def __init__(self, handle, **kwds):
kwds.pop('viewRect', None)
self.data = handle.read()
self.groupitem = pg.ItemGroup()
self.pipettes = {}
for dev in self.data.devices():
arrow = pg.ArrowItem()
self.pipettes[dev] = arrow
arrow.setParentItem(self.groupitem)
opts = {'movable': False, 'rotatable': False, 'handle': handle}
opts.update(kwds)
if opts.get('name') is None:
opts['name'] = handle.shortName()
CanvasItem.__init__(self, self.groupitem, **opts)
self._timeSliderResolution = 10. # 10 ticks per second on the time slider
self._mpCtrlWidget = MultiPatchLogCtrlWidget()
self.layout.addWidget(self._mpCtrlWidget, self.layout.rowCount(), 0, 1,
2)
self._mpCtrlWidget.timeSlider.setMaximum(
self._timeSliderResolution *
(self.data.lastTime() - self.data.firstTime()))
self._mpCtrlWidget.timeSlider.valueChanged.connect(
self.timeSliderChanged)
self._mpCtrlWidget.createMarkersBtn.clicked.connect(
self.createMarkersClicked)
self.timeSliderChanged(0)
def __init__(self, **opts):
if 'scale' not in opts:
opts['scale'] = [20e-6, 20e-6]
item = QtGui.QGraphicsEllipseItem(-0.5, -0.5, 1., 1.)
item.setPen(pg.mkPen((255, 255, 255)))
item.setBrush(pg.mkBrush((0, 100, 255)))
opts.setdefault('scalable', False)
opts.setdefault('rotatable', False)
CanvasItem.__init__(self, item, **opts)
self.selectBox.addTranslateHandle([0.5, 0.5])
def __init__(self, points=None, **kwds):
vr = kwds.pop('viewRect', None)
if points is None:
if vr is None:
points = ((0, 0), (1, 1))
else:
p1 = vr.center()
p2 = p1 + 0.2 * (vr.topRight() - p1)
points = ((p1.x(), p1.y()), (p2.x(), p2.y()))
item = pg.graphicsItems.ROI.RulerROI(points)
CanvasItem.__init__(self, item, **kwds)
def __init__(self, **opts):
if 'scale' not in opts:
opts['scale'] = [20e-6, 20e-6]
#opts['size'] = [20e-6, 20e-6]
#opts['scale'] = [1., 1.]
item = QtGui.QGraphicsEllipseItem(-0.5, -0.5, 1., 1.)
item.setPen(pg.mkPen((255,255,255)))
item.setBrush(pg.mkBrush((0,100,255)))
opts['scalable'] = False
opts['rotatable'] = False
CanvasItem.__init__(self, item, **opts)
self.selectBox.addTranslateHandle([0.5,0.5])
def addGraphicsItem(self, item, **opts):
"""Add a new GraphicsItem to the scene at pos.
Common options are name, pos, scale, and z
"""
citem = CanvasItem(item, **opts)
item._canvasItem = citem
self.addItem(citem)
return citem
def __init__(self, parent=None, allowTransforms=True, hideCtrl=False, name=None):
QtGui.QWidget.__init__(self, parent)
self.ui = Ui_Form()
self.ui.setupUi(self)
#self.view = self.ui.view
self.view = ViewBox()
self.ui.view.setCentralItem(self.view)
self.itemList = self.ui.itemList
self.itemList.setSelectionMode(self.itemList.ExtendedSelection)
self.allowTransforms = allowTransforms
self.multiSelectBox = SelectBox()
self.view.addItem(self.multiSelectBox)
self.multiSelectBox.hide()
self.multiSelectBox.setZValue(1e6)
self.ui.mirrorSelectionBtn.hide()
self.ui.reflectSelectionBtn.hide()
self.ui.resetTransformsBtn.hide()
self.redirect = None ## which canvas to redirect items to
self.items = []
#self.view.enableMouse()
self.view.setAspectLocked(True)
self.view.invertY()
grid = GridItem()
self.grid = CanvasItem(grid, name='Grid', movable=False)
self.addItem(self.grid)
self.hideBtn = QtGui.QPushButton('>', self)
self.hideBtn.setFixedWidth(20)
self.hideBtn.setFixedHeight(20)
self.ctrlSize = 200
self.sizeApplied = False
self.hideBtn.clicked.connect(self.hideBtnClicked)
self.ui.splitter.splitterMoved.connect(self.splitterMoved)
self.ui.itemList.itemChanged.connect(self.treeItemChanged)
self.ui.itemList.sigItemMoved.connect(self.treeItemMoved)
self.ui.itemList.itemSelectionChanged.connect(self.treeItemSelected)
self.ui.autoRangeBtn.clicked.connect(self.autoRange)
self.ui.storeSvgBtn.clicked.connect(self.storeSvg)
self.ui.storePngBtn.clicked.connect(self.storePng)
self.ui.redirectCheck.toggled.connect(self.updateRedirect)
self.ui.redirectCombo.currentIndexChanged.connect(self.updateRedirect)
self.multiSelectBox.sigRegionChanged.connect(self.multiSelectBoxChanged)
self.multiSelectBox.sigRegionChangeFinished.connect(self.multiSelectBoxChangeFinished)
self.ui.mirrorSelectionBtn.clicked.connect(self.mirrorSelectionClicked)
self.ui.reflectSelectionBtn.clicked.connect(self.reflectSelectionClicked)
