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June 6, 2019 15:48
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field assignment
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| """ | |
| FileIO GUIs in pyoviz | |
| """ | |
| import difflib | |
| from pathlib import Path | |
| import ezc3d | |
| import numpy as np | |
| from PyQt5 import QtWidgets | |
| class FieldsAssignment(QtWidgets.QMainWindow): | |
| """ | |
| FieldsAssignment allows to assign a list of targets to a list of channels dynamically. | |
| Use the export method to get the output dictionary. | |
| Parameters | |
| ---------- | |
| directory : str, Path | |
| Directory which contains all data | |
| targets : list | |
| List of target strings | |
| kind : str | |
| "emg", "analogs" or "markers" | |
| prefix : str | |
| Prefix in channel names (keeps the part after prefix) | |
| """ | |
| def __init__(self, directory, targets, kind, prefix=":", previous=None): | |
| # set parameters | |
| self.trials = [ | |
| ifile for idir in directory for ifile in Path(idir).glob("*.c3d") | |
| ] | |
| self.targets = targets | |
| self.kind = kind | |
| self.prefix = prefix | |
| self.previous = previous | |
| self.iassigned, self.assigned = [], [] | |
| self.i, self.itarget = -1, 0 | |
| # init gui | |
| app = QtWidgets.QApplication([]) | |
| super().__init__() | |
| self.init_layout() | |
| self.init_window() | |
| self.read_and_check() | |
| app.exec() | |
| # --- Init methods | |
| def init_window(self): | |
| """Initialize main window.""" | |
| self.setWindowTitle(f"Pyoviz's fields assignment") | |
| self.resize(1200, 700) | |
| self.show() | |
| def init_layout(self): | |
| """Initialize layout.""" | |
| self.central_widget = QtWidgets.QWidget(self) | |
| self.grid_layout = QtWidgets.QGridLayout(self.central_widget) | |
| # gui's elements | |
| self.init_labels() | |
| self.init_lists() | |
| self.init_buttons() | |
| self.init_progress_bar() | |
| self.init_bars() | |
| self.setCentralWidget(self.central_widget) | |
| def init_labels(self): | |
| """Initialize labels.""" | |
| # current trial label | |
| self.current_trial = QtWidgets.QLabel(self.central_widget) | |
| self.grid_layout.addWidget(self.current_trial, 0, 3, 1, 1) | |
| self.current_trial.setText("Current trial") | |
| # current fields label | |
| self.current_fields = QtWidgets.QLabel(self.central_widget) | |
| self.grid_layout.addWidget(self.current_fields, 1, 0, 1, 1) | |
| self.current_fields.setText("Current fields") | |
| # target fields label | |
| self.target_fields = QtWidgets.QLabel(self.central_widget) | |
| self.grid_layout.addWidget(self.target_fields, 1, 4, 1, 1) | |
| self.target_fields.setText("Assigned fields") | |
| # current target label | |
| self.current_target = QtWidgets.QLabel(self.central_widget) | |
| self.grid_layout.addWidget(self.current_target, 0, 0, 1, 1) | |
| self.current_target.setStyleSheet("font-size: 16pt") | |
| self.current_target.setText(f"Current target: {self.targets[self.itarget]}") | |
| def init_lists(self): | |
| """Initialize lists.""" | |
| # current fields list | |
| self.current_list = QtWidgets.QListWidget(self.central_widget) | |
| self.current_list.setStyleSheet("font-size: 16pt") | |
| self.grid_layout.addWidget(self.current_list, 5, 0, 1, 1) | |
| # assigned fields list | |
| self.assigned_list = QtWidgets.QListWidget(self.central_widget) | |
| self.assigned_list.setStyleSheet("font-size: 16pt") | |
| self.grid_layout.addWidget(self.assigned_list, 5, 4, 1, 1) | |
| def init_buttons(self): | |
| """Initialize buttons.""" | |
| # assign push button | |
| self.button_assign = QtWidgets.QPushButton(self.central_widget) | |
| self.grid_layout.addWidget(self.button_assign, 6, 3, 1, 1) | |
