def set_cw(self, fig=None):
# we create the figure canvas here because the fig parameter must be defined and depend on what kind of
# chart want to make
fig = fig or Figure(dpi=self.options[('General', 'figure-format',
'dpi-plot')])
self.figure_canvas = FigureCanvas(fig)
self.fig = self.figure_canvas.figure
self.mainwidgetmdi.setCentralWidget(self.figure_canvas)
# similar to figure canvas
self.mpl_toolbar = NavigationToolbar(self.figure_canvas, self)
self.mpl_toolbar.setVisible(self.options['General', 'toolbar'])
self.mpl_toolbar.update_options({
'save-format':
self.options[('General', 'figure-format', 'save-format')],
'dpi-save':
self.options[('General', 'figure-format', 'dpi-save')],
'filename':
self.options['subtitle']
})
self.mainwidgetmdi.addToolBar(Qt.ToolBarArea.BottomToolBarArea,
self.mpl_toolbar)
self.fbtn = QPushButton(
self.style().standardIcon(
QStyle.StandardPixmap.SP_FileDialogDetailedView), '',
self.figure_canvas)
self.fbtn.setToolTip('Show or Hide the Navigation Toolbar')
self.fbtn.toggled.connect(self.mpl_toolbar.setVisible)
self.fbtn.setCheckable(True)
self.fbtn.setChecked(False)
def __init__(self,
parent=None,
name=None,
width=5,
height=4,
dpi=100,
bgcolor=None):
self.parent = parent
if self.parent:
bgc = parent.backgroundBrush().color()
bgcolor = float(bgc.red()) / 255.0, float(
bgc.green()) / 255.0, float(bgc.blue()) / 255.0
#bgcolor = "#%02X%02X%02X" % (bgc.red(), bgc.green(), bgc.blue())
self.fig = Figure(figsize=(width, height),
dpi=dpi,
facecolor=bgcolor,
edgecolor=bgcolor)
self.axes = self.fig.add_subplot(111)
# We want the axes cleared every time plot() is called
self.axes.hold(False)
self.compute_initial_figure()
FigureCanvas.__init__(self, self.fig)
self.reparent(parent, QPoint(0, 0))
FigureCanvas.setSizePolicy(self, QSizePolicy.Expanding,
QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def changeEvent(self, event: QtCore.QEvent):
if event.type() == QtCore.QEvent.StyleChange:
setup_matplotlib()
self._figure.clear()
self.main_layout.removeWidget(self._canvas)
self._canvas.setVisible(False)
self._figure = plt.figure(figsize=self._figure.get_size_inches())
self._canvas = FigureCanvas(self._figure)
self._toolbar = NavigationToolbar(self._canvas, self)
self.main_layout.addWidget(self._canvas, 0, 0)
self.update_chart()
elif event.type() == QtCore.QEvent.LanguageChange:
self.retranslate()
def test_canvas_reinit():
from matplotlib.backends.backend_qtagg import FigureCanvasQTAgg
called = False
def crashing_callback(fig, stale):
nonlocal called
fig.canvas.draw_idle()
called = True
fig, ax = plt.subplots()
fig.stale_callback = crashing_callback
# this should not raise
canvas = FigureCanvasQTAgg(fig)
fig.stale = True
assert called
def __init__(self, parent=None, width=5, height=4, dpi=100):
self.fig = Figure(figsize=(width, height), dpi=dpi)
self.axes = self.fig.add_subplot(111)
# We want the axes cleared every time plot() is called
self.axes.hold(False)
self.compute_initial_figure()
FigureCanvas.__init__(self, self.fig)
self.reparent(parent, QPoint(0, 0))
FigureCanvas.setSizePolicy(self, QSizePolicy.Expanding, QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def __init__(self, parent, world_list: WorldList):
super().__init__(parent)
self.world_list = world_list
fig = Figure(figsize=(7, 5),
dpi=65,
facecolor=(1, 1, 1),
edgecolor=(0, 0, 0))
self.canvas = FigureCanvas(fig)
self.toolbar = NavigationToolbar(self.canvas, self)
lay = QtWidgets.QVBoxLayout(self)
lay.addWidget(self.toolbar)
lay.addWidget(self.canvas)
self.ax = fig.add_subplot(111)
self.line, *_ = self.ax.plot([])
self._world_to_node_positions = {}
def __init__(self, parent=None, width=5, height=4, dpi=100):
self.fig = Figure(figsize=(width, height), dpi=dpi)
self.axes = self.fig.add_subplot(111)
# We want the axes cleared every time plot() is called
self.axes.hold(False)
self.compute_initial_figure()
FigureCanvas.__init__(self, self.fig)
self.reparent(parent, QPoint(0, 0))
FigureCanvas.setSizePolicy(self, QSizePolicy.Expanding,
QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
def __init__(self, parent=None, figsize=(4, 3)):
super().__init__(parent=parent)
self._figure: plt.Figure = plt.figure(figsize=figsize)
self._canvas = FigureCanvas(self._figure)
self._toolbar = NavigationToolbar(self._canvas, self)
self.main_layout = QtWidgets.QGridLayout(self)
self.main_layout.setContentsMargins(0, 0, 0, 0)
self.main_layout.addWidget(self._canvas, 0, 0)
self.menu = QtWidgets.QMenu(self._canvas)
self.menu.setShortcutAutoRepeat(True)
self.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.customContextMenuRequested.connect(self.show_menu)
self.edit_figure_action = self.menu.addAction(self.tr("Edit Figure"))
self.edit_figure_action.triggered.connect(
lambda: self._toolbar.edit_parameters())
self.save_figure_action = self.menu.addAction(self.tr("Save Figure"))
self.save_figure_action.triggered.connect(
lambda: self._toolbar.save_figure())
self.normal_msg = QtWidgets.QMessageBox(parent=self)
self._animation: Optional[FuncAnimation] = None
def __init__(self, parent=None, name=None, width=5, height=4, dpi=100, bgcolor=None):
self.parent = parent
if self.parent:
bgc = parent.backgroundBrush().color()
bgcolor = float(bgc.red())/255.0, float(bgc.green())/255.0, float(bgc.blue())/255.0
#bgcolor = "#%02X%02X%02X" % (bgc.red(), bgc.green(), bgc.blue())
self.fig = Figure(figsize=(width, height), dpi=dpi, facecolor=bgcolor, edgecolor=bgcolor)
self.axes = self.fig.add_subplot(111)
# We want the axes cleared every time plot() is called
self.axes.hold(False)
self.compute_initial_figure()
FigureCanvas.__init__(self, self.fig)
self.reparent(parent, QPoint(0, 0))
FigureCanvas.setSizePolicy(self,
QSizePolicy.Expanding,
QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
class MatplotlibWidget(QtWidgets.QWidget):
ax: Axes
def __init__(self, parent, world_list: WorldList):
super().__init__(parent)
self.world_list = world_list
fig = Figure(figsize=(7, 5),
dpi=65,
facecolor=(1, 1, 1),
edgecolor=(0, 0, 0))
self.canvas = FigureCanvas(fig)
self.toolbar = NavigationToolbar(self.canvas, self)
lay = QtWidgets.QVBoxLayout(self)
lay.addWidget(self.toolbar)
lay.addWidget(self.canvas)
self.ax = fig.add_subplot(111)
self.line, *_ = self.ax.plot([])
self._world_to_node_positions = {}
def _positions_for_world(self, world: World, state: State):
g = networkx.DiGraph()
for area in world.areas:
