celldetective 1.4.2__py3-none-any.whl → 1.5.0b0__py3-none-any.whl

celldetective/gui/table_ops/_maths.py

@@ -0,0 +1,295 @@
+import numpy as np
+from PyQt5.QtCore import Qt
+from PyQt5.QtGui import QDoubleValidator
+from PyQt5.QtWidgets import (
+    QVBoxLayout,
+    QComboBox,
+    QHBoxLayout,
+    QLabel,
+    QRadioButton,
+    QButtonGroup,
+    QPushButton,
+    QMessageBox,
+    QLineEdit,
+)
+from superqt import QLabeledSlider
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.gui_utils import PandasModel, GenericOpColWidget
+from celldetective import get_logger
+from celldetective.utils.maths import differentiate_per_track, safe_log
+
+logger = get_logger(__name__)
+
+
+class DifferentiateColWidget(CelldetectiveWidget):
+
+    def __init__(self, parent_window, column=None):
+
+        super().__init__()
+        self.parent_window = parent_window
+        self.column = column
+
+        self.setWindowTitle("d/dt")
+        # Create the QComboBox and add some items
+        center_window(self)
+
+        layout = QVBoxLayout(self)
+        layout.setContentsMargins(30, 30, 30, 30)
+
+        self.measurements_cb = QComboBox()
+        self.measurements_cb.addItems(list(self.parent_window.data.columns))
+        if self.column is not None:
+            idx = self.measurements_cb.findText(self.column)
+            self.measurements_cb.setCurrentIndex(idx)
+
+        measurement_layout = QHBoxLayout()
+        measurement_layout.addWidget(QLabel("measurements: "), 25)
+        measurement_layout.addWidget(self.measurements_cb, 75)
+        layout.addLayout(measurement_layout)
+
+        self.window_size_slider = QLabeledSlider()
+        self.window_size_slider.setRange(
+            1, int(np.nanmax(self.parent_window.data.FRAME.to_numpy()))
+        )
+        self.window_size_slider.setValue(3)
+        window_layout = QHBoxLayout()
+        window_layout.addWidget(QLabel("window size: "), 25)
+        window_layout.addWidget(self.window_size_slider, 75)
+        layout.addLayout(window_layout)
+
+        self.backward_btn = QRadioButton("backward")
+        self.bi_btn = QRadioButton("bi")
+        self.bi_btn.click()
+        self.forward_btn = QRadioButton("forward")
+        self.mode_btn_group = QButtonGroup()
+        self.mode_btn_group.addButton(self.backward_btn)
+        self.mode_btn_group.addButton(self.bi_btn)
+        self.mode_btn_group.addButton(self.forward_btn)
+
+        mode_layout = QHBoxLayout()
+        mode_layout.addWidget(QLabel("mode: "), 25)
+        mode_sublayout = QHBoxLayout()
+        mode_sublayout.addWidget(self.backward_btn, 33, alignment=Qt.AlignCenter)
+        mode_sublayout.addWidget(self.bi_btn, 33, alignment=Qt.AlignCenter)
+        mode_sublayout.addWidget(self.forward_btn, 33, alignment=Qt.AlignCenter)
+        mode_layout.addLayout(mode_sublayout, 75)
+        layout.addLayout(mode_layout)
+
+        self.submit_btn = QPushButton("Compute")
+        self.submit_btn.setStyleSheet(self.button_style_sheet)
+        self.submit_btn.clicked.connect(self.compute_derivative_and_add_new_column)
+        layout.addWidget(self.submit_btn, 30)
+
+        self.setAttribute(Qt.WA_DeleteOnClose)
+
+    def compute_derivative_and_add_new_column(self):
+
+        if self.bi_btn.isChecked():
+            mode = "bi"
+        elif self.forward_btn.isChecked():
+            mode = "forward"
+        elif self.backward_btn.isChecked():
+            mode = "backward"
+        self.parent_window.data = differentiate_per_track(
+            self.parent_window.data,
+            self.measurements_cb.currentText(),
