def addActiveRegion(self, rgnType):
rgn = pTypes.SimpleParameter(name=rgnType, autoIncrementName=True,
type='bool', value=True,
removable=True, renamable=True)
self.params.param('Active Regions').addChild(rgn)
pos = self.getViewBox().viewRect().center()
size = self.params.param('spacing').value()*4
if rgnType == 'Rectangle':
roi = pg.ROI(pos=pos, size=size, angle=self.angle())
roi.addScaleHandle([0, 0], [1, 1])
roi.addScaleHandle([1, 1], [0, 0])
roi.addRotateHandle([0, 1], [0.5, 0.5])
roi.addRotateHandle([1, 0], [0.5, 0.5])
elif rgnType == 'Polygon':
roi = pg.PolyLineROI((pos, pos+pg.Point(0,1)*size, pos+pg.Point(1,0)*size), closed=True)
else:
raise Exception('Not sure how to add region of type:%s' % rgnType)
rgn.item = roi
self.rgns.append(rgn)
self.getViewBox().addItem(roi)
roi.sigRegionChanged.connect(self.invalidatePoints)
roi.sigRegionChangeFinished.connect(self.stateChangeFinished)
rgn.sigValueChanged.connect(self.rgnToggled)
self.invalidatePoints()
self.stateChangeFinished()
def addNew(self):
rgn = ptree.Parameter.create(name='region',
autoIncrementName=True,
renamable=True,
removable=True,
type='bool',
value=True,
children=[
dict(name='DB Column',
type='str',
value='Region'),
dict(name='Color', type='color'),
])
self.addChild(rgn)
## find the center of the view
view = self.canvas.view
center = view.viewRect().center()
size = [x * 50 for x in view.viewPixelSize()]
pts = [
center, center + pg.Point(size[0], 0),
center + pg.Point(0, size[1])
]
roi = pg.PolyLineROI(pts, closed=True)
roi.setZValue(1000)
view.addItem(roi)
rgn.roi = roi
roi.rgn = rgn
roi.sigRegionChangeFinished.connect(self.regionChanged)
def saveState(self):
## Saves the position/configuration of the cortexROI, as well as transforms for mapping to atlas coordinates
if self.sliceDir is None:
return
## get state of ROI
cortexROI = self.roi.saveState()
quads = self.roi.getQuadrilaterals()
newQuads = []
for q in quads:
newQuads.append([(p.x(), p.y()) for p in q])
rects = self.roi.getNormalizedRects()
matrices = []
for i, q in enumerate(quads):
matrix = self.atlas.solveBilinearTransform([pg.Point(x) for x in q], [pg.Point(x) for x in rects[i]])
matrices.append([list(matrix[0]), list(matrix[1])])
state = {
'cortexROI':cortexROI,
'quadrilaterals':newQuads,
'normalizedRects': rects,
'transformMatrices': matrices
}
## write to slice directory meta-info
atlasInfo = self.sliceDir.info().get('atlas', {}).deepcopy()
atlasInfo[self.atlas.name()] = state
self.sliceDir.setInfo(atlas=atlasInfo)
## set state for atlas object
self.atlas.setState(state)
def getBackground(self):
if self.background is None:
w, h = self.params['sensorSize']
tr = self.globalTransform()
tr = pg.SRTTransform(tr)
m = QtGui.QTransform()
m.scale(3e6, 3e6)
m.translate(0.0005, 0.0005)
tr = tr * m
origin = tr.map(pg.Point(0, 0))
x = (tr.map(pg.Point(1, 0)) - origin)
y = (tr.map(pg.Point(0, 1)) - origin)
origin = np.array([origin.x(), origin.y()])
x = np.array([x.x(), x.y()])
y = np.array([y.x(), y.y()])
## slice fractal from pre-rendered data
vectors = (x, y)
self.background = pg.affineSlice(self.bgData, (w, h),
origin,
vectors, (0, 1),
order=1)
return self.background
def transformChanged(self):
# manipulator's global transform has changed; update the center arrow and orientation axis
dev = self.getDevice()
pos = dev.mapToGlobal([0, 0, 0])
x = dev.mapToGlobal([1, 0, 0])
