Coverage for ibllib/qc/task_qc_viewer/ViewEphysQC.py: 16%

1"""An interactive PyQT QC data frame."""

3import logging (empty)

5from PyQt5 import QtWidgets (empty)

6from PyQt5.QtCore import ( (empty)

7 Qt,

8 QModelIndex,

9 pyqtSignal,

10 pyqtSlot,

11 QCoreApplication,

12 QSettings,

13 QSize,

14 QPoint,

15)

16from PyQt5.QtGui import QPalette, QShowEvent (empty)

17from PyQt5.QtWidgets import QMenu, QAction (empty)

18from iblqt.core import ColoredDataFrameTableModel (empty)

19from matplotlib.figure import Figure (empty)

20from matplotlib.backends.backend_qt5agg import FigureCanvasQTAgg, NavigationToolbar2QT (empty)

21import pandas as pd (empty)

22import numpy as np (empty)

24from ibllib.misc import qt (empty)

26_logger = logging.getLogger(__name__) (empty)

29class PlotCanvas(FigureCanvasQTAgg): (empty)

30 def __init__(self, parent=None, width=5, height=4, dpi=100, wheel=None): (empty)

31 fig = Figure(figsize=(width, height), dpi=dpi)

33 FigureCanvasQTAgg.__init__(self, fig)

34 self.setParent(parent)

36 FigureCanvasQTAgg.setSizePolicy(self, QtWidgets.QSizePolicy.Expanding, QtWidgets.QSizePolicy.Expanding)

37 FigureCanvasQTAgg.updateGeometry(self)

38 if wheel:

39 self.ax, self.ax2 = fig.subplots(2, 1, gridspec_kw={'height_ratios': [2, 1]}, sharex=True)

40 else:

41 self.ax = fig.add_subplot(111)

42 self.draw()

45class PlotWindow(QtWidgets.QWidget): (empty)

46 def __init__(self, parent=None, wheel=None): (empty)

47 QtWidgets.QWidget.__init__(self, parent=None)

48 self.canvas = PlotCanvas(wheel=wheel)

49 self.vbl = QtWidgets.QVBoxLayout() # Set box for plotting

50 self.vbl.addWidget(self.canvas)

51 self.setLayout(self.vbl)

52 self.vbl.addWidget(NavigationToolbar2QT(self.canvas, self))

55class GraphWindow(QtWidgets.QWidget): (empty)

56 _pinnedColumns = [] (empty)

58 def __init__(self, parent=None, wheel=None): (empty)

59 QtWidgets.QWidget.__init__(self, parent=parent)

61 self.columnPinned = pyqtSignal(int, bool)

63 # load button

64 self.pushButtonLoad = QtWidgets.QPushButton('Select File', self)

65 self.pushButtonLoad.clicked.connect(self.loadFile)

67 # define table model & view

68 self.tableModel = ColoredDataFrameTableModel(self)

69 self.tableView = QtWidgets.QTableView(self)

70 self.tableView.setModel(self.tableModel)

71 self.tableView.setSortingEnabled(True)

72 self.tableView.horizontalHeader().setDefaultAlignment(Qt.AlignLeft | Qt.AlignVCenter)

73 self.tableView.horizontalHeader().setSectionsMovable(True)

74 self.tableView.horizontalHeader().setContextMenuPolicy(Qt.CustomContextMenu)

75 self.tableView.horizontalHeader().customContextMenuRequested.connect(self.contextMenu)

76 self.tableView.verticalHeader().hide()

77 self.tableView.doubleClicked.connect(self.tv_double_clicked)

79 # define colors for highlighted cells

80 p = self.tableView.palette()

81 p.setColor(QPalette.Highlight, Qt.black)

82 p.setColor(QPalette.HighlightedText, Qt.white)

83 self.tableView.setPalette(p)

85 # QAction for pinning columns

86 self.pinAction = QAction('Pin column', self)

87 self.pinAction.setCheckable(True)

88 self.pinAction.toggled.connect(self.pinColumn)

90 # Filter columns by name

91 self.lineEditFilter = QtWidgets.QLineEdit(self)

