romainmartinez · June 6, 2019 15:48
diff --git a/FieldsAssignment b/FieldsAssignment
 """
 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")
	"""
	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")