def set_sounds_and_volume(self):
self.soundsGroup = QtGui.QActionGroup(self.menuSounds)
self.soundsGroup.setExclusive(True)
self.actionBeep.setActionGroup(self.soundsGroup)
self.actionBeep.triggered.connect(self.toggle_sounds)
self.actionClick.setActionGroup(self.soundsGroup)
self.actionClick.triggered.connect(self.toggle_sounds)
self.actionPunch.setActionGroup(self.soundsGroup)
self.actionPunch.triggered.connect(self.toggle_sounds)
self.actionWhack.setActionGroup(self.soundsGroup)
self.actionWhack.triggered.connect(self.toggle_sounds)
self.actionSharp.setActionGroup(self.soundsGroup)
self.actionSharp.triggered.connect(self.toggle_sounds)
self.actionGlass.setActionGroup(self.soundsGroup)
self.actionGlass.triggered.connect(self.toggle_sounds)
self.sound = 'beep'
self.volumeGroup = QtGui.QActionGroup(self.menuVolume)
self.volumeGroup.setExclusive(True)
self.actionHigh.setActionGroup(self.volumeGroup)
self.actionHigh.triggered.connect(self.toggle_volume)
self.actionMedium.setActionGroup(self.volumeGroup)
self.actionMedium.triggered.connect(self.toggle_volume)
self.actionLow.setActionGroup(self.volumeGroup)
self.actionLow.triggered.connect(self.toggle_volume)
self.volume = 1
def _center_widget(self, widget):
w = QtGui.QWidget(self)
hbox = QtGui.QHBoxLayout(w)
hbox.setAlignment(QtCore.Qt.AlignCenter)
hbox.setContentsMargins(0, 0, 0, 0)
hbox.addWidget(widget)
return w
def _update_meanmap_transform(self):
translate_transform = QtGui.QTransform().translate(
self.mm_ymin, self.mm_xmin)
scale_transform = QtGui.QTransform().scale(self.mm_dy, self.mm_dx)
transpose_transform = QtGui.QTransform()
transpose_transform *= QtGui.QTransform(0, 1, 0, 1, 0, 0, 0, 0, 1)
self.meanmap_transform = scale_transform * translate_transform * transpose_transform
def _set_subscription(self, source, title, value):
for row in range(0, self.table.rowCount()):
if (self.table.item(row, 0).text() == source.name()
and self.table.item(row, 1).text() == title):
if (value):
brush = QtGui.QBrush(QtGui.QColor(230, 255, 230))
else:
brush = QtGui.QBrush()
for column in range(0, self.table.columnCount()):
self.table.item(row, column).setBackground(brush)
def _image_transform(self, img, source, title):
"""Returns the appropriate transform for the content"""
conf = source.conf[title]
xmin = conf.get('xmin', 0)
ymin = conf.get('ymin', 0)
xmax = img.shape[-1] + xmin
ymax = img.shape[-2] + ymin
if "xmax" in conf:
if (conf['xmax'] <= xmin):
logging.warning(
"xmax <= xmin for title %s on %s. Ignoring xmax", title,
source.name())
else:
xmax = conf['xmax']
if "ymax" in conf:
if (conf['ymax'] <= ymin):
logging.warning(
"ymax <= ymin for title %s on %s. Ignoring xmax", title,
source.name())
else:
ymax = conf['ymax']
translate_transform = QtGui.QTransform().translate(ymin, xmin)