g.add_node(area)
for area in world.areas:
nearby_areas = set()
for node in area.nodes:
if isinstance(node, DockNode):
try:
target_node = self.world_list.resolve_dock_node(
node, state.patches)
if target_node is not None:
nearby_areas.add(
self.world_list.nodes_to_area(target_node))
except IndexError as e:
logging.error(
f"For {node.name} in {area.name}, received {e}")
continue
for other_area in nearby_areas:
g.add_edge(area, other_area)
return networkx.drawing.spring_layout(g)
def update_for(self, world: World, state: State,
nodes_in_reach: set[Node]):
g = networkx.DiGraph()
for area in world.areas:
g.add_node(area)
context = state.node_context()
for area in world.areas:
nearby_areas = set()
for node in area.nodes:
if node not in nodes_in_reach:
continue
for other_node, requirement in node.connections_from(context):
if requirement.satisfied(state.resources, state.energy,
state.resource_database):
other_area = self.world_list.nodes_to_area(other_node)
if other_area in world.areas:
nearby_areas.add(other_area)
for other_area in nearby_areas:
g.add_edge(area, other_area)
self.ax.clear()
cf = self.ax.get_figure()
cf.set_facecolor("w")
if world.name not in self._world_to_node_positions:
self._world_to_node_positions[
world.name] = self._positions_for_world(world, state)
pos = self._world_to_node_positions[world.name]
networkx.draw_networkx_nodes(g, pos, ax=self.ax)
networkx.draw_networkx_edges(g, pos, arrows=True, ax=self.ax)
networkx.draw_networkx_labels(
g,
pos,
ax=self.ax,
labels={area: area.name
for area in world.areas},
verticalalignment='top')
self.ax.set_axis_off()
plt.draw_if_interactive()
self.canvas.draw()
class BaseChart(QtWidgets.QWidget):
logger = logging.getLogger("QGrain.charts")
def __init__(self, parent=None, figsize=(4, 3)):
super().__init__(parent=parent)
self._figure: plt.Figure = plt.figure(figsize=figsize)
self._canvas = FigureCanvas(self._figure)
self._toolbar = NavigationToolbar(self._canvas, self)
self.main_layout = QtWidgets.QGridLayout(self)
self.main_layout.setContentsMargins(0, 0, 0, 0)
self.main_layout.addWidget(self._canvas, 0, 0)
self.menu = QtWidgets.QMenu(self._canvas)
self.menu.setShortcutAutoRepeat(True)
self.setContextMenuPolicy(QtCore.Qt.CustomContextMenu)
self.customContextMenuRequested.connect(self.show_menu)
self.edit_figure_action = self.menu.addAction(self.tr("Edit Figure"))
self.edit_figure_action.triggered.connect(
lambda: self._toolbar.edit_parameters())
self.save_figure_action = self.menu.addAction(self.tr("Save Figure"))
self.save_figure_action.triggered.connect(
lambda: self._toolbar.save_figure())
self.normal_msg = QtWidgets.QMessageBox(parent=self)
self._animation: Optional[FuncAnimation] = None
def show_message(self, title: str, message: str):
self.normal_msg.setWindowTitle(title)
self.normal_msg.setText(message)
self.normal_msg.exec_()
def show_info(self, message: str):
self.show_message(self.tr("Info"), message)
def show_warning(self, message: str):
self.show_message(self.tr("Warning"), message)
def show_error(self, message: str):
self.show_message(self.tr("Error"), message)
def show_menu(self, pos: QtCore.QPoint):
self.menu.popup(QtGui.QCursor.pos())
def update_chart(self):
pass
def save_chart(self, filename: str, **kwargs):
self._figure.savefig(filename, **kwargs)
def save_animation(self, filename: str = None):
if self._animation is None:
return
self._animation.pause()
if filename is None:
filename, format_str = QtWidgets.QFileDialog.getSaveFileName(
self,
self.
tr("Choose a filename to save the animation of this SSU result"
), ".",
"MPEG-4 Video File (*.mp4);;Html Animation (*.html);;Graphics Interchange Format (*.gif)"
)
if filename is None or filename == "":
return
progress_dialog = QtWidgets.QProgressDialog(
self.tr("Saving Animation Frames..."), self.tr("Cancel"), 0, 100,
self)
progress_dialog.setWindowTitle("QGrain")
progress_dialog.setWindowModality(QtCore.Qt.WindowModal)
def callback(frame_number, total_frames):
if progress_dialog.wasCanceled():
raise StopIteration()
progress_dialog.setValue(int(frame_number / total_frames * 100))
QtCore.QCoreApplication.processEvents()
try:
if filename[-5:] == ".html":
if not FFMpegWriter.isAvailable():
self.show_error(self.tr("FFMpeg is not installed."))
else:
self.show_info(
self.
tr("Rendering the animation to a html5 video, it will take several minutes."
))
html = self._animation.to_html5_video()
with open(filename, "w") as f:
f.write(html)
elif filename[-4:] == ".gif":
if not ImageMagickWriter.isAvailable():
self.show_error(self.tr("ImageMagick is not installed."))
else:
self._animation.save(filename,
writer="imagemagick",
fps=10,
progress_callback=callback)
elif filename[-4:] == ".mp4":
if not FFMpegWriter.isAvailable():
self.show_error(self.tr("FFMpeg is not installed."))
else:
self._animation.save(filename,
writer="ffmpeg",
fps=10,
progress_callback=callback)
except StopIteration:
self.logger.info("The saving task was canceled.")
finally:
progress_dialog.close()
def retranslate(self):
pass
def changeEvent(self, event: QtCore.QEvent):
if event.type() == QtCore.QEvent.StyleChange:
setup_matplotlib()
self._figure.clear()
self.main_layout.removeWidget(self._canvas)
self._canvas.setVisible(False)
self._figure = plt.figure(figsize=self._figure.get_size_inches())
self._canvas = FigureCanvas(self._figure)
self._toolbar = NavigationToolbar(self._canvas, self)
self.main_layout.addWidget(self._canvas, 0, 0)
self.update_chart()
elif event.type() == QtCore.QEvent.LanguageChange:
self.retranslate()
def __init__(self, graphMode=None, parent=None, name=None, width=5, height=4,
dpi=100, bgColor=None, valueRange=None,
maskLabels=None):
"""
Create matplotlib 'front-end' widget which can render 1D,2D,3D data as
1D or 2D graphs and handle masks.
"""
if debug : print '**xndarrayViewRenderer.__init__ ...'
self.parent = parent
if graphMode: self.graphMode = graphMode
else: self.graphMode = viewModes.MODE_2D
self.fwidth = width
self.fheight = height
self.dpi = dpi
# Will define the range of the colormap associated to values:
if debug: print 'valueRange :', valueRange
#valueRange = [0.001, 0.2] #noise var
#valueRange = [0.001, 0.5] #noise ARp
#valueRange = [0, 11]
if valueRange is not None:
self.norm = Normalize(valueRange[0],
valueRange[1]+_N.abs(valueRange[1])*.01,
clip=True)
self.backgroundValue = valueRange[0] - 100
else:
self.norm = None
self.backgroundValue = 0 #?
