Error with example data of statphysbio_synthetic

[Hugo-Blanc]

Hello,

I get the following error when I run 01_convert_simulation_to_experiment.py in examples/statphysbio_synthetic :

Traceback (most recent call last):
  File "/home/equipex/Documents/Github/merfish3d-analysis/examples/statphysbio_synthetic/01_convert_simulation_to_experiment.py", line 135, in <module>
    convert_simulation(root_path=root_path)
  File "/home/equipex/Documents/Github/merfish3d-analysis/examples/statphysbio_synthetic/01_convert_simulation_to_experiment.py", line 52, in convert_simulation
    reshaped_simulation_data = simulation_data.reshape(
ValueError: cannot reshape array of size 5242880 into shape (8,3,16,256,256)

I downloaded the data from the google drive linked in 00_readme.txt.
Inspecting aligned_1.tiff, it is only composed of 82 images of 256x256 pixels, but it should be a stack of 8x3x16 = 384 images according to scan_metadata.csv.

[dpshepherd]

Hi @Hugo-Blanc,

Let me check, it's possible the Google Drive link contains the wrong data. We are still cleaning everything up, so thank you for testing!

[Hugo-Blanc]

I tested with the new link and 01_convert_simulation_to_experiment.py runs fine.

[dpshepherd]

Great, thanks! If you are interested, happy to work with you to write a data converter for any real data you'd like to try the package out with.