p1 = pg.Point(x[:2])
p2 = pg.Point(pos[:2])
p3 = pg.Point(1, 0)
angle = (p1 - p2).angle(p3)
if angle is None:
angle = 0
self.centerArrow.setPos(pos[0], pos[1])
self.centerArrow.setStyle(angle=180 - angle)
# self.depthLine.setValue(pos[2])
self.depthArrow.setPos(0, pos[2])
self.target.setLabelAngle(dev.getYawAngle())
if self.ui.setOrientationBtn.isChecked():
return
with pg.SignalBlock(self.calibrateAxis.sigRegionChangeFinished,
self.calibrateAxisChanged):
self.calibrateAxis.setPos(pos[:2])
self.calibrateAxis.setAngle(angle)
ys = self.calibrateAxis.size()[1]
def addROI(self, roiType):
pen = pg.mkPen(pg.intColor(len(self.ROIs)))
center = self.view.viewRect().center()
#print 'camerawindow.py: addROI:: ', self.view.viewPixelSize()
size = [x * 50 for x in self.view.viewPixelSize()]
if roiType == 'rect':
roi = PlotROI(center, size)
elif roiType == 'ellipse':
roi = pg.EllipseROI(center, size, removable=True)
elif roiType == 'polygon':
pts = [
center, center + pg.Point(0, size[1]),
center + pg.Point(size[0], 0)
]
roi = pg.PolyLineROI(pts, closed=True, removable=True)
elif roiType == 'ruler':
pts = [center, center + pg.Point(size[0], size[1])]
roi = RulerROI(pts, removable=True)
else:
raise ValueError("Invalid ROI type %s" % roiType)
roi.setZValue(40000)
roi.setPen(pen)
self.view.addItem(roi)
plot = self.roiPlot.plot(pen=pen)
self.ROIs.append({'roi': roi, 'plot': plot, 'vals': [], 'times': []})
roi.sigRemoveRequested.connect(self.removeROI)
def boundingRect(self):
w = self.pixelLength(pg.Point(1, 0))
if w is None:
return QtCore.QRectF()
w *= 25
h = 25 * self.pixelLength(pg.Point(0, 1))
r = QtCore.QRectF(-w * 2, -h * 2, w * 4, h * 4)
return r
def pixelVectors(self):
tr = self.globalTransform()
origin = tr.map(pg.Point(0, 0))
x = (tr.map(pg.Point(1, 0)) - origin)
y = (tr.map(pg.Point(0, 1)) - origin)
origin = np.array([origin.x(), origin.y()])
x = np.array([x.x(), x.y()])
y = np.array([y.x(), y.y()])
return x, y
def setScanPosFromRoi(self):
# Update the position of the scan rectangle from the ROI
roi = self.currentRoi
w, h = roi.size()
# get top-left ROI corner in global coordinates
p0 = roi.mapToView(pg.Point(0,h))
if p0 is None:
# could not map point; probably view has been closed.
return
rparam = self.scanProgram.components[0].ctrlParameter()
rparam.system.p0 = pg.Point(p0) # top-left
rparam.system.p1 = pg.Point(roi.mapToView(pg.Point(w,h))) # rop-right
def viewTransformChanged(self):
w = self.pixelLength(pg.Point(1, 0))
if w is None:
self._pxLen = [None, None]
return
h = self.pixelLength(pg.Point(0, 1))
if self.size()[1] < 0:
h = -h
self._pxLen = [w, h]
self.blockSignals(True)
try:
self.setSize([w * 50, h * 50])
finally:
self.blockSignals(False)
self.updateText()
self.prepareGeometryChange()
def restoreROI(self):
if self.storedROI is not None:
(width, height, x, y) = self.storedROI
self.currentRoi.setSize([width, height])
self.currentRoi.setPos([x, y])
self.roiChanged()
else:
cpos = self.cameraModule.ui.view.viewRect().center() # center position, stage coordinates
csize = pg.Point([x*400 for x in self.cameraModule.ui.view.viewPixelSize()])
width = csize[0]*2 # width is x in M
height = csize[1]*2
csize = pg.Point(width, height)
cpos = cpos - csize/2.
self.currentRoi.setSize([width, height])
self.currentRoi.setPos(cpos)
def newFrames(self):
"""Return a list of all frames acquired since the last call to newFrames."""
