problem loading tutorial data

[mkunst23]

Hi,

I have trouble loading the example data for the tutorial. I already update the path in the notebook to point towards the resource folder

fix_path = '/mnt/sda/git/bigstream/resources/fix.n5'
mov_path = '/mnt/sda/git/bigstream/resources/mov.n5'

But when I try to load the ow res dapi sections I get this error message

---

KeyError Traceback (most recent call last)
in
4 # get pointers to the low res scale level
5 # still just pointers, no data loaded into memory yet
----> 6 fix_lowres = fix_zarr['/dapi/lowres']
7 mov_lowres = mov_zarr['/dapi/lowres']
8

~/anaconda3/envs/bigstream/lib/python3.8/site-packages/zarr/hierarchy.py in getitem(self, item)
347 synchronizer=self._synchronizer)
348 else:
--> 349 raise KeyError(item)
350
351 def setitem(self, item, value):

KeyError: '/dapi/lowres'

Thanks,
Michael

[GFleishman]

Hi Michael!

If your tutorial is looking for a dataset called '/dapi/lowres' then you are likely working with an old version of BigStream.
Try getting the most recent version, v0.1.1, just released last night. There are many updates to the tutorial and code base - please do keep in touch as you're trying things out so I can help and make improvements based on your feedback.

install

pip install bigstream --upgrade

get source, which includes new tutorial data

rm -r /path/to/old/repository (up to you, you could keep it)
git clone https://github.com/GFleishman/bigstream

you could also try:

cd /path/to/your/current/old/version
git pull origin master

[mkunst23]

Thanks that worked. But the path needs to be update it should be

fix_lowres = fix_zarr['/lowres']
mov_lowres = mov_zarr['/lowres']

instead of

fix_lowres = fix_zarr['/dapi/lowres']
mov_lowres = mov_zarr['/dapi/lowres']

Michael

[GFleishman]

The new BigStream version includes new tutorial data - and also a new tutorial! Make sure you're using the new tutorial located in the notebooks directory of the repository. The old tutorial will not work with the new version of BigStream - some function APIs have changed (for the better I hope). The new tutorial has these file paths correct so I recommend you double check to make sure you're using the new one.