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 addPinnedFrame(self):
"""Make a copy of the current camera frame and pin it to the view background"""
data = self.frameDisplay.visibleImage()
if data is None:
return
hist = self.frameDisplay.contrastCtrl.ui.histogram
im = pg.ImageItem(data,
levels=hist.getLevels(),
lut=hist.getLookupTable(img=data),
removable=True)
im.sigRemoveRequested.connect(self.removePinnedFrame)
if len(self.pinnedFrames) == 0:
z = -10000
else:
z = self.pinnedFrames[-1].zValue() + 1
im.setZValue(z)
self.pinnedFrames.append(im)
view = self.frameDisplay.imageItem().getViewBox()
if view is not None:
view.addItem(im)
im.setTransform(
self.frameDisplay.currentFrame.globalTransform().as2D())
def __init__(self, parent=None):
Qt.QWidget.__init__(self, parent)
self.layout = Qt.QGridLayout()
self.setLayout(self.layout)
self.view = pg.ImageView()
self.layout.addWidget(self.view, 0, 0)
self.ctrlWidget = Qt.QWidget()
self.layout.addWidget(self.ctrlWidget, 0, 1)
self.maskItem = pg.ImageItem()
self.maskItem.setZValue(10)
self.maskItem.setCompositionMode(Qt.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 errorSurface(axes=[3, 0],
v1=None,
v2=None,
bounds=None,
noise=0.0,
n=5000):
## compute sum of squares error between two templates over a range of differences in v
## the two templates are generated from the parameters in v1 and v2
## the error surface is computed by varying v2[axis[n]] from bounds[axis[n]][0] to bounds[axis[n]][1] on
## each axis of the surface.
## displays and returns the error surface,
## also returns an array of all the v2 parameters used for each point in the surface.
x = np.linspace(0, 0.5, 5000)
v = [1.0, 0.05, 0.05, 0.1] ## defaults used if v1 / v2 are not given
if v1 is None:
v1 = v[:]
if v2 is None:
v2 = v1[:]
if bounds is None:
bounds = [(0.0, 2.0), (0.0, 0.1), (0.01, 0.1), (0.01, 0.5)]
template1 = pspFunc(v1, x) + np.random.normal(size=len(x), scale=noise)
## number of iterations per axis
n = int(n**(1.0 / len(axes)))
axv = []
for ax in axes:
axv.append(np.linspace(bounds[ax][0], bounds[ax][1], n))
err = np.empty((n, ) * len(axes))
vals = np.empty(err.shape, dtype=object)
inds = np.indices(err.shape).reshape((len(axes), err.size))
for i in xrange(inds.shape[1]):
ind = tuple(inds[:, i])
v2a = v2[:]
for j in range(len(axes)):
v2a[axes[j]] = axv[j][ind[j]]
template2 = pspFunc(v2a, x)
err[ind] = np.sum((template2 - template1)**2)
vals[ind] = v2a
if len(axes) == 2:
p = pg.plot()
img = pg.ImageItem(err)
p.addItem(img)
b1 = bounds[axes[0]]
b2 = bounds[axes[1]]
img.setRect(QtCore.QRectF(b1[0], b2[0], b1[1] - b1[0], b2[1] - b2[0]))
elif len(axes) == 3:
pg.image(err)
return err, vals
def __init__(self, *args):
AnalysisModule.__init__(self, *args)
self.layout = Qt.QGridLayout()
self.setLayout(self.layout)
self.splitter = Qt.QSplitter()
self.layout.addWidget(self.splitter)
self.ptree = ParameterTree()
self.splitter.addWidget(self.ptree)
self.imageView = pg.ImageView()
self.splitter.addWidget(self.imageView)
self.params = Parameter(name='imager', children=[
dict(name='scanner', type='interface', interfaceTypes=['scanner']),
dict(name='detectors', type='group', addText="Add detector.."),
dict(name='decomb', type='float', readonly=False, value=20e-6, suffix='s', siPrefix=True, bounds=[0, 1e-3], step=1e-6, decimals=5, children=[
dict(name='auto', type='action'),
dict(name='subpixel', type='bool', value=False),
]),
dict(name='downsample', type='int', value=1, suffix='x', bounds=[1,None]),
dict(name='display', type='bool', value=True),
dict(name='scanProgram', type='list', values=[]),
dict(name='Objective', type='str', value='Unknown', readonly=True),