now = ptime.time()
dt = now - self.lastFrameTime
exp = self.getParam('exposure')
bin = self.getParam('binning')
fps = 1.0 / (exp + (40e-3 / (bin[0] * bin[1])))
nf = int(dt * fps)
if nf == 0:
return []
region = self.getParam('region')
bg = self.getBackground()[region[0]:region[0] + region[2],
region[1]:region[1] + region[3]]
## update cells
spikes = np.random.poisson(min(dt, 0.4) * self.cells['rate'])
self.cells['value'] *= np.exp(-dt / self.cells['decayTau'])
self.cells['value'] = np.clip(self.cells['value'] + spikes * 0.2, 0, 1)
shape = region[2:]
self.lastFrameTime = now + exp
data = self.getNoise(shape)
data[data < 0] = 0
data += bg * (exp * 1000)
## draw cells
px = (self.pixelVectors()[0]**2).sum()**0.5
## Generate transform that maps grom global coordinates to image coordinates
cameraTr = pg.SRTTransform3D(self.inverseGlobalTransform())
# note we use binning=(1,1) here because the image is downsampled later.
frameTr = self.makeFrameTransform(region, [1, 1]).inverted()[0]
tr = pg.SRTTransform(frameTr * cameraTr)
for cell in self.cells:
w = cell['size'] / px
pos = pg.Point(cell['x'], cell['y'])
imgPos = tr.map(pos)
start = (int(imgPos.x()), int(imgPos.y()))
stop = (int(start[0] + w), int(start[1] + w))
val = cell['intensity'] * cell['value'] * self.getParam('exposure')
data[max(0, start[0]):max(0, stop[0]),
max(0, start[1]):max(0, stop[1])] += val
data = fn.downsample(data, bin[0], axis=0)
data = fn.downsample(data, bin[1], axis=1)
data = data.astype(np.uint16)
self.frameId += 1
frames = []
for i in range(nf):
frames.append({
'data': data,
'time': now + (i / fps),
'id': self.frameId
})
return frames
def getSnapPosition(self, pos):
## Given that pos has been requested, return the nearest snap-to position
## optionally, snap may be passed in to specify a rectangular snap grid.
## override this function for more interesting snap functionality..
layout = self.params['layout']
spacing = self.params['spacing']
if layout == 'Square':
snap = pg.Point(spacing, spacing)
w = round(pos[0] / snap[0]) * snap[0]
h = round(pos[1] / snap[1]) * snap[1]
return pg.Point(w, h)
elif layout == 'Hexagonal':
snap1 = pg.Point(spacing, spacing*3.0**0.5)
dx = 0.5*snap1[0]
dy = 0.5*snap1[1]
w1 = round(pos[0] / snap1[0]) * snap1[0]
h1 = round(pos[1] / snap1[1]) * snap1[1]
w2 = round((pos[0]-dx) / snap1[0]) * snap1[0] + dx
h2 = round((pos[1]-dy) / snap1[1]) * snap1[1] + dy
if (pg.Point(w1, h1)-pos).length() < (pg.Point(w2,h2) - pos).length():
return pg.Point(w1, h1)
else:
return pg.Point(w2, h2)
def saveState(self):
center = self.roi.mapToView(pg.Point(0, 0))
return {
'startTime': self.params['startTime'],
'duration': self.params['duration'],
'radius': self.params['radius'],
'thickness': self.params['thickness'],
'spacing': self.params['spacing'],
'center': (center.x(), center.y()),
}
def targetChanged(self, dev, pos):
self.target.setPos(pg.Point(pos[:2]))
self.depthTarget.setPos(0, pos[2])
self.target.setVisible(True)
self._haveTarget = True
self.depthTarget.setVisible(True)
self.ui.targetBtn.setEnabled(True)
self.ui.approachBtn.setEnabled(True)
self.ui.setTargetBtn.setChecked(False)
self.focusChanged()
def generatePoints(self):
layout = self.params['layout']
# get x/y point spacing
sepx = sepy = self.params['spacing']
if layout == 'Hexagonal':
sepy *= 3 ** 0.5
# find grid points inside each active region
points = []
for rgn in self.rgns:
if not rgn.value():
continue
roi = rgn.item
