[SciPy-User] 2D slice of transformed data

David Baddeley david_baddeley@yahoo.com...
Wed Mar 23 19:07:42 CDT 2011

I think you are on to the right idea with using transformed coordinates with 
map_coordinates. I think the easiest way (and fastest way) to get your set of 
transformed coordinates might be something like the following:

assuming Ai is the inverse of your transformation matrix ...

X, Y, Z, T = mgrid[whatever your goal slices are]

Xt = Ai[0,0]*X + Ai[0,1]*Y + Ai[0,2]*Z .....
Yt = Ai[1,0]*X ........
Tt = ...
Tt = ...

this lets you still exploit scipys vector operations on your arrays of 
coordinates, rather than having to separately multiply each tuple with the 
matrix. I'm you can probably write that as a loop to avoid all the redundant 
code. eg:

def transformCoords(coords, A): 
    #coords is a list of coordinate arrays eg [X, Y, Z, T]
    #A is the transformation matrix

    ret = []
    for i in range(len(coords)):
         r_i = 0
         for j in range(len(coords)):
               r_j += A[i,j]*coords[j]


   return ret


From: Chris Weisiger <cweisiger@msg.ucsf.edu>
To: scipy-user@scipy.org
Sent: Thu, 24 March, 2011 11:00:39 AM
Subject: [SciPy-User] 2D slice of transformed data

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 

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. 


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