Local affine aligments

[IamJuanHilario]

I am trying to run the tutorial, however I get these errors which I cannot find a way to solve them. I would sincerely appreciate any help. I am using the values and blocksize that were provided with the tutorial

---

ValueError Traceback (most recent call last)
Input In [21], in <cell line: 3>()
1 # Note use of mov_lowres_aligned as moving image rather than mov_lowres_data
2 # Note also that fix_lowres_spacing is used as the "moving" voxel spacing here
----> 3 local_affines = affine.prepare_piecewise_ransac_affine(
4 fix_lowres_data, mov_lowres_aligned,
5 fix_lowres_spacing, fix_lowres_spacing,
6 min_radius=6, max_radius=20, match_threshold=0.75,
7 blocksize=[128,]*3,
8 )
11 # not a numpy array
12 print(type(local_affines))

File ~/envsternson/lib/python3.8/site-packages/bigstream/affine.py:111, in prepare_piecewise_ransac_affine(fix, mov, fix_spacing, mov_spacing, min_radius, max_radius, match_threshold, blocksize, **kwargs)
109 # wrap images as dask arrays
110 fix_da = da.from_array(fix, chunks=blocksize)
--> 111 mov_da = da.from_array(mov, chunks=blocksize)
113 # wrap affine function
114 def wrapped_ransac_affine(x, y, block_info=None):
115
116 # compute affine

File ~/envsternson/lib/python3.8/site-packages/dask/array/core.py:3335, in from_array(x, chunks, name, lock, asarray, fancy, getitem, meta, inline_array)
3189 """Create dask array from something that looks like an array.
3190
3191 Input must have a .shape, .ndim, .dtype and support numpy-style slicing.
(...)
3332 >>> a = da.from_array(x, chunks=((67, 33), (6,)))
3333 """
3334 if isinstance(x, Array):
-> 3335 raise ValueError(
3336 "Array is already a dask array. Use 'asarray' or " "'rechunk' instead."
3337 )
3338 elif is_dask_collection(x):
3339 warnings.warn(
3340 "Passing an object to dask.array.from_array which is already a "
3341 "Dask collection. This can lead to unexpected behavior."
3342 )

ValueError: Array is already a dask array. Use 'asarray' or 'rechunk' instead.

[GFleishman]

Hi - thanks for trying bigstream. I'm sorry to have never gotten to this issue to help you last year. I am not only the developer of bigstream, I also use it every day to process a constant stream of incoming new datasets. It has been hard to find time to support external users, but I am making some extra time for it this year.

Bigstream has changed a lot since you posted this issue and the code which was giving you an error has been considerably refactored. So I'm going to close this issue for now. I hope you'll give bigstream another try if you have data for it, and I will be more able to help if so.