+            window_size=self.window_size_slider.value(),
+            mode=mode,
+        )
+        self.parent_window.model = PandasModel(self.parent_window.data)
+        self.parent_window.table_view.setModel(self.parent_window.model)
+        self.close()
+
+
+class OperationOnColsWidget(CelldetectiveWidget):
+
+    def __init__(self, parent_window, column1=None, column2=None, operation="divide"):
+
+        super().__init__()
+        self.parent_window = parent_window
+        self.column1 = column1
+        self.column2 = column2
+        self.operation = operation
+
+        self.setWindowTitle(self.operation)
+        # Create the QComboBox and add some items
+        center_window(self)
+
+        layout = QVBoxLayout(self)
+        layout.setContentsMargins(30, 30, 30, 30)
+
+        self.col1_cb = QComboBox()
+        self.col1_cb.addItems(list(self.parent_window.data.columns))
+        if self.column1 is not None:
+            idx = self.col1_cb.findText(self.column1)
+            self.col1_cb.setCurrentIndex(idx)
+
+        numerator_layout = QHBoxLayout()
+        numerator_layout.addWidget(QLabel("column 1: "), 25)
+        numerator_layout.addWidget(self.col1_cb, 75)
+        layout.addLayout(numerator_layout)
+
+        self.col2_cb = QComboBox()
+        self.col2_cb.addItems(list(self.parent_window.data.columns))
+        if self.column2 is not None:
+            idx = self.col2_cb.findText(self.column2)
+            self.col2_cb.setCurrentIndex(idx)
+
+        denominator_layout = QHBoxLayout()
+        denominator_layout.addWidget(QLabel("column 2: "), 25)
+        denominator_layout.addWidget(self.col2_cb, 75)
+        layout.addLayout(denominator_layout)
+
+        self.submit_btn = QPushButton("Compute")
+        self.submit_btn.setStyleSheet(self.button_style_sheet)
+        self.submit_btn.clicked.connect(self.compute)
+        layout.addWidget(self.submit_btn, 30)
+
+        self.setAttribute(Qt.WA_DeleteOnClose)
+
+    def compute(self):
+
+        test = self._check_cols_before_operation()
+        if not test:
+            msg_box = QMessageBox()
+            msg_box.setIcon(QMessageBox.Warning)
+            msg_box.setText(
+                f"Operation could not be performed, one of the column types is object..."
+            )
+            msg_box.setWindowTitle("Warning")
+            msg_box.setStandardButtons(QMessageBox.Ok)
+            return_value = msg_box.exec()
+            if return_value == QMessageBox.Ok:
+                return None
+            else:
+                return None
+        else:
+            if self.operation == "divide":
+                name = f"{self.col1_txt}/{self.col2_txt}"
+                with np.errstate(divide="ignore", invalid="ignore"):
+                    res = np.true_divide(self.col1, self.col2)
+                    res[res == np.inf] = np.nan
+                    res[self.col1 != self.col1] = np.nan
+                    res[self.col2 != self.col2] = np.nan
+                    self.parent_window.data[name] = res
+
+            elif self.operation == "multiply":
+                name = f"{self.col1_txt}*{self.col2_txt}"
+                res = np.multiply(self.col1, self.col2)
+
+            elif self.operation == "add":
+                name = f"{self.col1_txt}+{self.col2_txt}"
+                res = np.add(self.col1, self.col2)
+
+            elif self.operation == "subtract":
+                name = f"{self.col1_txt}-{self.col2_txt}"
+                res = np.subtract(self.col1, self.col2)
+            else:
+                logger.info(f"Operation {self.operation} not implemented...")