| self.button_assign.setText("Assign [1]") | |
| self.button_assign.setShortcut("1") | |
| self.button_assign.clicked.connect(self.action_assign) | |
| # nan push button | |
| self.button_nan = QtWidgets.QPushButton(self.central_widget) | |
| self.grid_layout.addWidget(self.button_nan, 7, 3, 1, 1) | |
| self.button_nan.setText("NaN [2]") | |
| self.button_nan.setShortcut("2") | |
| self.button_nan.clicked.connect(self.action_nan) | |
| # undo push button | |
| self.button_undo = QtWidgets.QPushButton(self.central_widget) | |
| self.grid_layout.addWidget(self.button_undo, 8, 3, 1, 1) | |
| self.button_undo.setText("Undo [3]") | |
| self.button_undo.setShortcut("3") | |
| self.button_undo.clicked.connect(self.action_undo) | |
| # done push button | |
| self.button_done = QtWidgets.QPushButton(self.central_widget) | |
| self.grid_layout.addWidget(self.button_done, 9, 3, 1, 1) | |
| self.button_done.setText("Done [q]") | |
| self.button_done.setShortcut("q") | |
| self.button_done.clicked.connect(self.action_done) | |
| def init_progress_bar(self): | |
| """Initialize progress bar.""" | |
| self.progress_bar = QtWidgets.QProgressBar(self.central_widget) | |
| self.grid_layout.addWidget(self.progress_bar, 1, 3, 1, 1) | |
| def init_bars(self): | |
| """Initialize menu and status bar.""" | |
| # menu bar | |
| self.menu_bar = QtWidgets.QMenuBar(self) | |
| self.setMenuBar(self.menu_bar) | |
| # status bar | |
| self.status_bar = QtWidgets.QStatusBar(self) | |
| self.setStatusBar(self.status_bar) | |
| # --- Action methods | |
| def read_and_check(self): | |
| self.i += 1 | |
| if self.i >= len(self.trials): | |
| self.close() | |
| self.export() | |
| else: | |
| channel_names = self.action_read_file() | |
| self.action_check_fields(channel_names) | |
| def sort_list(self): | |
| items = [] | |
| for index in range(self.current_list.count()): | |
| items.append(self.current_list.item(index)) | |
| labels = [i.text() for i in items] | |
| closest = difflib.get_close_matches(self.targets[self.itarget], labels, n=1) | |
| if closest: | |
| self.current_list.clear() | |
| names = [i for i in labels if i != closest[0]] | |
| names.insert(0, closest[0]) | |
| self.current_list.addItems(names) | |
| self.current_list.setCurrentRow(0) | |
| def action_assign(self): | |
| """Assign a field to the item selected in current_list.""" | |
| choice = { | |
| "index": self.current_list.currentIndex().row(), | |
| "item": self.current_list.currentItem().text(), | |
| } | |
| self.current_list.takeItem(choice["index"]) | |
| self.assigned_list.addItem(choice["item"]) | |
| self.iassigned.append(choice["item"]) | |
| if len(self.iassigned) >= len(self.targets): | |
| self.assigned.append(self.iassigned) # append this file's assignment | |
| self.iassigned = [] | |
| self.current_list.clear() | |
| self.assigned_list.clear() | |
| self.read_and_check() | |
| else: | |
| self.itarget += 1 | |
| self.current_target.setText(f"Current target: {self.targets[self.itarget]}") | |
| self.sort_list() | |
| def action_nan(self): | |
| """Assign a field to a nan.""" | |
| self.assigned_list.addItem("NaN") | |
| self.iassigned.append("") | |
| if len(self.iassigned) >= len(self.targets): | |
| self.assigned.append(self.iassigned) # append this file's assignment | |
| self.iassigned = [] | |
| self.current_list.clear() | |
| self.assigned_list.clear() | |
| self.read_and_check() | |
| else: | |
| self.itarget += 1 | |
| self.current_target.setText(f"Current target: {self.targets[self.itarget]}") | |
| self.sort_list() | |
| def action_undo(self): | |
| """Undo an assign or nan action.""" | |
| choice = self.assigned_list.item(0) | |
| self.assigned_list.takeItem(0) | |
| if choice.text() != "NaN": | |