# Define the range of the colormap associated to the mask:
# will be used to draw contours of mask
self.maskCm = None
self.maskLabels = maskLabels
if debug: print '######### maskLabels :', maskLabels
if maskLabels is not None:
_N.random.seed(1) # ensure we get always the same random colors
#TODO: put the random seed back in the same state as before!!!
rndm = _N.random.rand(len(maskLabels),3)
# black:
#fixed = _N.zeros((len(maskLabels),3)) + _N.array([0.,0.,0.])
# green:
#fixed = _N.zeros((len(maskLabels),3)) + _N.array([0.,1.,0.])
#white:
fixed = _N.zeros((len(maskLabels),3)) + _N.array([1.,1.,1.])
# Create uniform colormaps for every mask label
# self.maskCm = dict(zip(maskLabels,
# [ListedColormap([ tuple(r) ]) for r in rndm]))
self.maskCm = dict(zip(maskLabels,
[ListedColormap([tuple(r)]) for r in fixed]))
self.displayMaskFlag = self.MASK_HIDDEN
# Set the color of the widget background
if self.parent:
bgc = parent.backgroundBrush().color()
#bgcolor = float(bgc.red())/255.0, float(bgc.green())/255.0, \
# float(bgc.blue())/255.0
bgcolor = "#%02X%02X%02X" % (bgc.red(), bgc.green(), bgc.blue())
else: bgcolor = 'w'
# Create the matplotlib figure:
self.fig = Figure(figsize=(width, height), dpi=dpi,
facecolor=bgcolor, edgecolor=bgcolor)
# Size of the grid of plots:
self.subplotsH = 0
self.subplotsW = 0
self.axes = None
self.showAxesFlag = True
self.showAxesLabels = True
# Init the parent Canvas:
FigureCanvas.__init__(self, self.fig)
# Some QT size stuffs
self.reparent(parent, QPoint(0, 0))
FigureCanvas.setSizePolicy(self, QSizePolicy.Expanding,
QSizePolicy.Expanding)
FigureCanvas.updateGeometry(self)
# Color bar related stuffs:
self.showColorBar = False
self.colorBars = None
# color associated to position where mask=0 :
self.bgColor = 'w'#QColor('white') if bgColor==None else bgColor
# Default colormap (~rainbow) : black-blue-green-yellow-red
self.colorMapString = '0;0;0.5;0.0;0.75;1.0;1.;1.0#' \
'0;0;0.5;1;0.75;1;1;0.#' \
'0;0;0.25;1;0.5;0;1;0.'
self.setColorMapFromString(self.colorMapString)
self.update()
# Signal stuffs:
#self.mpl_connect('button_release_event', self.onRelease)
self.mpl_connect('motion_notify_event', self.onMove)
self.mpl_connect('button_press_event', self.onClick)
class ChartsBase(QMdiSubWindow):
def __init__(self,
button: QToolButton,
options: dict = None,
item_parent=None):
super(ChartsBase, self).__init__()
self.setMinimumSize(400, 400)
self.options = options
self.item_parent = item_parent
self.setWindowIcon(QIcon(logo))
self.mainwidgetmdi = QMainWindow(
) # must be QMainWindow to handle the toolbar
sns.set_theme(style=self.options[('General', 'theme')])
self.plot = None
self.frange = [] # Frames range with which it was created
self.button = button
self.setWidget(self.mainwidgetmdi)
def set_cw(self, fig=None):
# we create the figure canvas here because the fig parameter must be defined and depend on what kind of
# chart want to make
fig = fig or Figure(dpi=self.options[('General', 'figure-format',
'dpi-plot')])
self.figure_canvas = FigureCanvas(fig)
self.fig = self.figure_canvas.figure
self.mainwidgetmdi.setCentralWidget(self.figure_canvas)
# similar to figure canvas
self.mpl_toolbar = NavigationToolbar(self.figure_canvas, self)
self.mpl_toolbar.setVisible(self.options['General', 'toolbar'])
self.mpl_toolbar.update_options({
'save-format':
self.options[('General', 'figure-format', 'save-format')],
'dpi-save':
self.options[('General', 'figure-format', 'dpi-save')],
'filename':
self.options['subtitle']
})
self.mainwidgetmdi.addToolBar(Qt.ToolBarArea.BottomToolBarArea,
self.mpl_toolbar)
self.fbtn = QPushButton(
self.style().standardIcon(
QStyle.StandardPixmap.SP_FileDialogDetailedView), '',
self.figure_canvas)
self.fbtn.setToolTip('Show or Hide the Navigation Toolbar')
self.fbtn.toggled.connect(self.mpl_toolbar.setVisible)
self.fbtn.setCheckable(True)
self.fbtn.setChecked(False)
def draw(self):
self.fig.tight_layout()
self.figure_canvas.draw()
def setup_text(self,
ax,
options,
key='',
title='',
xlabel='',
ylabel='Energy (kcal/mol)'):
key_list = [key] if isinstance(key, str) else key
ax.set_title(title,
fontdict={
'fontsize':
options[tuple(key_list + ['fontsize', 'suptitle'])]
})
if 'Line Plot' in key_list:
ax.legend(prop={
'size': options[tuple(key_list + ['fontsize', 'legend'])]
})
if xlabel:
ax.set_xlabel(xlabel,
fontdict={
'fontsize':
options[tuple(key_list +
['fontsize', 'x-label'])]
})
if ylabel:
ax.set_ylabel(ylabel,
fontdict={
'fontsize':
options[tuple(key_list +
['fontsize', 'y-label'])]
})
for label in ax.get_xticklabels():
label.set_rotation(options[tuple(key_list +
['axes', 'x-rotation'])])
if options[tuple(key_list + ['axes', 'x-rotation'])] < 0:
label.set_horizontalalignment('left')
else:
label.set_horizontalalignment('right')
label.set_fontsize(options[tuple(key_list +
['fontsize', 'x-ticks'])])
for label in ax.get_yticklabels():
label.set_rotation(options[tuple(key_list +
['axes', 'y-rotation'])])
if options[tuple(key_list + ['axes', 'y-rotation'])] < 0:
label.set_horizontalalignment('left')
else:
label.set_horizontalalignment('right')
label.set_fontsize(options[tuple(key_list +
['fontsize', 'y-ticks'])])
def closeEvent(self, closeEvent: QCloseEvent) -> None:
self.button.setChecked(False)
def initUI(self):
self.grid = QGridLayout(self)
self.file_control_grid = QGridLayout()
self.file_control_grid.setSpacing(3)
self.grid.addLayout(self.file_control_grid, 0, 0)
self.file_tree_grid = QGridLayout()
self.file_tree_grid.setSpacing(3)
self.grid.addLayout(self.file_tree_grid, 1, 0)
self.group_control_grid = QGridLayout()
self.group_control_grid.setSpacing(3)
self.grid.addLayout(self.group_control_grid, 0, 1)
self.attribute_grid = QGridLayout()
self.attribute_grid.setSpacing(3)
self.grid.addLayout(self.attribute_grid, 1, 1)
self.roi_control_grid = QGridLayout()
self.roi_control_grid.setSpacing(3)
self.grid.addLayout(self.roi_control_grid, 0, 2)
self.plot_grid = QGridLayout()
self.plot_grid.setSpacing(3)
self.grid.addLayout(self.plot_grid, 1, 2)
# # # # File control browser: # # # # # # # # (0,0)
loadButton = QPushButton("Load expt. file", self)
loadButton.clicked.connect(self.selectDataFile)
# Label with current expt file
self.currentExperimentLabel = QLabel('')
self.file_control_grid.addWidget(loadButton, 0, 0)
