def __init__(self, mosaic_editor):
self.mosaic_editor = mosaic_editor
QtGui.QWidget.__init__(self)
self.layout = QtGui.QGridLayout()
self.setLayout(self.layout)
self.load_btn = QtGui.QPushButton("Download 20x")
self.layout.addWidget(self.load_btn, 0, 0)
self.load_btn.clicked.connect(self.load_clicked)
self.submit_btn = pg.FeedbackButton("Submit cell positions to LIMS")
self.layout.addWidget(self.submit_btn, 1, 0)
self.submit_btn.clicked.connect(self.submit)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = multipatch_nwb_viewer.MultipatchNwbViewer()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.vsplit.insertWidget(0, self.load_from_dm_btn)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = submit_expt.ExperimentSubmitUi()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.left_layout.insertWidget(0, self.load_from_dm_btn)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = vimaging.VImagingAnalyzer()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.ui.layout.addWidget(self.load_from_dm_btn,
self.ui.layout.rowCount(), 0)
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self, manager, name, config):
Module.__init__(self, manager, name, config)
self.ui = vimaging.VImagingAnalyzer2()
self.ui.resize(1600, 900)
self.ui.show()
self.load_from_dm_btn = QtGui.QPushButton("load from data manager")
self.load_from_dm_btn.setParent(self.ui)
self.load_from_dm_btn.resize(160, 30)
self.load_from_dm_btn.show()
self.load_from_dm_btn.clicked.connect(self.load_from_dm_clicked)
def __init__(self):
QtGui.QWidget.__init__(self)
self.resize(800, 1000)
self.layout = QtGui.QGridLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
self.gw = pg.GraphicsLayoutWidget()
self.layout.addWidget(self.gw)
self.vb1 = self.gw.addViewBox()
self.img1 = pg.ImageItem()
self.vb1.addItem(self.img1)
self.vb2 = self.gw.addViewBox(row=1, col=0)
self.img2 = pg.ImageItem()
self.vb2.addItem(self.img2)
for vb in (self.vb1, self.vb2):
vb.invertY()
vb.setAspectLocked(True)
self.plt1 = self.gw.addPlot(row=2, col=0)
self.plt1.setLabels(bottom=('time', 's'))
self.plt1_items = []
self.rois = [
pg.RectROI([0, 0], [10, 10], pen=(i, 4)) for i in range(2)
]
for roi in self.rois:
self.vb1.addItem(roi)
roi.sigRegionChangeFinished.connect(self.roi_changed)
self.ignore_roi_change = False
self.plt2 = self.gw.addPlot(row=3, col=0)
self.plt2.setXLink(self.plt1)
self.plt2.setLabels(bottom=('time', 's'))
self.base_time_rgn = pg.LinearRegionItem([0.0, 0.1])
self.test_time_rgn = pg.LinearRegionItem([0.1, 0.11])
for time_rgn in (self.base_time_rgn, self.test_time_rgn):
self.plt1.addItem(time_rgn)
time_rgn.sigRegionChangeFinished.connect(self.time_rgn_changed)
time_rgn.sigRegionChangeFinished.connect(
self.update_sequence_analysis)
self.clamp_plots = []
self.plt3 = self.gw.addPlot(row=4, col=0)
self.plt3.setLabels(left="dF / F", bottom="trial")
self.show()
def __init__(self):
QtGui.QWidget.__init__(self)
self.layout = QtGui.QGridLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.setLayout(self.layout)
# Set up filter buttons
self.btns = OrderedDict()
row, col = 0, 0
for name in ['Mean', 'Max', 'Max w/Gaussian', 'Max w/Median', 'Edge']:
btn = QtGui.QPushButton(name)
self.btns[name] = btn