+
+            self.parent_window.data[name] = res
+            self.parent_window.model = PandasModel(self.parent_window.data)
+            self.parent_window.table_view.setModel(self.parent_window.model)
+            self.close()
+
+    def _check_cols_before_operation(self):
+
+        self.col1_txt = self.col1_cb.currentText()
+        self.col2_txt = self.col2_cb.currentText()
+
+        self.col1 = self.parent_window.data[self.col1_txt].to_numpy()
+        self.col2 = self.parent_window.data[self.col2_txt].to_numpy()
+
+        test = np.all([self.col1.dtype != "O", self.col2.dtype != "O"])
+
+        return test
+
+
+class CalibrateColWidget(GenericOpColWidget):
+
+    def __init__(self, *args, **kwargs):
+
+        super().__init__(title="Calibrate data", *args, **kwargs)
+
+        self.floatValidator = QDoubleValidator()
+        self.calibration_factor_le = QLineEdit("1")
+        self.calibration_factor_le.setPlaceholderText(
+            "multiplicative calibration factor..."
+        )
+        self.calibration_factor_le.setValidator(self.floatValidator)
+
+        self.units_le = QLineEdit("um")
+        self.units_le.setPlaceholderText("units...")
+
+        self.calibration_factor_le.textChanged.connect(self.check_valid_params)
+        self.units_le.textChanged.connect(self.check_valid_params)
+
+        calib_layout = QHBoxLayout()
+        calib_layout.addWidget(QLabel("calibration factor: "), 33)
+        calib_layout.addWidget(self.calibration_factor_le, 66)
+        self.sublayout.addLayout(calib_layout)
+
+        units_layout = QHBoxLayout()
+        units_layout.addWidget(QLabel("units: "), 33)
+        units_layout.addWidget(self.units_le, 66)
+        self.sublayout.addLayout(units_layout)
+
+        # info_layout = QHBoxLayout()
+        # info_layout.addWidget(QLabel('For reference: '))
+        # self.sublayout.addLayout(info_layout)
+
+        # info_layout2 = QHBoxLayout()
+        # info_layout2.addWidget(QLabel(f'PxToUm = {self.parent_window.parent_window.parent_window.PxToUm}'), 50)
+        # info_layout2.addWidget(QLabel(f'FrameToMin = {self.parent_window.parent_window.parent_window.FrameToMin}'), 50)
+        # self.sublayout.addLayout(info_layout2)
+
+    def check_valid_params(self):
+
+        try:
+            factor = float(self.calibration_factor_le.text().replace(",", "."))
+            factor_valid = True
+        except Exception as _:
+            factor_valid = False
+
+        if self.units_le.text() == "":
+            units_valid = False
+        else:
+            units_valid = True
+
+        if factor_valid and units_valid:
+            self.submit_btn.setEnabled(True)
+        else:
+            self.submit_btn.setEnabled(False)
+
+    def compute(self):
+        self.parent_window.data[
+            self.measurements_cb.currentText() + f"[{self.units_le.text()}]"
+        ] = self.parent_window.data[self.measurements_cb.currentText()] * float(
+            self.calibration_factor_le.text().replace(",", ".")
