Multi-Objective Ant Colony (MACO) - Pygmo","Self-Adaptive DE (SADE) - Pygmo", - "Particle Swarm (PSO) - Pygmo","Exponential Natural ES (XNES) - Pygmo", - "Simple Genetic Algorithm (SGA) - Pygmo","Covariance Matrix Adaptation ES (CMAES) - Pygmo", - "Differential Evolution (DE1220) - Pygmo", "Bee Colony (ABC) - Pygmo","Praxis - Pygmo","Nelder-Mead (NM) - Pygmo"] #"FullGrid - Pygmo","Single Differential Evolution (SDE) - Pygmo" - self.algos={ - 'Recommended':self.Recom, - 'Inspyred': self.Inspyred, - 'Scipy': self.Scipy, - 'Bluepyopt': self.Bluepyopt, - 'Pygmo': self.Pygmo} + self.resolution = 0 + self.Recom = [ + "Classical Evolution Strategy (CES) - Inspyred", + "Covariance Matrix Adaptation ES (CMAES) - Cmaes", + "Covariance Matrix Adaptation ES (CMAES) - Pygmo", + "Particle Swarm (PSO) - Inspyred", + "Particle Swarm Gen (PSOG) - Pygmo", + "Indicator Based (IBEA) - Bluepyopt", + "L-BFGS-B - Scipy", + "Random Search", + ] + self.Inspyred = [ + "Classical Evolution Strategy (CES) - Inspyred", + "Particle Swarm (PSO) - Inspyred", + "Differential Evolution (DE) - Inspyred", + "Nondominated Sorted GA (NSGA2) - Inspyred", + "Pareto Archived ES (PAES) - Inspyred", + "Simulated Annealing (SA) - Inspyred", + ] + self.Scipy = [ + "Basinhopping (BH) - Scipy", + "Nelder-Mead (NM) - Scipy", + "L-BFGS-B - Scipy", + ] + self.Bluepyopt = [ + "Nondominated Sorted GA (NSGA2) - Bluepyopt", + "Indicator Based (IBEA) - Bluepyopt", + ] + self.Pygmo = [ + "Particle Swarm Gen (PSOG) - Pygmo", + "Nondominated Sorted Particle Swarm (NSPSO) - Pygmo", + "Nondominated Sorted GA (NSGA2) - Pygmo", + "Differential Evolution (DE) - Pygmo", + "Extended Ant Colony (GACO) - Pygmo", + "Multi-Objective Ant Colony (MACO) - Pygmo", + "Self-Adaptive DE (SADE) - Pygmo", + "Particle Swarm (PSO) - Pygmo", + "Exponential Natural ES (XNES) - Pygmo", + "Simple Genetic Algorithm (SGA) - Pygmo", + "Covariance Matrix Adaptation ES (CMAES) - Pygmo", + # "FullGrid - Pygmo","Single Differential Evolution (SDE) - Pygmo" + "Differential Evolution (DE1220) - Pygmo", + "Bee Colony (ABC) - Pygmo", + "Praxis - Pygmo", + "Nelder-Mead (NM) - Pygmo", + ] + self.algos = { + "Recommended": self.Recom, + "Inspyred": self.Inspyred, + "Scipy": self.Scipy, + "Bluepyopt": self.Bluepyopt, + "Pygmo": self.Pygmo, + } self.algolist.setRowCount(len(self.Recom)) - for index,item in enumerate(self.Recom): - self.algolist.setItem(index, 0, QTableWidgetItem(item)) - - self.algo_param_dict = {"ker" : "Kernel: number of solutions stored in the solution archive.", - "q" : "Convergence speed parameter: this parameter is useful for managing \nthe convergence speed towards the found minima (the smaller the faster).", - "oracle" : "Oracle parameter: this is the oracle parameter used in the penalty method.", - "acc" : "Accuracy parameter: for maintaining a minimum penalty function's values distances.", - "threshold" : "Threshold parameter: when the generations reach the threshold \nthen q is set to 0.01 automatically.", - "n_gen_mark" : "Standard deviations convergence speed parameter: this parameters \ndetermines the convergence speed of the standard deviations values.", - "impstop" : "Improvement stopping criterion: if a positive integer is assigned here, \nthe algorithm will count the runs without improvements, \nif this number will exceed impstop value, the algorithm will be stopped.", - "evalstop" : "Evaluation stopping criterion: same as previous one, but with function evaluations.", - "focus" : "Focus parameter: this parameter makes the search for the optimum greedier \nand more focused on local improvements (the higher the greedier). \nIf the value is very high, the search is more focused around the current best solutions.", - "memory" : " Memory parameter: if true, memory is activated in the algorithm for multiple calls", - "cc" : "backward time horizon for the evolution path", - "cs" : "makes partly up for the small variance loss in case the indicator is zero", - "c1" : "CMAES: learning rate for the rank-one update of the covariance matrix \nNSPSO: magnitude of the force, applied to the particle's velocity, in the direction of its previous best position.", - "cmu" : "learning rate for the rank - update of the covariance matrix", - "sigma0" : "initial step-size", - "ftol" : "stopping criteria on the x tolerance", - "xtol" : "stopping criteria on the f tolerance", - "memory" : "when true the adapted parameters are not reset between successive calls to the evolve method", - "force_bounds" : "when true the box bounds are enforced. The fitness will never be called outside the bounds but the covariance matrix adaptation mechanism will worsen", - "omega" : "particles' inertia weight, or alternatively, the constriction coefficient (definition depends on the variant used)", - "eta1" : "magnitude of the force, applied to the particle's velocity, in the direction of its previous best position", - "eta2" : "magnitude of the force, applied to the particle's velocity, in the direction of the best position in its neighborhood", - "max_vel" : "maximum allowed particle velocity (as a fraction of the box bounds)", - "variant" : "PSO: algorithm variant to use (one of 1 .. 6) \nDE: mutation variant", - "neighb_type" : "swarm topology to use (one of 1 .. 4) [gbest, lbest, Von Neumann, adaptive random]", - "neighb_param" : "the neighbourhood parameter. If the lbest topology is selected (neighb_type=2), it represents each particle's indegree (also outdegree) in the swarm topology. Particles have neighbours up to a radius of k = neighb_param / 2 in the ring. If the Randomly-varying neighbourhood topology is selected (neighb_type=4), it represents each particle's maximum outdegree in the swarm topology. The minimum outdegree is 1 (the particle always connects back to itself). If neighb_type is 1 or 3 this parameter is ignored.", - "F" : "weight coefficient", - "CR" : "crossover probability", - "cr" : "crossover probability", - "variant_adptv" : "weight coefficient and crossover probability parameter adaptation scheme to be used (one of 1..2)", - "c2" : "magnitude of the force, applied to the particle's velocity, in the direction of its global best (i.e., leader).", - "chi" : "velocity scaling factor.", - "v_coeff" : "velocity coefficient (determining the maximum allowed particle velocity).", - "leader_selection_range" : "leader selection range parameter (i.e., the leader of each particle is selected among the best).", - "diversity_mechanism" : "the diversity mechanism used to maintain diversity on the Pareto front.", - "cr" : "Crossover probability.", - "eta_c" : "Distribution index for crossover.", - "m" : "Mutation probability.", - "eta_m" : "Distribution index for mutation.", - "eta_c" : "distribution index for “sbx” crossover. This is an inactive parameter if other types of crossovers are selected.", - "m" : "mutation probability.", - "param_m" : "distribution index (“polynomial” mutation), gaussian width (“gaussian” mutation) or inactive (“uniform” mutation)", - "param_s" : "when “truncated” selection is used this indicates the number of best individuals to use. When “tournament” selection is used this indicates the size of the tournament.", - "eta_mu" : "learning rate for mean update ", - "eta_sigma" : "learning rate for step-size update", - "eta_b" : "learning rate for the covariance matrix update", - "fatol" : "stopping criteria on the x tolerance", - "xatol" : "stopping criteria on the f tolerance", - "mutpb" : "Mutation probability", - "cxpb" : "Crossover probability", - "sigma" : "coordinate wise standard deviation (step size)" - } - - - self.algo_dict=self.core.option_handler.algorithm_parameters_dict.copy() - self.tabwidget.setTabText(self.tabwidget.indexOf(self.results_tab), _translate("Neuroptimus", "Results")) + for index, item in enumerate(self.Recom): + self.algolist.setItem(index, 0, QTableWidgetItem(item)) + + self.algo_param_dict = { + "ker": + "Kernel: number of solutions stored in the solution archive.", + "q": + "Convergence speed parameter: this parameter is useful for managing \nthe convergence speed towards the found minima (the smaller the faster).", + "oracle": + "Oracle parameter: this is the oracle parameter used in the penalty method.", + "acc": + "Accuracy parameter: for maintaining a minimum penalty function's values distances.", + "threshold": + "Threshold parameter: when the generations reach the threshold \nthen q is set to 0.01 automatically.", + "n_gen_mark": + "Standard deviations convergence speed parameter: this parameters \ndetermines the convergence speed of the standard deviations values.", + "impstop": + "Improvement stopping criterion: if a positive integer is assigned here, \nthe algorithm will count the runs without improvements, \nif this number will exceed impstop value, the algorithm will be stopped.", + "evalstop": + "Evaluation stopping criterion: same as previous one, but with function evaluations.", + "focus": + "Focus parameter: this parameter makes the search for the optimum greedier \nand more focused on local improvements (the higher the greedier). \nIf the value is very high, the search is more focused around the current best solutions.", + "memory": + " Memory parameter: if true, memory is activated in the algorithm for multiple calls", + "cc": "backward time horizon for the evolution path", + "cs": + "makes partly up for the small variance loss in case the indicator is zero", + "c1": + "CMAES: learning rate for the rank-one update of the covariance matrix \nNSPSO: magnitude of the force, applied to the particle's velocity, in the direction of its previous best position.", + "cmu": + "learning rate for the rank - update of the covariance matrix", + "sigma0": "initial step-size", + "ftol": "stopping criteria on the x tolerance", + "xtol": "stopping criteria on the f tolerance", + "memory": + "when true the adapted parameters are not reset between successive calls to the evolve method", + "force_bounds": + "when true the box bounds are enforced. The fitness will never be called outside the bounds but the covariance matrix adaptation mechanism will worsen", + "omega": + "particles' inertia weight, or alternatively, the constriction coefficient (definition depends on the variant used)", + "eta1": + "magnitude of the force, applied to the particle's velocity, in the direction of its previous best position", + "eta2": + "magnitude of the force, applied to the particle's velocity, in the direction of the best position in its neighborhood", + "max_vel": + "maximum allowed particle velocity (as a fraction of the box bounds)", + "variant": + "PSO: algorithm variant to use (one of 1 .. 6) \nDE: mutation variant", + "neighb_type": + "swarm topology to use (one of 1 .. 4) [gbest, lbest, Von Neumann, adaptive random]", + "neighb_param": + "the neighbourhood parameter. If the lbest topology is selected (neighb_type=2), it represents each particle's indegree (also outdegree) in the swarm topology. Particles have neighbours up to a radius of k = neighb_param / 2 in the ring. If the Randomly-varying neighbourhood topology is selected (neighb_type=4), it represents each particle's maximum outdegree in the swarm topology. The minimum outdegree is 1 (the particle always connects back to itself). If neighb_type is 1 or 3 this parameter is ignored.", + "F": "weight coefficient", + "CR": "crossover probability", + "cr": "crossover probability", + "variant_adptv": + "weight coefficient and crossover probability parameter adaptation scheme to be used (one of 1..2)", + "c2": + "magnitude of the force, applied to the particle's velocity, in the direction of its global best (i.e., leader).", + "chi": "velocity scaling factor.", + "v_coeff": + "velocity coefficient (determining the maximum allowed particle velocity).", + "leader_selection_range": + "leader selection range parameter (i.e., the leader of each particle is selected among the best).", + "diversity_mechanism": + "the diversity mechanism used to maintain diversity on the Pareto front.", + "cr": "Crossover probability.", + "eta_c": "Distribution index for crossover.", + "m": "Mutation probability.", + "eta_m": "Distribution index for mutation.", + "eta_c": + "distribution index for “sbx” crossover. This is an inactive parameter if other types of crossovers are selected.", + "m": "mutation probability.", + "param_m": + "distribution index (“polynomial” mutation), gaussian width (“gaussian” mutation) or inactive (“uniform” mutation)", + "param_s": + "when “truncated” selection is used this indicates the number of best individuals to use. When “tournament” selection is used this indicates the size of the tournament.", + "eta_mu": "learning rate for mean update ", + "eta_sigma": "learning rate for step-size update", + "eta_b": "learning rate for the covariance matrix update", + "fatol": "stopping criteria on the x tolerance", + "xatol": "stopping criteria on the f tolerance", + "mutpb": "Mutation probability", + "cxpb": "Crossover probability", + "sigma": "coordinate wise standard deviation (step size)", + } + + self.algo_dict = self.core.option_handler.algorithm_parameters_dict.copy( + ) + self.tabwidget.setTabText( + self.tabwidget.indexOf(self.results_tab), + _translate("Neuroptimus", "Results"), + ) self.label_72.setText(_translate("Neuroptimus", "Final Result")) - self.figure2, self.results_tab_axes = plt.subplots( dpi=80) + self.figure2, self.results_tab_axes = plt.subplots(dpi=80) self.canvas2 = FigureCanvas(self.figure2) self.canvas2.setParent(self.plot_widget) hbox2 = QtWidgets.QHBoxLayout(self.plot_widget) hbox2.addWidget(self.canvas2) self.plot_widget.setLayout(hbox2) - - self.pushButton_34.setText(_translate("Neuroptimus", "Save Parameters")) - self.pushButton_34.clicked.connect(self.SaveParam) + self.pushButton_34.setText(_translate("Neuroptimus", + "Save Parameters")) + self.pushButton_34.clicked.connect(self.SaveParam) - self.tabwidget.setTabText(self.tabwidget.indexOf(self.stat_tab), _translate("Neuroptimus", "Statistics")) + self.tabwidget.setTabText( + self.tabwidget.indexOf(self.stat_tab), + _translate("Neuroptimus", "Statistics"), + ) self.label_74.setText(_translate("Neuroptimus", "Analysis")) - self.pushButton_35.setText(_translate("Neuroptimus", "Generation Plot")) + self.pushButton_35.setText(_translate("Neuroptimus", + "Generation Plot")) self.pushButton_35.clicked.connect(self.PlotGen) self.pushButton_37.setText(_translate("Neuroptimus", "Error Details")) self.pushButton_37.clicked.connect(self.ShowErrorDialog) self.errorlist.setColumnCount(4) - self.errorlist.setHorizontalHeaderLabels(["Error Functions","Value","Weight","Weighted Value"]) - self.errorlist.