# The order of dimensions in the scale call is (y,x) as in the numpy
# array the last dimension corresponds to the x.
scale_transform = QtGui.QTransform().scale(
(ymax - ymin) / img.shape[-2], (xmax - xmin) / img.shape[-1])
#rotate_transform = QtGui.QTransform()
#if source.data_type[title] == 'image':
# if "angle" in conf:
# rotate_transform = QtGui.QTransform(numpy.cos(conf["angle"]), numpy.sin(conf["angle"]), -numpy.sin(conf["angle"]), numpy.cos(conf["angle"]), 0, 0)
transpose_transform = QtGui.QTransform()
if source.data_type[title] == 'image':
transpose_transform *= QtGui.QTransform(0, 1, 0, 1, 0, 0, 0, 0, 1)
if (self.settingsWidget.ui.transpose.currentText() == 'Yes'
or (self.settingsWidget.ui.transpose.currentText() == 'Auto'
and "transpose" in conf)):
transpose_transform *= QtGui.QTransform(0, 1, 0, 1, 0, 0, 0, 0, 1)
transform = scale_transform * translate_transform * transpose_transform
#transform = scale_transform * translate_transform * rotate_transform * transpose_transform
# print '|%f %f %f|' % (transform.m11(), transform.m12(), transform.m13())
# print '|%f %f %f|' % (transform.m21(), transform.m22(), transform.m23())
# print '|%f %f %f|' % (transform.m31(), transform.m32(), transform.m33())
return transform
def add_row(self, source, plotdata, row=None):
if row is None:
row = self.table.rowCount()
self.table.insertRow(row)
item = QtGui.QTableWidgetItem(source.name())
item.setData(QtCore.Qt.UserRole, source)
item.setFlags(item.flags() & ~QtCore.Qt.ItemIsEditable)
self.table.setItem(row, 0, item)
item = QtGui.QTableWidgetItem(plotdata.title)
item.setData(QtCore.Qt.UserRole, plotdata)
item.setFlags(item.flags() & ~QtCore.Qt.ItemIsEditable)
self.table.setItem(row, 1, item)
bar = QtGui.QProgressBar()
self.table.setItem(row, 2, QtGui.QTableWidgetItem())
self.table.setCellWidget(row, 2, self._center_widget(bar))
checkbox = QtGui.QCheckBox()
checkbox.setChecked(plotdata.restored)
self.table.setItem(row, 3, QtGui.QTableWidgetItem())
self.table.setCellWidget(row, 3, self._center_widget(checkbox))
checkbox = QtGui.QCheckBox()
checkbox.setEnabled(plotdata.ishistory)
checkbox.setChecked(plotdata.recordhistory)
self.table.setItem(row, 4, QtGui.QTableWidgetItem())
self.table.setCellWidget(row, 4, self._center_widget(checkbox))
# Mark existing subscriptions
if (plotdata.title in source.subscribed_titles):
self._set_subscription(source, plotdata.title, True)
def _finish_layout(self):
"""This is called after the derived classes finish settings up so
that the lower common section of the window can be setup. Kinda ugly."""
layout = QtGui.QVBoxLayout(self.plotFrame)
layout.addWidget(self.plot)
self.plot_title = str(self.title.text())
self.title.textChanged.connect(self._on_title_change)
def add_backend(self, data_source):
"""Add backend to menu if it's not there yet
and append to _data_sources"""
actions = self._backends_menu.actions()
unique = True
for a in actions:
if (a.text() == data_source.name()):
unique = False
if (not unique):
QtGui.QMessageBox.warning(
self, "Duplicate backend",
"Duplicate backend. Ignoring %s" % data_source.name())
return
self._data_sources.append(data_source)
logging.debug("Registering data source '%s' in the GUI",
data_source.name())
action = QtGui.QAction(data_source.name(), self)
action.setData(data_source)
action.setCheckable(True)
action.setChecked(True)
self._backends_menu.addAction(action)