btn.setCheckable(True)
self.layout.addWidget(btn, row, col)
btn.clicked.connect(self.filterBtnClicked)
col += 1
if col > 1:
col = 0
row += 1
# show flowchart control panel inside a collapsible group box
self.fcGroup = pg.GroupBox('Filter Settings')
fgl = QtGui.QVBoxLayout()
self.fcGroup.setLayout(fgl)
fgl.setContentsMargins(0, 0, 0, 0)
self.layout.addWidget(self.fcGroup, row + 1, 0, 1, 2)
self.fc = pg.flowchart.Flowchart(terminals={
'dataIn': {
'io': 'in'
},
'dataOut': {
'io': 'out'
}
})
fgl.addWidget(self.fc.widget())
self.fcGroup.setCollapsed(True)
self.fc.sigStateChanged.connect(self.sigStateChanged)
def __init__(self, parent=None):
QtGui.QWidget.__init__(self, parent)
self.layout = QtGui.QGridLayout()
self.setLayout(self.layout)
self.view = pg.ImageView()
self.layout.addWidget(self.view, 0, 0)
self.ctrlWidget = QtGui.QWidget()
self.layout.addWidget(self.ctrlWidget, 0, 1)
self.maskItem = pg.ImageItem()
self.maskItem.setZValue(10)
self.maskItem.setCompositionMode(QtGui.QPainter.CompositionMode_Multiply)
lut = np.zeros((256, 3), dtype='ubyte')
lut[:,0:2] = np.arange(256).reshape(256,1)
self.maskItem.setLookupTable(lut)
kern = np.fromfunction(lambda x,y: np.clip(((5 - (x-5)**2+(y-5)**2)**0.5 * 255), 0, 255), (11, 11))
self.maskItem.setDrawKernel(kern, mask=kern, center=(5,5), mode='add')
self.view.addItem(self.maskItem)
self.view.sigTimeChanged.connect(self.updateMaskImage)
def __init__(self):
QtGui.QWidget.__init__(self)
self.layout = QtGui.QVBoxLayout()
self.setLayout(self.layout)
self.imv1 = pg.ImageView()
self.layout.addWidget(self.imv1)
self.plt1 = pg.PlotWidget()
self.layout.addWidget(self.plt1)
self.base_time_rgn = pg.LinearRegionItem([0.07, 0.099])
self.test_time_rgn = pg.LinearRegionItem([0.104, 0.112])
for time_rgn in (self.base_time_rgn, self.test_time_rgn):
self.plt1.addItem(time_rgn)
time_rgn.sigRegionChangeFinished.connect(self.time_rgn_changed)
self.plot_data = []
def __init__(self, image=None, **opts):
## If no image was specified, check for a file handle..
if image is None:
image = opts.get('handle', None)
item = None
self.data = None
if isinstance(image, QtGui.QGraphicsItem):
item = image
elif isinstance(image, np.ndarray):
self.data = image
elif isinstance(image, DataManager.FileHandle):
opts['handle'] = image
self.handle = image
self.data = self.handle.read()
if 'name' not in opts:
opts['name'] = self.handle.shortName()
try:
if 'transform' in self.handle.info():
tr = pg.SRTTransform3D(self.handle.info()['transform'])
tr = pg.SRTTransform(tr) ## convert to 2D
opts['pos'] = tr.getTranslation()
opts['scale'] = tr.getScale()
opts['angle'] = tr.getRotation()
else: ## check for older info formats
if 'imagePosition' in self.handle.info():
opts['scale'] = self.handle.info()['pixelSize']
opts['pos'] = self.handle.info()['imagePosition']
elif 'Downsample' in self.handle.info():
### Needed to support an older format stored by 2p imager
if 'pixelSize' in self.handle.info():
opts['scale'] = self.handle.info()['pixelSize']
if 'microscope' in self.handle.info():
m = self.handle.info()['microscope']
opts['pos'] = m['position'][0:2]
else:
info = self.data._info[-1]
opts['pos'] = info.get('imagePosition', None)
elif hasattr(self.data, '_info'):
info = self.data._info[-1]