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) - + self.errorlist.setHorizontalHeaderLabels( + ["Error Functions", "Value", "Weight", "Weighted Value"]) + self.errorlist.setEditTriggers( + QtWidgets.QAbstractItemView.NoEditTriggers) self.fileMenu.setTitle(_translate("Neuroptimus", "File")) self.actionunlock.setText(_translate("Neuroptimus", "Unlock Tabs")) self.actionexit.setText(_translate("Neuroptimus", "Exit")) - self.actionSaveSettings.setText(_translate("Neuroptimus", "Save Settings")) - self.actionLoadSettings.setText(_translate("Neuroptimus", "Load Settings")) - - self.tabwidget.setTabEnabled(1,False) - self.tabwidget.setTabEnabled(2,False) - self.tabwidget.setTabEnabled(3,False) - self.tabwidget.setTabEnabled(4,False) - self.tabwidget.setTabEnabled(5,False) - self.tabwidget.setTabEnabled(6,False) + self.actionSaveSettings.setText( + _translate("Neuroptimus", "Save Settings")) + self.actionLoadSettings.setText( + _translate("Neuroptimus", "Load Settings")) + + self.tabwidget.setTabEnabled(1, False) + self.tabwidget.setTabEnabled(2, False) + self.tabwidget.setTabEnabled(3, False) + self.tabwidget.setTabEnabled(4, False) + self.tabwidget.setTabEnabled(5, False) + self.tabwidget.setTabEnabled(6, False) self.result_labels = [] self.algorithm_parameter_list.cellChanged.connect(self.aspect_changed) - for curr_tab in [self.results_tab,self.stat_tab]: + for curr_tab in [self.results_tab, self.stat_tab]: label = QtWidgets.QLabel() font = QtGui.QFont() font.setFamily("Ubuntu") @@ -2195,24 +2465,23 @@ def retranslateUi(self, Neuroptimus): self.result_labels.append(label) scroll_area = QtWidgets.QScrollArea(curr_tab) # scroll_area.setGeometry(QtCore.QRect(10, 100, 170, 256)) - scroll_area.setGeometry(QtCore.QRect(10, 100, 300+50, 500)) + scroll_area.setGeometry(QtCore.QRect(10, 100, 300 + 50, 500)) scroll_area.setWidget(label) scroll_area.setWidgetResizable(True) - - - if curr_tab is self.results_tab: - scroll_area.setSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding) - self.canvas2.setSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding) - self.results_tab_grid.addWidget(self.label_72, 0, 0, 1, 2) + scroll_area.setSizePolicy(QtWidgets.QSizePolicy.Expanding, + QtWidgets.QSizePolicy.Expanding) + self.canvas2.setSizePolicy(QtWidgets.QSizePolicy.Expanding, + QtWidgets.QSizePolicy.Expanding) + self.results_tab_grid.addWidget(self.label_72, 0, 0, 1, 2) self.results_tab_grid.addWidget(scroll_area, 1, 0, 1, 2) self.results_tab_grid.addWidget(self.plot_widget, 0, 3, 2, 3) elif curr_tab is self.stat_tab: self.statLayout.addWidget(self.label_74, 0, 0, 1, 2) - self.statLayout.addWidget(scroll_area,1,0,2,2) + self.statLayout.addWidget(scroll_area, 1, 0, 2, 2) self.scroll_area2_stat = QtWidgets.QScrollArea(self.stat_tab) self.stats_label = QtWidgets.QLabel(self.stat_tab) self.stats_label.setGeometry(QtCore.QRect(300, 80, 250, 146)) @@ -2224,181 +2493,200 @@ def retranslateUi(self, Neuroptimus): self.stats_label.setFont(font) self.stats_label.setObjectName("label") # scroll_area_2.setSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding) - self.scroll_area2_stat.setGeometry(QtCore.QRect(300,80, 350, 100)) + self.scroll_area2_stat.setGeometry( + QtCore.QRect(300, 80, 350, 100)) self.scroll_area2_stat.setWidgetResizable(True) self.statLayout.addWidget(self.pushButton_35, 3, 0, 1, 2) - - self.statLayout.addWidget(self.fitstat, 0, 4, 1, 4) #label + self.statLayout.addWidget(self.fitstat, 0, 4, 1, 4) # label self.statLayout.addWidget(self.scroll_area2_stat, 1, 4, 1, 2) - #making a bold label + # making a bold label font = QtGui.QFont() font.setFamily("Ubuntu") font.setPointSize(10) font.setBold(True) font.setWeight(75) self.fitstat.setFont(font) - self.statLayout.addWidget(self.errorlist, 2, 4, 1, 4) + self.statLayout.addWidget(self.errorlist, 2, 4, 1, 4) self.statLayout.addWidget(self.pushButton_37, 3, 4, 1, 1) - self.errorlist.setSizePolicy(QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding) + self.errorlist.setSizePolicy(QtWidgets.QSizePolicy.Expanding, + QtWidgets.QSizePolicy.Expanding) self.errorlist.horizontalHeader().setStretchLastSection(True) # self.statLayout.setColumnStretch(0, 1) # self.statLayout.setColumnStretch(1, 2) - - - - # def startFittingThread(self): - # # Create a new thread for optimization # optimization_thread = threading.Thread(target=self.runsim) # optimization_thread.start() - def tabchange(self): """if current tab changed to second tab and the file is loaded with Hippounit mode selected, then disable the simulation type selection""" # if self.tabwidget.currentIndex()==1: self.model_name_label.setEnabled(True) self.model_name_input.setEnabled(True) # self.simtab_neuroptimus_group_boxes.setEnabled(True) - [widget.setEnabled(True) for widget in self.simtab_neuroptimus_group_boxes] - if self.type_selector.currentText() == "HippoUnit" : + [ + widget.setEnabled(True) + for widget in self.simtab_neuroptimus_group_boxes + ] + if self.type_selector.currentText() == "HippoUnit": self.dd_type.setEnabled(False) - [widget.setEnabled(False) for widget in self.simtab_neuroptimus_group_boxes] + [ + widget.setEnabled(False) + for widget in self.simtab_neuroptimus_group_boxes + ] else: self.dd_type.setEnabled(True) - def startFittingThread(self): + """ """ # Create a new thread for optimization self.fitting_thread = FittingThread(self) # self.fitting_thread.finished.connect(self.on_fitting_finished) # self.fitting_thread.error.connect(self.on_fitting_error) # Start the thread - self.fitting_thread.start() + self.fitting_thread.start() - def help_popup_fit(self): + """ """ msg = QtWidgets.QMessageBox() msg.setIcon(QtWidgets.QMessageBox.Question) - msg.setText("""Normalize button will adjust active fitness weights sum to 1 + msg.setText( + """Normalize button will adjust active fitness weights sum to 1 \nFitness functions with 0 values considered as inactive""") msg.exec() - def toggleTabLock(self): - """ - Unlock or lock the tabs in the tab widget based on the state of the 'actionunlock' checkbox. + """Unlock or lock the tabs in the tab widget based on the state of the 'actionunlock' checkbox. If the 'actionunlock' checkbox is checked, all tabs in the tab widget will be enabled. If the 'actionunlock' checkbox is unchecked, tabs after the currently selected tab will be disabled. - Parameters: - None - Returns: - None + :param None: + :returns: None + """ if self.actionunlock.isChecked(): for i in range(self.tabwidget.count()): self.tabwidget.setTabEnabled(i, True) else: - for i in range(self.tabwidget.currentIndex() + 1, self.tabwidget.count()): + for i in range(self.tabwidget.currentIndex() + 1, + self.tabwidget.count()): self.tabwidget.setTabEnabled(i, False) - - - def openFileNameDialog(self): - """ - File dialog for the file tab to open file. - """ + def openFileNameDialog(self): + """File dialog for the file tab to open file.""" options = QtWidgets.QFileDialog.Options() options |= QtWidgets.QFileDialog.DontUseNativeDialog - self.datfileName, _ = QFileDialog.getOpenFileName(None,"QFileDialog.getOpenFileName()", "","Data files (*.dat *.json);;All Files (*);;", options=options) + self.datfileName, _ = QFileDialog.getOpenFileName( + None, + "QFileDialog.getOpenFileName()", + "", + "Data files (*.dat *.json);;All Files (*);;", + options=options, + ) if self.datfileName: self.lineEdit_file.setText(self.datfileName) - self.lineEdit_folder.setText(os.path.dirname(os.path.realpath(self.datfileName))) + self.lineEdit_folder.setText( + os.path.dirname(os.path.realpath(self.datfileName))) self.pushButton_3.setEnabled(True) if self.time_checker.isChecked(): self.time_calc() def time_calc(self): + """ """ try: with open(str(self.lineEdit_file.text())) as data: - all_line=data.read().splitlines() - time_vec=[float(x.split()[0]) for x in all_line] + all_line = data.read().splitlines() + time_vec = [float(x.split()[0]) for x in all_line] self.length_ctrl.setText(str(round(max(time_vec)))) - self.freq_ctrl.setText(str(((len(time_vec)-1)*1000)/(max(time_vec)-min(time_vec)))) #frequency - self.size_ctrl.setText(str(len(all_line[0].split())-1)) #trace number + self.freq_ctrl.setText( + # frequency + str(((len(time_vec) - 1) * 1000) / + (max(time_vec) - min(time_vec)))) + self.size_ctrl.setText(str(len(all_line[0].split()) - + 1)) # trace number except: - print('No data file selected') + print("No data file selected") - def set_widgets_in_list(self, widget_list,enabled): - for widget in widget_list: - widget.setEnabled(enabled) + def set_widgets_in_list(self, widget_list, enabled): + """ + + :param widget_list: + :param enabled: - def openFolderNameDialog2(self): """ - File dialog for the model tab to open folder. - """ + for widget in widget_list: + widget.setEnabled(enabled) + + def openFolderNameDialog2(self): + """File dialog for the model tab to open folder.""" options = QtWidgets.QFileDialog.Options() options |= QtWidgets.QFileDialog.DontUseNativeDialog - folderName= QFileDialog.getExistingDirectory(None, options=options) + folderName = QFileDialog.getExistingDirectory(None, options=options) if folderName: self.lineEdit_folder2.setText(folderName) - def openFileNameDialog2(self): - """ - File dialog for the model tab to open file. - """ + def openFileNameDialog2(self): + """File dialog for the model tab to open file.""" options = QtWidgets.QFileDialog.Options() options |= QtWidgets.QFileDialog.DontUseNativeDialog - fileName, _ = QFileDialog.getOpenFileName(None,"QFileDialog.getOpenFileName()", "","Hoc Files (*.hoc);;All Files (*);;", options=options) + fileName, _ = QFileDialog.getOpenFileName( + None, + "QFileDialog.getOpenFileName()", + "", + "Hoc Files (*.hoc);;All Files (*);;", + options=options, + ) if fileName: self.lineEdit_file2.setText(fileName) - self.lineEdit_folder2.setText(os.path.dirname(os.path.realpath(fileName))) + self.lineEdit_folder2.setText( + os.path.dirname(os.path.realpath(fileName))) self.pushButton_3.setEnabled(True) def openFolderNameDialog(self): - """ - File dialog for the file tab to open folder. - """ + """File dialog for the file tab to open folder.""" options = QtWidgets.QFileDialog.Options() options |= QtWidgets.QFileDialog.DontUseNativeDialog - folderName= QFileDialog.getExistingDirectory(None, options=options) + folderName = QFileDialog.getExistingDirectory(None, options=options) if folderName: self.lineEdit_folder.setText(folderName) - if self.type_selector.currentText() == "HippoUnit" : + if self.type_selector.currentText() == "HippoUnit": self.pushButton_3.setEnabled(True) - def set_hippounit_output_dir(self): + """ """ options = QtWidgets.QFileDialog.Options() options |= QtWidgets.QFileDialog.DontUseNativeDialog - folderName = QFileDialog.getExistingDirectory(None, options=options, caption="Select HippoUnit output folder") + folderName = QFileDialog.getExistingDirectory( + None, options=options, caption="Select HippoUnit output folder") if folderName: # Add a trailing slash to the folder name based on the operating system - if os.name == 'posix': - if not folderName.endswith('/'): - folderName += '/' - elif os.name == 'nt': - if not folderName.endswith('\\'): - folderName += '\\' + if os.name == "posix": + if not folderName.endswith("/"): + folderName += "/" + elif os.name == "nt": + if not folderName.endswith("\\"): + folderName += "\\" self.output_dir_input.setText(folderName) - def prepare_fitnessFunctions_table(self): - """ - Prepares the table for HippoUnit fitness functions settings to be displayed in the GUI - """ - - #if type is hippounit: - if self.type_selector.currentText() == "HippoUnit" : + """Prepares the table for HippoUnit fitness functions settings to be displayed in the GUI""" + + # if type is hippounit: + if self.type_selector.currentText() == "HippoUnit": self.fitlist.setColumnCount(5) - self.fitlist.setHorizontalHeaderLabels(["Fitness functions","Weights", "Target data path","Stimuli file path","Feature penalty"]) + self.fitlist.setHorizontalHeaderLabels([ + "Fitness functions", + "Weights", + "Target data path", + "Stimuli file path", + "Feature penalty", + ]) # self.fitlist.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.Stretch) self.fitlist.resizeColumnToContents(2) self.fitlist.resizeColumnToContents(3) @@ -2406,138 +2694,187 @@ def prepare_fitnessFunctions_table(self): self.fitlist.verticalHeader().setVisible(False) self.fitlist.setRowCount(0) self.fitlist.setAlternatingRowColors(False) - self.fitlist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) - self.fitlist.setSelectionMode(QtWidgets.QAbstractItemView.SingleSelection) + self.fitlist.setSelectionBehavior( + QtWidgets.QAbstractItemView.SelectRows) + self.fitlist.setSelectionMode( + QtWidgets.QAbstractItemView.SingleSelection) # self.fitlist.