action.triggered.connect(self._data_source_triggered)
self.plotdata_widget.add_source(data_source)
data_source._recorder = self._recorder
self._status_message("Backend '%s' connected." % (data_source.name()),
5000)
def _setup_connections(self):
"""Initialize connections"""
self.menuData_Sources.aboutToShow.connect(self.on_menu_show)
self.actionSaveToPNG.triggered.connect(self.on_save_to_png)
self.actionSaveToPNG.setShortcut(QtGui.QKeySequence("Ctrl+P"))
self.actionSound_on_off.triggered.connect(self.toggle_alert)
self.alertBlinkTimer.timeout.connect(self.blink_alert)
def _setup_connections(self):
"""Initialize connections"""
self.menuData_Sources.aboutToShow.connect(self.on_menu_show)
self.actionSaveToPNG.triggered.connect(self.on_save_to_png)
self.actionSaveToPNG.setShortcut(QtGui.QKeySequence("Ctrl+P"))
self.alertBlinkTimer.timeout.connect(self.blink_alert)
self.title.installEventFilter(self)
self.timeLabel.installEventFilter(self)
self.dateLabel.installEventFilter(self)
def add_menu(title, menu, ds):
action = QtGui.QAction(title, self)
action.setData([ds, title])
action.setCheckable(True)
if (ds in self._enabled_sources
and title in self._enabled_sources[ds]):
action.setChecked(True)
else:
action.setChecked(False)
menu.addAction(action)
action.triggered.connect(self._source_title_triggered)
def start_interface(restore):
"""Initialize and show the Interface"""
# Catch Ctrl+c and such
signal.signal(signal.SIGINT, sigint_handler)
QtCore.QCoreApplication.setOrganizationName("SPI")
QtCore.QCoreApplication.setOrganizationDomain("spidocs.rtfd.org")
QtCore.QCoreApplication.setApplicationName("Hummingbird")
app = QtGui.QApplication(sys.argv)
app.setQuitOnLastWindowClosed(True)
GUI(restore).show()
sys.exit(app.exec_())
def updateFonts(self):
f = self.title.font()
size = int(self.settings.value("plotFontSize"))
f.setPointSize(size)
self.title.setFont(f)
f = QtGui.QFont()
f.setPointSize(size)
ax = self.plot.getAxis('left')
ax.setTickFont(f)
ax = self.plot.getAxis('bottom')
ax.setTickFont(f)
def add_header(self, name, row=None):
if row is None:
row = self.table.rowCount()
self.table.insertRow(row)
named_item = QtGui.QTableWidgetItem(name)
named_item.setFlags(QtCore.Qt.NoItemFlags)
header_font = QtGui.QFont()
header_font.setBold(True)
named_item.setFont(header_font)
named_item.setData(QtCore.Qt.UserRole, str(name))
self.table.setItem(row, 1, named_item)
separator_text = ""
item = QtGui.QTableWidgetItem(separator_text)
item.setFlags(QtCore.Qt.NoItemFlags)
self.table.setItem(row, 0, item)
item = QtGui.QTableWidgetItem(separator_text)
item.setFlags(QtCore.Qt.NoItemFlags)
self.table.setItem(row, 2, item)
item = QtGui.QTableWidgetItem(separator_text)
item.setFlags(QtCore.Qt.NoItemFlags)
self.table.setItem(row, 3, item)
item = QtGui.QTableWidgetItem(separator_text)
item.setFlags(QtCore.Qt.NoItemFlags)
self.table.setItem(row, 4, item)
return named_item
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
label = QtGui.QLabel('<center><b>Data Sources</b></center>')
vbox = QtGui.QVBoxLayout(self)
vbox.addWidget(label)
self.table = QtGui.QTableWidget()
self.table.setColumnCount(5)
self.table.setHorizontalHeaderLabels([
'Backend', 'Title', 'Buffer Capacity', 'Save on Exit',
'Record History'
])
self.table.horizontalHeader().setStretchLastSection(True)
self.table.horizontalHeader().setHighlightSections(False)
self.table.verticalHeader().hide()
