[SciPy-User] 2D slice of transformed data

Isaiah Norton isaiah.norton@gmail....
Wed Mar 23 20:22:46 CDT 2011


Hi Chris,

It's not strictly Python, but VTK and ITK are the heavy-iron for this sort
of thing (py wrappings available). There are several tools built on these
libraries to provide user-friendly 3D/4D registration, visualization, etc.

GoFigure2: http://gofigure2.sourceforge.net/
- very microscopy oriented. 4D support. linux/mac/win

 V3D: http://penglab.janelia.org/proj/v3d/V3D/About_V3D.html
- also 4D and triplatform.

BioImageXD
- mostly written in Python glue for vtk/itk.

If you want to build something custom in Python, check out MayaVi - it uses
VTK under the hood so the transforms will be handled fast in C++, but has
nice pythonic tvtk syntax and native numpy support.

-Isaiah




On Wed, Mar 23, 2011 at 6:00 PM, Chris Weisiger <cweisiger@msg.ucsf.edu>wrote:

> In preface, I'm not remotely an expert at array manipulation here. I'm an
> experienced programmer, but not an experienced *scientific* programmer. I'm
> sure what I want to do is possible, and I'm pretty certain it's even
> possible to do efficiently, but figuring out the actual implementation is
> giving me fits.
>
> I have two four-dimensional arrays of data: time, Z, Y, X. These represent
> microscopy data taken of the same sample with two different cameras. Their
> views don't quite match up if you overlay them, so we have a
> three-dimensional transform to align one array with the other. That
> transformation consists of X, Y, and Z translations (shifts), rotation about
> the Z axis, and equal scaling in X and Y -- thus, the transformation has 5
> parameters. I can perform the transformation on the data without difficulty
> with ndimage.affine_transform, but because we typically have hundreds of
> millions of pixels in one array, it takes a moderately long time. A
> representative array would be 30x50x512x512 or thereabouts.
>
> I'm writing a program to allow users to adjust the transformation and see
> how well-aligned the data looks from several perspectives. In addition to
> the traditional XY view, we also want to show XZ and YZ views, as well as
> kymographs (e.g. TX, TY, TZ views). Thus, I need to be able to show 2D
> slices of the transformed data in a timely fashion. These slices are always
> perpendicular to two axes (e.g. an XY slice passing through T = 0, Z = 20,
> or a TZ slice passing through X = 256, Y = 256), never diagonal. It seems
> like the fast way to do this would be to take each pixel in the desired
> slice, apply the reverse transform, and figure out where in the original
> data it came from. But I'm having trouble figuring out how to efficiently do
> this.
>
> I could construct a 3D array with shape (length of axis 1), (length of axis
> 2), (4), such that each position in the array is a 4-tuple of the
> coordinates of the pixel in the desired slice. For example, if doing a YX
> slice at T = 10, Z = 20, the array would look like [[[10, 20, 0, 0], [10,
> 20, 1, 0], [10, 20, 2, 0], ...], [[10, 20, 0, 1], 10, 20, 1, 1], ...]]. Then
> perhaps there'd be some way to efficiently apply the inverse transform to
> each coordinate tuple, then using ndimage.map_coordinates to turn those into
> pixel data. But I haven't managed to figure that out yet.
>
> By any chance is this already solved? If not, any suggestions / assistance
> would be wonderful.
>
> -Chris
>
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