Missing example file: filtered.matrix.tsv.gz

[huanlity]

Hi, I am trying to run ficture using the example scripts. In generric_III.sh file, the variable pixel was defined as pixel=${pixel:-${path}/filtered.matrix.tsv.gz}, but the filtered.matrix.tsv.gz cannot be found in the data folder. Could you please upload this file? Thank you!

Also, I got an error when running this, any idea how to fix it?

python [/Users/whuan/dev/ficture/script/make_spatial_minibatch.py](https://file+.vscode-resource.vscode-cdn.net/Users/whuan/dev/ficture/script/make_spatial_minibatch.py) --input [/Users/whuan/dev/ficture/examples/data/transcripts.tsv.gz](https://file+.vscode-resource.vscode-cdn.net/Users/whuan/dev/ficture/examples/data/transcripts.tsv.gz) --output [/Users/whuan/dev/ficture/examples/data/batched.matrix.tsv.gz](https://file+.vscode-resource.vscode-cdn.net/Users/whuan/dev/ficture/examples/data/batched.matrix.tsv.gz) --mu_scale 1 --batch_size 500 --batch_buff 30 --major_axis Y

error:

INFO:root:Random seed 1709301234.7678442
zcat: can't stat: [/Users/whuan/dev/ficture/examples/data/transcripts.tsv.gz](https://file+.vscode-resource.vscode-cdn.net/Users/whuan/dev/ficture/examples/data/transcripts.tsv.gz) (/Users/whuan/dev/ficture/examples/data/transcripts.tsv.gz.Z): No such file or directory
['X', 'random_index', 'Y', 'gene', 'MoleculeID', 'Count']
Traceback (most recent call last):
  File "/Users/whuan/dev/ficture/script/make_spatial_minibatch.py", line 106, in <module>
    x_min, y_min = df[["X","Y"]].values.min(axis = 0)
  File "/Users/whuan/opt/anaconda3/envs/ficture/lib/python3.9/site-packages/numpy/core/_methods.py", line 45, in _amin
    return umr_minimum(a, axis, None, out, keepdims, initial, where)
ValueError: zero-size array to reduction operation minimum which has no identity

Thanks, Huan

[Yichen-Si]

pixel=${pixel:-${path}/filtered.matrix.tsv.gz} mean using the input "pixel" and fallback to a default file name filtered.matrix.tsv.gz. In the example it is ${path}/transcripts.tsv.gz as set in the realdata.md

Thanks, Yichen