self.file_control_grid.addWidget(self.currentExperimentLabel, 1, 0)
directoryButton = QPushButton("Select data directory", self)
directoryButton.clicked.connect(self.selectDataDirectory)
self.file_control_grid.addWidget(directoryButton, 0, 1)
self.data_directory_display = QLabel('')
self.data_directory_display.setFont(QtGui.QFont('SansSerif', 8))
self.file_control_grid.addWidget(self.data_directory_display, 1, 1)
# Attach metadata to file
attachDatabutton = QPushButton("Attach metadata to file", self)
attachDatabutton.clicked.connect(self.attachData)
self.file_control_grid.addWidget(attachDatabutton, 2, 0, 1, 2)
# Select image data file
selectImageDataFileButton = QPushButton("Select image data file", self)
selectImageDataFileButton.clicked.connect(self.selectImageDataFile)
self.file_control_grid.addWidget(selectImageDataFileButton, 3, 0, 1, 2)
# # # # File tree: # # # # # # # # (1,0)
self.groupTree = QTreeWidget(self)
self.groupTree.setHeaderHidden(True)
self.groupTree.itemClicked.connect(self.onTreeItemClicked)
self.file_tree_grid.addWidget(self.groupTree, 3, 0, 2, 7)
# # # # Group control: # # # # # # # # (0, 1)
deleteGroupButton = QPushButton("Delete selected group", self)
deleteGroupButton.clicked.connect(self.deleteSelectedGroup)
self.group_control_grid.addWidget(deleteGroupButton, 0, 0, 1, 2)
# File name display
self.currentImageFileNameLabel = QLabel('')
self.group_control_grid.addWidget(self.currentImageFileNameLabel, 1, 0)
# Channel drop down
ch_label = QLabel('Channel:')
self.ChannelComboBox = QComboBox(self)
self.ChannelComboBox.addItem("1")
self.ChannelComboBox.addItem("0")
self.ChannelComboBox.activated.connect(self.selectChannel)
self.group_control_grid.addWidget(ch_label, 2, 0)
self.group_control_grid.addWidget(self.ChannelComboBox, 2, 1)
# # # # Attribute table: # # # # # # # # (1, 1)
self.tableAttributes = QTableWidget()
self.tableAttributes.setStyleSheet("")
self.tableAttributes.setColumnCount(2)
self.tableAttributes.setObjectName("tableAttributes")
self.tableAttributes.setRowCount(0)
item = QTableWidgetItem()
font = QtGui.QFont()
font.setPointSize(10)
item.setFont(font)
item.setBackground(QtGui.QColor(121, 121, 121))
brush = QtGui.QBrush(QtGui.QColor(91, 91, 91))
brush.setStyle(QtCore.Qt.BrushStyle.SolidPattern)
item.setForeground(brush)
self.tableAttributes.setHorizontalHeaderItem(0, item)
item = QTableWidgetItem()
item.setBackground(QtGui.QColor(123, 123, 123))
brush = QtGui.QBrush(QtGui.QColor(91, 91, 91))
brush.setStyle(QtCore.Qt.BrushStyle.SolidPattern)
item.setForeground(brush)
self.tableAttributes.setHorizontalHeaderItem(1, item)
self.tableAttributes.horizontalHeader().setCascadingSectionResizes(
True)
self.tableAttributes.horizontalHeader().setHighlightSections(False)
self.tableAttributes.horizontalHeader().setSortIndicatorShown(True)
self.tableAttributes.horizontalHeader().setStretchLastSection(True)
self.tableAttributes.verticalHeader().setVisible(False)
self.tableAttributes.verticalHeader().setHighlightSections(False)
item = self.tableAttributes.horizontalHeaderItem(0)
item.setText("Attribute")
item = self.tableAttributes.horizontalHeaderItem(1)
item.setText("Value")
self.tableAttributes.itemChanged.connect(self.update_attrs_to_file)
self.attribute_grid.addWidget(self.tableAttributes, 3, 0, 1, 8)
# # # # Roi control # # # # # # # # (0, 2)
# ROI type drop-down
self.RoiTypeComboBox = QComboBox(self)
self.RoiTypeComboBox.addItem("freehand")
radii = [1, 2, 3, 4, 6, 8]
for radius in radii:
self.RoiTypeComboBox.addItem("circle:" + str(radius))
self.RoiTypeComboBox.activated.connect(self.selectRoiType)
self.roi_control_grid.addWidget(self.RoiTypeComboBox, 0, 0)
# Clear all ROIs button
self.clearROIsButton = QPushButton("Clear ROIs", self)
self.clearROIsButton.clicked.connect(self.clearRois)
self.roi_control_grid.addWidget(self.clearROIsButton, 0, 2)
# Response display type dropdown
self.RoiResponseTypeComboBox = QComboBox(self)
self.RoiResponseTypeComboBox.addItem("RawTrace")
self.RoiResponseTypeComboBox.addItem("TrialAverage")
self.RoiResponseTypeComboBox.addItem("TrialResponses")
self.RoiResponseTypeComboBox.addItem("TrialAverageDFF")
self.roi_control_grid.addWidget(self.RoiResponseTypeComboBox, 2, 2)
# ROIset file name line edit box
self.defaultRoiSetName = "roi_set_name"
self.le_roiSetName = QLineEdit(self.defaultRoiSetName)
self.roi_control_grid.addWidget(self.le_roiSetName, 1, 1)
# Save ROIs button
self.saveROIsButton = QPushButton("Save ROIs", self)
self.saveROIsButton.clicked.connect(self.saveRois)
self.roi_control_grid.addWidget(self.saveROIsButton, 1, 0)
# Load ROI set combobox
self.loadROIsComboBox = QComboBox(self)
self.loadROIsComboBox.addItem("(load existing ROI set)")
self.loadROIsComboBox.activated.connect(self.selectedExistingRoiSet)
self.roi_control_grid.addWidget(self.loadROIsComboBox, 1, 2)
self.updateExistingRoiSetList()
# Delete current roi button
self.deleteROIButton = QPushButton("Delete ROI", self)
self.deleteROIButton.clicked.connect(self.deleteRoi)
self.roi_control_grid.addWidget(self.deleteROIButton, 2, 0)
# Current roi slider
self.roiSlider = QSlider(QtCore.Qt.Orientation.Horizontal, self)
self.roiSlider.setMinimum(0)
self.roiSlider.setMaximum(self.max_rois)
self.roiSlider.valueChanged.connect(self.sliderUpdated)
self.roi_control_grid.addWidget(self.roiSlider, 2, 1, 1, 1)
ctx = plt.rc_context({
'xtick.major.size': 1,
'axes.spines.top': False,
'axes.spines.right': False,
'xtick.labelsize': 'xx-small',
'ytick.labelsize': 'xx-small',
'xtick.major.size': 1.0,
'ytick.major.size': 1.0,
'xtick.major.pad': 1.0,
'ytick.major.pad': 1.0
})
with ctx:
self.responseFig = plt.figure(frameon=False, layout='constrained')
self.responsePlot = self.responseFig.add_subplot(111)
self.responseCanvas = FigureCanvas(self.responseFig)
self.responseCanvas.draw_idle()
self.plot_grid.addWidget(self.responseCanvas, 0, 0)
# # # # Image canvas # # # # # # # # (1, 2)
self.roi_fig = plt.figure()
self.roi_ax = self.roi_fig.add_subplot(111)
self.roi_canvas = FigureCanvas(self.roi_fig)
self.toolbar = NavigationToolbar(self.roi_canvas, self)
self.roi_ax.set_aspect('equal')
self.roi_ax.set_axis_off()
self.plot_grid.addWidget(self.toolbar, 1, 0)
self.plot_grid.addWidget(self.roi_canvas, 2, 0)
self.plot_grid.setRowStretch(0, 1)
self.plot_grid.setRowStretch(1, 3)