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) self.fitlist.setSortingEnabled(False) self.fitlist.setShowGrid(True) self.fitlist.setWordWrap(True) self.fitlist.setCornerButtonEnabled(True) self.fitlist.horizontalHeader().setStretchLastSection(True) - min_width = sum([self.fitlist.columnWidth(i) for i in range(self.fitlist.columnCount())]) + min_width = sum([ + self.fitlist.columnWidth(i) + for i in range(self.fitlist.columnCount()) + ]) self.fitlist.setMinimumWidth(min_width) - - - - - # if cell in column 2 or 3 doubel clicked, open file dialog - self.fitlist.cellDoubleClicked.connect(self.browse_file_for_hippounit_data_paths) - - - + # if cell in column 2 or 3 doubel clicked, open file dialog + self.fitlist.cellDoubleClicked.connect( + self.browse_file_for_hippounit_data_paths) # #selection is by cell not row - self.fitlist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectItems) - self.HippoTests_parameter_location_in_table = {"TrunkSecList_name":3 , "ObliqueSecList_name":4 , "TuftSecList_name":5, "num_of_dend_locations":6} - self.tests_ui_names = {"SomaticFeaturesTest":"Somatic Features Test", - "PSPAttenuationTest":"PSP Attenuation Test", - "BackpropagatingAPTest":"Backpropagating AP Test", - "PathwayInteraction":"Pathway Interaction Test", - "DepolarizationBlockTest":"Depolarization Block Test", - "ObliqueIntegrationTest":"Oblique Integration Test"} - self.HippoTests_required_parameters = {self.tests_ui_names["PSPAttenuationTest"]: ["TrunkSecList_name","num_of_dend_locations"], - self.tests_ui_names["BackpropagatingAPTest"]: ["TrunkSecList_name"], - self.tests_ui_names["ObliqueIntegrationTest"]: ["ObliqueSecList_name", "TrunkSecList_name"], - self.tests_ui_names["PathwayInteraction"]: ["TuftSecList_name","num_of_dend_locations"]} - - #inverse of the above dictionary - self.tests_real_names = {v: k for k, v in self.tests_ui_names.items()} + self.fitlist.setSelectionBehavior( + QtWidgets.QAbstractItemView.SelectItems) + self.HippoTests_parameter_location_in_table = { + "TrunkSecList_name": 3, + "ObliqueSecList_name": 4, + "TuftSecList_name": 5, + "num_of_dend_locations": 6, + } + self.tests_ui_names = { + "SomaticFeaturesTest": "Somatic Features Test", + "PSPAttenuationTest": "PSP Attenuation Test", + "BackpropagatingAPTest": "Backpropagating AP Test", + "PathwayInteraction": "Pathway Interaction Test", + "DepolarizationBlockTest": "Depolarization Block Test", + "ObliqueIntegrationTest": "Oblique Integration Test", + } + self.HippoTests_required_parameters = { + self.tests_ui_names["PSPAttenuationTest"]: [ + "TrunkSecList_name", + "num_of_dend_locations", + ], + self.tests_ui_names["BackpropagatingAPTest"]: + ["TrunkSecList_name"], + self.tests_ui_names["ObliqueIntegrationTest"]: [ + "ObliqueSecList_name", + "TrunkSecList_name", + ], + self.tests_ui_names["PathwayInteraction"]: [ + "TuftSecList_name", + "num_of_dend_locations", + ], + } + + # inverse of the above dictionary + self.tests_real_names = { + v: k + for k, v in self.tests_ui_names.items() + } # #fill the table with the test specific settings configurations paths # self.fitlist.setRowCount(0) # #row 0 SomaticFeaturesTest target_data_path , second column to be filled with stimuli_file_path - - - self.fitlist.insertRow(0) # self.fitlist.setItem(0, 0, QtWidgets.QTableWidgetItem(self.tests_ui_names["SomaticFeaturesTest"])) - self.fitlist.setItem(0, 0, QtWidgets.QTableWidgetItem(self.tests_ui_names["SomaticFeaturesTest"])) + self.fitlist.setItem( + 0, + 0, + QtWidgets.QTableWidgetItem( + self.tests_ui_names["SomaticFeaturesTest"]), + ) self.fitlist.setItem(0, 2, fitlistTableItem("")) self.fitlist.setItem(0, 3, fitlistTableItem("")) self.fitlist.setItem(0, 4, QtWidgets.QTableWidgetItem("250")) - - #row 1 PSPAttenuationTest + + # row 1 PSPAttenuationTest self.fitlist.insertRow(1) - self.fitlist.setItem(1, 0, QtWidgets.QTableWidgetItem(self.tests_ui_names["PSPAttenuationTest"])) + self.fitlist.setItem( + 1, + 0, + QtWidgets.QTableWidgetItem( + self.tests_ui_names["PSPAttenuationTest"]), + ) self.fitlist.setItem(1, 2, fitlistTableItem("")) self.fitlist.setItem(1, 3, fitlistTableItem("")) self.fitlist.setItem(1, 4, QtWidgets.QTableWidgetItem("250")) - #BackpropagatingAPTest + # BackpropagatingAPTest self.fitlist.insertRow(2) - self.fitlist.setItem(2, 0, QtWidgets.QTableWidgetItem(self.tests_ui_names["BackpropagatingAPTest"])) + self.fitlist.setItem( + 2, + 0, + QtWidgets.QTableWidgetItem( + self.tests_ui_names["BackpropagatingAPTest"]), + ) self.fitlist.setItem(2, 2, fitlistTableItem("")) self.fitlist.setItem(2, 3, fitlistTableItem("")) self.fitlist.setItem(2, 4, QtWidgets.QTableWidgetItem("250")) - #PathwayInteraction + # PathwayInteraction self.fitlist.insertRow(3) - self.fitlist.setItem(3, 0, QtWidgets.QTableWidgetItem(self.tests_ui_names["PathwayInteraction"])) + self.fitlist.setItem( + 3, + 0, + QtWidgets.QTableWidgetItem( + self.tests_ui_names["PathwayInteraction"]), + ) self.fitlist.setItem(3, 2, fitlistTableItem("")) self.fitlist.setItem(3, 3, fitlistTableItem("")) self.fitlist.setItem(3, 4, QtWidgets.QTableWidgetItem("250")) - #non editable and non selectable cell + # non editable and non selectable cell self.fitlist.item(3, 3).setFlags(QtCore.Qt.NoItemFlags) - #setting color to gray rgb(192,192,192) + # setting color to gray rgb(192,192,192) self.fitlist.item(3, 3).setBackground(GRAY) - #BackpropagatingAPTest + # BackpropagatingAPTest self.fitlist.insertRow(4) - self.fitlist.setItem(4, 0, QtWidgets.QTableWidgetItem(self.tests_ui_names["DepolarizationBlockTest"])) + self.fitlist.setItem( + 4, + 0, + QtWidgets.QTableWidgetItem( + self.tests_ui_names["DepolarizationBlockTest"]), + ) self.fitlist.setItem(4, 2, fitlistTableItem("")) self.fitlist.setItem(4, 3, QtWidgets.QTableWidgetItem("")) self.fitlist.setItem(4, 4, QtWidgets.QTableWidgetItem("250")) - - #non editable and non selectable cell + # non editable and non selectable cell self.fitlist.item(4, 3).setFlags(QtCore.Qt.NoItemFlags) - #setting color to gray rgb(192,192,192) + # setting color to gray rgb(192,192,192) self.fitlist.item(4, 3).setBackground(GRAY) - #non clickable cell + # non clickable cell # self.fitlist.horizontalHeader().setSectionResizeMode(QtWidgets.QHeaderView.ResizeToContents) # column 2 3 have fixed width enough for the header text # self.fitlist.horizontalHeader().setSectionResizeMode(2, QtWidgets.QHeaderView.Fixed) # self.fitlist.horizontalHeader().setSectionResizeMode(3, QtWidgets.QHeaderView.Fixed) - #set the width of column 2 3 to 200 + # set the width of column 2 3 to 200 self.fitlist.setColumnWidth(2, 130) self.fitlist.setColumnWidth(3, 130) - - #ObliqueIntegrationTest + # ObliqueIntegrationTest self.fitlist.insertRow(5) - self.fitlist.setItem(5, 0, QtWidgets.QTableWidgetItem(self.tests_ui_names["ObliqueIntegrationTest"])) + self.fitlist.setItem( + 5, + 0, + QtWidgets.QTableWidgetItem( + self.tests_ui_names["ObliqueIntegrationTest"]), + ) self.fitlist.setItem(5, 2, fitlistTableItem("")) self.fitlist.setItem(5, 3, QtWidgets.QTableWidgetItem(" ")) self.fitlist.setItem(5, 4, QtWidgets.QTableWidgetItem("250")) - #set its color to gray + # set its color to gray self.fitlist.item(5, 3).setBackground(GRAY) - - #make it non editable and non selectable + + # make it non editable and non selectable self.fitlist.item(5, 3).setFlags(QtCore.Qt.NoItemFlags) self.fitlist.resizeRowsToContents() - # write a hint text to the table cells "Double click to Browse" + # write a hint text to the table cells "Double click to Browse" for row in range(self.fitlist.rowCount()): for column in range(self.fitlist.columnCount()): - if column == 2 : - self.fitlist.item(row, column).setToolTip("click to Browse") + if column == 2: + self.fitlist.item(row, + column).setToolTip("click to Browse") elif column == 3: - #if last three rows: - if row >= self.fitlist.rowCount()-2: + # if last three rows: + if row >= self.fitlist.rowCount() - 2: self.fitlist.item(row, column).setToolTip("N/A") else: - self.fitlist.item(row, column).setToolTip("click to Browse") + self.fitlist.item( + row, column).setToolTip("click to Browse") # self.fitlist.horizontalHeader().setStretchLastSection(True) - - #gray #4th 5th 6th columns + + # gray #4th 5th 6th columns self.fitlist.blockSignals(True) for row in range(self.fitlist.rowCount()): - for column in range(2,5): - self.fitlist.item(row, column).setFlags(QtCore.Qt.NoItemFlags) + for column in range(2, 5): + self.fitlist.item(row, + column).setFlags(QtCore.Qt.NoItemFlags) self.fitlist.item(row, column).setBackground(GRAY) self.fitlist.blockSignals(False) - - #4th 5th 6th columns to be non editable and gray + # 4th 5th 6th columns to be non editable and gray # self.fitlist.blockSignals(True) # for row in range(self.fitlist.rowCount()): # for column in range(2,5): @@ -2545,108 +2882,133 @@ def prepare_fitnessFunctions_table(self): # self.fitlist.item(row, column).setBackground(GRAY) # self.fitlist.blockSignals(False) - #first row of test_specific_settings_table value be -20 - self.test_specific_settings_table.setItem(0, 1, QtWidgets.QTableWidgetItem("-20")) + # first row of test_specific_settings_table value be -20 + self.test_specific_settings_table.setItem( + 0, 1, QtWidgets.QTableWidgetItem("-20")) - - #populating SomaSecList_name, TrunkSecList_name, ObliqueSecList_name + # populating SomaSecList_name, TrunkSecList_name, ObliqueSecList_name # row 2 SomaSecList_name self.test_specific_settings_table.insertRow(2) - self.test_specific_settings_table.setItem(2, 0, QtWidgets.QTableWidgetItem("SomaSecList_name (leave empty if no template is used)")) - self.test_specific_settings_table.setItem(2, 1, QtWidgets.QTableWidgetItem("")) - self.test_specific_settings_table.item(2, 0).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.setItem( + 2, + 0, + QtWidgets.QTableWidgetItem( + "SomaSecList_name (leave empty if no template is used)"), + ) + self.test_specific_settings_table.setItem( + 2, 1, QtWidgets.QTableWidgetItem("")) + self.test_specific_settings_table.item(2, 0).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(2, 0).setForeground(BLACK) # row 3 TrunkSecList_name self.test_specific_settings_table.insertRow(3) - self.test_specific_settings_table.setItem(3, 0, QtWidgets.QTableWidgetItem("TrunkSecList_name")) - self.test_specific_settings_table.setItem(3, 1, QtWidgets.QTableWidgetItem("")) - self.test_specific_settings_table.item(3, 0).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.setItem( + 3, 0, QtWidgets.QTableWidgetItem("TrunkSecList_name")) + self.test_specific_settings_table.setItem( + 3, 1, QtWidgets.QTableWidgetItem("")) + self.test_specific_settings_table.item(3, 0).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(3, 0).setForeground(BLACK) # row 4 ObliqueSecList_name self.test_specific_settings_table.insertRow(4) - self.test_specific_settings_table.setItem(4, 0, QtWidgets.QTableWidgetItem("ObliqueSecList_name")) - self.test_specific_settings_table.setItem(4, 1, QtWidgets.QTableWidgetItem("")) - self.test_specific_settings_table.item(4, 0).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.setItem( + 4, 0, QtWidgets.QTableWidgetItem("ObliqueSecList_name")) + self.test_specific_settings_table.setItem( + 4, 1, QtWidgets.QTableWidgetItem("")) + self.test_specific_settings_table.item(4, 0).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(4, 0).setForeground(BLACK) # row 5 TuftSecList_name self.test_specific_settings_table.insertRow(5) - self.test_specific_settings_table.setItem(5, 0, QtWidgets.QTableWidgetItem("TuftSecList_name")) - self.test_specific_settings_table.setItem(5, 1, QtWidgets.QTableWidgetItem("")) - self.test_specific_settings_table.item(5, 0).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.setItem( + 5, 0, QtWidgets.QTableWidgetItem("TuftSecList_name")) + self.test_specific_settings_table.setItem( + 5, 1, QtWidgets.QTableWidgetItem("")) + self.test_specific_settings_table.item(5, 0).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(5, 0).setForeground(BLACK) - #row 6 num_of_dend_locations + # row 6 num_of_dend_locations self.test_specific_settings_table.insertRow(6) - self.test_specific_settings_table.setItem(6, 0, QtWidgets.QTableWidgetItem("num_of_dend_locations")) - self.test_specific_settings_table.setItem(6, 1, QtWidgets.QTableWidgetItem("15")) - self.test_specific_settings_table.item(6, 0).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.setItem( + 6, 0, QtWidgets.QTableWidgetItem("num_of_dend_locations")) + self.test_specific_settings_table.setItem( + 6, 1, QtWidgets.QTableWidgetItem("15")) + self.test_specific_settings_table.item(6, 0).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(6, 0).setForeground(BLACK) - - #make these rows gray TrunkSecList_name ObliqueSecList_name TuftSecList_name rows and make them non editable + # make these rows gray TrunkSecList_name ObliqueSecList_name TuftSecList_name rows and make them non editable # self.hippounit_test_sections_names_table.item(2, 1).setFlags(QtCore.Qt.NoItemFlags) # self.hippounit_test_sections_names_table.item(2, 1).setBackground(GRAY) # self.hippounit_test_sections_names_table.item(2, 0).setBackground(GRAY) - - self.test_specific_settings_table.item(3, 1).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.item(3, 1).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(3, 1).setBackground(GRAY) self.test_specific_settings_table.item(3, 0).setBackground(GRAY) - self.test_specific_settings_table.item(4, 1).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.item(4, 1).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(4, 1).setBackground(GRAY) self.test_specific_settings_table.item(4, 0).setBackground(GRAY) - self.test_specific_settings_table.item(5, 1).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.item(5, 1).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(5, 1).setBackground(GRAY) self.test_specific_settings_table.item(5, 0).setBackground(GRAY) - self.test_specific_settings_table.item(6, 1).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.item(6, 1).setFlags( + QtCore.Qt.NoItemFlags) self.test_specific_settings_table.item(6, 1).setBackground(GRAY) self.test_specific_settings_table.item(6, 0).setBackground(GRAY) - - - else: self.fitlist.setColumnCount(2) - #self.fitlist.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents) - #self.flist.setHorizontalHeaderLabels(("Section;Segment;Mechanism;Parameter").split(";")) + # self.fitlist.setSizeAdjustPolicy(QtWidgets.QAbstractScrollArea.AdjustToContents) + # self.flist.setHorizontalHeaderLabels(("Section;Segment;Mechanism;Parameter").split(";")) self.fitlist.resizeColumnsToContents() - - #self.fitlist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) - self.fitlist.setHorizontalHeaderLabels(["Fitness functions","Weights"]) - #self.fitlist.