self.table.setShowGrid(False)
self.table.setAlternatingRowColors(True)
self.table.setSelectionMode(QtGui.QAbstractItemView.SingleSelection)
self.table.setSelectionBehavior(QtGui.QAbstractItemView.SelectRows)
self.table.itemSelectionChanged.connect(self._on_selection_changed)
self._groups = {None: [[], None]}
vbox.addWidget(self.table)
hbox = QtGui.QHBoxLayout()
hbox.addStretch()
self.clear_buffer = QtGui.QPushButton('Clear Buffer', self)
self.clear_buffer.setEnabled(False)
self.clear_buffer.clicked.connect(self._on_clear_buffer_clicked)
hbox.addWidget(self.clear_buffer)
self.buffer_size = QtGui.QPushButton('Set Buffer Capacity', self)
self.buffer_size.setEnabled(False)
self.buffer_size.clicked.connect(self._on_buffer_size_clicked)
hbox.addWidget(self.buffer_size)
self.buffer_spin = QtGui.QSpinBox(self)
self.buffer_spin.setEnabled(False)
self.buffer_spin.setMaximum(1024 * 1024 * 1024)
hbox.addWidget(self.buffer_spin)
hbox.addStretch()
vbox.addLayout(hbox)
def replot(self):
"""Replot data"""
for source, title in self.source_and_titles():
if (title not in source.plotdata):
continue
pd = source.plotdata[title]
if (pd.y is None or len(pd.y) == 0):
continue
conf = source.conf[title]
if "alert" in conf and self.alert and conf['alert']:
os.system('afplay -v %f src/interface/ui/sounds/%s.wav &' %
(self.volume, self.sound))
if not self.alertBlinkTimer.isActive():
self.alertBlinkTimer.start()
else:
if self.alertBlinkTimer.isActive():
self.alertBlinkTimer.stop()
self.setStyleSheet("")
if (self.settingsWidget.ui.ignore_source.isChecked() is False):
if 'vmin' in conf and conf['vmin'] is not None:
cmin = self.settingsWidget.ui.colormap_min
cmin.setText(str(conf['vmin']))
if 'vmax' in conf and conf['vmax'] is not None:
cmax = self.settingsWidget.ui.colormap_max
cmax.setText(str(conf['vmax']))
if 'vmin' in conf or 'vmax' in conf:
self.set_colormap_range()
if conf["data_type"] == "running_hist":
if not self.running_hist_initialised:
self.init_running_hist(source, title)
window = int(self.settingsWidget.ui.runningHistWindow.text())
bins = int(self.settingsWidget.ui.runningHistBins.text())
hmin = int(self.settingsWidget.ui.runningHistMin.text())
hmax = int(self.settingsWidget.ui.runningHistMax.text())
v = pd.y[-1]
length = pd.maxlen
img = utils.array.runningHistogram(v, title, length, window,
bins, hmin, hmax)
if not img.shape[0]:
continue
else:
img = numpy.array(pd.y, copy=False)
self._configure_axis(source, title)
transform = self._image_transform(img, source, title)
if conf["data_type"] == "running_hist":
translate_transform = QtGui.QTransform().translate(0, hmin)
scale_transform = QtGui.QTransform().scale(
3. * float(hmax - hmin) / float(length),
float(hmax - hmin) / float(bins))
transform = scale_transform * translate_transform
if (self.plot.image is None or # Plot if first image
len(self.plot.image.shape) < 3
or # Plot if there's no history
self.plot.image.shape[0] - 1 == self.plot.currentIndex
): # Plot if we're at the last image in history
auto_levels = False
auto_range = False
auto_histogram = False
if (self.plot.image is None and self.restored == False):
# Turn on auto on the first image
auto_levels = True
auto_rage = True
auto_histogram = True
if "data_type" in conf and conf["data_type"] == "triple":
triples = numpy.array(pd.y, copy=False)
times = numpy.array(pd.x, copy=False)
img, transform, x, y = self._fill_meanmap(
times,
triples,