| self.current_list.addItem(choice.text()) | |
| self.iassigned.pop() | |
| self.itarget -= 1 | |
| self.current_target.setText(f"Current target: {self.targets[self.itarget]}") | |
| self.sort_list() | |
| def action_done(self): | |
| """When you are done and want to quit.""" | |
| choice = QtWidgets.QMessageBox.question( | |
| self, "Done?", "Exit?", QtWidgets.QMessageBox.Yes | QtWidgets.QMessageBox.No | |
| ) | |
| if choice == QtWidgets.QMessageBox.Yes: | |
| print("Assignment done.") | |
| self.export() | |
| self.close() | |
| def action_read_file(self): | |
| """Read a c3d file and return channel names""" | |
| # update current trial label and progress bar | |
| self.current_trial.setText(str(self.trials[self.i].parts[-1])) | |
| self.progress_bar.setValue(int(self.i / len(self.trials) * 100)) | |
| # ezc3d version | |
| reader = ezc3d.c3d(str(self.trials[self.i])) | |
| if self.kind == "markers": | |
| kind_str = "POINT" | |
| elif self.kind == "analogs" or self.kind == "emg": | |
| kind_str = "ANALOG" | |
| else: | |
| raise ValueError( | |
| f'`kind` shoud be "analogs", "emg" or "markers". You provided {self.kind}' | |
| ) | |
| channels = reader["parameters"][kind_str]["LABELS"]["value"] | |
| if self.prefix: | |
| channels = [i.split(self.prefix)[-1] for i in channels] | |
| return channels | |
| @staticmethod | |
| def test_in_assigned(x, channel_names): | |
| """test if one of the assigned contains all targets""" | |
| np.isin(x, channel_names).all() | |
| def action_check_fields(self, channel_names): | |
| """Check if targets are in channel names or already assigned fields. Update GUI if not""" | |
| if np.isin(self.targets, channel_names).all(): | |
| # test if channel_names contains all targets | |
| self.read_and_check() | |
| else: | |
| if ( | |
| self.assigned | |
| and np.isin(self.assigned, channel_names).any(axis=1).any() | |
| ): | |
| # test if one of the assigned contains al targets | |
| self.read_and_check() | |
| elif ( | |
| self.previous | |
| and np.isin(self.previous, channel_names).any(axis=1).any() | |
| ): | |
| print("\t\t\tfind previous assignment") | |
| self.assigned.append( | |
| self.previous[ | |
| np.argwhere(np.isin(self.previous, channel_names).any(axis=1))[ | |
| 0 | |
| ][0] | |
| ] | |
| ) | |
| else: | |
| self.iassigned, self.itarget = [], 0 | |
| self.current_list.addItems(channel_names) | |
| self.sort_list() | |
| def export(self): | |
| """Set the output dict to object""" | |
| self.output = {self.kind: {"targets": self.targets, "assigned": self.assigned}} | |
| if __name__ == "__main__": | |
| dir = "/media/romain/F/Data/Shoulder/RAW/IRSST_DapOd/trials" | |
| targets = [ | |
| "ASISl", | |
| "ASISr", | |
| "PSISl", | |
| "PSISr", | |
| "STER", | |
| "STERl", | |
| "STERr", | |
| "T1", | |
| "T10", | |
| "XIPH", | |
| "CLAVm", | |
| "CLAVl", | |
| "CLAV_ant", | |
| "CLAV_post", | |
| "CLAV_SC", | |
| "ACRO_tip", | |
| "SCAP_AA", | |
| "SCAPl", | |
| "SCAPm", | |
| "SCAP_CP", | |
| "SCAP_RS", | |
| "SCAP_SA", | |
| "SCAP_IA", | |
| "CLAV_AC", | |
| "DELT", | |
| "ARMl", | |
| "ARMm", | |
| "ARMp_up", | |
| "ARMp_do", | |
| "EPICl", | |
| "EPICm", | |
| "LARMm", | |
| "LARMl", | |
| "LARM_elb", | |
| "LARM_ant", | |
| "STYLr", | |
| "STYLr_up", | |
| "STYLu", | |
| "WRIST", | |
| "INDEX", | |
| "LASTC", | |
| "MEDH", | |
| "LATH", | |
| "boite_gauche_ext", | |
| "boite_gauche_int", | |
| "boite_droite_int", | |
| "boite_droite_ext", | |
| "boite_avant_gauche", | |
| "boite_avant_droit", | |
| "boite_arriere_droit", | |
| "boite_arriere_gauche", | |
| ] | |
| print("debug") | |
| fields = FieldsAssignment(directory=[dir], targets=targets, kind="markers") | |
| print("debug") |
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