rect = self.mapFromItem(roi, roi.boundingRect()).boundingRect()
## find 'snap' position of first spot
newPos = self.getSnapPosition((rect.x(), rect.y()))
x = newPos.x() - sepx
y = newPos.y() - sepy
w = rect.width() + 2*sepx
h = rect.height() + 2*sepy
if layout == "Hexagonal":
# make every other row of the grid starting from top
points.append(self.generateGrid([x, y], [x+w, y+h], [sepx, sepy]))
# make every other row of the grid starting with 2nd row
points.append(self.generateGrid([x+0.5*sepx, y+0.5*sepy], [x+w, y+h], [sepx, sepy]))
elif layout == "Square":
points.append(self.generateGrid([x, y], [x+w, y+h], [sepx, sepx]))
if len(points) == 0:
return np.empty((0,2), dtype=float)
# stack all point arrays together
points = np.ascontiguousarray(np.vstack(points))
# do some rounding to make it easier to detect duplicate points
dec = int(-np.log10(sepx) + 4)
points = np.round(points, dec)
# keep only unique points
points = np.unique(points.view(dtype=[('x', float), ('y', float)]))
# convert back to normal array
points = points.view(dtype=float).reshape(len(points), 2)
# get shape of total active region
activeArea = Qt.QPainterPath()
for rgn in self.rgns:
if rgn.value():
roi = rgn.item
activeArea |= self.mapFromItem(roi, roi.shape())
# filter for all points within active region
mask = np.array([activeArea.contains(pg.Point(*pt)) for pt in points], dtype=bool)
return points[mask]
def addItem(self, item, pos=(0,0), scale=(1,1), z=None):
"""Adds an item into the scene. The item is placed in the global coordinate system;
it will stay fixed on the subject even if the scope moves or changes objective."""
self.view.addItem(item)
if pos is None:
pos = self.view.viewRect().center()
item.setPos(pg.Point(pos))
item.scale(scale[0], scale[1])
if z is not None:
item.setZValue(z)
def analyzeTransform(self):
"""Return the position and yaw angle of the device transform
"""
p = pg.debug.Profiler(disabled=True)
dev = self.getDevice()
p('getdev')
pos = dev.mapToGlobal([0, 0, 0])
p('map1')
x = dev.mapToGlobal([1, 0, 0])
p('map2')
p1 = pg.Point(x[:2])
p2 = pg.Point(pos[:2])
p3 = pg.Point(1, 0)
p('points')
angle = (p1 - p2).angle(p3)
if angle is None:
angle = 0
p('angle')
return pos, angle
def paint(self, p, *args):
pg.LineSegmentROI.paint(self, p, *args)
h1 = self.handles[0]['item'].pos()
h2 = self.handles[1]['item'].pos()
p1 = p.transform().map(h1)
p2 = p.transform().map(h2)
vec = pg.Point(h2) - pg.Point(h1)
length = vec.length()
angle = vec.angle(pg.Point(1, 0))
pvec = p2 - p1
pvecT = pg.Point(pvec.y(), -pvec.x())
pos = 0.5 * (p1 + p2) + pvecT * 40 / pvecT.length()
p.resetTransform()
txt = pg.siFormat(length, suffix='m') + '\n%0.1f deg' % angle
p.drawText(QtCore.QRectF(pos.x() - 50,
pos.y() - 50, 100, 100),
QtCore.Qt.AlignCenter | QtCore.Qt.AlignVCenter, txt)
def roiChanged(self):
""" read the ROI rectangle width and height and repost
in the parameter tree """
if self.ignoreRoiChange:
return
self.scanVoltageCache = None # invalidate cache
# update scan position
self.setScanPosFromRoi()
# update scan shape if needed
roi = self.currentRoi
state = roi.getState()
w, h = state['size']
rparam = self.scanProgram.components[0].ctrlParameter()
param = self.param.child('Scan Control')
rows = int(param['Image Width'] * h / w)
if param['Image Height'] != rows:
# update image height; this will cause acq thread protocol to be updated
with param.treeChangeBlocker():
param['Image Height'] = rows
else:
