[SciPy-User] Projecting volumes down to 2D
Chris Weisiger
cweisiger@msg.ucsf....
Wed Aug 31 17:35:57 CDT 2011
Briefly, I'm working on a visualization tool for five-dimensional
microscopy data (X/Y/Z/time/wavelength). Different wavelengths can be
transformed with respect to each other: X/Y/Z translation, rotation
about the Z axis, and uniform scaling in X and Y. We can then show
various 2D slices of the data that pass through a specific XYZT point:
an X-Y slice, an X-Z slice, a Y-Z slice, and slices through time.
These slices are generated by transforming the view coordinates and
using scipy.ndimage.map_coordinates.
Now we want to be able to project an entire row/column/etc. of pixels
into a single pixel. For example, in the X-Y slice, each pixel shown
is actually the brightest pixel from the entire Z column. This example
is easily done by taking the maximum along the Z axis and then
proceeding as normal with generating the slice, albeit with a Z
transformation of 0. That's because the other transformation
parameters don't move data through the Z axis. Thus I still only have
to transform X by Y pixels.
I'm having trouble with an edge case for transformed data, though: if
the projection axis is X or Y, and there is a rotation/scale factor,
then I can't see a way to avoid having to transform every single pixel
in a 3D volume to obtain the projection -- that is, transforming X by
Y by Z pixels. This is expensive. Obviously each pixel in the volume
must be considered to generate these projections, but does every pixel
have to be transformed? I don't suppose anyone knows of a way to
simplify the problem?
-Chris
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