92 self.lineEditFilter.setPlaceholderText('Filter columns')

93 self.lineEditFilter.textChanged.connect(self.changeFilter)

94 self.lineEditFilter.setMinimumWidth(200)

96 # colormap picker

97 self.comboboxColormap = QtWidgets.QComboBox(self)

98 colormaps = {self.tableModel.colormap, 'inferno', 'magma', 'plasma', 'summer'}

99 self.comboboxColormap.addItems(sorted(list(colormaps)))

100 self.comboboxColormap.setCurrentText(self.tableModel.colormap)

101 self.comboboxColormap.currentTextChanged.connect(self.tableModel.setColormap)

102

103 # slider for alpha values

104 self.sliderAlpha = QtWidgets.QSlider(Qt.Horizontal, self)

105 self.sliderAlpha.setMaximumWidth(100)

106 self.sliderAlpha.setMinimum(0)

107 self.sliderAlpha.setMaximum(255)

108 self.sliderAlpha.setValue(self.tableModel.alpha)

109 self.sliderAlpha.valueChanged.connect(self.tableModel.setAlpha)

110

111 # Horizontal layout

112 hLayout = QtWidgets.QHBoxLayout()

113 hLayout.addWidget(self.lineEditFilter)

114 hLayout.addSpacing(50)

115 hLayout.addWidget(QtWidgets.QLabel('Colormap', self))

116 hLayout.addWidget(self.comboboxColormap)

117 hLayout.addWidget(QtWidgets.QLabel('Alpha', self))

118 hLayout.addWidget(self.sliderAlpha)

119 hLayout.addSpacing(50)

120 hLayout.addWidget(self.pushButtonLoad)

121

122 # Vertical layout

123 vLayout = QtWidgets.QVBoxLayout(self)

124 vLayout.addLayout(hLayout)

125 vLayout.addWidget(self.tableView)

126

127 # Recover layout from QSettings

128 self.settings = QSettings()

129 self.settings.beginGroup('MainWindow')

130 self.resize(self.settings.value('size', QSize(800, 600), QSize))

131 self.comboboxColormap.setCurrentText(self.settings.value('colormap', 'plasma', str))

132 self.sliderAlpha.setValue(self.settings.value('alpha', 255, int))

133 self.settings.endGroup()

134

135 self.wplot = PlotWindow(wheel=wheel)

136 self.wplot.show()

137 self.tableModel.dataChanged.connect(self.wplot.canvas.draw)

138

139 self.wheel = wheel

140

141 def closeEvent(self, _) -> bool: (empty)

142 self.settings.beginGroup('MainWindow')

143 self.settings.setValue('size', self.size())

144 self.settings.setValue('colormap', self.tableModel.colormap)

145 self.settings.setValue('alpha', self.tableModel.alpha)

146 self.settings.endGroup()

147 self.wplot.close()

148

149 def showEvent(self, a0: QShowEvent) -> None: (empty)

150 super().showEvent(a0)

151 self.activateWindow()

152

153 def contextMenu(self, pos: QPoint): (empty)

154 idx = self.sender().logicalIndexAt(pos)

155 action = self.pinAction

156 action.setData(idx)

157 action.setChecked(idx in self._pinnedColumns)

158 menu = QMenu(self)

159 menu.addAction(action)

160 menu.exec(self.sender().mapToGlobal(pos))

161

162 @pyqtSlot(bool) (empty)

163 @pyqtSlot(bool, int) (empty)

164 def pinColumn(self, pin: bool, idx: int | None = None): (empty)

165 idx = idx if idx is not None else self.sender().data()

166 if not pin and idx in self._pinnedColumns:

167 self._pinnedColumns.remove(idx)

168 if pin and idx not in self._pinnedColumns:

169 self._pinnedColumns.append(idx)

170 self.changeFilter(self.lineEditFilter.text())

171

172 def changeFilter(self, string: str): (empty)

173 headers = [

174 self.tableModel.headerData(x, Qt.Horizontal, Qt.DisplayRole).lower()

175 for x in range(self.tableModel.columnCount())