self.plot_grid.setRowStretch(2, 3)
# Current z slice slider
self.zSlider = QSlider(QtCore.Qt.Orientation.Horizontal, self)
self.zSlider.setMinimum(0)
self.zSlider.setMaximum(50)
self.zSlider.setValue(0)
self.zSlider.valueChanged.connect(self.zSliderUpdated)
self.plot_grid.addWidget(self.zSlider, 3, 0)
self.roi_fig.tight_layout()
self.setWindowTitle('Visanalysis')
self.setGeometry(200, 200, 1200, 600)
self.show()
class DataGUI(QWidget):
def __init__(self):
super().__init__()
self.experiment_file_name = None
self.experiment_file_directory = None
self.data_directory = None
self.max_rois = 50
self.roi_type = 'freehand'
self.roi_radius = None
self.existing_roi_set_paths = {}
self.current_roi_index = 0
self.current_z_slice = 0
self.current_channel = 1 # index
self.image_series_name = ''
self.series_number = None
self.roi_response = []
self.roi_mask = []
self.roi_path = []
self.roi_image = None
self.roi_path_list = []
self.blank_image = np.zeros((1, 1))
self.colors = [
mcolors.to_rgb(x) for x in list(mcolors.TABLEAU_COLORS)[:20]
]
self.initUI()
def initUI(self):
self.grid = QGridLayout(self)
self.file_control_grid = QGridLayout()
self.file_control_grid.setSpacing(3)
self.grid.addLayout(self.file_control_grid, 0, 0)
self.file_tree_grid = QGridLayout()
self.file_tree_grid.setSpacing(3)
self.grid.addLayout(self.file_tree_grid, 1, 0)
self.group_control_grid = QGridLayout()
self.group_control_grid.setSpacing(3)
self.grid.addLayout(self.group_control_grid, 0, 1)
self.attribute_grid = QGridLayout()
self.attribute_grid.setSpacing(3)
self.grid.addLayout(self.attribute_grid, 1, 1)
self.roi_control_grid = QGridLayout()
self.roi_control_grid.setSpacing(3)
self.grid.addLayout(self.roi_control_grid, 0, 2)
self.plot_grid = QGridLayout()
self.plot_grid.setSpacing(3)
self.grid.addLayout(self.plot_grid, 1, 2)
# # # # File control browser: # # # # # # # # (0,0)
loadButton = QPushButton("Load expt. file", self)
loadButton.clicked.connect(self.selectDataFile)
# Label with current expt file
self.currentExperimentLabel = QLabel('')
self.file_control_grid.addWidget(loadButton, 0, 0)
self.file_control_grid.addWidget(self.currentExperimentLabel, 1, 0)
directoryButton = QPushButton("Select data directory", self)
directoryButton.clicked.connect(self.selectDataDirectory)
self.file_control_grid.addWidget(directoryButton, 0, 1)
self.data_directory_display = QLabel('')
self.data_directory_display.setFont(QtGui.QFont('SansSerif', 8))
self.file_control_grid.addWidget(self.data_directory_display, 1, 1)
# Attach metadata to file
attachDatabutton = QPushButton("Attach metadata to file", self)
attachDatabutton.clicked.connect(self.attachData)
self.file_control_grid.addWidget(attachDatabutton, 2, 0, 1, 2)
# Select image data file
selectImageDataFileButton = QPushButton("Select image data file", self)
selectImageDataFileButton.clicked.connect(self.selectImageDataFile)
self.file_control_grid.addWidget(selectImageDataFileButton, 3, 0, 1, 2)
# # # # File tree: # # # # # # # # (1,0)
self.groupTree = QTreeWidget(self)
self.groupTree.setHeaderHidden(True)
self.groupTree.itemClicked.connect(self.onTreeItemClicked)
self.file_tree_grid.addWidget(self.groupTree, 3, 0, 2, 7)
# # # # Group control: # # # # # # # # (0, 1)
deleteGroupButton = QPushButton("Delete selected group", self)
deleteGroupButton.clicked.connect(self.deleteSelectedGroup)
self.group_control_grid.addWidget(deleteGroupButton, 0, 0, 1, 2)
# File name display
self.currentImageFileNameLabel = QLabel('')
self.group_control_grid.addWidget(self.currentImageFileNameLabel, 1, 0)
# Channel drop down
ch_label = QLabel('Channel:')
self.ChannelComboBox = QComboBox(self)
self.ChannelComboBox.addItem("1")
self.ChannelComboBox.addItem("0")
self.ChannelComboBox.activated.connect(self.selectChannel)
self.group_control_grid.addWidget(ch_label, 2, 0)
self.group_control_grid.addWidget(self.ChannelComboBox, 2, 1)
# # # # Attribute table: # # # # # # # # (1, 1)
self.tableAttributes = QTableWidget()
self.tableAttributes.setStyleSheet("")
self.tableAttributes.setColumnCount(2)
self.tableAttributes.setObjectName("tableAttributes")
self.tableAttributes.setRowCount(0)
item = QTableWidgetItem()
font = QtGui.QFont()
font.setPointSize(10)
item.setFont(font)
item.setBackground(QtGui.QColor(121, 121, 121))
brush = QtGui.QBrush(QtGui.QColor(91, 91, 91))
brush.setStyle(QtCore.Qt.BrushStyle.SolidPattern)
item.setForeground(brush)
self.tableAttributes.setHorizontalHeaderItem(0, item)
item = QTableWidgetItem()
item.setBackground(QtGui.QColor(123, 123, 123))
brush = QtGui.QBrush(QtGui.QColor(91, 91, 91))
brush.setStyle(QtCore.Qt.BrushStyle.SolidPattern)
item.setForeground(brush)
self.tableAttributes.setHorizontalHeaderItem(1, item)
self.tableAttributes.horizontalHeader().setCascadingSectionResizes(
True)
self.tableAttributes.horizontalHeader().setHighlightSections(False)
self.tableAttributes.horizontalHeader().setSortIndicatorShown(True)
self.tableAttributes.horizontalHeader().setStretchLastSection(True)
self.tableAttributes.verticalHeader().setVisible(False)
self.tableAttributes.verticalHeader().setHighlightSections(False)
item = self.tableAttributes.horizontalHeaderItem(0)
item.setText("Attribute")
item = self.tableAttributes.horizontalHeaderItem(1)
item.setText("Value")
self.tableAttributes.itemChanged.connect(self.update_attrs_to_file)
self.attribute_grid.addWidget(self.tableAttributes, 3, 0, 1, 8)
# # # # Roi control # # # # # # # # (0, 2)
# ROI type drop-down
self.RoiTypeComboBox = QComboBox(self)
self.RoiTypeComboBox.addItem("freehand")
radii = [1, 2, 3, 4, 6, 8]
for radius in radii:
self.RoiTypeComboBox.addItem("circle:" + str(radius))
self.RoiTypeComboBox.activated.connect(self.selectRoiType)
self.roi_control_grid.addWidget(self.RoiTypeComboBox, 0, 0)
# Clear all ROIs button
self.clearROIsButton = QPushButton("Clear ROIs", self)
self.clearROIsButton.clicked.connect(self.clearRois)
self.roi_control_grid.addWidget(self.clearROIsButton, 0, 2)
# Response display type dropdown
self.RoiResponseTypeComboBox = QComboBox(self)
self.RoiResponseTypeComboBox.addItem("RawTrace")
self.RoiResponseTypeComboBox.addItem("TrialAverage")
self.RoiResponseTypeComboBox.addItem("TrialResponses")
self.RoiResponseTypeComboBox.addItem("TrialAverageDFF")
self.roi_control_grid.addWidget(self.RoiResponseTypeComboBox, 2, 2)