self.ui.resetTransformsBtn.clicked.connect(self.resetTransformsClicked)
self.resizeEvent()
if hideCtrl:
self.hideBtnClicked()
if name is not None:
self.registeredName = CanvasManager.instance().registerCanvas(self, name)
self.ui.redirectCombo.setHostName(self.registeredName)
def saveState(self, **kwds):
state = CanvasItem.saveState(self, **kwds)
state['imagestate'] = self.histogram.saveState()
state['filter'] = self.filter.saveState()
state['composition'] = self.imgModeCombo.currentText()
return state
def __init__(self, handle, **opts):
opts['handle'] = handle
item = QtSvg.QGraphicsSvgItem(handle.name())
CanvasItem.__init__(self, item, **opts)
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)
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)
def saveState(self, **kwds):
state = CanvasItem.saveState(self, **kwds)
state['currentTime'] = self.currentTime()
return state
def __init__(self, handle, **opts):
opts['handle'] = handle
item = QtSvg.QGraphicsSvgItem(handle.name())
CanvasItem.__init__(self, item, **opts)
def __init__(self, **kwds):
kwds.pop('viewRect', None)
item = pg.GridItem()
CanvasItem.__init__(self, item, **kwds)
def __init__(self, **opts):
self.defaultSize = 1e-4 # set a default spot size as 100 um.
if 'handle' not in opts:
raise Exception(
"ScanCanvasItem must be initialized with 'handle' or 'handles' specified in opts"
)
## Top-level dirHandle tells us the default name of the item
## and may have a userTransform
dirHandle = opts['handle']
if 'name' not in opts:
opts['name'] = dirHandle.shortName()
## Get the specific list of subdirs to use from which to pull spot information
if 'subDirs' in opts:
dirs = opts['subDirs']
else:
model = acq4.Manager.getManager().dataModel
typ = model.dirType(dirHandle)
if typ == 'ProtocolSequence':
dirs = [dirHandle[d] for d in dirHandle.subDirs()]
elif typ == 'Protocol':
dirs = [dirHandle]
else:
raise Exception("Invalid dir type '%s'" % typ)
## Generate spot data and a scatterplotitem
pts = []
for d in dirs:
if 'Scanner' in d.info() and 'position' in d.info(
)['Scanner']: #Note: this is expected to fail (gracefully) when a protocol sequence is incomplete
pos = d.info()['Scanner']['position']
if 'spotSize' in d.info()['Scanner']:
size = d.info()['Scanner']['spotSize']
else:
size = self.defaultSize
pts.append({'pos': pos, 'size': size, 'data': d})
self.scatterPlotData = pts
if len(pts) == 0:
raise Exception(
"No data found in scan %s." %
dirHandle.name(relativeTo=dirHandle.parent().parent()))
gitem = pg.ScatterPlotItem(pts, pxMode=False, pen=(50, 50, 50, 200))
#citem = ScanCanvasItem(self, item, handle=dirHandle, **opts)
#self._addCanvasItem(citem)
#return [citem]
CanvasItem.__init__(self, gitem, **opts)
#self.scatterPlot = gitem
self.originalSpotSize = size
self._ctrlWidget = QtGui.QWidget()
self.ui = ScanCanvasItemTemplate.Ui_Form()
self.ui.setupUi(self._ctrlWidget)
self.layout.addWidget(self._ctrlWidget, self.layout.rowCount(), 0, 1,
2)
self.ui.outlineColorBtn.setColor((50, 50, 50, 200))
#self.transformGui.mirrorImageBtn.clicked.connect(self.mirrorY)
self.ui.sizeSpin.setOpts(dec=True,
step=1,
minStep=1e-6,
siPrefix=True,
suffix='m',
bounds=[1e-6, None])
self.ui.sizeSpin.setValue(self.originalSpotSize)
self.ui.sizeSpin.valueChanged.connect(self.sizeSpinEdited)
self.ui.sizeFromCalibrationRadio.clicked.connect(self.updateSpotSize)
self.ui.outlineColorBtn.sigColorChanging.connect(self.updateOutline)
self.addScanImageBtn = self.ui.loadSpotImagesBtn
#self.createGradientBtn = self.ui.createGradientBtn
#self.removeGradientBtn = self.ui.removeGradientBtn
self.addScanImageBtn.connect(self.addScanImageBtn,
QtCore.SIGNAL('clicked()'),
self.loadScanImage)
def restoreState(self, state):
CanvasItem.restoreState(self, state)
self.filter.restoreState(state['filter'])
self.imgModeCombo.setCurrentIndex(
self.imgModeCombo.findText(state['composition']))
self.histogram.restoreState(state['imagestate'])
def restoreState(self, state):
self.setCurrentTime(state.pop('currentTime'))
CanvasItem.restoreState(self, state)
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 __init__(self, **opts):
"""
Create a new CanvasItem representing a scan.