176 ]

177 tokens = [y.lower() for y in (x.strip() for x in string.split(',')) if len(y)]

178 showAll = len(tokens) == 0

179 for idx, column in enumerate(headers):

180 show = showAll or any((t in column for t in tokens)) or idx in self._pinnedColumns

181 self.tableView.setColumnHidden(idx, not show)

182

183 def loadFile(self): (empty)

184 fileName, _ = QtWidgets.QFileDialog.getOpenFileName(self, 'Open File', '', 'CSV Files (*.csv)')

185 if len(fileName) == 0:

186 return

187 df = pd.read_csv(fileName)

188 self.updateDataframe(df)

189

190 def updateDataframe(self, df: pd.DataFrame): (empty)

191 # clear pinned columns

192 self._pinnedColumns = []

193

194 # try to identify and sort columns containing timestamps

195 col_names = df.select_dtypes('number').columns

196 df_interp = df[col_names].replace([-np.inf, np.inf], np.nan)

197 df_interp = df_interp.interpolate(limit_direction='both')

198 cols_mono = col_names[[df_interp[c].is_monotonic_increasing for c in col_names]]

199 cols_mono = [c for c in cols_mono if df[c].nunique() > 1]

200 cols_mono = df_interp[cols_mono].mean().sort_values().keys()

201 for idx, col_name in enumerate(cols_mono):

202 df.insert(idx, col_name, df.pop(col_name))

203

204 # columns containing boolean values are sorted to the end

205 # of those, columns containing 'pass' in their title will be sorted by number of False values

206 col_names = df.columns

207 cols_bool = list(df.select_dtypes(['bool', 'boolean']).columns)

208 cols_pass = [c for c in cols_bool if 'pass' in c]

209 cols_bool = [c for c in cols_bool if c not in cols_pass] # I know. Friday evening, brain is fried ... sorry.

210 cols_pass = list((~df[cols_pass]).sum().sort_values().keys())

211 cols_bool += cols_pass

212 for col_name in cols_bool:

213 df = df.join(df.pop(col_name))

214

215 # trial_no should always be the first column

216 if 'trial_no' in col_names:

217 df.insert(0, 'trial_no', df.pop('trial_no'))

218

219 # define columns that should be pinned by default

220 for col in ['trial_no']:

221 self._pinnedColumns.append(df.columns.get_loc(col))

222

223 self.tableModel.setDataFrame(df)

224

225 def tv_double_clicked(self, index: QModelIndex): (empty)

226 data = self.tableModel.dataFrame.iloc[index.row()]

227 t0 = data['intervals_0']

228 t1 = data['intervals_1']

229 dt = t1 - t0

230 if self.wheel:

231 idx = np.searchsorted(self.wheel['re_ts'], np.array([t0 - dt / 10, t1 + dt / 10]))

232 period = self.wheel['re_pos'][idx[0]:idx[1]]

233 if period.size == 0:

234 _logger.warning('No wheel data during trial #%i', index.row())

235 else:

236 min_val, max_val = np.min(period), np.max(period)

237 self.wplot.canvas.ax2.set_ylim(min_val - 1, max_val + 1)

238 self.wplot.canvas.ax2.set_xlim(t0 - dt / 10, t1 + dt / 10)

239 self.wplot.canvas.ax.set_xlim(t0 - dt / 10, t1 + dt / 10)

240 self.wplot.setWindowTitle(f"Trial {data.get('trial_no', '?')}")

241 self.wplot.canvas.draw()

242

243

244def viewqc(qc=None, title=None, wheel=None): (empty)

245 app = qt.create_app()

246 app.setStyle('Fusion')

247 QCoreApplication.setOrganizationName('International Brain Laboratory')

248 QCoreApplication.setOrganizationDomain('internationalbrainlab.org')

249 QCoreApplication.setApplicationName('QC Viewer')

250 qcw = GraphWindow(wheel=wheel)

251 qcw.setWindowTitle(title)

252 if qc is not None:

253 qcw.updateDataframe(qc)

254 qcw.show()

255 return qcw