opts['scale'] = info.get('pixelSize', None)
opts['pos'] = info.get('imagePosition', None)
else:
opts['defaultUserTransform'] = {'scale': (1e-5, 1e-5)}
opts['scalable'] = True
except:
debug.printExc(
'Error reading transformation for image file %s:' %
image.name())
if item is None:
item = pg.ImageItem()
CanvasItem.__init__(self, item, **opts)
self.splitter = QtGui.QSplitter()
self.splitter.setOrientation(QtCore.Qt.Vertical)
self.layout.addWidget(self.splitter, self.layout.rowCount(), 0, 1, 2)
self.filterGroup = pg.GroupBox("Image Filter")
fgl = QtGui.QGridLayout()
fgl.setContentsMargins(3, 3, 3, 3)
fgl.setSpacing(1)
self.filterGroup.setLayout(fgl)
self.filter = ImageFilterWidget()
self.filter.sigStateChanged.connect(self.filterStateChanged)
fgl.addWidget(self.filter)
self.splitter.addWidget(self.filterGroup)
self.histogram = pg.HistogramLUTWidget()
self.histogram.setImageItem(self.graphicsItem())
# addWidget arguments: row, column, rowspan, colspan
self.splitter.addWidget(self.histogram)
self.imgModeCombo = QtGui.QComboBox()
self.imgModeCombo.addItems(
['SourceOver', 'Overlay', 'Plus', 'Multiply'])
self.layout.addWidget(self.imgModeCombo, self.layout.rowCount(), 0, 1,
1)
self.imgModeCombo.currentIndexChanged.connect(self.imgModeChanged)
self.autoBtn = QtGui.QPushButton("Auto")
self.autoBtn.setCheckable(True)
self.autoBtn.setChecked(True)
self.layout.addWidget(self.autoBtn,
self.layout.rowCount() - 1, 1, 1, 1)
self.timeSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
self.layout.addWidget(self.timeSlider, self.layout.rowCount(), 0, 1, 2)
self.timeSlider.valueChanged.connect(self.timeChanged)
# ## controls that only appear if there is a time axis
self.timeControls = [self.timeSlider]
if self.data is not None:
if isinstance(self.data, pg.metaarray.MetaArray):
self.filter.setInput(self.data.asarray())
else:
self.filter.setInput(self.data)
self.updateImage()
# Needed to ensure selection box wraps the image properly
tr = self.saveTransform()
self.resetUserTransform()
self.restoreTransform(tr)
# make a few variables available from the console
console.localNamespace.update({'man': m, 'view': v, 'nwb': None, 'sweeps': [], 'analyzer': None})
# make selected sweeps / analyzer available as well
def update_namespace():
console.localNamespace.update({'sweeps': v.selected_sweeps(), 'analyzer': v.selected_analyzer()})
v.analyzer_changed.connect(update_namespace)
v.explorer.selection_changed.connect(update_namespace)
# Set up code reloading shortcut
def reload_all():
acq4.pyqtgraph.reload.reloadAll(verbose=True)
reload_shortcut = QtGui.QShortcut(QtGui.QKeySequence('Ctrl+r'), v)
reload_shortcut.setContext(QtCore.Qt.ApplicationShortcut)
reload_shortcut.activated.connect(reload_all)
# load file or set base directory from argv
for arg in sys.argv[1:]:
if not os.path.exists(arg):
from aisynphys.experiment_list import cached_experiments
expts = cached_experiments()
try:
expt = expts[arg]
except Exception:
print("Could not find experiment %s" % arg)
sys.exit(-1)
arg = expt.nwb_file
def __init__(self):
QtGui.QSplitter.__init__(self, QtCore.Qt.Horizontal)
self.resize(800, 1000)
self.params = pg.parametertree.Parameter(
name='params',
type='group',
children=[
dict(name='sequence',