dict(name='Filter', type='str', value='Unknown', readonly=True),
])
self.ptree.setParameters(self.params, showTop=False)
self.params.sigTreeStateChanged.connect(self.update)
self.params.child('detectors').sigAddNew.connect(self.addDetectorClicked)
self.params.child('decomb', 'auto').sigActivated.connect(self.autoDecomb)
self.man = getManager()
self.scannerDev = self.man.getDevice(self.params['scanner'])
# find first scope device that is parent of scanner
dev = self.scannerDev
while dev is not None and not isinstance(dev, Microscope):
dev = dev.parentDevice()
self.scopeDev = dev
self.lastFrame = None
# self.SUF = SUFA.ScannerUtilities()
# self.ui.alphaSlider.valueChanged.connect(self.imageAlphaAdjust)
self.img = pg.ImageItem() ## image shown in camera module
self.img.setLookupTable(self.imageView.ui.histogram.getLookupTable) # image fetches LUT from the ImageView
self.imageView.ui.histogram.sigLevelsChanged.connect(self._updateCamModImage)
self.imageView.imageItem.setAutoDownsample(True)
def __init__(self):
Qt.QObject.__init__(self)
self._imageItem = pg.ImageItem()
self.contrastCtrl = self.contrastClass()
self.contrastCtrl.setImageItem(self._imageItem)
self.bgCtrl = self.bgSubtractClass()
self.bgCtrl.needFrameUpdate.connect(self.updateFrame)
self.nextFrame = None
self._updateFrame = False
self.currentFrame = None
self.lastDrawTime = None
self.displayFps = None
self.hasQuit = False
## Check for new frame updates every 16ms
## Some checks may be skipped even if there is a new frame waiting to avoid drawing more than
## 60fps.
self.frameTimer = Qt.QTimer()
self.frameTimer.timeout.connect(self.drawFrame)
self.frameTimer.start(30) ## draw frames no faster than 60Hz
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)
def show(dh=None):
"""
Display a graphic of the currently selected slice / cell
"""
global v, g, atlas
if dh is None:
dh = man.currentFile
v.clear()
if 'cell' in dh.shortName().lower():
cd = dh
sd = cd.parent()
else:
sd = dh
cd = None
atlas.loadState(sd)
g = atlas.schematicGraphicsItems()
v.addItem(g)
if cd is not None:
## small image to go over slice schematic
imgf = cd['morphology.png']
imgd = pg.colorToAlpha(imgf.read(), np.array([255,255,255]))
mimg1 = pg.ImageItem(imgd)
tr = pg.SRTTransform(imgf.info()['userTransform'])
mimg1.setTransform(tr)
mimg1.setParentItem(g.sliceGroup)
g.cellImg1 = mimg1
## larger image to be displayed above
cellGroup = pg.ItemGroup()
g.cellGroup = cellGroup
mimg2 = pg.ImageItem(imgd)
mimg2.setParentItem(cellGroup)
mimg2.setTransform(tr * g.sliceGroup.transform())
mimg2.scale(1.0 / g.sliceScaleFactor, 1.0 / g.sliceScaleFactor)
#angle = pg.SRTTransform(g.sliceGroup.transform()).getRotation()
#mimg2.rotate(angle)
cellScale = 50.
cellGroup.scale(cellScale, cellScale)
g.cellImg2 = mimg2
## reposition image above slice schematic
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
b2 = g.sliceClip.mapRectToParent(g.sliceClip.boundingRect())
bounds = b1 | b2
cellGroup.setParentItem(g)
imgBounds = g.mapRectFromItem(mimg2, mimg2.boundingRect())
pos = pg.Point(bounds.center().x() - imgBounds.center().x(), bounds.top()-imgBounds.bottom())
cellGroup.setPos(pos)
## add scale bar
sbLength = 25e-6
g.cellScale = Qt.QGraphicsLineItem(0.0, 0.0, sbLength, 0.0)
g.cellScale.setPen(pg.mkPen(color=0.0, width=100e-6/cellScale, cosmetic=False))
g.cellScale.setParentItem(cellGroup)
g.cellScale.setZValue(10)
g.cellScale.text = pg.TextItem(u"25 µm", anchor=(0.5, 1), color=(0,0,0))
g.cellScale.text.setParentItem(g.cellScale)
g.cellScale.text.setPos(sbLength*0.5, -50e-6/cellScale)
corner = mimg2.mapToParent(mimg2.boundingRect()).boundingRect().bottomRight()
g.cellScale.setPos(corner + pg.Point(-sbLength/2., -sbLength/3.))
