Atlas-Download-Tools
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BlueBrain
Search, download, and prepare brain atlas data.
Might be actually really useful (potentially simplifying our pipelines). http://help.brain-map.org/display/api/Downloading+3-D+Expression+Grid+Data TODO: - [ ] Can one choose the resolution or is it fixed to 200 microns? - [ ] How...
We currently hardcode the respace to be (in microns). I guess because it is the canonical setup. ```python refspace = ( ("coronal", (0, 13200), ("transverse", (0, 8000), ("sagittal", (0, 11400),...
https://github.com/BlueBrain/Atlas-Download-Tools/blob/829206f9a2a21720bebc8830d51971315fccde27/tox.ini#L70-L83 It seems like the `todo` and `slow` markers are not used in the code anymore. Do you think we should keep them? Additionally, there are some tests that requires...
At the moment `get_corners_in_ref_space` sends 4 queries to determine the corner locations in the reference space. Given we have the machinery to do the transformations locally using affine transformations we...
Regarding tracebacks / debugging, there are for sure different options. First of all, we already have a way because we added the `__main__.py` file. So now to debug some `atldld...
Whenever one calls `warp` the transformation needs to be computed from the displacements. https://github.com/BlueBrain/Atlas-Download-Tools/blob/60f0221916f4f9987a4728807be0b37934784cd0/src/atldld/base.py#L319 This operation requires `np.meshgrid` or `np.indices` and can be costly for big shapes. Anyway, the `DisplacementField`...
In `download_parallel_dataset` one can specify both the `downsample_ref` and `downsample_img` manually. However, it might be very useful to imply a reasonable `downsample_img` from the selected `downsample_ref` and the resolution of...
There are different ways to get monospaced font in docs: - `` :code:`stuff` `` - `` `stuff` `` - ``` ``stuff`` ``` According to the [some docs](https://docutils.sourceforge.io/docs/user/rst/quickref.html#inline-markup) - `` `stuff`...
In theory, nothing prevents us from downloading + synchronizing the images in parallel.