def __init__(self, atlas, host):
Atlas.AtlasCtrlWidget.__init__(self, atlas, host)
self.atlasDir = os.path.split(os.path.abspath(__file__))[0]
## add ThalamocorticalMarker to canvas
fh = DataManager.getHandle(os.path.join(self.atlasDir, 'images', 'ThalamocorticalMarker.svg'))
self.canvas.addFile(fh, pos=(-0.001283, -0.000205), scale=[3.78e-6, 3.78e-6], index=0, movable=False, z=10000)
## add CortexROI
self.roi = CortexROI([-1e-3, 0])
self.canvas.addGraphicsItem(self.roi, pos=(-1e-3, 1e-3), scale=[1e-3, 1e-3], name='CortexROI', movable=False)
self.roi.sigRegionChangeFinished.connect(self.roiChanged)
class A1AtlasCtrlWidget(Atlas.AtlasCtrlWidget):
def __init__(self, atlas, host):
Atlas.AtlasCtrlWidget.__init__(self, atlas, host)
self.atlasDir = os.path.split(os.path.abspath(__file__))[0]
## add ThalamocorticalMarker to canvas
fh = DataManager.getHandle(os.path.join(self.atlasDir, 'images', 'ThalamocorticalMarker.svg'))
self.canvas.addFile(fh, pos=(-0.001283, -0.000205), scale=[3.78e-6, 3.78e-6], index=0, movable=False, z=10000)
## add CortexROI
self.roi = CortexROI([-1e-3, 0])
self.canvas.addGraphicsItem(self.roi, pos=(-1e-3, 1e-3), scale=[1e-3, 1e-3], name='CortexROI', movable=False)
self.roi.sigRegionChangeFinished.connect(self.roiChanged)
def loadState(self):
if self.sliceDir is None:
return
state = self.sliceDir.info()['atlas'][self.atlas.name()]
self.roi.setState(state['cortexROI'])
self.atlas.setState(state)
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 generateDataArray(self, positions, dirType):
prof = Profiler("A1Atlas.generateDataArray", disabled=True)
if self.atlas.state is None:
self.saveState()
prof.mark('saved atlas state')
dirColumn = dirType + 'Dir'
if dirType == 'Protocol':
data = np.empty(len(positions), dtype=[('SliceDir', object),
(dirColumn, object),
#('layer', float),
#('depth', float),
('yPosSlice', float),
('yPosCell', float),
('percentDepth', float),
('xPosSlice', float),
('xPosCell', float),
('modXPosSlice', float),
('modXPosCell', float)])
fields = collections.OrderedDict([
('SliceDir', 'directory:Slice'),
(dirColumn, 'directory:'+dirType),
('yPosSlice', 'real'),
('yPosCell', 'real'),
('percentDepth', 'real'),
('xPosSlice', 'real'),
('xPosCell', 'real'),
('modXPosSlice', 'real'),
('modXPosCell', 'real')])
prof.mark("defined Protocol data array")
for i in range(len(positions)):
dh, pos = positions[i]
cellPos = self.dataModel.getCellInfo(dh)['userTransform']['pos']
mapped = self.atlas.mapToAtlas(pg.Point(pos)) ## needs to return %depth and modXPosSlice
#data[i] = (self.sliceDir, dh, mapped.x(), mapped.y(), mapped.z())
data[i]['SliceDir'] = self.sliceDir
data[i][dirColumn] = dh
data[i]['yPosSlice'] = pos[1]
data[i]['yPosCell'] = pos[1]-cellPos[1]
data[i]['percentDepth'] = mapped[1]
data[i]['xPosSlice'] = pos[0]
data[i]['xPosCell'] = pos[0]-cellPos[0]
data[i]['modXPosSlice'] = mapped[0]
data[i]['modXPosCell'] = mapped[0]-self.atlas.mapToAtlas(pg.Point(cellPos))[0]
prof.mark("filled protocol data array")
elif dirType == 'Cell':
data = np.empty(len(positions), dtype=[('SliceDir', object),
(dirColumn, object),
#('layer', float),
#('depth', float),
('yPosSlice', float),
#('yPosCell', float),
('percentDepth', float),
('xPosSlice', float),
#('xPosCell', float),
('modXPosSlice', float),
#('modXPosCell', float)
])
fields = collections.OrderedDict([
('SliceDir', 'directory:Slice'),
(dirColumn, 'directory:'+dirType),
('yPosSlice', 'real'),
('percentDepth', 'real'),
('xPosSlice', 'real'),
('modXPosSlice', 'real')])
prof.mark("defined cell data array")
for i in range(len(positions)):
dh, pos = positions[i]
#cellPos = self.dataModel.getCellInfo(dh)['pos']
mapped = self.atlas.mapToAtlas(pg.Point(pos)) ## needs to return %depth and modXPosSlice
#data[i] = (self.sliceDir, dh, mapped.x(), mapped.y(), mapped.z())
data[i]['SliceDir'] = self.sliceDir
data[i][dirColumn] = dh
data[i]['yPosSlice'] = pos[1]
#data['yPosCell'] = pos[1]-cellPos[1]
data[i]['percentDepth'] = mapped[1]
data[i]['xPosSlice'] = pos[0]
#data['xPosCell'] = pos[0]-cellPos[0]
data[i]['modXPosSlice'] = mapped[0]
#data['modXPosCell'] = mapped[0]-self.atlas.mapToAtlas(pg.Point(cellPos))[0]
prof.mark("filled cell data array")
else:
prof.finish()
raise Exception("Not sure how to structure data array for dirType=%s"%dirType)
prof.finish()
return data, fields
def roiChanged(self):
self.saveState()