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) - self.fitlist.setColumnWidth(0,200) - self.fitlist.setColumnWidth(1,80) - self.fitlist.setSelectionMode(QtWidgets.QAbstractItemView.SingleSelection) - #self.fitlist.itemSelectionChanged.connect(self.fitselect) - #self.fitlist.cellClicked.connect(self.fitselect) + + # self.fitlist.setSelectionBehavior(QtWidgets.QAbstractItemView.SelectRows) + self.fitlist.setHorizontalHeaderLabels( + ["Fitness functions", "Weights"]) + # self.fitlist.setEditTriggers(QtWidgets.QAbstractItemView.NoEditTriggers) + self.fitlist.setColumnWidth(0, 200) + self.fitlist.setColumnWidth(1, 80) + self.fitlist.setSelectionMode( + QtWidgets.QAbstractItemView.SingleSelection) + # self.fitlist.itemSelectionChanged.connect(self.fitselect) + # self.fitlist.cellClicked.connect(self.fitselect) # self.fitlist.horizontalHeader().setStretchLastSection(True) - #set value of the first row to 0 - self.test_specific_settings_table.setItem(0, 1, QtWidgets.QTableWidgetItem("0.0")) - #if hippounit_test_sections_names_table has more than 2 rows, remove them + # set value of the first row to 0 + self.test_specific_settings_table.setItem( + 0, 1, QtWidgets.QTableWidgetItem("0.0")) + # if hippounit_test_sections_names_table has more than 2 rows, remove them if self.test_specific_settings_table.rowCount() > 2: - for row in range(self.test_specific_settings_table.rowCount()-1,1,-1): + for row in range( + self.test_specific_settings_table.rowCount() - 1, 1, + -1): self.test_specific_settings_table.removeRow(row) - + self._disable_column_editing(self.fitlist, 0) - #stretch the last column + # stretch the last column # self.fitlist.horizontalHeader().setStretchLastSection(True) def _disable_column_editing(self, table_widget, column_index): - """ - Disables editing of a column in a table widget + """Disables editing of a column in a table widget + + :param table_widget: + :param column_index: + """ for row in range(table_widget.rowCount()): - table_widget.item(row, column_index).setFlags(QtCore.Qt.NoItemFlags) + table_widget.item(row, + column_index).setFlags(QtCore.Qt.NoItemFlags) table_widget.item(row, column_index).setForeground(BLACK) def disable_mod_path(self): - """ - Disables mod files path if checked for usage - """ + """Disables mod files path if checked for usage""" if self.load_mods_checkbox.isChecked(): self.lineEdit_folder2.setEnabled(True) self.pushButton_14.setEnabled(True) @@ -2654,82 +3016,83 @@ def disable_mod_path(self): self.lineEdit_folder2.setEnabled(False) self.pushButton_14.setEnabled(False) - - def type_change(self): - """ - Sets units for drop down widget selecting simulation type. - """ + """Sets units for drop down widget selecting simulation type.""" self.dropdown.clear() # if not is_hippounit_installed(): # self.type_selector[2] = None - self.set_widgets_in_list(self.target_data_ui_components,True) - self.set_widgets_in_list(self.simtab_neuroptimus_group_boxes,True) - type_index=self.type_selector.currentIndex() - #block signals to avoid triggering the signal handler + self.set_widgets_in_list(self.target_data_ui_components, True) + self.set_widgets_in_list(self.simtab_neuroptimus_group_boxes, True) + type_index = self.type_selector.currentIndex() + # block signals to avoid triggering the signal handler self.fitlist.blockSignals(True) self.prepare_fitnessFunctions_table() self.fitlist.blockSignals(False) - if type_index in [0,1,2]: + if type_index in [0, 1, 2]: self.pushButton_3.setText("Load data") self.hippounit_group.setEnabled(False) # self.spike_group_box.setEnabled(True) # self.set_widgets_in_list(self.hippounit_settings_widgets,False) - if self.type_selector.currentIndex()==0: - self.dropdown.addItems(["uV","mV","V"]) - elif self.type_selector.currentIndex()==1: - self.dropdown.addItems(["pA","nA","uA"]) - elif self.type_selector.currentIndex()==2: - self.dropdown.addItems(["uV","mV","V","pA","nA","uA"]) - - elif self.type_selector.currentIndex()==3: #Hippounit + if self.type_selector.currentIndex() == 0: + self.dropdown.addItems(["uV", "mV", "V"]) + elif self.type_selector.currentIndex() == 1: + self.dropdown.addItems(["pA", "nA", "uA"]) + elif self.type_selector.currentIndex() == 2: + self.dropdown.addItems(["uV", "mV", "V", "pA", "nA", "uA"]) + + elif self.type_selector.currentIndex() == 3: # Hippounit self.pushButton_3.setText("Confirm") - self.set_widgets_in_list(self.target_data_ui_components,False) #first tab - self.set_widgets_in_list(self.simtab_neuroptimus_group_boxes,False) #settings tab (3rd) + self.set_widgets_in_list(self.target_data_ui_components, + False) # first tab + self.set_widgets_in_list( + # settings tab (3rd) + self.simtab_neuroptimus_group_boxes, + False, + ) self.hippounit_group.setEnabled(True) # self.set_widgets_in_list(self.hippounit_settings_widgets,True) # self.spike_group_box.setEnabled(False) - + else: self.dropdown.addItems(["none"]) self.dropdown.setCurrentIndex(1) self.settings_tab_mode_change() - + def settings_tab_mode_change(self): - if self.type_selector.currentText() == "HippoUnit" : - #hide all group boxes in self.neuroptimus_settings_widgets list + """ """ + if self.type_selector.currentText() == "HippoUnit": + # hide all group boxes in self.neuroptimus_settings_widgets list for widget in self.neuroptimus_settings_widgets: widget.hide() - #add self.hippounit_group to first place self.settings_tab_grid and hide the rest + # add self.hippounit_group to first place self.settings_tab_grid and hide the rest self.settings_tab_grid.addWidget(self.hippounit_group, 0, 0, 1, 2) self.hippounit_group.show() - elif self.type_selector.currentIndex() in [0,1,2]: - #unhide all group boxes in self.neuroptimus_settings_widgets list + elif self.type_selector.currentIndex() in [0, 1, 2]: + # unhide all group boxes in self.neuroptimus_settings_widgets list for widget in self.neuroptimus_settings_widgets: widget.show() self.settings_tab_grid.addWidget(self.hippounit_group, 6, 1, 7, 1) self.hippounit_group.hide() - - def add_data_dict(self,data_dict): - """ - Creates Input tree *not implemented yet* - :param data_dict: - :param root: + + def add_data_dict(self, data_dict): + """Creates Input tree *not implemented yet* + + :param data_dict: param root: + """ - + stack = data_dict - string="" + string = "" while stack: key, value = stack.popitem() if isinstance(value, dict): - string+=str("{0} : ".format(key))+"\n" + string += str("{0} : ".format(key)) + "\n" stack.update(value) else: - string+=str(" {0} : {1}".format(key, value))+"\n" - - + string += str(" {0} : {1}".format(key, value)) + "\n" + return string - + # def save_state_decorator(func): # @wraps(func) # def wrapper( *args, **kwargs): @@ -2748,98 +3111,122 @@ def add_data_dict(self,data_dict): # return result # return wrapper - + @save_state_decorator - def Load(self,*args): - """ - Loads the model after the 'Load Trace' clicked + def Load(self, *args): + """Loads the model after the 'Load Trace' clicked First creates a dictionary with the paths and options and call the First step, giving these as argument Plots the trace in matplotlib on the file tab. + :param *args: + """ # self.gui_elements_state["pushButton_3"] = {"type": "QPushButton", "value": True} - if (self.type_selector.currentText() == 'Features'): + if self.type_selector.currentText() == "Features": try: - kwargs = {"file" : str(self.lineEdit_folder.text()), - "input" : [str(self.lineEdit_file.text()), - None, - str(self.dropdown.currentText()), - None, - None, - None, - self.type_selector.currentText().split()[0].lower()]} - + kwargs = { + "file": + str(self.lineEdit_folder.text()), + "input": [ + str(self.lineEdit_file.text()), + None, + str(self.dropdown.currentText()), + None, + None, + None, + self.type_selector.currentText().split()[0].lower(), + ], + } + except ValueError as ve: print(ve) traceback.print_exc() - elif self.type_selector.currentIndex()==3: #Hippounit - self.tabwidget.setTabEnabled(1,True) - kwargs = {"file" : str(self.lineEdit_folder.text()), - "input": [ ""]*6 + ["hippounit"]} + elif self.type_selector.currentIndex() == 3: # Hippounit + self.tabwidget.setTabEnabled(1, True) + kwargs = { + "file": str(self.lineEdit_folder.text()), + "input": [""] * 6 + ["hippounit"], + } # "input":[str(self.lineEdit_file.text()),None,None,None,None,None,"hippounit"]} self.kwargs = kwargs - pass #TODO load_neuroptimus() + pass # TODO load_neuroptimus() else: try: - kwargs = {"file" : str(self.lineEdit_folder.text()), - "input" : [str(self.lineEdit_file.text()), - int(self.size_ctrl.text()), - str(self.dropdown.currentText()), - float(self.length_ctrl.text()), - float(self.freq_ctrl.text()), - self.time_checker.isChecked(), - self.type_selector.currentText().split()[0].lower()]} - + kwargs = { + "file": + str(self.lineEdit_folder.text()), + "input": [ + str(self.lineEdit_file.text()), + int(self.size_ctrl.text()), + str(self.dropdown.currentText()), + float(self.length_ctrl.text()), + float(self.freq_ctrl.text()), + self.time_checker.isChecked(), + self.type_selector.currentText().split()[0].lower(), + ], + } + except ValueError as ve: print(ve) traceback.print_exc() - + self.core.FirstStep(kwargs) - self.tabwidget.setTabEnabled(1,True) - if self.type_selector.currentText().lower() in ["voltage trace", "current trace"]: - + self.tabwidget.setTabEnabled(1, True) + if self.type_selector.currentText().lower() in [ + "voltage trace", + "current trace", + ]: + f = self.core.option_handler.input_freq t = self.core.option_handler.input_length - no_traces=self.core.option_handler.input_size - _type="voltage" if self.type_selector.currentIndex==0 else "current" if self.type_selector.currentIndex==1 else "unkown" + no_traces = self.core.option_handler.input_size + _type = ("voltage" + if self.type_selector.currentIndex == 0 else "current" + if self.type_selector.currentIndex == 1 else "unkown") exp_data = [] - - freq=float(self.freq_ctrl.text()) + + freq = float(self.freq_ctrl.text()) for k in range(self.core.data_handler.number_of_traces()): exp_data.extend(self.core.data_handler.data.GetTrace(k)) - + self.figure.clf() ax = self.figure.add_subplot(111) ax.cla() if self.time_checker.isChecked(): - ax.plot([x/freq*1000 for x in range(len(exp_data))],exp_data) + ax.plot([x / freq * 1000 for x in range(len(exp_data))], + exp_data) else: ax.plot(exp_data) self.canvas.draw() - - - + for k in range(self.core.data_handler.number_of_traces()): exp_data.extend(self.core.data_handler.data.GetTrace(k)) self.model.insertRow(0) - if self.type_selector.currentIndex()==0: - for n in [x for x in enumerate(self.loaded_input_types) if x[1]!=None and x[0]!=2]: - self.loaded_input_types[n[0]]=None - input_string="Voltage trace \n" - self.loaded_input_types[0]=self.tvoltage - - input_string+=str(str(self.lineEdit_file.text()).split("/")[-1])+"\n" - elif self.type_selector.currentIndex()==1: - for n in [x for x in enumerate(self.loaded_input_types) if x[1]!=None and x[0]!=2]: - self.loaded_input_types[n[0]]=None - input_string="Current trace" - self.loaded_input_types[1]=self.tcurrent - input_string+=str(str(self.lineEdit_file.text()).split("/")[-1])+"\n" - - ''' + if self.type_selector.currentIndex() == 0: + for n in [ + x for x in enumerate(self.loaded_input_types) + if x[1] != None and x[0] != 2 + ]: + self.loaded_input_types[n[0]] = None + input_string = "Voltage trace \n" + self.loaded_input_types[0] = self.tvoltage + + input_string += ( + str(str(self.lineEdit_file.text()).split("/")[-1]) + "\n") + elif self.type_selector.currentIndex() == 1: + for n in [ + x for x in enumerate(self.loaded_input_types) + if x[1] != None and x[0] != 2 + ]: + self.loaded_input_types[n[0]] = None + input_string = "Current trace" + self.loaded_input_types[1] = self.tcurrent + input_string += ( + str(str(self.lineEdit_file.text()).split("/")[-1]) + "\n") + """ elif self.type_selector.GetSelection()==3: try: self.input_tree.Delete(self.tspike_t) @@ -2847,172 +3234,204 @@ def Load(self,*args): pass self.tspike_t=self.input_tree.AppendItem(self.troot,"Spike times") self.input_tree.AppendItem(self.tspike_t,self.input_file_controll.GetValue().split("/")[-1]) - ''' - + """ elif self.type_selector.currentText().lower() == "features": - for n in [x for x in enumerate(self.loaded_input_types) if x[1]!=None and x[0]!=2]: - self.loaded_input_types[n[0]]=None - input_string="Features" - input_string+=str(str(self.lineEdit_file.text()).split("/")[-1])+"\n" - input_string+=self.add_data_dict(self.core.data_handler.features_dict) - - elif self.type_selector.currentText().lower() == "hippounit": - input_string="Hippounit" + for n in [ + x for x in enumerate(self.loaded_input_types) + if x[1] != None and x[0] != 2 + ]: + self.loaded_input_types[n[0]] = None + input_string = "Features" + input_string += str(str( + self.lineEdit_file.text()).split("/")[-1]) + "\n" + input_string += self.add_data_dict( + self.core.data_handler.features_dict) + + elif self.type_selector.currentText().lower() == "hippounit": + input_string = "Hippounit" # self.tabwidget.setTabEnabled(1,True) # pass #TODO load_neuroptimus() else: raise NotImplementedError("Input type not implemented yet") - - self.input_label.setText(QtCore.QCoreApplication.translate("Neuroptimus", input_string)) - if self.core.option_handler.type[-1].lower() in ["voltage", "current"]: - self.my_list = copy(self.core.ffun_calc_list) + + self.input_label.setText( + QtCore.QCoreApplication.translate("Neuroptimus", input_string)) + if self.core.option_handler.type[-1].lower() in ["voltage", "current"]: + self.my_list = copy(self.core.ffun_calc_list) elif self.core.option_handler.type[-1].lower() == "hippounit": - verbose("hippounit tests loading in table") - self.my_list = copy(self.core.hippounit_tests_names) - else: #features - self.my_list=list(self.core.data_handler.features_data.keys())[3:] + verbose("hippounit tests loading in table") + self.my_list = copy(self.core.hippounit_tests_names) + else: # features + self.my_list = list( + self.core.data_handler.features_data.keys())[3:] self.param_list = [[]] * len(self.my_list) if self.core.option_handler.type[-1].lower() in ["voltage", "current"]: - self.param_list[2] = [("Spike detection thres. (mV)",0.0)] - self.param_list[1] = [("Spike detection thres. (mV)",0.0), ("Spike Window (ms)",1.0)] - + self.param_list[2] = [("Spike detection thres. (mV)", 0.0)] + self.param_list[1] = [ + ("Spike detection thres. (mV)", 0.0), + ("Spike Window (ms)", 1.0), + ] + elif self.core.option_handler.type[-1].lower() == "features": - self.param_list[0] = [("Spike detection thres. (mV)",0.0)] + self.param_list[0] = [("Spike detection thres. (mV)", 0.0)] - if self.core.option_handler.type[-1]=="features": - for l in range(len(self.core.data_handler.features_data["stim_amp"])): - self.container.append(float(self.core.data_handler.features_data["stim_amp"][l])) + if self.core.option_handler.type[-1] == "features": + for l in range( + len(self.core.data_handler.features_data["stim_amp"])): + self.container.append( + float(self.core.data_handler.features_data["stim_amp"][l])) self.fitlist.setRowCount(len(self.my_list)) - for index,elems in enumerate(self.my_list): - item = QTableWidgetItem(self.tests_ui_names[elems] if self.core.option_handler.type[-1].lower() == "hippounit" else elems) - item.