+        )
+
+
+class AbsColWidget(GenericOpColWidget):
+
+    def __init__(self, *args, **kwargs):
+
+        super().__init__(title="abs(.)", *args, **kwargs)
+
+    def compute(self):
+        self.parent_window.data["|" + self.measurements_cb.currentText() + "|"] = (
+            self.parent_window.data[self.measurements_cb.currentText()].abs()
+        )
+
+
+class LogColWidget(GenericOpColWidget):
+
+    def __init__(self, *args, **kwargs):
+
+        super().__init__(title="log10(.)", *args, **kwargs)
+
+    def compute(self):
+        self.parent_window.data["log10(" + self.measurements_cb.currentText() + ")"] = (
+            safe_log(self.parent_window.data[self.measurements_cb.currentText()].values)
+        )

celldetective/gui/table_ops/_merge_groups.py

@@ -0,0 +1,140 @@
+from typing import List
+
+import numpy as np
+from PyQt5.QtCore import QSize, Qt
+from PyQt5.QtWidgets import (
+    QComboBox,
+    QHBoxLayout,
+    QLabel,
+    QLineEdit,
+    QPushButton,
+    QVBoxLayout,
+)
+from fonticon_mdi6 import MDI6
+from superqt.fonticon import icon
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.gui_utils import PandasModel
+from celldetective.gui.base.utils import center_window
+
+
+class MergeGroupWidget(CelldetectiveWidget):
+    def __init__(self, parent_window, columns: List[str] = [], n_cols_init: int = 3):
+
+        super().__init__()
+        self.parent_window = parent_window
+
+        self.setWindowTitle("Merge classifications")
+        self.group_cols = [
+            c
+            for c in list(self.parent_window.data.columns)
+            if c.startswith("group_") or c.startswith("status_")
+        ]
+        self.group_cols.insert(0, "--")
+        if len(columns) > n_cols_init:
+            n_cols_init = len(columns)
+
+        center_window(self)
+
+        layout = QVBoxLayout(self)
+        layout.setContentsMargins(30, 10, 30, 30)
+
+        label = QLabel(
+            "Merge several binary or multi-label classification features into a multi-label classification feature where each state is one of the possible combinations.\n"
+        )
+
+        label.setWordWrap(True)  # enables automatic line breaking
+        label.setTextInteractionFlags(
+            Qt.TextSelectableByMouse
+        )  # optional, to allow copy
+        label.setStyleSheet("color: gray;")  # optional style
+
+        layout.addWidget(label)
+
+        self.name_le = QLineEdit("group_multilabel")
+        name_layout = QHBoxLayout()
+        name_layout.addWidget(QLabel("name: "), 25)
+        name_layout.addWidget(self.name_le, 75)
+        layout.addLayout(name_layout)
+
+        self.cbs_layout = QVBoxLayout()
+        self.cbs_layout.setContentsMargins(0, 10, 0, 0)
+
+        self.cbs = []
+        for i in range(n_cols_init):
+            cb_i = QComboBox()
+            cb_i.addItems(self.group_cols)
+            if i < len(columns):
+                selection = columns[i]
+                idx = cb_i.findText(selection)
+                if idx >= 0:
+                    cb_i.setCurrentIndex(idx)
+                else:
+                    cb_i.setCurrentIndex(0)
+            self.cbs.append(cb_i)
+
+            col_layout = QHBoxLayout()
+            col_layout.addWidget(QLabel(f"state {i}: "), 25)
+            col_layout.addWidget(cb_i, 75)
+            self.cbs_layout.addLayout(col_layout)
+
+        layout.addLayout(self.cbs_layout)
+
+        self.add_feature_btn = QPushButton()
+        self.add_feature_btn.setIcon(icon(MDI6.plus, color=self.help_color))
+        self.add_feature_btn.setIconSize(QSize(20, 20))
+        self.add_feature_btn.clicked.connect(self.add_col)
+        self.add_feature_btn.setStyleSheet(self.button_select_all)
+        layout.addWidget(self.add_feature_btn, alignment=Qt.AlignRight)
+
+        self.submit_btn = QPushButton("Compute")
+        self.submit_btn.setStyleSheet(self.button_style_sheet)
+        self.submit_btn.clicked.connect(self.compute)
+        layout.addWidget(self.submit_btn, 30)
+
+        self.setAttribute(Qt.WA_DeleteOnClose)
+
+    def add_col(self):
+        cb_i = QComboBox()
+        cb_i.addItems(self.group_cols)
+        self.cbs.append(cb_i)
+
+        col_layout = QHBoxLayout()
+        col_layout.addWidget(QLabel(f"state {len(self.cbs)}: "), 25)
+        col_layout.addWidget(cb_i, 75)
+
+        self.cbs_layout.addLayout(col_layout)
+
+    def compute(self):
+
+        cols_to_merge = [
+            cb_i.currentText() for cb_i in self.cbs if cb_i.currentText() != "--"
+        ]
+        name = self.name_le.text()
+        if " " in name:
+            name.replace(" ", "_")
+        if name == "":
+            name = "multilabel"
+        if not name.startswith("group_"):
+            name = "group_" + name
+
+        if len(cols_to_merge) > 1:
+            print(
+                "Computing a multi-label classification from the classification feature sources..."