Options:
handle: DirHandle where scan data is stored (required)
subDirs: list of DirHandles to the individual Protocols for each spot
(optional; this allows the inclusion of only part of a scan sequence)
"""
self.defaultSize = 1e-4 # set a default spot size as 100 um.
if 'handle' not in opts:
raise Exception("ScanCanvasItem must be initialized with 'handle' or 'handles' specified in opts")
## Top-level dirHandle tells us the default name of the item
## and may have a userTransform
dirHandle = opts['handle']
if 'name' not in opts:
opts['name'] = dirHandle.shortName()
## Get the specific list of subdirs to use from which to pull spot information
if 'subDirs' in opts:
dirs = opts['subDirs']
else:
model = acq4.Manager.getManager().dataModel
typ = model.dirType(dirHandle)
if typ == 'ProtocolSequence':
dirs = [dirHandle[d] for d in dirHandle.subDirs()]
elif typ == 'Protocol':
dirs = [dirHandle]
else:
raise Exception("Invalid dir type '%s'" % typ)
## Generate spot data and a scatterplotitem
pts = []
for d in dirs:
if 'Scanner' in d.info() and 'position' in d.info()['Scanner']: #Note: this is expected to fail (gracefully) when a protocol sequence is incomplete
pos = d.info()['Scanner']['position']
if 'spotSize' in d.info()['Scanner']:
size = d.info()['Scanner']['spotSize']
else:
size = self.defaultSize
pts.append({'pos': pos, 'size': size, 'data': d})
self.scatterPlotData = pts
if len(pts) == 0:
raise Exception("No data found in scan %s." % dirHandle.name(relativeTo=dirHandle.parent().parent()))
gitem = pg.ScatterPlotItem(pts, pxMode=False, pen=(50,50,50,200))
#citem = ScanCanvasItem(self, item, handle=dirHandle, **opts)
#self._addCanvasItem(citem)
#return [citem]
CanvasItem.__init__(self, gitem, **opts)
#self.scatterPlot = gitem
self.originalSpotSize = size
self._ctrlWidget = QtGui.QWidget()
self.ui = ScanCanvasItemTemplate.Ui_Form()
self.ui.setupUi(self._ctrlWidget)
self.layout.addWidget(self._ctrlWidget, self.layout.rowCount(), 0, 1, 2)
self.ui.outlineColorBtn.setColor((50,50,50,200))
#self.transformGui.mirrorImageBtn.clicked.connect(self.mirrorY)
self.ui.sizeSpin.setOpts(dec=True, step=1, minStep=1e-6, siPrefix=True, suffix='m', bounds=[1e-6, None])
self.ui.sizeSpin.setValue(self.originalSpotSize)
self.ui.sizeSpin.valueChanged.connect(self.sizeSpinEdited)
self.ui.sizeFromCalibrationRadio.clicked.connect(self.updateSpotSize)
self.ui.outlineColorBtn.sigColorChanging.connect(self.updateOutline)
self.addScanImageBtn = self.ui.loadSpotImagesBtn
#self.createGradientBtn = self.ui.createGradientBtn
#self.removeGradientBtn = self.ui.removeGradientBtn
self.addScanImageBtn.connect(self.addScanImageBtn, QtCore.SIGNAL('clicked()'), self.loadScanImage)