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsEditable) + for index, elems in enumerate(self.my_list): + item = QTableWidgetItem(self.tests_ui_names[elems] if self.core. + option_handler.type[-1].lower() == + "hippounit" else elems) + item.setFlags(QtCore.Qt.ItemIsSelectable + | QtCore.Qt.ItemIsEnabled + | QtCore.Qt.ItemIsEditable) self.fitlist.setItem(index, 0, item) - if self.core.option_handler.type[-1]=="features": - itemv = QTableWidgetItem(str(self.core.data_handler.features_data[self.my_list[index]]["weight"])) + if self.core.option_handler.type[-1] == "features": + itemv = QTableWidgetItem( + str(self.core.data_handler.features_data[ + self.my_list[index]]["weight"])) else: itemv = QTableWidgetItem("0") self.fitlist.setItem(index, 1, itemv) self._disable_column_editing(self.fitlist, 0) if self.core.option_handler.type[-1].lower() in ["voltage", "current"]: - self.kwargs={"runparam" : [self.core.data_handler.data.t_length, - self.core.data_handler.data.step, - "record", - "soma", - "pos", - "vrest"] - } + self.kwargs = { + "runparam": [ + self.core.data_handler.data.t_length, + self.core.data_handler.data.step, + "record", + "soma", + "pos", + "vrest", + ] + } elif self.core.option_handler.type[-1].lower() == "features": - self.kwargs={"runparam" : [self.core.data_handler.features_data["stim_delay"] + self.core.data_handler.features_data["stim_duration"]+100, - 0.05, - "record", - "soma", - "pos", - "vrest"]} - if self.core.option_handler.output_level=="1": + self.kwargs = { + "runparam": [ + self.core.data_handler.features_data["stim_delay"] + + self.core.data_handler.features_data["stim_duration"] + + 100, + 0.05, + "record", + "soma", + "pos", + "vrest", + ] + } + if self.core.option_handler.output_level == "1": self.core.Print() - self.fit_container=[] + self.fit_container = [] if self.core.option_handler.type[-1].lower() in ["voltage", "current"]: - self.lineEdit_tstop.setText(str(self.core.data_handler.data.t_length)) + self.lineEdit_tstop.setText( + str(self.core.data_handler.data.t_length)) elif self.core.option_handler.type[-1].lower() == "features": - self.lineEdit_tstop.setText(str(self.core.data_handler.features_data["stim_delay"] + self.core.data_handler.features_data["stim_duration"]+100)) - self.lineEdit_delay.setText(str(self.core.data_handler.features_data["stim_delay"])) - self.lineEdit_duration.setText(str(self.core.data_handler.features_data["stim_duration"])) - - + self.lineEdit_tstop.setText( + str(self.core.data_handler.features_data["stim_delay"] + + self.core.data_handler.features_data["stim_duration"] + + 100)) + self.lineEdit_delay.setText( + str(self.core.data_handler.features_data["stim_delay"])) + self.lineEdit_duration.setText( + str(self.core.data_handler.features_data["stim_duration"])) - - @save_state_decorator def Set(self, e): - """ - Set the selected parameters to optimize on the model. + """Set the selected parameters to optimize on the model. Loop through every selected line. + + :param e: + """ items = self.modellist.selectionModel().selectedRows() - #save the selected items rows to self.gui_elements_state - self.modellist_selected_rows.add_selected_rows_index([x.row() for x in items]) + # save the selected items rows to self.gui_elements_state + self.modellist_selected_rows.add_selected_rows_index( + [x.row() for x in items]) self.modellist_selected_rows.set_table_widget("modellist") self.remover.setEnabled(True) for item_selected in items: - selected_row=item_selected.row() - section = str(self.modellist.item(selected_row, 0).text()) - segment = str(self.modellist.item(selected_row, 1).text()) - chan = str(self.modellist.item(selected_row, 2).text()) - morph="" - par = str(self.modellist.item(selected_row, 3).text()) - if chan == "morphology": - chan = "None" - par= "None" - morph = str(self.modellist.item(selected_row, 3).text()) - - - - kwargs = {"section" : section, - "segment" : segment, - "channel" : chan, - "morph" : morph, - "params" : par, - "values" : 0} - - - for j in range(4): - self.modellist.item(selected_row,j).setBackground(QtGui.QColor(255,0,0)) - - - self.core.SetModel2(kwargs) - - + selected_row = item_selected.row() + section = str(self.modellist.item(selected_row, 0).text()) + segment = str(self.modellist.item(selected_row, 1).text()) + chan = str(self.modellist.item(selected_row, 2).text()) + morph = "" + par = str(self.modellist.item(selected_row, 3).text()) + if chan == "morphology": + chan = "None" + par = "None" + morph = str(self.modellist.item(selected_row, 3).text()) + + kwargs = { + "section": section, + "segment": segment, + "channel": chan, + "morph": morph, + "params": par, + "values": 0, + } + + for j in range(4): + self.modellist.item(selected_row, + j).setBackground(QtGui.QColor(255, 0, 0)) + + self.core.SetModel2(kwargs) def Remove(self, e): - """ - Remove the selected parameters to optimize on the model. + """Remove the selected parameters to optimize on the model. Loop through every selected line. + + :param e: + """ items = self.modellist.selectionModel().selectedRows() - self.modellist_selected_rows.remove_selected_rows_indices([x.row() for x in items]) + self.modellist_selected_rows.remove_selected_rows_indices( + [x.row() for x in items]) for item_selected in items: - selected_row=item_selected.row() - section = str(self.modellist.item(selected_row, 0).text()) - segment = str(self.modellist.item(selected_row, 1).text()) - chan = str(self.modellist.item(selected_row, 2).text()) - morph="" - par = str(self.modellist.item(selected_row, 3).text()) - if chan == "morphology": - chan = "None" - par= "None" - morph = str(self.modellist.item(selected_row, 3).text()) - - kwargs = {"section" : section, - "segment" : segment, - "channel" : chan, - "morph" : morph, - "params" : par} - - if kwargs["channel"] == "None": - temp = kwargs["section"] + " " + kwargs["morph"] - else: - temp = kwargs["section"] + " " + kwargs["segment"] + " " + kwargs["channel"] + " " + kwargs["params"] - self.core.option_handler.param_vals.pop(self.core.option_handler.GetObjTOOpt().index(temp)) - self.core.option_handler.adjusted_params.remove(temp) - if len(self.core.option_handler.GetObjTOOpt()) == 0: - self.remover.setEnabled(False ) - for j in range(4): - self.modellist.item(selected_row,j).setBackground(WHITE) - - + selected_row = item_selected.row() + section = str(self.modellist.item(selected_row, 0).text()) + segment = str(self.modellist.item(selected_row, 1).text()) + chan = str(self.modellist.item(selected_row, 2).text()) + morph = "" + par = str(self.modellist.item(selected_row, 3).text()) + if chan == "morphology": + chan = "None" + par = "None" + morph = str(self.modellist.item(selected_row, 3).text()) + + kwargs = { + "section": section, + "segment": segment, + "channel": chan, + "morph": morph, + "params": par, + } + + if kwargs["channel"] == "None": + temp = kwargs["section"] + " " + kwargs["morph"] + else: + temp = (kwargs["section"] + " " + kwargs["segment"] + " " + + kwargs["channel"] + " " + kwargs["params"]) + self.core.option_handler.param_vals.pop( + self.core.option_handler.GetObjTOOpt().index(temp)) + self.core.option_handler.adjusted_params.remove(temp) + if len(self.core.option_handler.GetObjTOOpt()) == 0: + self.remover.setEnabled(False) + for j in range(4): + self.modellist.item(selected_row, j).setBackground(WHITE) def sim_plat(self): - """ - Called when simulation platform changed, locks unnecessary widgets and swap Label of Load button. - """ - if self.dd_type.currentIndex()==1: + """Called when simulation platform changed, locks unnecessary widgets and swap Label of Load button.""" + if self.dd_type.currentIndex() == 1: self.sim_path.show() self.sim_param.show() - self.pushButton_13.setText(QtCore.QCoreApplication.translate("Neuroptimus", "Set")) + self.pushButton_13.setText( + QtCore.QCoreApplication.translate("Neuroptimus", "Set")) self.pushButton_12.show() self.pushButton_14.hide() self.pushButton_15.hide() @@ -3027,10 +3446,11 @@ def sim_plat(self): self.label_26.show() self.label_27.show() self.load_mods_checkbox.hide() - elif self.dd_type.currentIndex()==2: + elif self.dd_type.currentIndex() == 2: self.sim_path.show() self.sim_param.show() - self.pushButton_13.setText(QtCore.QCoreApplication.translate("Neuroptimus", "Set")) + self.pushButton_13.setText( + QtCore.QCoreApplication.translate("Neuroptimus", "Set")) self.pushButton_12.hide() self.pushButton_14.hide() self.pushButton_15.hide() @@ -3046,7 +3466,8 @@ def sim_plat(self): self.label_27.show() self.load_mods_checkbox.hide() else: - self.pushButton_13.setText(QtCore.QCoreApplication.translate("Neuroptimus", "Load")) + self.pushButton_13.setText( + QtCore.QCoreApplication.translate("Neuroptimus", "Load")) self.sim_path.hide() self.sim_param.hide() self.pushButton_12.hide() @@ -3065,27 +3486,40 @@ def sim_plat(self): self.load_mods_checkbox.show() def Loadpython(self, e): + """ + + :param e: + + """ options = QtWidgets.QFileDialog.Options() options |= QtWidgets.QFileDialog.DontUseNativeDialog - fileName, _ = QFileDialog.getOpenFileName(None,"QFileDialog.getOpenFileName()", "","Python files (*.py);;All Files (*);;", options=options) + fileName, _ = QFileDialog.getOpenFileName( + None, + "QFileDialog.getOpenFileName()", + "", + "Python files (*.py);;All Files (*);;", + options=options, + ) if fileName: - self.sim_path.setText("python "+str(fileName)) + self.sim_path.setText("python " + str(fileName)) @save_state_decorator - def Load2(self,e): - """ - Load the selected Neuron model and displays the sections in a tablewidget + def Load2(self, e): + """Load the selected Neuron model and displays the sections in a tablewidget + + :param e: + """ self.model_file = self.lineEdit_file2.text() if not os.path.isfile(self.model_file): - #focus on the model path input + # focus on the model path input self.lineEdit_file2.setFocus() - #error popup + # error popup popup("Invalid model path") return None - self.tabwidget.setTabEnabled(2,True) - self.tabwidget.setTabEnabled(3,True) - self.tabwidget.setTabEnabled(4,True) + self.tabwidget.setTabEnabled(2, True) + self.tabwidget.setTabEnabled(3, True) + self.tabwidget.setTabEnabled(4, True) if self.load_mods_checkbox.isChecked(): self.spec_file = self.lineEdit_folder2.text() else: @@ -3097,31 +3531,38 @@ def Load2(self,e): self.model_name = self.model_name_input.text() self._write_on_status_bar("Model loaded Successfully!") - - return try: - self.core.LoadModel({"model" : [self.model_file, self.spec_file], - "simulator" : simulator_selected, - "sim_command" : self.sim_path.text() if not self.dd_type else self.sim_path.text()+" "+self.sim_param.text()}) + self.core.LoadModel({ + "model": [self.model_file, self.spec_file], + "simulator": + simulator_selected, + "sim_command": + (self.sim_path.text() if not self.dd_type else + self.sim_path.text() + " " + self.sim_param.text()), + }) temp = self.core.model_handler.GetParameters() - if temp!=None: - with open("model.txt", 'w+') as out: + if temp != None: + with open("model.txt", "w+") as out: for i in temp: out.write(str(i)) out.write("\n") - index=0 + index = 0 self.modellist.setRowCount(self.recursive_len(temp)) for row in temp: - for k in (row[1]): + for k in row[1]: if k != []: - for s in (k[2]): - self.modellist.setItem(index, 0, QTableWidgetItem(row[0])) - self.modellist.setItem(index, 1, QTableWidgetItem(str(k[0]))) - self.modellist.setItem(index, 2, QTableWidgetItem(k[1])) - self.modellist.setItem(index, 3, QTableWidgetItem(s)) - index+=1 + for s in k[2]: + self.modellist.setItem( + index, 0, QTableWidgetItem(row[0])) + self.modellist.setItem( + index, 1, QTableWidgetItem(str(k[0]))) + self.modellist.setItem(index, 2, + QTableWidgetItem(k[1])) + self.modellist.setItem(index, 3, + QTableWidgetItem(s)) + index += 1 self.modellist.setRowCount(index) else: pass @@ -3131,9 +3572,9 @@ def Load2(self,e): except Exception as e: print("Error in Load2:") traceback.print_exc() - if not self.dd_type.currentIndex(): + if not self.dd_type.currentIndex(): try: - tmp=self.core.ReturnSections() + tmp = self.core.ReturnSections() [tmp.remove("None") for i in range(tmp.count("None"))] self.section_rec.addItems(tmp) self.section_stim.addItems(tmp) @@ -3144,67 +3585,87 @@ def Load2(self,e): popup("Section error") def typeChange(self): + """ """ _translate = QtCore.QCoreApplication.translate - if self.stimulus_type.currentIndex()==0:#step prot + if self.stimulus_type.currentIndex() == 0: # step prot self.lineEdit_delay.setDisabled(False) self.lineEdit_duration.setDisabled(False) - self.base_dir_controll9.clicked.disconnect(self.openFileNameDialogWaveform) + self.base_dir_controll9.clicked.disconnect( + self.openFileNameDialogWaveform) self.base_dir_controll9.clicked.connect(self.amplitudes_fun) - self.base_dir_controll9.setText(_translate("Neuroptimus", "Amplitude(s)")) - if self.stimulus_type.currentIndex()==1:#wave prot + self.base_dir_controll9.setText( + _translate("Neuroptimus", "Amplitude(s)")) + if self.stimulus_type.currentIndex() == 1: # wave prot self.lineEdit_delay.setDisabled(True) self.lineEdit_delay.setText("0") self.lineEdit_duration.setDisabled(True) self.lineEdit_duration.setText("1e9") - self.base_dir_controll9.setText(_translate("Neuroptimus", "Load Waveform")) + self.base_dir_controll9.setText( + _translate("Neuroptimus", "Load Waveform")) self.base_dir_controll9.clicked.disconnect(self.amplitudes_fun) - self.base_dir_controll9.clicked.connect(self.openFileNameDialogWaveform) + self.base_dir_controll9.clicked.connect( + self.openFileNameDialogWaveform) - def openFileNameDialogWaveform(self): - """ - File dialog for the file tab to open file. - """ + def openFileNameDialogWaveform(self): + """File dialog for the file tab to open file.""" options = QtWidgets.QFileDialog.Options() options |= QtWidgets.QFileDialog.DontUseNativeDialog - fileName, _ = QFileDialog.getOpenFileName(None,"QFileDialog.getOpenFileName()", "","Data files (*.dat *.json);;All Files (*);;", options=options) + fileName, _ = QFileDialog.getOpenFileName( + None, + "QFileDialog.getOpenFileName()", + "", + "Data files (*.dat *.json);;All Files (*);;", + options=options, + ) if fileName: - self.container=[fileName] - + self.container = [fileName] + def _write_on_status_bar(self, message, color="green", timeout=5000): - - self.statusbar.setStyleSheet("color: "+color) + """ + + :param message: + :param color: (Default value = "green") + :param timeout: (Default value = 5000) + + """ + + self.statusbar.setStyleSheet("color: " + color) self.statusbar.showMessage(message, timeout) - def recursive_len(self,item): + def recursive_len(self, item): + """ + + :param item: + + """ if type(item) == list: return sum(self.recursive_len(subitem) for subitem in item) else: return 1 - def UF(self): - """ - Calls the user function window for the Model tab. - """ + """Calls the user function window for the Model tab.""" - # self.SW = SecondWindow(self) + # self.SW = SecondWindow(self) # self.SW.setObjectName("Neuroptimus") # self.SW.resize(500, 500) self.SW.show() + @save_state_decorator - def amplitudes_fun(self,*args): - """ - Calls the amplitude window for the Options tab. + def amplitudes_fun(self, *args): + """Calls the amplitude window for the Options tab. + + :param *args: + """ - # self.SiW = StimuliWindow(self) + # self.SiW = StimuliWindow(self) # self.SiW.setObjectName("Neuroptimus") # self.SiW.resize(400, 500) self.SiW.initialize() self.SiW.show() - # def fitselect(self): # """ # Calls when fitness functions selected, colours the item and adds them to a set. @@ -3221,158 +3682,198 @@ def amplitudes_fun(self,*args): # self.fitlist.item(item_selected.row(),0).setBackground(QtGui.QColor(0,255,0)) # self.fitset.add(current_item) + def _check_fitlist_weight(self, selected_row): + """ - def _check_fitlist_weight(self,selected_row): - if self.fitlist.item(selected_row, 1) != None and self.fitlist.item(selected_row, 1).text() != "" and float(self.fitlist.item(selected_row, 1).text()) != 0: - return True - + :param selected_row: + """ + if (self.fitlist.item(selected_row, 1) != None + and self.fitlist.item(selected_row, 1).text() != "" + and float(self.fitlist.item(selected_row, 1).text()) != 0): + return True def fitchanged(self): - """ - Calls when the weights changed for the fitness functions. Checks which Hippounit test is selected and enables the corresponding row in the settings table. - """ - - - #first check if hippounit test is selected + """Calls when the weights changed for the fitness functions. Checks which Hippounit test is selected and enables the corresponding row in the settings table.""" + + # first check if hippounit test is selected if self.type_selector.currentText().lower() == "hippounit": - - + # self.HippoTests_required_parameters = {self.tests_ui_names["PSPAttenuationTest"]: ["TrunkSecList_name","num_of_dend_locations"], # self.tests_ui_names["BackpropagatingAPTest"]: ["TrunkSecList_name"], # self.tests_ui_names["ObliqueIntegrationTest"]: ["ObliqueSecList_name", "TrunkSecList_name"], # self.tests_ui_names["PathwayInteraction"]: ["TuftSecList_name","num_of_dend_locations"]} - - + # self.HippoTests_parameter_location_in_table = {"TrunkSecList_name":3 , "ObliqueSecList_name":4 , "TuftSecList_name":5, "num_of_dend_locations":6} - #get currently selected row + # get currently selected row selected_row = self.fitlist.currentRow() # verbose("Current selected row ---------->",selected_row) - #get the name of the test if not its's weight (2nd column) is not none and not empty and not 0 + # get the name of the test if not its's weight (2nd column) is not none and not empty and not 0 try: test_name = self.fitlist.item(selected_row, 0).text() is_test_weighted = self._check_fitlist_weight(selected_row) - if is_test_weighted: #Weight is a number and not 0 - #make its corresponding property row in the table to the selected row be editable and non grayed - #enable the row in fitlist and make it white columns 2 , 3 ,4 + if is_test_weighted: # Weight is a number and not 0 + # make its corresponding property row in the table to the selected row be editable and non grayed + # enable the row in fitlist and make it white columns 2 , 3 ,4 self.fitlist.blockSignals(True) - for column in range(2,5): #do this except cells (5,2) , (5,3), (4,2) , (4,3) + # do this except cells (5,2) , (5,3), (4,2) , (4,3) + for column in range(2, 5): # #set text "Double click to Browse" if it is not last column - is_penalty_coulmn = column == self.fitlist.columnCount() - 1 + is_penalty_coulmn = column == self.fitlist.columnCount( + ) - 1 if is_penalty_coulmn: - is_penalty_already_set = self.fitlist.item(selected_row, column).text().isnumeric() + is_penalty_already_set = (self.fitlist.item( + selected_row, column).text().isnumeric()) if not is_penalty_already_set: - self.fitlist.item(selected_row, column).setText("250") + self.fitlist.item(selected_row, + column).setText("250") else: - pass #keep the value - elif not os.path.isfile(self.fitlist.item(selected_row, column).text()) : + pass # keep the value + elif not os.path.isfile( + self.fitlist.item(selected_row, + column).text()): self.fitlist.item(selected_row, column).setText("") - - else : + + else: pass # if column == 4:#set value to 255 # #if it's text is not numeric (not already set to a number), set it to 250 # if not self.fitlist.item(selected_row, column).text().isnumeric(): - # self.fitlist.item(selected_row, column).setText("250") - # self.fitlist.item(selected_row, column).setPlaceholderText("250") - if (column == 3 and selected_row == 4) or (column == 3 and selected_row == 5) : - self.fitlist.item(selected_row, column).setBackground(GRAY) - self.fitlist.item(selected_row, column).setForeground(BLACK) - self.fitlist.item(selected_row, column).setFlags(QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled) - self.fitlist.item(selected_row, column).setFlags(QtCore.Qt.NoItemFlags) + # self.fitlist.item(selected_row, column).setText("250") + # self.fitlist.item(selected_row, column).setPlaceholderText("250") + if (column == 3 and selected_row + == 4) or (column == 3 and selected_row == 5): + self.fitlist.item(selected_row, + column).setBackground(GRAY) + self.fitlist.item(selected_row, + column).setForeground(BLACK) + self.fitlist.item( + selected_row, + column).setFlags(QtCore.Qt.ItemIsEditable + | QtCore.Qt.ItemIsEnabled) + self.fitlist.item(selected_row, column).setFlags( + QtCore.Qt.NoItemFlags) self.fitlist.item(selected_row, column).setText("") - + else: - self.fitlist.item(selected_row, column).setBackground(WHITE) - self.fitlist.item(selected_row, column).setForeground(BLACK) - self.fitlist.item(selected_row, column).setFlags(QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled) - + self.fitlist.item(selected_row, + column).setBackground(WHITE) + self.fitlist.item(selected_row, + column).setForeground(BLACK) + self.fitlist.item( + selected_row, + column).setFlags(QtCore.Qt.ItemIsEditable + | QtCore.Qt.ItemIsEnabled) + self.fitlist.blockSignals(False) - #disable callbacks for the table - + # disable callbacks for the table if test_name in self.HippoTests_required_parameters.keys(): - required_properties_by_test = self.HippoTests_required_parameters[test_name] + required_properties_by_test = ( + self.HippoTests_required_parameters[test_name]) for property in required_properties_by_test: - property_row = self.HippoTests_parameter_location_in_table[property] - self.test_specific_settings_table.item(property_row, 1).setFlags(QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled) - self.test_specific_settings_table.item(property_row, 1).setBackground(WHITE) - self.test_specific_settings_table.item(property_row, 0).setBackground(WHITE) - - - else : # Weight is 0 or none - #make uneditable and grayed out rows if the weight is 0 or none + property_row = self.HippoTests_parameter_location_in_table[ + property] + self.test_specific_settings_table.item( + property_row, + 1).setFlags(QtCore.Qt.ItemIsEditable + | QtCore.Qt.ItemIsEnabled) + self.test_specific_settings_table.item( + property_row, 1).setBackground(WHITE) + self.test_specific_settings_table.item( + property_row, 0).setBackground(WHITE) + + else: # Weight is 0 or none + # make uneditable and grayed out rows if the weight is 0 or none self.fitlist.blockSignals(True) - for column in range(2,5): - self.fitlist.item(selected_row, column).setBackground(GRAY) - self.fitlist.item(selected_row, column).setForeground(BLACK) - self.fitlist.item(selected_row, column).setFlags(QtCore.Qt.ItemIsEditable | QtCore.Qt.ItemIsEnabled) - self.fitlist.item(selected_row, column).setFlags(QtCore.Qt.NoItemFlags) - self.fitlist.item(selected_row, column).setText("") - + for column in range(2, 5): + self.fitlist.item(selected_row, + column).setBackground(GRAY) + self.fitlist.item(selected_row, + column).setForeground(BLACK) + self.fitlist.item( + selected_row, + column).setFlags(QtCore.Qt.ItemIsEditable + | QtCore.Qt.ItemIsEnabled) + self.fitlist.item(selected_row, column).setFlags( + QtCore.Qt.NoItemFlags) + self.fitlist.item(selected_row, column).setText("") + self.fitlist.blockSignals(False) - - + if test_name in self.HippoTests_required_parameters.keys(): - required_properties_by_test = self.HippoTests_required_parameters[test_name] + required_properties_by_test = ( + self.HippoTests_required_parameters[test_name]) # print("required_properties_by_test",required_properties_by_test) for property in required_properties_by_test: # print("property",property) - property_row = self.HippoTests_parameter_location_in_table[property] - self.test_specific_settings_table.item(property_row, 1).setFlags(QtCore.Qt.NoItemFlags) - self.test_specific_settings_table.item(property_row, 1).setBackground(GRAY) - self.test_specific_settings_table.item(property_row, 0).setBackground(GRAY) - + property_row = self.HippoTests_parameter_location_in_table[ + property] + self.test_specific_settings_table.item( + property_row, + 1).setFlags(QtCore.Qt.NoItemFlags) + self.test_specific_settings_table.item( + property_row, 1).setBackground(GRAY) + self.test_specific_settings_table.item( + property_row, 0).setBackground(GRAY) + except AttributeError as ae: - pass - + pass + except Exception as e: traceback.print_exc() # print(e) pass - - def browse_file_for_hippounit_data_paths(self): - """ - File dialog for the file tab to open file. - """ - row = self.fitlist.currentRow() #get the selected row - column = self.fitlist.currentColumn() #get the selected column - if column in [0, 1, 4]: #if the selected cell is the first column - return #do nothing - - + """File dialog for the file tab to open file.""" + row = self.fitlist.currentRow() # get the selected row + column = self.fitlist.currentColumn() # get the selected column + if column in [0, 1, 4]: # if the selected cell is the first column + return # do nothing + options = QtWidgets.QFileDialog.Options() options |= QtWidgets.QFileDialog.DontUseNativeDialog - filePath, _ = QFileDialog.getOpenFileName(None,"QFileDialog.getOpenFileName()", "","Data files (*.json);;All Files (*);;", options=options) + filePath, _ = QFileDialog.getOpenFileName( + None, + "QFileDialog.getOpenFileName()", + "", + "Data files (*.json);;All Files (*);;", + options=options, + ) if filePath: - #set the file name to the selected cell, do not resize the column - self.fitlist.setItem(self.fitlist.currentRow(),self.fitlist.currentColumn(), QTableWidgetItem(filePath)) - - - - + # set the file name to the selected cell, do not resize the column + self.fitlist.setItem( + self.fitlist.currentRow(), + self.fitlist.currentColumn(), + QTableWidgetItem(filePath), + ) def Fit_normalize(self, e): - """ - Normalize the weigths of only the selected fitness functions. + """Normalize the weigths of only the selected fitness functions. Iterates through all fitness functions and scans the ones contained in the fitness set (selected ones) with an 'if' statement. + + :param e: + """ try: - #self.fitselect() - #self.432eanged() + # self.fitselect() + # self.432eanged() allRows = self.fitlist.rowCount() - self.weights=[float(self.fitlist.item(row, 1).text()) for row in range(0,allRows)] + self.weights = [ + float(self.fitlist.item(row, 1).text()) + for row in range(0, allRows) + ] sum_o_weights = float(sum(self.weights)) - for row in range(0,allRows): - current_fun=str(self.fitlist.item(row, 0).text()) - current_weight=float(str(self.fitlist.item(row, 1).text())) + for row in range(0, allRows): + current_fun = str(self.fitlist.item(row, 0).text()) + current_weight = float(str(self.fitlist.item(row, 1).text())) if current_weight: try: - self.fitlist.item(row, 1).setText(str(round(current_weight / sum_o_weights,4))) + self.fitlist.item(row, 1).setText( + str(round(current_weight / sum_o_weights, 4))) except: continue else: @@ -3381,68 +3882,84 @@ def Fit_normalize(self, e): except: continue except Exception as e: - popup("Wrong values given. "+str(e)) + popup("Wrong values given. " + str(e)) - - def packageselect(self,pack_name): - """ - Writes the given aspects to algorithm in an other table, where the user can change the option (generation, population size, etc.). - Iterates through the selected algorithms options list and writes the names of it to the first column and sets the cell immutable, - and the values to the second row. - """ + def packageselect(self, pack_name): + """Writes the given aspects to algorithm in an other table, where the user can change the option (generation, population size, etc.). + Iterates through the selected algorithms options list and writes the names of it to the first column and sets the cell immutable, + and the values to the second row. - selected_package = self.algos.get(pack_name) - self.algolist.setRowCount(len(selected_package)) - for index,elems in enumerate(selected_package): - item = QTableWidgetItem(str(elems)) - self.algolist.setItem(index, 0, item) - self.algolist.item(0,0) + :param pack_name: - def algoselect(self): """ - Writes the given aspects to algorithm in an other table, where the user can change the option (generation, population size, etc.). - Iterates through the selected algorithms options list and writes the names of it to the first column and sets the cell immutable, + + selected_package = self.algos.get(pack_name) + self.algolist.setRowCount(len(selected_package)) + for index, elems in enumerate(selected_package): + item = QTableWidgetItem(str(elems)) + self.algolist.setItem(index, 0, item) + self.algolist.item(0, 0) + + def algoselect(self): + """Writes the given aspects to algorithm in an other table, where the user can change the option (generation, population size, etc.). + Iterates through the selected algorithms options list and writes the names of it to the first column and sets the cell immutable, and the values to the second row. + + """ try: - selected_algo = self.algolist.selectionModel().selectedRows()[0].row() - algo_name = str(self.algolist.item(selected_algo, 0).text()).upper() - self.aspects = self.algo_dict[algo_name[algo_name.find("(")+1:].replace(")","").replace(" - ","_").replace("-","_").replace(" ","_")] - self.algorithm_parameter_list.setRowCount(len(self.aspects)+1) - item = QTableWidgetItem('Seed') - item.