xmin=conf["xmin"],
xmax=conf["xmax"],
ymin=conf["ymin"],
ymax=conf["ymax"],
ybins=conf["ybins"],
xbins=conf["xbins"],
dynamic_extent=conf.get("dynamic_extent", False),
initial_reset=conf.get("initial_reset", False),
)
else:
x, y = (0, 0)
if (self.settingsWidget.ui.show_trend.isChecked()):
_trend = getattr(
numpy,
str(self.settingsWidget.ui.trend_options.currentText())
)
img = _trend(img, axis=0)
if self.settingsWidget.ui.modelVisibility.value() > 0:
# We should overwrite part of the image with a model
dirty = False
centerx = float(self.settingsWidget.ui.modelCenterX.text())
if 'centerx' not in self.modelParameters or centerx != self.modelParameters[
'centerx']:
dirty = True
self.modelParameters['centerx'] = centerx
centery = float(self.settingsWidget.ui.modelCenterY.text())
if 'centery' not in self.modelParameters or centery != self.modelParameters[
'centery']:
dirty = True
self.modelParameters['centery'] = centery
diameter = float(
self.settingsWidget.ui.modelDiameter.text()) * 1e-9
if 'diameter' not in self.modelParameters or diameter != self.modelParameters[
'diameter']:
dirty = True
self.modelParameters['diameter'] = diameter
intensity = float(self.settingsWidget.ui.pulseIntensity.
text()) * 1e-3 / 1e-12
if 'intensity' not in self.modelParameters or intensity != self.modelParameters[
'intensity']:
dirty = True
self.modelParameters['intensity'] = intensity
wavelength = 1239.84193 / float(
self.settingsWidget.ui.photonEnergy.text()) * 1e-9
if 'wavelength' not in self.modelParameters or wavelength != self.modelParameters[
'wavelength']:
dirty = True
self.modelParameters['wavelength'] = wavelength
distance = float(
self.settingsWidget.ui.detectorDistance.text())
if 'distance' not in self.modelParameters or distance != self.modelParameters[
'distance']:
dirty = True
self.modelParameters['distance'] = distance
pixelsize = float(
self.settingsWidget.ui.detectorPixelSize.text()) * 1e-6
if 'pixelsize' not in self.modelParameters or pixelsize != self.modelParameters[
'pixelsize']:
dirty = True
self.modelParameters['pixelsize'] = pixelsize
if dirty:
material = 'virus'
quantum_efficiency = 1.0
adu_per_photon = float(
self.settingsWidget.ui.detectorGain.text()
) / float(
self.settingsWidget.ui.photonEnergy.text()) * 1e3
self.modelParameters['adu_per_photon'] = adu_per_photon
size = self.spimage.sphere_model_convert_diameter_to_size(
diameter, wavelength, pixelsize, distance)
scaling = self.spimage.sphere_model_convert_intensity_to_scaling(
intensity, diameter, wavelength, pixelsize,
distance, quantum_efficiency, adu_per_photon,
material)
fit = self.spimage.I_sphere_diffraction(
scaling,
self.spimage.rgrid(img[0].shape,
(centerx, centery)), size)
self.modelParameters['fit'] = fit
else:
fit = self.modelParameters['fit']
adu_per_photon = self.modelParameters['adu_per_photon']
extent = numpy.ceil(
img.shape[2] *
self.settingsWidget.ui.modelVisibility.value() / 100.0)
if self.settingsWidget.ui.modelPoisson.isChecked():
fit = numpy.random.poisson(
fit[:, :extent] / adu_per_photon) * adu_per_photon
else:
fit = fit[:, :extent]
img[-1, :, :extent] = fit
self.plot.setImage(img,
transform=transform,
autoRange=auto_range,
autoLevels=auto_levels,
autoHistogramRange=auto_histogram)
self._show_crosshair(x, y)
if (len(self.plot.image.shape) > 2):
# Make sure to go to the last image
last_index = self.plot.image.shape[0] - 1
self.plot.setCurrentIndex(