type='group',
children=[
dict(name='analysis',
type='list',
values=['dF / F', 'SNR', 'noise']),
]),
])
self.ptree = pg.parametertree.ParameterTree()
self.ptree.setParameters(self.params)
self.params.child('sequence').sigTreeStateChanged.connect(
self.update_sequence_analysis)
self.leftPanel = QtGui.QWidget()
self.addWidget(self.leftPanel)
self.layout = QtGui.QGridLayout()
self.layout.setContentsMargins(0, 0, 0, 0)
self.leftPanel.setLayout(self.layout)
self.layout.addWidget(self.ptree, 0, 0)
self.gw = pg.GraphicsLayoutWidget()
self.addWidget(self.gw)
self.vb1 = self.gw.addViewBox()
self.img1 = pg.ImageItem()
self.vb1.addItem(self.img1)
self.vb2 = self.gw.addViewBox(row=1, col=0)
self.img2 = pg.ImageItem()
self.vb2.addItem(self.img2)
for vb in (self.vb1, self.vb2):
vb.invertY()
vb.setAspectLocked(True)
self.plt1 = self.gw.addPlot(row=2, col=0)
self.plt1.setLabels(bottom=('time', 's'))
self.plt1_items = []
self.rois = [
pg.EllipseROI([0, 0], [10, 10], pen=(i, 4)) for i in range(2)
]
for roi in self.rois:
self.vb1.addItem(roi)
roi.sigRegionChangeFinished.connect(self.roi_changed)
self.ignore_roi_change = False
self.plt2 = self.gw.addPlot(row=3, col=0)
self.plt2.setXLink(self.plt1)
self.plt2.setLabels(bottom=('time', 's'))
self.noise_time_rgn = pg.LinearRegionItem([0.01, 0.02],
brush=(255, 0, 0, 30))
self.base_time_rgn = pg.LinearRegionItem([0.025, 0.95],
brush=(0, 255, 0, 30))
self.test_time_rgn = pg.LinearRegionItem([0.1, 0.11],
brush=(0, 0, 255, 30))
for time_rgn in (self.base_time_rgn, self.test_time_rgn,
self.noise_time_rgn):
self.plt1.addItem(time_rgn)
time_rgn.sigRegionChangeFinished.connect(self.time_rgn_changed)
time_rgn.sigRegionChangeFinished.connect(
self.update_sequence_analysis)
self.clamp_plots = []
self.plt3 = self.gw.addPlot(row=4, col=0)
self.plt3.setLabels(left="dF / F", bottom="trial")
self.show()
def __init__(self, image=None, **opts):
"""
CanvasItem displaying an image.
The image may be 2 or 3-dimensional.
Options:
image: May be a fileHandle, ndarray, or GraphicsItem.
handle: May optionally be specified in place of image
"""
## If no image was specified, check for a file handle..
if image is None:
image = opts.get('handle', None)
item = None
self.data = None
self.currentT = None
if isinstance(image, QtGui.QGraphicsItem):
item = image
elif isinstance(image, np.ndarray):
self.data = image
elif isinstance(image, DataManager.FileHandle):
opts['handle'] = image
self.handle = image
self.data = self.handle.read()
if 'name' not in opts:
opts['name'] = self.handle.shortName()
try:
if 'transform' in self.handle.info():
tr = pg.SRTTransform3D(self.handle.info()['transform'])
tr = pg.SRTTransform(tr) ## convert to 2D
opts['pos'] = tr.getTranslation()
opts['scale'] = tr.getScale()
opts['angle'] = tr.getRotation()
else: ## check for older info formats
if 'imagePosition' in self.handle.info():
opts['scale'] = self.handle.info()['pixelSize']
opts['pos'] = self.handle.info()['imagePosition']
elif 'Downsample' in self.handle.info():
### Needed to support an older format stored by 2p imager
if 'pixelSize' in self.handle.info():
opts['scale'] = self.handle.info()['pixelSize']
if 'microscope' in self.handle.info():
m = self.handle.info()['microscope']