+            )
+            bases = [int(self.parent_window.data[c].max()) + 1 for c in cols_to_merge]
+            multipliers = np.concatenate(([1], np.cumprod(bases[:-1])))
+            self.parent_window.data[name] = (
+                self.parent_window.data[cols_to_merge] * multipliers
+            ).sum(axis=1)
+            self.parent_window.data.loc[
+                self.parent_window.data[cols_to_merge].isna().any(axis=1), name
+            ] = np.nan
+
+            self.parent_window.model = PandasModel(self.parent_window.data)
+            self.parent_window.table_view.setModel(self.parent_window.model)
+            self.close()
+        elif len(cols_to_merge) == 1:
+            print("Only one classification feature was selected, nothing to merge...")
+        else:
+            print("No classification feature was selected...")

celldetective/gui/table_ops/_merge_one_hot.py

@@ -0,0 +1,95 @@
+from PyQt5.QtCore import Qt
+from PyQt5.QtWidgets import QVBoxLayout, QHBoxLayout, QLabel, QLineEdit, QPushButton
+from fonticon_mdi6 import MDI6
+from superqt import QSearchableComboBox
+from superqt.fonticon import icon
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.gui_utils import PandasModel
+
+
+class MergeOneHotWidget(CelldetectiveWidget):
+
+    def __init__(self, parent_window, selected_columns=None):
+
+        super().__init__()
+        self.parent_window = parent_window
+        self.selected_columns = selected_columns
+
+        self.setWindowTitle("Merge one-hot encoded columns...")
+        # Create the QComboBox and add some items
+        center_window(self)
+
+        self.layout = QVBoxLayout(self)
+        self.layout.setContentsMargins(30, 30, 30, 30)
+
+        if self.selected_columns is not None:
+            n_cols = len(self.selected_columns)
+        else:
+            n_cols = 2
+
+        name_hbox = QHBoxLayout()
+        name_hbox.addWidget(QLabel("New categorical column: "), 33)
+        self.new_col_le = QLineEdit()
+        self.new_col_le.setText("categorical_")
+        self.new_col_le.textChanged.connect(self.allow_merge)
+        name_hbox.addWidget(self.new_col_le, 66)
+        self.layout.addLayout(name_hbox)
+
+        self.layout.addWidget(QLabel("Source columns: "))
+
+        self.cbs = [QSearchableComboBox() for _ in range(n_cols)]
+        self.cbs_layout = QVBoxLayout()
+
+        for i in range(n_cols):
+            lay = QHBoxLayout()
+            lay.addWidget(QLabel(f"column {i}: "), 33)
+            self.cbs[i].addItems(["--"] + list(self.parent_window.data.columns))
+            if self.selected_columns is not None:
+                self.cbs[i].setCurrentText(self.selected_columns[i])
+            lay.addWidget(self.cbs[i], 66)
+            self.cbs_layout.addLayout(lay)
+
+        self.layout.addLayout(self.cbs_layout)
+
+        hbox = QHBoxLayout()
+        self.add_col_btn = QPushButton("Add column")
+        self.add_col_btn.clicked.connect(self.add_col)
+        self.add_col_btn.setStyleSheet(self.button_add)
+        self.add_col_btn.setIcon(icon(MDI6.plus, color="black"))
+
+        hbox.addWidget(QLabel(""), 50)
+        hbox.addWidget(self.add_col_btn, 50, alignment=Qt.AlignRight)
+        self.layout.addLayout(hbox)
+
+        self.submit_btn = QPushButton("Merge")
+        self.submit_btn.setStyleSheet(self.button_style_sheet)
+        self.submit_btn.clicked.connect(self.merge_cols)
+        self.layout.addWidget(self.submit_btn, 30)
+
+        self.setAttribute(Qt.WA_DeleteOnClose)
+
+    def add_col(self):
+        self.cbs.append(QSearchableComboBox())
+        self.cbs[-1].addItems(["--"] + list(self.parent_window.data.columns))