# ROIset file name line edit box
self.defaultRoiSetName = "roi_set_name"
self.le_roiSetName = QLineEdit(self.defaultRoiSetName)
self.roi_control_grid.addWidget(self.le_roiSetName, 1, 1)
# Save ROIs button
self.saveROIsButton = QPushButton("Save ROIs", self)
self.saveROIsButton.clicked.connect(self.saveRois)
self.roi_control_grid.addWidget(self.saveROIsButton, 1, 0)
# Load ROI set combobox
self.loadROIsComboBox = QComboBox(self)
self.loadROIsComboBox.addItem("(load existing ROI set)")
self.loadROIsComboBox.activated.connect(self.selectedExistingRoiSet)
self.roi_control_grid.addWidget(self.loadROIsComboBox, 1, 2)
self.updateExistingRoiSetList()
# Delete current roi button
self.deleteROIButton = QPushButton("Delete ROI", self)
self.deleteROIButton.clicked.connect(self.deleteRoi)
self.roi_control_grid.addWidget(self.deleteROIButton, 2, 0)
# Current roi slider
self.roiSlider = QSlider(QtCore.Qt.Orientation.Horizontal, self)
self.roiSlider.setMinimum(0)
self.roiSlider.setMaximum(self.max_rois)
self.roiSlider.valueChanged.connect(self.sliderUpdated)
self.roi_control_grid.addWidget(self.roiSlider, 2, 1, 1, 1)
ctx = plt.rc_context({
'xtick.major.size': 1,
'axes.spines.top': False,
'axes.spines.right': False,
'xtick.labelsize': 'xx-small',
'ytick.labelsize': 'xx-small',
'xtick.major.size': 1.0,
'ytick.major.size': 1.0,
'xtick.major.pad': 1.0,
'ytick.major.pad': 1.0
})
with ctx:
self.responseFig = plt.figure(frameon=False, layout='constrained')
self.responsePlot = self.responseFig.add_subplot(111)
self.responseCanvas = FigureCanvas(self.responseFig)
self.responseCanvas.draw_idle()
self.plot_grid.addWidget(self.responseCanvas, 0, 0)
# # # # Image canvas # # # # # # # # (1, 2)
self.roi_fig = plt.figure()
self.roi_ax = self.roi_fig.add_subplot(111)
self.roi_canvas = FigureCanvas(self.roi_fig)
self.toolbar = NavigationToolbar(self.roi_canvas, self)
self.roi_ax.set_aspect('equal')
self.roi_ax.set_axis_off()
self.plot_grid.addWidget(self.toolbar, 1, 0)
self.plot_grid.addWidget(self.roi_canvas, 2, 0)
self.plot_grid.setRowStretch(0, 1)
self.plot_grid.setRowStretch(1, 3)
self.plot_grid.setRowStretch(2, 3)
# Current z slice slider
self.zSlider = QSlider(QtCore.Qt.Orientation.Horizontal, self)
self.zSlider.setMinimum(0)
self.zSlider.setMaximum(50)
self.zSlider.setValue(0)
self.zSlider.valueChanged.connect(self.zSliderUpdated)
self.plot_grid.addWidget(self.zSlider, 3, 0)
self.roi_fig.tight_layout()
self.setWindowTitle('Visanalysis')
self.setGeometry(200, 200, 1200, 600)
self.show()
def _populateTree(self, widget, dict):
widget.clear()
self.fill_item(widget.invisibleRootItem(), dict)
def fill_item(self, item, value):
item.setExpanded(True)
if type(value) is dict:
for key, val in sorted(value.items()):
child = QTreeWidgetItem()
child.setText(0, key)
item.addChild(child)
self.fill_item(child, val)
elif type(value) is list:
for val in value:
child = QTreeWidgetItem()
item.addChild(child)
if type(val) is dict:
child.setText(0, '[dict]')
self.fill_item(child, val)
elif type(val) is list:
child.setText(0, '[list]')
self.fill_item(child, val)
else:
child.setText(0, val)
child.setExpanded(True)
else:
child = QTreeWidgetItem()
child.setText(0, value)
item.addChild(child)
def onTreeItemClicked(self, item, column):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
group_path = h5io.getPathFromTreeItem(
self.groupTree.selectedItems()[0])
self.clearRois()
self.series_number = None
if 'series_' in group_path:
self.series_number = int(
group_path.split('series_')[-1].split('/')[0])
if self.plugin.dataIsAttached(file_path, self.series_number):
self.plugin.updateImagingDataObject(
self.experiment_file_directory, self.experiment_file_name,
self.series_number)
# look for image_file_name or ask user to select it
if self.data_directory is not None:
image_file_name = h5io.readImageFileName(
file_path, self.series_number)
if image_file_name is None or image_file_name == '':
image_file_path, _ = QFileDialog.getOpenFileName(
self, "Select image file")
print('User selected image file at {}'.format(
image_file_path))
image_file_name = os.path.split(image_file_path)[-1]
self.data_directory = os.path.split(
image_file_path)[:-1][0]
h5io.attachImageFileName(file_path, self.series_number,
image_file_name)
print('Attached image_file_name {} to series {}'.format(
image_file_name, self.series_number))
print('Data directory is {}'.format(self.data_directory))
self.image_file_name = image_file_name
self.currentImageFileNameLabel.setText(self.image_file_name)
else: # clicked part of the tree upstream of any series
self.series_number = None
if item.parent() is not None:
if item.parent().text(
column) == 'rois': # selected existing roi group
roi_set_name = item.text(column)
# print('Selected roi set {} from series {}'.format(roi_set_name, self.series_number))
self.le_roiSetName.setText(roi_set_name)
roi_set_path = h5io.getPathFromTreeItem(
self.groupTree.selectedItems()[0])
self.loadRois(roi_set_path)
self.redrawRoiTraces()
if group_path != '':
attr_dict = h5io.getAttributesFromGroup(file_path, group_path)
editable_values = True # user can edit metadata
self.populate_attrs(attr_dict=attr_dict,
editable_values=editable_values)
# show roi image
if self.series_number is not None: # Clicked on node of the tree associated with a single series
if self.data_directory is not None: # user has selected a raw data directory
if self.plugin.dataIsAttached(file_path, self.series_number):
self.plugin.updateImageSeries(
data_directory=self.data_directory,
image_file_name=self.image_file_name,
series_number=self.series_number,
channel=self.current_channel)
self.roi_image = self.plugin.mean_brain
self.zSlider.setValue(0)
self.zSlider.setMaximum(self.roi_image.shape[2] - 1)
self.redrawRoiTraces()
else:
print('Attach metadata to file before drawing rois')
else:
print('Select a data directory before drawing rois')
# # # TEST # # #
memory_usage = psutil.Process(os.getpid()).memory_info().rss * 10**-9
print('Current Memory Usage: {:.2f}GB'.format(memory_usage))
sys.stdout.flush()
# # # TEST # # #
def updateExistingRoiSetList(self):
if self.experiment_file_name is not None:
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
self.existing_roi_set_paths = self.plugin.getRoiSetPaths(
file_path) # dictionary of name: full path
