def overlayPoints(dataSource,
pointSource,
sink=None,
pointColor=[1, 0, 0],
x=all,
y=all,
z=all):
"""Overlay points on 3D data and return as color image
Arguments:
dataSouce (str or array): volumetric image data
pointSource (str or array): point data to be overlayed on the image data
pointColor (array): RGB color for the overlayed points
x, y, z (all or tuple): sub-range specification
Returns:
(str or array): image overlayed with points
See Also:
:func:`overlayLabel`
"""
data = io.readData(dataSource, x=x, y=y, z=z)
points = io.readPoints(pointSource, x=x, y=y, z=z, shift=True)
#print data.shape
if not pointColor is None:
dmax = data.max()
dmin = data.min()
if dmin == dmax:
dmax = dmin + 1
cimage = numpy.repeat((data - dmin) / (dmax - dmin), 3)
cimage = cimage.reshape(data.shape + (3, ))
if data.ndim == 2:
for p in points: # faster version using voxelize ?
cimage[p[0], p[1], :] = pointColor
elif data.ndim == 3:
for p in points: # faster version using voxelize ?
cimage[p[0], p[1], p[2], :] = pointColor
else:
raise RuntimeError(
'overlayPoints: data dimension %d not suported' % data.ndim)
else:
cimage = vox.voxelize(points, data.shape, voxelizationMethod='Pixel')
cimage = cimage.astype(data.dtype) * data.max()
data.shape = data.shape + (1, )
cimage.shape = cimage.shape + (1, )
cimage = numpy.concatenate((data, cimage), axis=3)
#print cimage.shape
return io.writeData(sink, cimage)
def overlayPoints(dataSource, pointSource, sink = None, pointColor = [1,0,0], x = all, y = all, z = all):
"""Overlay points on 3D data and return as color image
Arguments:
dataSouce (str or array): volumetric image data
pointSource (str or array): point data to be overlayed on the image data
pointColor (array): RGB color for the overlayed points
x, y, z (all or tuple): sub-range specification
Returns:
(str or array): image overlayed with points
See Also:
:func:`overlayLabel`
"""
data = io.readData(dataSource, x = x, y = y, z = z);
points = io.readPoints(pointSource, x = x, y = y, z = z, shift = True);
#print data.shape
if not pointColor is None:
dmax = data.max(); dmin = data.min();
if dmin == dmax:
dmax = dmin + 1;
cimage = numpy.repeat( (data - dmin) / (dmax - dmin), 3);
cimage = cimage.reshape(data.shape + (3,));
if data.ndim == 2:
for p in points: # faster version using voxelize ?
cimage[p[0], p[1], :] = pointColor;
elif data.ndim == 3:
for p in points: # faster version using voxelize ?
cimage[p[0], p[1], p[2], :] = pointColor;
else:
raise RuntimeError('overlayPoints: data dimension %d not suported' % data.ndim);
else:
cimage = vox.voxelize(points, data.shape, method = 'Pixel');
cimage = cimage.astype(data.dtype) * data.max();
data.shape = data.shape + (1,);
cimage.shape = cimage.shape + (1,);
cimage = numpy.concatenate((data, cimage), axis = 3);
#print cimage.shape
return io.writeData(sink, cimage);