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEnabled ) + selected_algo = self.algolist.selectionModel().selectedRows( + )[0].row() + algo_name = str(self.algolist.item(selected_algo, + 0).text()).upper() + self.aspects = self.algo_dict[algo_name[algo_name.find("(") + + 1:].replace( + ")", "").replace( + " - ", + "_").replace( + "-", + "_").replace( + " ", "_")] + self.algorithm_parameter_list.setRowCount(len(self.aspects) + 1) + item = QTableWidgetItem("Seed") + item.setFlags(QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEnabled) self.algorithm_parameter_list.setItem(0, 0, item) - item2 = QTableWidgetItem('1234') + item2 = QTableWidgetItem("1234") self.algorithm_parameter_list.setItem(0, 1, item2) for index, (key, value) in enumerate(self.aspects.items()): item = QTableWidgetItem(key) if self.algo_param_dict.get(key): - item.setToolTip(str(self.algo_param_dict.get(key)).rjust(30)) - item.setFlags( QtCore.Qt.ItemIsSelectable | QtCore.Qt.ItemIsEnabled ) - self.algorithm_parameter_list.setItem(index+1, 0, item) + item.setToolTip( + str(self.algo_param_dict.get(key)).rjust(30)) + item.setFlags(QtCore.Qt.ItemIsSelectable + | QtCore.Qt.ItemIsEnabled) + self.algorithm_parameter_list.setItem(index + 1, 0, item) item2 = QTableWidgetItem(str(value)) - if str(value)=='True' or str(value)=='False': + if str(value) == "True" or str(value) == "False": item2 = QTableWidgetItem() - #select the cell if checked - item2.setFlags(QtCore.Qt.ItemIsUserCheckable | QtCore.Qt.ItemIsEnabled | QtCore.Qt.ItemIsSelectable) - if str(value)=='True': - item2.setCheckState(QtCore.Qt.Checked) + # select the cell if checked + item2.setFlags(QtCore.Qt.ItemIsUserCheckable + | QtCore.Qt.ItemIsEnabled + | QtCore.Qt.ItemIsSelectable) + if str(value) == "True": + item2.setCheckState(QtCore.Qt.Checked) else: - item2.setCheckState(QtCore.Qt.Unchecked) - self.algorithm_parameter_list.setItem(index+1, 1, item2) - self.algorithm_parameter_list.resizeColumnsToContents() #setSectionResizeMode(0,QtWidgets.QHeaderView.ResizeToContents) + item2.setCheckState(QtCore.Qt.Unchecked) + self.algorithm_parameter_list.setItem(index + 1, 1, item2) + # setSectionResizeMode(0,QtWidgets.QHeaderView.ResizeToContents) + self.algorithm_parameter_list.resizeColumnsToContents() except Exception as e: - print('Algorithm parameter error') + print("Algorithm parameter error") print(e) - def aspect_changed(self): - """ - Stores the options value separately for each algorithm. + """Stores the options value separately for each algorithm. Clears selection, because if other algorithm clicked after change, it's counts as a change again. So the same value is going to be stored for the next algorirhm selection. + + """ - #get current cell focused in self.algorithm_parameter_list + # get current cell focused in self.algorithm_parameter_list current_row = self.algorithm_parameter_list.currentRow() item = self.algorithm_parameter_list.item(current_row, 1) if item is not None: @@ -3454,213 +3971,238 @@ def aspect_changed(self): val = False else: val = True - self.aspects[str(self.algorithm_parameter_list.item(0, 0).text())] = val + self.aspects[str( + self.algorithm_parameter_list.item(0, 0).text())] = val return # if val is numeric if val.isnumeric(): val = float(val) - else: #string + else: # string val = str(val) - if val.lower()== "none" or val.lower() == "null": + if val.lower() == "none" or val.lower() == "null": val = None # store the value - self.aspects[str(self.algorithm_parameter_list.item(0, 0).text())] = val + self.aspects[str(self.algorithm_parameter_list.item( + 0, 0).text())] = val self.algorithm_parameter_list.clearSelection() - - - def hippounit_gui_to_json(self): - self.hippounit_config = {"model":{}, "tests":{}} + """ """ + self.hippounit_config = {"model": {}, "tests": {}} - #collect the following information from the GUI, the info found in this json config file - - #the model name + # collect the following information from the GUI, the info found in this json config file + + # the model name self.hippounit_config["model"]["name"] = self.model_name_input.text() if self.hippounit_config["model"]["name"] == "": - + # go to the Model tab self.tabwidget.setCurrentIndex(1) - #focus on the model name input + # focus on the model name input self.model_name_input.setFocus() popup("Model name must be set") return None - #the model path - self.hippounit_config["model"]["mod_files_path"] = add_trailing_slash(self.lineEdit_folder2.text()) - #if the path is not valid or empty popup error - if not os.path.isdir(self.hippounit_config["model"]["mod_files_path"]): #TODO: Do we always need to have mod files path? - + # the model path + self.hippounit_config["model"]["mod_files_path"] = add_trailing_slash( + self.lineEdit_folder2.text()) + # if the path is not valid or empty popup error + # TODO: Do we always need to have mod files path? + if not os.path.isdir(self.hippounit_config["model"]["mod_files_path"]): + # go to the Model tab self.tabwidget.setCurrentIndex(1) - #focus on the model path input + # focus on the model path input self.lineEdit_folder2.setFocus() popup("Mod Files Path must be set to a valid directory") - return None - + return None - #the output path - self.hippounit_config["model"]["output_dir"] = self.output_dir_input.text() - #if the path is not valid or empty popup error + # the output path + self.hippounit_config["model"][ + "output_dir"] = self.output_dir_input.text() + # if the path is not valid or empty popup error if not os.path.isdir(self.hippounit_config["model"]["output_dir"]): - + # go to the Model tab self.tabwidget.setCurrentIndex(2) - #focus on the output path input + # focus on the output path input self.output_dir_input.setFocus() popup("Output path must be set to a valid directory") return None - #the template name - self.hippounit_config["model"]["template_name"] = self.template_name_input.text() if self.template_name_input.text() != "" else None - #threshold + # the template name + self.hippounit_config["model"]["template_name"] = ( + self.template_name_input.text() + if self.template_name_input.text() != "" else None) + # threshold try: - #first row, second column - self.hippounit_config["model"]["threshold"] = float(self.test_specific_settings_table.item(0,1).text()) + # first row, second column + self.hippounit_config["model"]["threshold"] = float( + self.test_specific_settings_table.item(0, 1).text()) except: - self.test_specific_settings_table.item(0,1).setBackground(QtGui.QColor(255,0,0)) - #goto to tab 3 + self.test_specific_settings_table.item(0, 1).setBackground( + QtGui.QColor(255, 0, 0)) + # goto to tab 3 self.tabwidget.setCurrentIndex(3) - #focus on the threshold input - self.test_specific_settings_table.item(0,1).setSelected(True) - #error popup + # focus on the threshold input + self.test_specific_settings_table.item(0, 1).setSelected(True) + # error popup popup("Spike detection thres. (mV) must be set to a number") return None - - #v_init + + # v_init try: - self.hippounit_config["model"]["v_init"] = float(self.v_init_input.text()) + self.hippounit_config["model"]["v_init"] = float( + self.v_init_input.text()) except: - #goto to tab 3 + # goto to tab 3 self.tabwidget.setCurrentIndex(2) - #focus on the v_init input + # focus on the v_init input self.v_init_input.setFocus() - #error popup + # error popup popup("v_init must be set to a number") return None try: - #celsius - self.hippounit_config["model"]["celsius"] = float(self.celsius_input.text()) + # celsius + self.hippounit_config["model"]["celsius"] = float( + self.celsius_input.text()) except: - #goto to tab 2 + # goto to tab 2 self.tabwidget.setCurrentIndex(2) - #focus on the celsius input + # focus on the celsius input self.celsius_input.setFocus() - #error popup + # error popup popup("Temperature must be set to a number") return None - #the soma section name + # the soma section name try: self.hippounit_config["model"]["soma"] = self.soma_input.text() except: - #goto to tab 2 + # goto to tab 2 self.tabwidget.setCurrentIndex(2) - #focus on the soma section name input + # focus on the soma section name input self.soma_input.setFocus() - #error popup + # error popup popup("Soma Section Name must be set") return None if self.hippounit_config["model"]["soma"] == "": - #goto to tab 2 + # goto to tab 2 self.tabwidget.setCurrentIndex(2) - #focus on the soma section name input + # focus on the soma section name input self.soma_input.setFocus() - #error popup + # error popup popup("Soma Section Name must be set") return None # #the soma section list name - self.hippounit_config["model"]["SomaSecList_name"] = self.test_specific_settings_table.item(2,1).text() if self.test_specific_settings_table.item(2,1).text() != "" else None - - #the trunk section list name - hippo_paramaters_to_check = ["TrunkSecList_name", "ObliqueSecList_name", "TuftSecList_name", "num_of_dend_locations"] - #Assign the values of these parameters to the config file, if they are not empty or none and was supposed to be set + self.hippounit_config["model"]["SomaSecList_name"] = ( + self.test_specific_settings_table.item(2, 1).text() + if self.test_specific_settings_table.item( + 2, 1).text() != "" else None) + + # the trunk section list name + hippo_paramaters_to_check = [ + "TrunkSecList_name", + "ObliqueSecList_name", + "TuftSecList_name", + "num_of_dend_locations", + ] + # Assign the values of these parameters to the config file, if they are not empty or none and was supposed to be set for param in hippo_paramaters_to_check: # get the value of the parameter based on the configuaration dictionary HippoTests_parameter_location_in_table which maps the parameter name to the row in the table property_row = self.HippoTests_parameter_location_in_table[param] - value_of_param = self.test_specific_settings_table.item(property_row, 1).text() - - #if their cell not grayed, it means they are supposed to be set, the color is handled in the fitchanged function - if self.test_specific_settings_table.item(property_row, 1).flags() != QtCore.Qt.NoItemFlags: - #if their cell is not empty or none + value_of_param = self.test_specific_settings_table.item( + property_row, 1).text() + + # if their cell not grayed, it means they are supposed to be set, the color is handled in the fitchanged function + if (self.test_specific_settings_table.item(property_row, + 1).flags() + != QtCore.Qt.NoItemFlags): + # if their cell is not empty or none if value_of_param != "" and value_of_param != None: self.hippounit_config["model"][param] = value_of_param else: - #go to tab 3 + # go to tab 3 self.tabwidget.setCurrentIndex(3) - #focus on the parameter input - self.test_specific_settings_table.item(property_row, 1).setSelected(True) - #error popup - popup(param+" must be set") + # focus on the parameter input + self.test_specific_settings_table.item(property_row, + 1).setSelected(True) + # error popup + popup(param + " must be set") return None else: self.hippounit_config["model"][param] = None - + self.hippounit_config["model"]["tests"] = [] - #fil tests from fitlist 1st row cellls whoose 2nd columns are not 0 or empty - for row in range(0,self.fitlist.rowCount()): - #fitness weight - fitness_weight = self.fitlist.item(row,1).text() - #if not a number (int or float) or 0 or empty - + # fil tests from fitlist 1st row cellls whoose 2nd columns are not 0 or empty + for row in range(0, self.fitlist.rowCount()): + # fitness weight + fitness_weight = self.fitlist.item(row, 1).text() + # if not a number (int or float) or 0 or empty - if float(self.fitlist.item(row,1).text()) != 0 and self.fitlist.item(row,1).text() != "": - self.hippounit_config["model"]["tests"].append(self.tests_real_names[self.fitlist.item(row,0).text()]) + if (float(self.fitlist.item(row, 1).text()) != 0 + and self.fitlist.item(row, 1).text() != ""): + self.hippounit_config["model"]["tests"].append( + self.tests_real_names[self.fitlist.item(row, 0).text()]) if not self.hippounit_config["model"]["tests"]: - #go to tab 4 + # go to tab 4 self.tabwidget.setCurrentIndex(3) - #focus on the test list - self.fitlist.item(0,0).setSelected(True) + # focus on the test list + self.fitlist.item(0, 0).setSelected(True) popup("At least one test must be selected") return None self.hippounit_config["model"]["dataset"] = "test_dataset" - - - - # from self.fitlist get the test name and the path to the json file of tests that are in self.hippounit_config["tests"] - for row in range(0,self.fitlist.rowCount()): + for row in range(0, self.fitlist.rowCount()): # if self.fitlist.item(row,0).text() in self.hippounit_config["model"]["tests"]: - test_name = self.fitlist.item(row,0).text() + test_name = self.fitlist.item(row, 0).text() test_real_name = self.tests_real_names[test_name] - if test_real_name in self.hippounit_config["model"]["tests"]: - test_name = self.fitlist.item(row,0).text() - test_path = self.fitlist.item(row,2).text() - stimuli_path = self.fitlist.item(row,3).text() + if test_real_name in self.hippounit_config["model"]["tests"]: + test_name = self.fitlist.item(row, 0).text() + test_path = self.fitlist.item(row, 2).text() + stimuli_path = self.fitlist.item(row, 3).text() self.hippounit_config["tests"][test_real_name] = {} - #if not valid path, popup error + # if not valid path, popup error if not os.path.isfile(test_path): - #go to tab 4 + # go to tab 4 self.tabwidget.setCurrentIndex(3) - #focus on the test path input - self.fitlist.item(row,2).setSelected(True) - self.fitlist.setCurrentCell(row,2) + # focus on the test path input + self.fitlist.item(row, 2).setSelected(True) + self.fitlist.setCurrentCell(row, 2) popup("Test path must be set to a valid file path!") return None - - self.hippounit_config["tests"][test_real_name]["target_data_path"] = test_path - if test_real_name not in ["DepolarizationBlockTest","ObliqueIntegrationTest","PathwayInteraction"]: - #if not valid path, popup error + + self.hippounit_config["tests"][test_real_name][ + "target_data_path"] = test_path + if test_real_name not in [ + "DepolarizationBlockTest", + "ObliqueIntegrationTest", + "PathwayInteraction", + ]: + # if not valid path, popup error if not os.path.isfile(stimuli_path): - #go to tab 4 + # go to tab 4 self.tabwidget.setCurrentIndex(3) - #focus on the stimuli path input - self.fitlist.item(row,3).setSelected(True) - self.fitlist.setCurrentCell(row,3) + # focus on the stimuli path input + self.fitlist.item(row, 3).setSelected(True) + self.fitlist.setCurrentCell(row, 3) popup("Stimuli path must be set to a valid file path!") return None - self.hippounit_config["tests"][test_real_name]["stimuli_file_path"] = stimuli_path - #get penalty of missing feature for the test, the 