# ..otherwise we need to request the update here.
if self.imagingThread.isRunning():
self.updateImagingProtocol()
# record position of ROI in Scanner's local coordinate system
# we can use this later to allow the ROI to track stage movement
tr = self.scannerDev.inverseGlobalTransform() # maps from global to device local
pt1 = pg.Point(*state['pos'])
pt2 = pt1 + pg.Point(*state['size'])
self.currentRoi.scannerCoords = [
tr.map(pt1),
tr.map(pt2),
]
def segmentClicked(self, segment, ev=None, pos=None): ## ev/pos should be in this item's coordinate system
if ev != None:
pos = ev.pos()
elif pos != None:
pos = pos
else:
raise Exception("Either an event or a position must be specified")
## figure out which segment to add corresponding handle to
n = len(self.segments)
ind = self.segments.index(segment)
#mirrorInd = (n - ind) - 2
mirrorInd= n-ind
## figure out position at which to add second handle:
h1 = pg.Point(self.mapFromItem(segment, segment.handles[0]['item'].pos()))
h2 = pg.Point(self.mapFromItem(segment, segment.handles[1]['item'].pos()))
dist = (h1-pos).length()/(h1-h2).length()
h3 = pg.Point(self.mapFromItem(self.segments[mirrorInd], self.segments[mirrorInd].handles[0]['item'].pos()))
h4 = pg.Point(self.mapFromItem(self.segments[mirrorInd], self.segments[mirrorInd].handles[1]['item'].pos()))
mirrorPos = h4 - (h4-h3)*dist
## add handles:
if mirrorInd > ind:
ROI.PolyLineROI.segmentClicked(self, self.segments[mirrorInd], pos=mirrorPos)
ROI.PolyLineROI.segmentClicked(self, segment, pos=pos)
ROI.LineSegmentROI([pos, mirrorPos], [0,0], handles=(self.segments[ind].handles[1]['item'], self.segments[mirrorInd+1].handles[1]['item']), pen=self.pen, movable=False, parent=self)
else:
ROI.PolyLineROI.segmentClicked(self, segment, pos=pos)
ROI.PolyLineROI.segmentClicked(self, self.segments[mirrorInd], pos=mirrorPos)
ROI.LineSegmentROI([mirrorPos, pos], [0,0], handles=(self.segments[mirrorInd].handles[1]['item'], self.segments[ind+1].handles[1]['item']), pen=self.pen, movable=False, parent=self)
def createROI(self, roiColor='r'):
# the initial ROI will be nearly as big as the field, and centered.
cpos = self.scannerDev.mapToGlobal((0,0)) # get center position in scanner coordinates
csize = self.scannerDev.mapToGlobal((self.fieldSize, self.fieldSize))
objScale = self.scannerDev.parentDevice().getObjective().scale().x()
height = width = self.fieldSize*objScale
csize = pg.Point(width, height)
cpos = cpos - csize/2.
roiColor = self.getObjectiveColor(self.scopeDev.currentObjective) # pick up an objective color...
roi = RegionCtrl(cpos, csize, roiColor) # Note that the position actually gets over ridden by the camera additem below..
self.cameraModule.window().addItem(roi)
roi.setPos(cpos)
roi.sigRegionChangeFinished.connect(self.roiChanged)
return roi
def roiChanged(self):
""" read the ROI rectangle width and height and repost
in the parameter tree """
state = self.roi.getState()
w, h = state['size']
# Remember: ROI origin is in bottom-left because camera module has +y pointing upward.
self.params.system.p0 = pg.Point(self.roi.mapToView(pg.Point(
0, h))) # top-left
self.params.system.p1 = pg.Point(self.roi.mapToView(pg.Point(
w, h))) # rop-right
self.params.system.p2 = pg.Point(self.roi.mapToView(pg.Point(
0, 0))) # bottom-left
self.params.updateSystem()
def writeArray(self, array, mapping=None):
# Compute start/end indexes
start, npts = self._arrayIndexes()
# Generate spiral path
sg = self.spiralGeometry()
path = sg.path(npts, uniform=True)
# Move to center position
center = self.roi.mapToView(pg.Point(0, 0))
path += np.array([center.x(), center.y()])
# map to scanner voltage and write into array
x, y = (path[:, 0], path[:, 1])
if mapping is not None:
x, y = mapping(x, y)
array[start:start + npts, 0] = x
array[start:start + npts, 1] = y
return start, start + npts
def getMatrix(self, pos):
"""Return the transformMatrix to use for the given pos."""