cell = dh
sl = cell.parent()
day = sl.parent()
name = day.shortName() + "_" + sl.shortName() + "_" + cell.shortName()
g.cellName = pg.TextItem(name, color=(0,0,0))
g.cellName.setParentItem(cellGroup)
g.cellName.setPos(corner + pg.Point(-sbLength*4,-sbLength/4.))
def showMap(dh=None):
"""
Display a graphic of an input map for the currently selected cell
"""
global v, g, atlas
if dh is None:
dh = man.currentFile
db = man.getModule('Data Manager').currentDatabase()
v.clear()
cd = dh
sd = cd.parent()
atlas.loadState(sd)
g = atlas.schematicGraphicsItems(contours=False, sliceScale=10, cellDir=cd)
v.addItem(g)
cellGroup = pg.ItemGroup()
g.cellGroup = cellGroup
cellScale = 10.
cellGroup.scale(cellScale, cellScale)
cellGroup.setParentItem(g)
g.atlasScale.hide()
g.arrowGroup.hide()
## reposition/rescale atlas group
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
b2 = g.sliceClip.mapRectToParent(g.sliceClip.boundingRect())
g.atlasGroup.setPos(b2.right()-b1.left()+0.001, b2.top()-b1.top())
b1 = g.atlasGroup.mapRectToParent(g.atlasGroup.childrenBoundingRect())
bounds = b1 | b2
if cd.exists('morphology.png'):
## small image to go over slice schematic
imgf = cd['morphology.png']
imgd = pg.colorToAlpha(imgf.read(), np.array([255,255,255]))
mimg1 = pg.ImageItem(imgd)
tr = pg.SRTTransform(imgf.info()['userTransform'])
mimg1.setTransform(tr)
mimg1.setParentItem(g.sliceGroup)
mimg1.setZValue(100)
g.cellImg1 = mimg1
## larger image to be displayed above
mimg2 = pg.ImageItem(imgd)
mimg2.setParentItem(cellGroup)
mimg2.setTransform(tr * g.sliceGroup.transform())
mimg2.scale(1.0 / g.sliceScaleFactor, 1.0 / g.sliceScaleFactor)
#angle = pg.SRTTransform(g.sliceGroup.transform()).getRotation()
#mimg2.rotate(angle)
g.cellImg2 = mimg2
cellGroup.scale(5,5)
## reposition next to slice schematic
imgBounds = g.mapRectFromItem(mimg2, mimg2.boundingRect())
pos = pg.Point(bounds.right()-imgBounds.left(), bounds.bottom()-imgBounds.bottom())
cellGroup.setPos(pos)
## add scale bar
sbLength = 50e-6
g.cellScale = Qt.QGraphicsLineItem(0.0, 0.0, sbLength, 0.0)
g.cellScale.setPen(pg.mkPen(color=0.0, width=5))
g.cellScale.setZValue(10)
g.cellScale.text = pg.TextItem(u"%d µm" % int(sbLength*1e6), anchor=(0.5, 1), color=(0,0,0))
g.cellScale.text.setParentItem(g.cellScale)
g.cellScale.text.setPos(sbLength*0.5, -50e-6/cellScale)
#g.cellScale = pg.ScaleBar(sbLength)
g.cellScale.setParentItem(cellGroup)
corner = mimg2.mapToParent(mimg2.boundingRect()).boundingRect().bottomRight()
g.cellScale.setPos(corner + pg.Point(-sbLength/2., -sbLength/3.))
