class Controller(PgImageController):
"""
TopView Controller
"""
def __init__(self, qmain: TopView, res=25):
super(Controller, self).__init__(qmain)
self.atlas = AllenAtlas(res)
self.fig_top = self.qwidget = qmain
# Setup Coronal slice: width: ml, height: dv, depth: ap
self.fig_coronal = SliceView(qmain, waxis=0, haxis=2, daxis=1)
self.fig_coronal.setWindowTitle('Coronal Slice')
self.set_slice(self.fig_coronal)
self.fig_coronal.show()
# Setup Sagittal slice: width: ap, height: dv, depth: ml
self.fig_sagittal = SliceView(qmain, waxis=1, haxis=2, daxis=0)
self.fig_sagittal.setWindowTitle('Sagittal Slice')
self.set_slice(self.fig_sagittal)
self.fig_sagittal.show()
def set_slice(self, fig, coord=0):
waxis, haxis, daxis = (fig.ctrl.waxis, fig.ctrl.haxis, fig.ctrl.daxis)
# construct the transform matrix image 2 ibl coordinates
dw = self.atlas.bc.dxyz[waxis]
dh = self.atlas.bc.dxyz[haxis]
wl = self.atlas.bc.lim(waxis) - dw / 2
hl = self.atlas.bc.lim(haxis) - dh / 2
fig.ctrl.set_image(self.atlas.slice(coord, axis=daxis, mode='clip'),
dw, dh, wl[0], hl[0])
fig.ctrl.slice_coord = coord
def set_top(self):
img = self.atlas.top.transpose()
img[np.isnan(img)] = np.nanmin(img) # img has dims ml, ap
dw, dh = (self.atlas.bc.dxyz[0], self.atlas.bc.dxyz[1])
wl, hl = (self.atlas.bc.xlim, self.atlas.bc.ylim)
self.set_image(img, dw, dh, wl[0], hl[0])
class ControllerTopView(PgImageController):
"""
TopView ControllerTopView
"""
def __init__(self,
qmain: TopView,
res: int = 25,
volume='image',
brainmap='Allen'):
super(ControllerTopView, self).__init__(qmain)
self.volume = volume
self.atlas = AllenAtlas(res, brainmap=brainmap)
self.fig_top = self.qwidget = qmain
# Setup Coronal slice: width: ml, height: dv, depth: ap
self.fig_coronal = SliceView(qmain, waxis=0, haxis=2, daxis=1)
self.fig_coronal.setWindowTitle('Coronal Slice')
self.set_slice(self.fig_coronal)
self.fig_coronal.show()
# Setup Sagittal slice: width: ap, height: dv, depth: ml
self.fig_sagittal = SliceView(qmain, waxis=1, haxis=2, daxis=0)
self.fig_sagittal.setWindowTitle('Sagittal Slice')
self.set_slice(self.fig_sagittal)
self.fig_sagittal.show()
def set_slice(self, fig, coord=0, mapping="Allen"):
waxis, haxis, daxis = (fig.ctrl.waxis, fig.ctrl.haxis, fig.ctrl.daxis)
# construct the transform matrix image 2 ibl coordinates
dw = self.atlas.bc.dxyz[waxis]
dh = self.atlas.bc.dxyz[haxis]
wl = self.atlas.bc.lim(waxis) - dw / 2
hl = self.atlas.bc.lim(haxis) - dh / 2
# the ImageLayer object carries slice kwargs and pyqtgraph ImageSet kwargs
# reversed order so the self.im is set with the base layer
for layer in reversed(fig.ctrl.image_layers):
_slice = self.atlas.slice(coord,
axis=daxis,
mapping=mapping,
**layer.slice_kwargs)
fig.ctrl.set_image(layer.image_item, _slice, dw, dh, wl[0], hl[0],
**layer.pg_kwargs)
fig.ctrl.slice_coord = coord
def set_top(self):
img = self.atlas.top.transpose()
img[np.isnan(img)] = np.nanmin(img) # img has dims ml, ap
dw, dh = (self.atlas.bc.dxyz[0], self.atlas.bc.dxyz[1])
wl, hl = (self.atlas.bc.xlim, self.atlas.bc.ylim)
self.set_image(self.image_layers[0].image_item, img, dw, dh, wl[0],
hl[0])
def set_scatter(self, fig, coord=0):
waxis = fig.ctrl.waxis
# dealing with coronal slice
if waxis == 0:
idx = np.where(
self.scatter_data_ind[:, 1] == self.atlas.bc.y2i(coord))[0]
x = self.scatter_data[idx, 0]
y = self.scatter_data[idx, 2]
else:
idx = np.where(
self.scatter_data_ind[:, 0] == self.atlas.bc.x2i(coord))[0]
x = self.scatter_data[idx, 1]
y = self.scatter_data[idx, 2]
fig.ctrl.set_points(x, y)
def set_volume(self, volume):
self.volume = volume