quads = self.state['quadrilaterals']
ind=None
for i, q in enumerate(quads):
if QtGui.QPolygonF([QtCore.QPointF(*x) for x in q]).containsPoint(QtCore.QPointF(pos), QtCore.Qt.OddEvenFill):
ind = i
if ind == None: ## in case pos is outside the quadrilaterals
bestMin = 1000
for i, q in enumerate(quads):
dist = [pg.Point(x-pos).length() for x in q]
minDist = min(dist)
dist.remove(minDist)
minDist += min(dist)
if minDist < bestMin:
bestMin = minDist
ind = i
m = self.state['transformMatrices'][ind]
return np.array([m[0], m[1]])
def paint(self, p, *args):
p.setRenderHint(p.Antialiasing)
px = self.pixelLength(pg.Point(1, 0))
py = self.pixelLength(pg.Point(0, 1))
w = 5 * px
h = 5 * py
r = QtCore.QRectF(-w, -h, w * 2, h * 2)
p.setPen(pg.mkPen('y'))
p.setBrush(pg.mkBrush(0, 0, 255, 100))
p.drawEllipse(r)
p.drawLine(pg.Point(-w * 2, 0), pg.Point(w * 2, 0))
p.drawLine(pg.Point(0, -h * 2), pg.Point(0, h * 2))
if self.label is not None:
angle = self.labelAngle * np.pi / 180.
pos = p.transform().map(QtCore.QPointF(
0, 0)) + 15 * QtCore.QPointF(np.cos(angle), -np.sin(angle))
p.resetTransform()
p.drawText(QtCore.QRectF(pos.x() - 10,
pos.y() - 10, 20, 20),
QtCore.Qt.AlignCenter | QtCore.Qt.AlignVCenter,
self.label)
def runCalibration(self):
"""The scanner calibration routine:
1) Measure background frame, then scan mirrors
while collecting frames as fast as possible (self.scan())
2) Locate spot in every frame using gaussian fit
3) Map image spot locations to coordinate system of Scanner device's parent
3) Do parabolic fit to determine mapping between voltage and position
"""
camera = str(self.ui.cameraCombo.currentText())
laser = str(self.ui.laserCombo.currentText())
blurRadius = 5
## Do fast scan of entire allowed command range
(background, cameraResult, positions) = self.scan()
#self.calibrationResult = {'bg': background, 'frames': cameraResult, 'pos': positions}
with pg.ProgressDialog("Calibrating scanner: Computing spot positions...", 0, 100) as dlg:
dlg.show()
dlg.raise_() # Not sure why this is needed here..
## Forget first 2 frames since some cameras can't seem to get these right.
frames = cameraResult.asArray()
frames = frames[2:]
positions = positions[2:]
## Do background subtraction
## take out half the data until it can do the calculation without having a MemoryError.
finished = False
gc.collect()
while not finished:
try:
frames = frames.astype(np.float32)
frames -= background.astype(np.float32)
finished=True
except MemoryError:
frames = frames[::2,:,:]
positions = positions[::2]
finished = False
## Find a frame with a spot close to the center (within center 1/3)
cx = frames.shape[1] / 3
cy = frames.shape[2] / 3
centerSlice = blur(frames[:, cx:cx*2, cy:cy*2], (0, 5, 5)).max(axis=1).max(axis=1)
maxIndex = argmax(centerSlice)
maxFrame = frames[maxIndex]
dlg.setValue(5)
## Determine spot intensity and width
mfBlur = blur(maxFrame, blurRadius)
amp = mfBlur.max() - median(mfBlur) ## guess intensity of spot
(x, y) = argwhere(mfBlur == mfBlur.max())[0] ## guess location of spot
fit = fitGaussian2D(maxFrame, [amp, x, y, maxFrame.shape[0] / 10, 0.])[0] ## gaussian fit to locate spot exactly
# convert sigma to full width at 1/e
fit[3] = abs(2 * (2 ** 0.5) * fit[3]) ## sometimes the fit for width comes out negative. *shrug*
someFrame = cameraResult.frames()[0]
frameTransform = pg.SRTTransform(someFrame.globalTransform())
pixelSize = someFrame.info()['pixelSize'][0]
spotAmplitude = fit[0]
spotWidth = abs(fit[3] * pixelSize)