pos = pg.SRTTransform(cd.info()['userTransform']).map(pg.Point(0,0))
size = pg.Point(30e-6, 30e-6)
g.cellMarker = Qt.QGraphicsEllipseItem(Qt.QRectF(pos-size, pos+size))
g.cellMarker.setBrush(pg.mkBrush(100,100,255,150))
g.cellMarker.setPen(pg.mkPen('k', width=0.5))
g.cellMarker.setParentItem(g.sliceGroup)
g.cellMarker.setZValue(90)
sites = db.select('map_site_view', ['ProtocolDir', 'HasInput'], where={'CellDir': cd})
if len(sites) > 0:
tr = sites[0]['ProtocolDir'].parent().info().get('userTransform', None)
if tr is None:
tr = pg.SRTTransform()
else:
tr = pg.SRTTransform(tr)
pos = []
size = sites[0]['ProtocolDir'].info()['Scanner']['spotSize']
brushes = []
for site in sites:
pd = site['ProtocolDir']
x,y = pd.info()['Scanner']['position']
p2 = tr.map(pg.Point(x,y))
pos.append((p2.x(), p2.y()))
if site['HasInput']:
brushes.append(pg.mkBrush('w'))
else:
brushes.append(pg.mkBrush(None))
inputMap = pg.ScatterPlotItem(pos=np.array(pos), size=size, brush=brushes, pen=(0,0,0,50), pxMode=False, antialias=True)
g.sliceGroup.addItem(inputMap)
g.inputMap = inputMap
inputMap.setZValue(50)
cell = dh
sl = cell.parent()
day = sl.parent()
name = day.shortName() + "_" + sl.shortName() + "_" + cell.shortName()
rec = db.select('DirTable_Cell', '*', where={'Dir': cd})[0]
name += "\nType: " + str(rec['CellType']) + " Temp: " + str(rec['Temperature']) + " Internal: " + str(rec['Internal']) + " Age:" + str(rec['Age']) + " Raccess: " + str(rec['AccessResistance'])
name += "\nDirect Area: %s>0pA %s>20pA %s>100pA" % (str(rec['DirectAreaGt0']), str(rec['DirectAreaGt20']), str(rec['DirectAreaGt100']))
name += " Direct n spikes: " + str(rec['DirectNSpikes'])
name += "\nSpont Ex Decay: %s Spont In Decay: %s" % (str(rec['SpontExDecay1']), str(rec['SpontInDecay']))
name += "\nExcitatory input" if (rec['EvokedExDecay'] is not None or rec['EvokedExAmp'] is not None) else ""
print(rec)
#name += '\nDirect Slow Decay: %s %s' % (str(rec['DirectAreaGT0']), str(rec['DirectAreaGT0']))
g.cellName = pg.TextItem(name, color=(0,0,0))
g.cellName.setParentItem(g)
g.cellName.setPos(0, bounds.bottom())
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()
'labels': {}
}])
label.write(labelFile, mappable=True)
label = metaarray.MetaArray(file=labelFile, mmap=True, writable=True)
labelCache = None
labelInfo = {}
#ui.view.enableMouse()
#ui.view.setAspectLocked(True)
vb = pg.ViewBox()
ui.view.setCentralItem(vb)
vb.setAspectLocked(True)
vb.invertY(False)
dataImg = pg.ImageItem()
labelImg = pg.ImageItem() # mode=Qt.QPainter.CompositionMode_Plus)
#labelImg.setCompositionMode(Qt.QPainter.CompositionMode_Overlay)
labelImg.setZValue(10)
labelImg.setOpacity(1)
vb.addItem(dataImg)
vb.addItem(labelImg)
def connectSignals():
for r in [ui.rightRadio, ui.dorsalRadio, ui.rostralRadio]:
r.toggled.connect(imageChanged)
ui.zSlider.valueChanged.connect(updateImage)
ui.radiusSpin.valueChanged.connect(updateKernel)
ui.greyCheck.toggled.connect(updateImage)
ui.labelSlider.valueChanged.connect(imageChanged)
pw1.setLabel('bottom', 'Decay Tau', 's')
spl2 = Qt.QSplitter()
spl2.setOrientation(Qt.Qt.Horizontal)
spl1.addWidget(spl2)
pw2 = pg.PlotWidget(labels={'bottom': ('time', 's')})
spl2.addWidget(pw2)
tab = Qt.QTabWidget()
spl2.addWidget(tab)
## For viewing cell morphology
gv = pg.GraphicsView()
gv.setBackgroundBrush(pg.mkBrush('w'))
image = pg.ImageItem()
gv.addItem(image)
gv.enableMouse()
gv.setAspectLocked(True)
tab.addTab(gv, 'Morphology')
## 3D atlas
import acq4.analysis.atlas.CochlearNucleus as CN
atlas = CN.CNAtlasDisplayWidget()
atlas.showLabel('DCN')
atlas.showLabel('AVCN')
atlas.showLabel('PVCN')
tab.addTab(atlas, 'Atlas')
atlasPoints = gl.GLScatterPlotItem()
atlas.addItem(atlasPoints)
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)