print 'm: ', m
print 'mpos: ', m['position']
opts['pos'] = m['position'][0:2]
else:
info = self.data._info[-1]
opts['pos'] = info.get('imagePosition', None)
elif hasattr(self.data, '_info'):
info = self.data._info[-1]
opts['scale'] = info.get('pixelSize', None)
opts['pos'] = info.get('imagePosition', None)
else:
opts['defaultUserTransform'] = {'scale': (1e-5, 1e-5)}
opts['scalable'] = True
except:
debug.printExc(
'Error reading transformation for image file %s:' %
image.name())
if item is None:
item = pg.ImageItem()
CanvasItem.__init__(self, item, **opts)
self.histogram = pg.PlotWidget()
self.blockHistogram = False
self.histogram.setMaximumHeight(100)
self.levelRgn = pg.LinearRegionItem()
self.histogram.addItem(self.levelRgn)
self.updateHistogram(autoLevels=True)
# addWidget arguments: row, column, rowspan, colspan
self.layout.addWidget(self.histogram, self.layout.rowCount(), 0, 1, 3)
self.timeSlider = QtGui.QSlider(QtCore.Qt.Horizontal)
#self.timeSlider.setMinimum(0)
#self.timeSlider.setMaximum(self.data.shape[0]-1)
self.layout.addWidget(self.timeSlider, self.layout.rowCount(), 0, 1, 3)
self.timeSlider.valueChanged.connect(self.timeChanged)
self.timeSlider.sliderPressed.connect(self.timeSliderPressed)
self.timeSlider.sliderReleased.connect(self.timeSliderReleased)
thisRow = self.layout.rowCount()
self.edgeBtn = QtGui.QPushButton('Edge')
self.edgeBtn.clicked.connect(self.edgeClicked)
self.layout.addWidget(self.edgeBtn, thisRow, 0, 1, 1)
self.meanBtn = QtGui.QPushButton('Mean')
self.meanBtn.clicked.connect(self.meanClicked)
self.layout.addWidget(self.meanBtn, thisRow + 1, 0, 1, 1)
self.tvBtn = QtGui.QPushButton('tv denoise')
self.tvBtn.clicked.connect(self.tvClicked)
self.layout.addWidget(self.tvBtn, thisRow + 2, 0, 1, 1)
self.maxBtn = QtGui.QPushButton('Max no Filter')
self.maxBtn.clicked.connect(self.maxClicked)
self.layout.addWidget(self.maxBtn, thisRow, 1, 1, 1)
self.maxBtn2 = QtGui.QPushButton('Max w/Gaussian')
self.maxBtn2.clicked.connect(self.max2Clicked)
self.layout.addWidget(self.maxBtn2, thisRow + 1, 1, 1, 1)
self.maxMedianBtn = QtGui.QPushButton('Max w/Median')
self.maxMedianBtn.clicked.connect(self.maxMedianClicked)
self.layout.addWidget(self.maxMedianBtn, thisRow + 2, 1, 1, 1)
self.filterOrder = QtGui.QComboBox()
self.filterLabel = QtGui.QLabel('Order')
for n in range(1, 11):
self.filterOrder.addItem("%d" % n)
self.layout.addWidget(self.filterLabel, thisRow + 3, 2, 1, 1)
self.layout.addWidget(self.filterOrder, thisRow + 3, 3, 1, 1)
self.zPlanes = QtGui.QComboBox()
self.zPlanesLabel = QtGui.QLabel('# planes')
for s in ['All', '1', '2', '3', '4', '5']:
self.zPlanes.addItem("%s" % s)
self.layout.addWidget(self.zPlanesLabel, thisRow + 3, 0, 1, 1)
self.layout.addWidget(self.zPlanes, thisRow + 3, 1, 1, 1)
## controls that only appear if there is a time axis
self.timeControls = [
self.timeSlider, self.edgeBtn, self.maxBtn, self.meanBtn,
self.maxBtn2, self.maxMedianBtn, self.filterOrder, self.zPlanes
]
if self.data is not None:
self.updateImage(self.data)
self.graphicsItem().sigImageChanged.connect(self.updateHistogram)
self.levelRgn.sigRegionChanged.connect(self.levelsChanged)
self.levelRgn.sigRegionChangeFinished.connect(
self.levelsChangeFinished)