size = self.spotSize(mfBlur)
dlg.setValue(50)
## Determine location of spot within each frame,
## ignoring frames where the spot is too dim or too close to the frame edge
spotLocations = []
globalSpotLocations = []
spotCommands = []
spotFrames = []
margin = fit[3]
for i in range(len(positions)):
dlg.setValue(50. + 50. * i / frames.shape[0])
if dlg.wasCanceled():
raise HelpfulException('Calibration canceled by user.', msgType='warning')
frame = frames[i]
fBlur = blur(frame.astype(np.float32), blurRadius)
mx = fBlur.max()
diff = mx - fBlur.min()
ss = self.spotSize(fBlur)
if ss < size * 0.6:
#print "Ignoring spot:", ss
continue
#else:
#print "Keeping spot:", ss
(x, y) = argwhere(fBlur == mx)[0] # guess location of spot
if x < margin or x > frame.shape[0] - margin:
#print " ..skipping; too close to edge", x, y
continue
if y < margin or y > frame.shape[1] - margin:
#print " ..skipping; too close to edge", x, y
continue
frame[x,y] = -1 ## mark location of peak in image
## convert pixel location to coordinate system of scanner's parent
globalPos = frameTransform.map(pg.Point(x, y)) ## Map from frame pixel location to global coordinates
localPos = self.dev.mapGlobalToParent(globalPos) ## map from global to parent coordinate system. This is the position we calibrate to.
#print (x, y), (globalPos.x(), globalPos.y()), (localPos.x(), localPos.y())
spotLocations.append([localPos.x(), localPos.y()])
globalSpotLocations.append([globalPos.x(), globalPos.y()])
spotCommands.append(positions[i])
spotFrames.append(frame[newaxis])
## sanity check on spot frame
if len(spotFrames) == 0:
self.ui.view.setImage(frames)
raise HelpfulException('Calibration never detected laser spot! Looking for spots that are %f pixels wide.'% fit[3], reasons=['shutter is disabled', 'mirrors are disabled', 'objective is not clean', 'spot is not visible or not bright enough when shutter is open'])
spotFrameMax = concatenate(spotFrames).max(axis=0)
self.ui.view.setImage(spotFrameMax, transform=frameTransform)
self.clearSpots()
for sl in globalSpotLocations:
#self.addSpot(sl, fit[3]*binning[0])
self.addSpot(sl, spotWidth)
self.ui.view.autoRange()
if len(spotFrames) < 10:
raise HelpfulException('Calibration detected only %d frames with laser spot; need minimum of 10.' % len(spotFrames), reasons=['spot is too dim for camera sensitivity', 'objective is not clean', 'mirrors are scanning too quickly', 'mirror scanning region is not within the camera\'s view'])
## Fit all data to a map function
mapParams = self.generateMap(array(spotLocations), array(spotCommands))
#print
#print "Map parameters:", mapParams
if spotWidth < 0:
raise Exception()
return (mapParams, (spotAmplitude, spotWidth))
def getBackground(self):
if self.background is None:
w, h = self.params['sensorSize']
tr = self.globalTransform()
if isinstance(self.bgData, dict):
# select data based on objective
obj = self.getObjective()
data = self.bgData[obj]
info = self.bgInfo[obj]
px = info['pixelSize']
pz = info['depths'][1] - info['depths'][0]
m = pg.QtGui.QMatrix4x4()
pos = info['transform']['pos']
m.scale(1 / px[0], 1 / px[1], 1 / pz)
m.translate(-pos[0], -pos[1], -info['depths'][0])
tr2 = m * tr
origin = tr2.map(pg.Vector(0, 0, 0))
#print(origin)
origin = [int(origin.x()), int(origin.y()), origin.z()]
## slice data
camRect = QtCore.QRect(origin[0], origin[1], w, h)
dataRect = QtCore.QRect(0, 0, data.shape[1], data.shape[2])
overlap = camRect.intersected(dataRect)
tl = overlap.topLeft() - camRect.topLeft()
