search

schwartzlab-methods / NEST

Implementation of NEST method
GNU General Public License v3.0
2 stars 1 forks source link

Error durion visualization #1

Open iaaka opened 5 months ago

iaaka commented 5 months ago

Hello, thank you for your tool! I encountered few errors while running nest visualize from your tutorial (within your singularity). I managed to fix the problems by:

  1. commenting out example lines 9-16 in altairThemes.py (that otherwise caused NameError: name 'alt' is not defined)
  2. Replacing np.float with np.float64 in two places in output_visualization_NEST.py that otherwise caused AttributeError: module 'numpy' has no attribute 'float'. I'm happy to make pull request if it is helpful.

That also seems that nest output_graph_picture doesn't work as intended at least it produces attached image which looks strange and doesn't seem useful (all text and spots overlap each other). I haven't managed to fix it.

anne04 commented 5 months ago

@iaaka Thank you for trying out our tool.

  1. Thank you for the fix. I have also updated those statements
  2. Yes, please make a pull request
  3. nest output_graph_picture -- Is this error happening with the same human lymph node data or are you using something else? Also, I need to figure out if this error is happening during conversion to the .pdf/.svg or during making the NetworkX graph. So, could you please also check how does the mygraph.html look like? You may send me a screenshot.
iaaka commented 5 months ago

Hi, thank you for reply, seems I have to rights to commit to the repo, but it probably doesn't deserve pull request, one just need to replace np.float with np.float64 here and there. Re to images, it is human lymph node, I followed your tutorial with only deviation that I used just one run instead of five. mygraph.html looks fine: image I'm attaching dot file and html in case it can help nest_human_lymph.zip