+        lay = QHBoxLayout()
+        lay.addWidget(QLabel(f"column {len(self.cbs)-1}: "), 33)
+        lay.addWidget(self.cbs[-1], 66)
+        self.cbs_layout.addLayout(lay)
+
+    def merge_cols(self):
+
+        self.parent_window.data[self.new_col_le.text()] = self.parent_window.data.loc[
+            :, list(self.selected_columns)
+        ].idxmax(axis=1)
+        self.parent_window.model = PandasModel(self.parent_window.data)
+        self.parent_window.table_view.setModel(self.parent_window.model)
+        self.close()
+
+    def allow_merge(self):
+
+        if self.new_col_le.text() == "":
+            self.submit_btn.setEnabled(False)
+        else:
+            self.submit_btn.setEnabled(True)

celldetective/gui/table_ops/_query_table.py

@@ -0,0 +1,43 @@
+from PyQt5.QtWidgets import QHBoxLayout, QLineEdit, QPushButton
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+
+
+class QueryWidget(CelldetectiveWidget):
+
+    def __init__(self, parent_window):
+
+        super().__init__()
+        self.parent_window = parent_window
+
+        self.setWindowTitle("Filter table")
+        # Create the QComboBox and add some items
+
+        layout = QHBoxLayout(self)
+        layout.setContentsMargins(30, 30, 30, 30)
+        self.query_le = QLineEdit()
+        layout.addWidget(self.query_le, 70)
+
+        self.submit_btn = QPushButton("submit")
+        self.submit_btn.clicked.connect(self.filter_table)
+        layout.addWidget(self.submit_btn, 30)
+        center_window(self)
+
+    def filter_table(self):
+        from celldetective.gui.tableUI import TableUI
+
+        try:
+            query_text = self.query_le.text()  # .replace('class', '`class`')
+            tab = self.parent_window.data.query(query_text)
+            self.subtable = TableUI(
+                tab,
+                query_text,
+                plot_mode="static",
+                population=self.parent_window.population,
+            )
+            self.subtable.show()
+            self.close()
+        except Exception as e:
+            print(e)
+            return None

celldetective/gui/table_ops/_rename_col.py

@@ -0,0 +1,44 @@
+from PyQt5.QtCore import Qt
+from PyQt5.QtWidgets import QHBoxLayout, QLineEdit, QPushButton
+
+from celldetective.gui.base.components import CelldetectiveWidget
+from celldetective.gui.base.utils import center_window
+from celldetective.gui.gui_utils import PandasModel
+
+
+class RenameColWidget(CelldetectiveWidget):
+
+    def __init__(self, parent_window, column=None):
+
+        super().__init__()
+        self.parent_window = parent_window
+        self.column = column
+        if self.column is None:
+            self.column = ""
+
+        self.setWindowTitle("Rename column")
+        # Create the QComboBox and add some items
+        center_window(self)
+
+        layout = QHBoxLayout(self)
+        layout.setContentsMargins(30, 30, 30, 30)
+        self.new_col_name = QLineEdit()
+        self.new_col_name.setText(self.column)
+        layout.addWidget(self.new_col_name, 70)
+
+        self.submit_btn = QPushButton("rename")
+        self.submit_btn.clicked.connect(self.rename_col)
+        layout.addWidget(self.submit_btn, 30)
+        self.setAttribute(Qt.WA_DeleteOnClose)
+
+    def rename_col(self):
+
+        old_name = self.column
+        new_name = self.new_col_name.text()
+        self.parent_window.data = self.parent_window.data.rename(
+            columns={old_name: new_name}
+        )
+
+        self.parent_window.model = PandasModel(self.parent_window.data)
+        self.parent_window.table_view.setModel(self.parent_window.model)
+        self.close()