z = origin[2]
z1 = np.floor(z)
z2 = np.ceil(z)
s = (z - z1) / (z2 - z1)
z1 = int(np.clip(z1, 0, data.shape[0] - 1))
z2 = int(np.clip(z2, 0, data.shape[0] - 1))
src1 = data[z1,
overlap.left():overlap.left() + overlap.width(),
overlap.top():overlap.top() + overlap.height()]
src2 = data[z2,
overlap.left():overlap.left() + overlap.width(),
overlap.top():overlap.top() + overlap.height()]
src = src1 * (1 - s) + src2 * s
bg = np.empty((w, h), dtype=data.dtype)
bg[:] = 100
bg[tl.x():tl.x() + overlap.width(),
tl.y():tl.y() + overlap.height()] = src
self.background = bg
#vectors = ([1, 0, 0], [0, 1, 0])
#self.background = pg.affineSlice(data, (w,h), origin, vectors, (1, 2, 0), order=1)
else:
tr = pg.SRTTransform(tr)
m = QtGui.QTransform()
m.scale(3e6, 3e6)
m.translate(0.0005, 0.0005)
tr = tr * m
origin = tr.map(pg.Point(0, 0))
x = (tr.map(pg.Point(1, 0)) - origin)
y = (tr.map(pg.Point(0, 1)) - origin)
origin = np.array([origin.x(), origin.y()])
x = np.array([x.x(), x.y()])
y = np.array([y.x(), y.y()])
## slice fractal from pre-rendered data
vectors = (x, y)
self.background = pg.affineSlice(self.bgData, (w, h),
origin,
vectors, (0, 1),
order=1)
return self.background
def generateVoltageArray(self, arr):
"""
Use a polyline to make a scan that covers multiple regions in an
interleaved fashion. Alternate line segments of the polyline
are either the "scan" or the "interscan", allowing rapid movement
between successive points.
Interscan intervals are green on the line, scan intervals are white
"""
pts = list(map(pg.Point, cmd['points']))
startPos = pts[0]
stopPos = pts[-1]
#scanPoints = cmd['sweepDuration']/dt # in point indices, not time.
#interTracePoints = cmd['intertraceDuration']/dt
#scanPause = np.ones(int(interTracePoints))
#cmd['samplesPerScan'] = scanPoints
#cmd['samplesPerPause'] = interTracePoints
sweepSpeed = 1000 * cmd['sweepSpeed'] # in m/msec
interSweepSpeed = 1000 * cmd['interSweepSpeed']
ScanFlag = False
xp = np.array([])
yp = np.array([])
pockels = np.array([])
nSegmentScans = 0
nIntersegmentScans = 0
scanPointList = []
interScanFlag = False
for k in range(len(pts)): # loop through the list of points
k2 = k + 1
if k2 > len(pts) - 1:
k2 = 0
dist = (pg.Point(pts[k] - pts[k2])).length()
if interScanFlag is False:
scanPoints = int((dist / sweepSpeed) / dt)
xPos = np.linspace(pts[k].x(), pts[k2].x(), scanPoints)
yPos = np.linspace(pts[k].y(), pts[k2].y(), scanPoints)
pockels = np.append(pockels, np.ones(scanPoints))
nSegmentScans += 1
scanPointList.append(scanPoints)
else:
interSweepPoints = int((dist / interSweepSpeed) / dt)
xPos = np.linspace(pts[k].x(), pts[k2].x(), interSweepPoints)
yPos = np.linspace(pts[k].y(), pts[k2].y(), interSweepPoints)
pockels = np.append(pockels, np.zeros(interSweepPoints))
nIntersegmentScans += 1
scanPointList.append(interSweepPoints)
x, y = dev.mapToScanner(xPos, yPos, cmd['laser'])
xp = np.append(xp, x)
yp = np.append(yp, y)
interScanFlag = not interScanFlag
cmd['nSegmentScans'] = nSegmentScans
cmd['nIntersegmentScans'] = nIntersegmentScans
cmd['scanPointList'] = scanPointList
x = np.tile(xp, cmd['nScans'])
y = np.tile(yp, cmd['nScans'])
arr[0, startInd:startInd + len(x)] = x
arr[1, startInd:startInd + len(y)] = y
arr[0, startInd + len(x):stopInd] = arr[
0, startInd + len(x) -
1] # fill in any unused sample on this scan section
arr[1, startInd + len(y):stopInd] = arr[1, startInd + len(y) - 1]
lastPos = (x[-1], y[-1])
return stopInd
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.))