self.loadROIsComboBox.clear()
for r_path in self.existing_roi_set_paths:
self.loadROIsComboBox.addItem(r_path)
self.show()
def selectedExistingRoiSet(self):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
roi_set_key = self.loadROIsComboBox.currentText()
roi_set_path = self.existing_roi_set_paths[roi_set_key]
_, _, self.roi_path, self.roi_mask = self.plugin.loadRoiSet(
file_path, roi_set_path)
if self.series_number is not None:
self.roi_response = []
for new_path in self.roi_path:
new_roi_resp = self.plugin.getRoiDataFromPath(
roi_path=new_path)
self.roi_response.append(new_roi_resp)
# update slider to show most recently drawn roi response
self.current_roi_index = len(self.roi_response) - 1
self.roiSlider.setValue(self.current_roi_index)
# Update figures
self.redrawRoiTraces()
def selectDataFile(self):
filePath, _ = QFileDialog.getOpenFileName(
self, "Open experiment (hdf5) file")
self.experiment_file_name = os.path.split(filePath)[1].split('.')[0]
self.experiment_file_directory = os.path.split(filePath)[0]
if self.experiment_file_name != '':
self.currentExperimentLabel.setText(self.experiment_file_name)
self.initializeDataAnalysis()
self.populateGroups()
self.updateExistingRoiSetList()
def selectDataDirectory(self):
filePath = str(
QFileDialog.getExistingDirectory(self, "Select data directory"))
self.data_directory = filePath
self.data_directory_display.setText('..' + self.data_directory[-24:])
def initializeDataAnalysis(self):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
data_type = h5io.getDataType(file_path)
# Load plugin based on Rig name in hdf5 file
if data_type == 'Bruker':
from visanalysis.plugin import bruker
self.plugin = bruker.BrukerPlugin()
elif data_type == 'AODscope':
from visanalysis.plugin import aodscope
self.plugin = aodscope.AodScopePlugin()
else:
self.plugin = h5io.BasePlugin()
self.plugin.parent_gui = self
# # # TEST # # #
memory_usage = psutil.Process(os.getpid()).memory_info().rss * 10**-9
print('Current memory usage: {:.2f}GB'.format(memory_usage))
sys.stdout.flush()
# # # TEST # # #
def attachData(self):
if self.data_directory is not None:
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
self.plugin.attachData(self.experiment_file_name, file_path,
self.data_directory)
print('Data attached')
else:
print('Select a data directory before attaching new data')
def selectImageDataFile(self):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
image_file_path, _ = QFileDialog.getOpenFileName(
self, "Select image file")
print('User selected image file at {}'.format(image_file_path))
self.image_file_name = os.path.split(image_file_path)[-1]
self.data_directory = os.path.split(image_file_path)[:-1][0]
h5io.attachImageFileName(file_path, self.series_number,
self.image_file_name)
print('Attached image_file_name {} to series {}'.format(
self.image_file_name, self.series_number))
print('Data directory is {}'.format(self.data_directory))
self.currentImageFileNameLabel.setText(self.image_file_name)
# show roi image
if self.series_number is not None:
if self.data_directory is not None: # user has selected a raw data directory
self.plugin.updateImageSeries(
data_directory=self.data_directory,
image_file_name=self.image_file_name,
series_number=self.series_number,
channel=self.current_channel)
self.roi_image = self.plugin.mean_brain
self.zSlider.setValue(0)
self.zSlider.setMaximum(self.roi_image.shape[2] - 1)
self.redrawRoiTraces()
else:
print('Select a data directory before drawing rois')
def deleteSelectedGroup(self):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
group_path = h5io.getPathFromTreeItem(
self.groupTree.selectedItems()[0])
group_name = group_path.split('/')[-1]
buttonReply = QMessageBox.question(
self, 'Delete series',
"Are you sure you want to delete group {}?".format(group_name),
QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
QMessageBox.StandardButton.No)
if buttonReply == QMessageBox.StandardButton.Yes:
h5io.deleteGroup(file_path=file_path, group_path=group_path)
print('Deleted group {}'.format(group_name))
self.updateExistingRoiSetList()
self.populateGroups()
else:
print('Delete aborted')
def populateGroups(self):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
self.group_dset_dict = h5io.getHierarchy(file_path)
self._populateTree(self.groupTree, self.group_dset_dict)
def populate_attrs(self, attr_dict=None, editable_values=False):
"""Populate attribute for currently selected group."""
self.tableAttributes.blockSignals(
True) # block udpate signals for auto-filled forms
self.tableAttributes.setRowCount(0)
self.tableAttributes.setColumnCount(2)
self.tableAttributes.setSortingEnabled(False)
if attr_dict:
for num, key in enumerate(attr_dict):
self.tableAttributes.insertRow(self.tableAttributes.rowCount())
key_item = QTableWidgetItem(key)
key_item.setFlags(QtCore.Qt.ItemFlag.ItemIsSelectable
| QtCore.Qt.ItemFlag.ItemIsEnabled)
self.tableAttributes.setItem(num, 0, key_item)
val_item = QTableWidgetItem(str(attr_dict[key]))
if editable_values:
val_item.setFlags(QtCore.Qt.ItemFlag.ItemIsSelectable
| QtCore.Qt.ItemFlag.ItemIsEditable
| QtCore.Qt.ItemFlag.ItemIsEnabled)
else:
val_item.setFlags(QtCore.Qt.ItemFlag.ItemIsSelectable
| QtCore.Qt.ItemFlag.ItemIsEnabled)
self.tableAttributes.setItem(num, 1, val_item)
self.tableAttributes.blockSignals(False)
def update_attrs_to_file(self, item):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
group_path = h5io.getPathFromTreeItem(
self.groupTree.selectedItems()[0])
attr_key = self.tableAttributes.item(item.row(), 0).text()
attr_val = item.text()
# update attr in file
h5io.changeAttribute(file_path=file_path,
group_path=group_path,
attr_key=attr_key,
attr_val=attr_val)
print('Changed attr {} to = {}'.format(attr_key, attr_val))
# %% # # # # # # # # ROI SELECTOR WIDGET # # # # # # # # # # # # # # # # # # #
def refreshLassoWidget(self, keep_paths=False):
self.roi_ax.clear()
init_lasso = False
if self.roi_image is not None:
if len(self.roi_mask) > 0:
newImage = plot_tools.overlayImage(
self.roi_image[:, :, self.current_z_slice],
self.roi_mask,
0.5,
self.colors,
z=self.current_z_slice)
else:
newImage = self.roi_image[:, :, self.current_z_slice]
self.roi_ax.imshow(newImage, cmap=cm.gray)
init_lasso = True
else:
self.roi_ax.imshow(self.blank_image)
self.roi_ax.set_axis_off()