last_index, autoHistogramRange=auto_histogram)
self._set_logscale(source, title)
self.setWindowTitle(pd.title)
dt, msg = self.get_time_and_msg()
self.infoLabel.setText(msg)
# Round to miliseconds
self.timeLabel.setText(
'%02d:%02d:%02d.%03d' %
(dt.hour, dt.minute, dt.second, dt.microsecond / 1000))
self.dateLabel.setText(str(dt.date()))
def __init__(self, parent=None):
# This also sets up the UI part
DataWindow.__init__(self, parent)
# This is imported here to prevent problems with sphinx
from .image_view import ImageView
self.plot = ImageView(self, view=pyqtgraph.PlotItem())
self._finish_layout()
self.infoLabel.setText('')
self.acceptable_data_types = [
'image', 'vector', 'triple', 'running_hist'
]
self.exclusive_source = True
self.meanmap = None
self.last_x = None
self.last_y = None
self.mm_last = None
self.vline = None
self.hline = None
self.settingsWidget.setVisible(self.actionPlotSettings.isChecked())
self.settingsWidget.ui.colormap_min.editingFinished.connect(
self.set_colormap_range)
self.settingsWidget.ui.colormap_max.editingFinished.connect(
self.set_colormap_range)
self.settingsWidget.ui.colormap_min.setValidator(
QtGui.QDoubleValidator())
self.settingsWidget.ui.colormap_max.setValidator(
QtGui.QDoubleValidator())
self.settingsWidget.ui.colormap_full_range.clicked.connect(
self.set_colormap_full_range)
self.settingsWidget.ui.histogram_show.toggled.connect(
self.plot.getHistogramWidget().setVisible)
self.actionHistogram.triggered.connect(
self.plot.getHistogramWidget().setVisible)
self.actionHistogram.triggered.connect(
self.settingsWidget.ui.histogram_show.setChecked)
self.settingsWidget.ui.histogram_show.toggled.connect(
self.actionHistogram.setChecked)
self.settingsWidget.ui.x_show.toggled.connect(self.toggle_axis)
self.actionX_axis.triggered.connect(self.toggle_axis)
self.settingsWidget.ui.y_show.toggled.connect(self.toggle_axis)
self.actionY_axis.triggered.connect(self.toggle_axis)
self.settingsWidget.ui.histogram_show.toggled.connect(self.toggle_axis)
self.actionHistogram.triggered.connect(self.toggle_axis)
self.settingsWidget.ui.modelCenterX.setValidator(
QtGui.QDoubleValidator())
self.settingsWidget.ui.modelCenterY.setValidator(
QtGui.QDoubleValidator())
self.settingsWidget.ui.modelDiameter.setValidator(
QtGui.QDoubleValidator())
self.settingsWidget.ui.photonEnergy.setValidator(
QtGui.QDoubleValidator())
self.settingsWidget.ui.detectorGain.setValidator(
QtGui.QDoubleValidator())
self.settingsWidget.ui.detectorDistance.setValidator(
QtGui.QDoubleValidator())
self.settingsWidget.ui.detectorPixelSize.setValidator(
QtGui.QDoubleValidator())
self.modelParameters = {}
success, spimage = utils.io.load_spimage()
if not success:
# no spimage available, we need to disable the model settings
self.settingsWidget.ui.modelTab.setEnabled(False)
else:
self.spimage = spimage
self.settingsWidget.ui.colormap_max.setValidator(
QtGui.QDoubleValidator())
self.plot.getHistogramWidget().region.sigRegionChangeFinished.connect(
self.set_colormap_range)
self.actionPlotSettings.triggered.connect(self.toggle_settings)
# Make sure to disable native menus
self.plot.getView().setMenuEnabled(False)
self.plot.getHistogramWidget().vb.setMenuEnabled(False)
self.x_axis_name = 'left'
self.y_axis_name = 'bottom'
self._set_logscale_lookuptable()
self.running_hist_initialised = False
self.actionReset_cache.triggered.connect(self.on_reset_cache)