5th column of the row + self.hippounit_config["tests"][test_real_name][ + "stimuli_file_path"] = stimuli_path + # get penalty of missing feature for the test, the 5th column of the row try: - self.hippounit_config["tests"][test_real_name]["unevaluated_feature_penalty"] = float(self.fitlist.item(row,4).text()) + self.hippounit_config["tests"][test_real_name][ + "unevaluated_feature_penalty"] = float( + self.fitlist.item(row, 4).text()) except: - #go to tab 4 + # go to tab 4 self.tabwidget.setCurrentIndex(3) - #focus on the penalty input - self.fitlist.item(row,4).setSelected(True) + # focus on the penalty input + self.fitlist.item(row, 4).setSelected(True) popup("Missing feature penalty must be set to a number!") return None # print(self.hippounit_config) @@ -3669,92 +4211,108 @@ def hippounit_gui_to_json(self): # Now we will preparet the neuroptimus json config file from the GUI # get paramaters from self.BW.boundary_table save them to ordered dict self.adjusted_params_boundaries = OrderedDict() - try : - for row in range(0,self.BW.boundary_table.rowCount()): + try: + for row in range(0, self.BW.boundary_table.rowCount()): try: - self.adjusted_params_boundaries[self.BW.boundary_table.item(row,0).text()] = [float(self.BW.boundary_table.item(row,1).text()),float(self.BW.boundary_table.item(row,2).text())] + self.adjusted_params_boundaries[ + self.BW.boundary_table.item(row, 0).text()] = [ + float(self.BW.boundary_table.item(row, 1).text()), + float(self.BW.boundary_table.item(row, 2).text()), + ] except: - #go to tab 5 + # go to tab 5 self.tabwidget.setCurrentIndex(4) - #open boundary window - self.BW.show() + # open boundary window + self.BW.show() popup("Boundary values must be numbers") return None except: popup("You must set boundaries for all parameters") return None base_dir = self.lineEdit_folder.text() - #boundaries is a list of 2 lists, the first list contains the lower boundaries, the second list contains the upper boundaries - boundaries = [list(self.adjusted_params_boundaries.values())[i][0] for i in range(len(self.adjusted_params_boundaries.values()))] , [list(self.adjusted_params_boundaries.values())[i][1] for i in range(len(self.adjusted_params_boundaries.values()))] + # boundaries is a list of 2 lists, the first list contains the lower boundaries, the second list contains the upper boundaries + boundaries = [ + list(self.adjusted_params_boundaries.values())[i][0] + for i in range(len(self.adjusted_params_boundaries.values())) + ], [ + list(self.adjusted_params_boundaries.values())[i][1] + for i in range(len(self.adjusted_params_boundaries.values())) + ] num_params = len(boundaries[0]) # print("algos list", self.algolist.selectionModel().selectedRows()) - algo_ui_name = self.algolist.item(self.algolist.selectionModel().selectedRows()[0].row(),0).text() - algo_name = algo_ui_name[algo_ui_name.find("(")+1:].replace(")","").replace(" - ","_").replace("-","_").replace(" ","_") + algo_ui_name = self.algolist.item( + self.algolist.selectionModel().selectedRows()[0].row(), 0).text() + algo_name = (algo_ui_name[algo_ui_name.find("(") + 1:].replace( + ")", "").replace(" - ", "_").replace("-", "_").replace(" ", "_")) model_path = self.model_file mods_path = self.spec_file type_ = "hippounit" u_fun_string = self.SW.plaintext.toPlainText() simulator = "hippounit" algo_param_dict = {} - weights = [float(self.fitlist.item(row,1).text()) for row in range(0,self.fitlist.rowCount())] - #get parameters from self.algorithm_parameter_list - for row in range(1,self.algorithm_parameter_list.rowCount()): - val = self.algorithm_parameter_list.item(row,1).text() + weights = [ + float(self.fitlist.item(row, 1).text()) + for row in range(0, self.fitlist.rowCount()) + ] + # get parameters from self.algorithm_parameter_list + for row in range(1, self.algorithm_parameter_list.rowCount()): + val = self.algorithm_parameter_list.item(row, 1).text() # handling cell has checkbox - if val == "": #bool - val = self.algorithm_parameter_list.item(row,1).checkState() + if val == "": # bool + val = self.algorithm_parameter_list.item(row, 1).checkState() if val == 0: val = False else: val = True elif val.isnumeric(): val = float(val) - else: #string + else: # string val = str(val) - if val.lower()== "none" or val.lower() == "null": + if val.lower() == "none" or val.lower() == "null": val = None - algo_param_dict[self.algorithm_parameter_list.item(row,0).text()] = val - + algo_param_dict[self.algorithm_parameter_list.item(row, + 0).text()] = val - - - - #save to json file - #base directory path + # save to json file + # base directory path base_dir = self.lineEdit_folder.text() hippounit_settings_file_name = "hippounit_config_from_gui.json" - hippounit_settings_path = os.path.join(base_dir,hippounit_settings_file_name) - with open(hippounit_settings_path, 'w+') as out: - json.dump(self.hippounit_config,out,indent=4) - verbose(f"hippounit_config_from_gui.json saved to {hippounit_settings_path}") - + hippounit_settings_path = os.path.join(base_dir, + hippounit_settings_file_name) + with open(hippounit_settings_path, "w+") as out: + json.dump(self.hippounit_config, out, indent=4) + verbose( + f"hippounit_config_from_gui.json saved to {hippounit_settings_path}" + ) neuroptimus_settings_name = "neuroptimus_config_from_gui.json" - neuroptimus_settings_path = os.path.join(base_dir,neuroptimus_settings_name) - - - #create a dictionary with the above structure from my variables + neuroptimus_settings_path = os.path.join(base_dir, + neuroptimus_settings_name) + + # create a dictionary with the above structure from my variables - neuroptimus_settings = {"attributes":{}} - #seed + neuroptimus_settings = {"attributes": {}} + # seed try: - neuroptimus_settings["attributes"]["seed"] = int(self.algorithm_parameter_list.item(0,1).text()) + neuroptimus_settings["attributes"]["seed"] = int( + self.algorithm_parameter_list.item(0, 1).text()) except: - #go to tab 5 + # go to tab 5 self.tabwidget.setCurrentIndex(4) popup("Seed must be set to a number!") return None - #check model_path if valid path + # check model_path if valid path if not os.path.isfile(model_path): - #go to tab 1 + # go to tab 1 self.tabwidget.setCurrentIndex(1) - #focus on the model path input + # focus on the model path input self.lineEdit_file2.setFocus() - #error popup + # error popup popup("Invalid model path") return None - - neuroptimus_settings["attributes"]["adjusted_params"] = list(self.adjusted_params_boundaries.keys()) + + neuroptimus_settings["attributes"]["adjusted_params"] = list( + self.adjusted_params_boundaries.keys()) neuroptimus_settings["attributes"]["boundaries"] = boundaries neuroptimus_settings["attributes"]["num_params"] = num_params neuroptimus_settings["attributes"]["base_dir"] = base_dir @@ -3764,53 +4322,34 @@ def hippounit_gui_to_json(self): neuroptimus_settings["attributes"]["weights"] = weights neuroptimus_settings["attributes"]["type"] = [type_] neuroptimus_settings["attributes"]["simulator"] = simulator - neuroptimus_settings["attributes"]["hippounit_settings_path"] = hippounit_settings_path - neuroptimus_settings["attributes"]["param_vals"] = [0.1 for i in range(num_params)] - neuroptimus_settings["attributes"]["current_algorithm"] = {algo_name:algo_param_dict} + neuroptimus_settings["attributes"][ + "hippounit_settings_path"] = hippounit_settings_path + neuroptimus_settings["attributes"]["param_vals"] = [ + 0.1 for i in range(num_params) + ] + neuroptimus_settings["attributes"]["current_algorithm"] = { + algo_name: algo_param_dict + } - #save to json file - with open(neuroptimus_settings_path, 'w+') as out: - json.dump(neuroptimus_settings,out,indent=4) + # save to json file + with open(neuroptimus_settings_path, "w+") as out: + json.dump(neuroptimus_settings, out, indent=4) # print("neuroptimus_config_from_gui.json saved") - verbose(f"neuroptimus_config_from_gui.json saved to {neuroptimus_settings_path}") - - - - - + verbose( + f"neuroptimus_config_from_gui.json saved to {neuroptimus_settings_path}" + ) - - - - - - - - - - - - - - - - - - - - - - return neuroptimus_settings_path - - - - def updateProgressBar(self, value): + """ + + :param value: + + """ # painter = QtGui.QPainter(self.progressBar) # painter.begin(self.progressBar) - if self.total_evaluations_required == 1 and value !=-1: + if self.total_evaluations_required == 1 and value != -1: QtWidgets.QApplication.processEvents() self.progressBar.setMaximum(0) self.progressBar.setMinimum(0) @@ -3818,8 +4357,8 @@ def updateProgressBar(self, value): self.progressBar.repaint() QtWidgets.QApplication.processEvents() elif value == -1: - #means that special call for 100% fill - #stop the progress bar + # means that special call for 100% fill + # stop the progress bar self.progressBar.setMinimum(0) self.progressBar.setMaximum(100) self.progressBar.setValue(100) @@ -3827,7 +4366,7 @@ def updateProgressBar(self, value): # QtWidgets.QApplication.processEvents() else: - percenatge = value * 100/ self.total_evaluations_required + percenatge = value * 100 / self.total_evaluations_required # self.progressBar.setMinimum(0) # self.progressBar.setMaximum(100) self.progressBar.setValue(percenatge) @@ -3835,152 +4374,210 @@ def updateProgressBar(self, value): self.progressBar.repaint() QtWidgets.QApplication.processEvents() - - - - - def runsim(self,singlerun=False)->bool: - """ - Check all the tabs and sends the options to the Core. + def runsim(self, singlerun=False) -> bool: + """Check all the tabs and sends the options to the Core. Check the fitness values and if they are normalized. Check the selected algorithm and the options for it then launch the optimization. Calls the last step if the optimization ended. If an error happens, stores the number of tab in a list and it's error string in an other list. Switch to the tab, where the error happened and popup the erro. + + :param singlerun: (Default value = False) + """ if self.is_optimization_active: popup("Optimization is already running") return False - - self.is_optimization_active = True + self.is_optimization_active = True - - if self.core.option_handler.type[-1].lower() == "hippounit": - json_filename = self.hippounit_gui_to_json() + json_filename = self.hippounit_gui_to_json() if json_filename is None: - popup("There was an error in the Hippounit settings, please check them") + popup( + "There was an error in the Hippounit settings, please check them" + ) return try: with open(json_filename, "r") as f: json_data = json.load(f) - + except IOError as ioe: popup("File not found!\n") print(ioe) sys.exit("File not found!\n") try: - self.core.option_handler.ReadJson(json_data['attributes']) + self.core.option_handler.ReadJson(json_data["attributes"]) except Exception as e: # print(e) traceback.print_exc() popup("Error in reading json file") return # self.core.option_handler.ReadJson(json_data['attributes']) - - err=[] - errpop=[] - if self.core.option_handler.type[-1].lower() != "hippounit" and (not self.dd_type.currentIndex()): + + err = [] + errpop = [] + if self.core.option_handler.type[-1].lower() != "hippounit" and ( + not self.dd_type.currentIndex()): try: - self.core.SecondStep({"stim" : [str(self.stimprot.currentText()), float(self.lineEdit_pos.text()), str(self.section_rec.currentText())], - "stimparam" : [self.container, float(self.lineEdit_delay.text()), float(self.lineEdit_duration.text())]}) - self.kwargs = {"runparam":[float(self.lineEdit_tstop.text()), - float(self.lineEdit_dt.text()), - str(self.param_to_record.currentText()), - str(self.section_stim.currentText()), - float(self.lineEdit_posins.text()), - float(self.lineEdit_initv.text())]} + self.core.SecondStep({ + "stim": [ + str(self.stimprot.currentText()), + float(self.lineEdit_pos.text()), + str(self.section_rec.currentText()), + ], + "stimparam": [ + self.container, + float(self.lineEdit_delay.text()), + float(self.lineEdit_duration.text()), + ], + }) + self.kwargs = { + "runparam": [ + float(self.lineEdit_tstop.text()), + float(self.lineEdit_dt.text()), + str(self.param_to_record.currentText()), + str(self.section_stim.currentText()), + float(self.lineEdit_posins.text()), + float(self.lineEdit_initv.text()), + ] + } except AttributeError: err.append(2) errpop.append("No stimulus amplitude was selected!") - + except ValueError: - errpop.append('Some of the cells are empty. Please fill out all of them!') + errpop.append( + "Some of the cells are empty. Please fill out all of them!" + ) err.append(2) except Exception as e: err.append(2) print(e) errpop.append("There was an error") - self.fitfun_list=[] - self.weights=[] + self.fitfun_list = [] + self.weights = [] allRows = self.fitlist.rowCount() try: - for row in range(0,allRows): - current_fun=str(self.fitlist.item(row, 0).text()) - current_weight=float(self.fitlist.item(row, 1).text()) + for row in range(0, allRows): + current_fun = str(self.fitlist.item(row, 0).text()) + current_weight = float(self.fitlist.item(row, 1).text()) if current_weight: self.fitfun_list.append(current_fun) - self.weights.append(current_weight) - if self.core.option_handler.type[-1].lower() in ["voltage", "current"]: - spike_threshold = self.test_specific_settings_table.item(0,1).text() - spike_window = self.test_specific_settings_table.item(1,1).text() - self.kwargs.update({"feat": - [{"Spike Detection Thres. (mv)": float(self.test_specific_settings_table.item(0,1).text()), "Spike Window (ms)":float(self.test_specific_settings_table.item(1,1).text())}, - self.fitfun_list] - }) - self.kwargs.update({"weights" : self.weights}) + self.weights.append(current_weight) + if self.core.option_handler.type[-1].lower() in [ + "voltage", "current" + ]: + spike_threshold = self.test_specific_settings_table.item( + 0, 1).text() + spike_window = self.test_specific_settings_table.item( + 1, 1).text() + self.kwargs.update({ + "feat": [ + { + "Spike Detection Thres. (mv)": + float( + self.test_specific_settings_table.item( + 0, 1).text()), + "Spike Window (ms)": + float( + self.test_specific_settings_table.item( + 1, 1).text()), + }, + self.fitfun_list, + ] + }) + self.kwargs.update({"weights": self.weights}) elif self.core.option_handler.type[-1].lower() == "features": - self.kwargs.update({"feat": - [{"Spike Detection Thres. (mv)": float(self.test_specific_settings_table.item(0,1).text()), "Spike Window (ms)":float(self.test_specific_settings_table.item(1,1).text())}, - self.fitfun_list] - }) - self.kwargs.update({"weights" : self.weights}) - if not(0.99