self.roi_canvas.draw()
if not keep_paths:
self.roi_path_list = []
if init_lasso:
if self.roi_type == 'circle':
self.lasso_1 = EllipseSelector(self.roi_ax,
onselect=self.newEllipse,
button=1)
elif self.roi_type == 'freehand':
self.lasso_1 = LassoSelector(self.roi_ax,
onselect=self.newFreehand,
button=1)
self.lasso_2 = LassoSelector(self.roi_ax,
onselect=self.appendFreehand,
button=3)
else:
print(
'Warning ROI type not recognized. Choose circle or freehand'
)
def newFreehand(self, verts):
new_roi_path = path.Path(verts)
new_roi_path.z_level = self.zSlider.value()
new_roi_path.channel = self.current_channel
self.updateRoiSelection([new_roi_path])
def appendFreehand(self, verts):
print('Appending rois, hit Enter/Return to finish')
new_roi_path = path.Path(verts)
new_roi_path.z_level = self.zSlider.value()
new_roi_path.channel = self.current_channel
self.roi_path_list.append(new_roi_path)
def keyPressEvent(self, event):
if type(event) == QtGui.QKeyEvent:
if np.any([
event.key() == QtCore.Qt.Key.Key_Return,
event.key() == QtCore.Qt.Key.Key_Enter
]):
if len(self.roi_path_list) > 0:
event.accept()
self.updateRoiSelection(self.roi_path_list)
else:
event.ignore()
else:
event.ignore()
else:
event.ignore()
def newEllipse(self, pos1, pos2, definedRadius=None):
x1 = np.round(pos1.xdata)
x2 = np.round(pos2.xdata)
y1 = np.round(pos1.ydata)
y2 = np.round(pos2.ydata)
radiusX = np.sqrt((x1 - x2)**2) / 2
radiusY = np.sqrt((y1 - y2)**2) / 2
if self.roi_radius is not None:
radiusX = self.roi_radius
center = (np.round((x1 + x2) / 2), np.round((y1 + y2) / 2))
new_roi_path = path.Path.circle(center=center, radius=radiusX)
new_roi_path.z_level = self.zSlider.value()
new_roi_path.channel = self.current_channel
self.updateRoiSelection([new_roi_path])
def updateRoiSelection(self, new_roi_path):
mask = self.plugin.getRoiMaskFromPath(new_roi_path)
new_roi_resp = self.plugin.getRoiDataFromPath(roi_path=new_roi_path)
if mask.sum() == 0:
print('No pixels in the roi you just drew')
return
# update list of roi data
self.roi_mask.append(mask)
self.roi_path.append(new_roi_path) # list of lists of paths
self.roi_response.append(new_roi_resp)
# update slider to show most recently drawn roi response
self.current_roi_index = len(self.roi_response) - 1
self.roiSlider.setValue(self.current_roi_index)
# Update figures
self.redrawRoiTraces()
def sliderUpdated(self):
self.current_roi_index = self.roiSlider.value()
self.redrawRoiTraces()
def zSliderUpdated(self):
self.current_z_slice = self.zSlider.value()
if self.roi_image is not None:
self.refreshLassoWidget(keep_paths=True)
def redrawRoiTraces(self):
self.clearRoiArtists()
if self.current_roi_index < len(self.roi_response):
current_raw_trace = np.squeeze(
self.roi_response[self.current_roi_index])
fxn_name = self.RoiResponseTypeComboBox.currentText()
display_trace = getattr(self.plugin,
'getRoiResponse_{}'.format(fxn_name))(
[current_raw_trace])
self.responsePlot.plot(display_trace,
color=self.colors[self.current_roi_index],
linewidth=1,
alpha=0.5)
self.responsePlot.set_xlim([0, len(display_trace)])
y_min = np.nanmin(display_trace)
y_max = np.nanmax(display_trace)
self.responsePlot.set_ylim([y_min, y_max])
self.responseCanvas.draw()
self.refreshLassoWidget(keep_paths=False)
# %% # # # # # # # # LOADING / SAVING / COMPUTING ROIS # # # # # # # # # # # # # # # # # # #
def loadRois(self, roi_set_path):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
self.roi_response, self.roi_image, self.roi_path, self.roi_mask = self.plugin.loadRoiSet(
file_path, roi_set_path)
self.zSlider.setValue(0)
self.zSlider.setMaximum(self.roi_image.shape[2] - 1)
def saveRois(self):
file_path = os.path.join(self.experiment_file_directory,
self.experiment_file_name + '.hdf5')
roi_set_name = self.le_roiSetName.text()
if roi_set_name in h5io.getAvailableRoiSetNames(
file_path, self.series_number):
buttonReply = QMessageBox.question(
self, 'Overwrite roi set',
"Are you sure you want to overwrite roi set: {}?".format(
roi_set_name),
QMessageBox.StandardButton.Yes | QMessageBox.StandardButton.No,
QMessageBox.StandardButton.No)
if buttonReply == QMessageBox.StandardButton.Yes:
self.plugin.saveRoiSet(file_path,
series_number=self.series_number,
roi_set_name=roi_set_name,
roi_mask=self.roi_mask,
roi_response=self.roi_response,
roi_image=self.roi_image,
roi_path=self.roi_path)
print('Saved roi set {} to series {}'.format(
roi_set_name, self.series_number))
self.populateGroups()
self.updateExistingRoiSetList()
else:
print('Overwrite aborted - pick a unique roi set name')
else:
self.plugin.saveRoiSet(file_path,
series_number=self.series_number,
roi_set_name=roi_set_name,
roi_mask=self.roi_mask,
roi_response=self.roi_response,
roi_image=self.roi_image,
roi_path=self.roi_path)
print('Saved roi set {} to series {}'.format(
roi_set_name, self.series_number))
self.populateGroups()
self.updateExistingRoiSetList()
def deleteRoi(self):
if self.current_roi_index < len(self.roi_response):
self.roi_mask.pop(self.current_roi_index)
self.roi_response.pop(self.current_roi_index)
self.roi_path.pop(self.current_roi_index)
self.roiSlider.setValue(self.current_roi_index - 1)
self.redrawRoiTraces()
def clearRois(self):
self.roi_mask = []
self.roi_response = []
self.roi_path = []
self.roi_image = None
self.clearRoiArtists()
self.redrawRoiTraces()
self.roi_ax.clear()
def clearRoiArtists(self):
for artist in self.responsePlot.lines + self.responsePlot.collections:
artist.remove()
def selectRoiType(self):
self.roi_type = self.RoiTypeComboBox.currentText().split(':')[0]
if 'circle' in self.RoiTypeComboBox.currentText():
self.roi_radius = int(
self.RoiTypeComboBox.currentText().split(':')[1])
else:
self.roi_radius = None
self.redrawRoiTraces()
def selectChannel(self):
self.current_channel = int(self.ChannelComboBox.currentText())
# show roi image
if self.series_number is not None:
if self.data_directory is not None: # user has selected a raw data directory
self.plugin.updateImageSeries(
data_directory=self.data_directory,
image_file_name=self.image_file_name,
series_number=self.series_number,
channel=self.current_channel)
self.roi_image = self.plugin.mean_brain
self.zSlider.setValue(0)
self.zSlider.setMaximum(self.roi_image.shape[2] - 1)
self.redrawRoiTraces()
else:
print('Select a data directory before drawing rois')
