francklab/single-layer-3d-tfm

Repository for single-layer 3D TFM for measuring cellular displacements and tractions with epifluorescence microscopy

single-layer-3d-tfm's Issues

Issue with running code

I've successfully downloaded Matlab (+ necessary add ons), Docker Desktop, the code which is added to the Matlab path. The first issue I have is that when running

SL3DTFM_runscript.m

I get the error

Unable to resolve the name 'SL3DTFM_runscript.m'.

When inspecting the code files, I found a similar file called SL3DTFM_runfile.m and when I ran that, I got the error:

Error using save
Cannot create 'example_data_example_saved_data_all_settings.mat' because
'C:\Users\Pacu-2\Documents\MATLAB\single-layer-3D-TFM-master\SL_3D_TFM_code\example_data'
does not exist.

Error in SL3DTFM_runfile (line 58)
save([data_dir,data_name,'',save_file_descriptor,'','all','_settings.mat'], '-v7.3')

In the instructions, it says to download the example data in the example folder, which I can do, but since the files are named differently I want to confirm that I'm using the correct code.

Error With inpaint_nans3.m

I successfully ran SL3DTFM_runfile.m in Matlab and run_sl_tfm_ps.ps1 in PowerShell and saved my sl_tfm_call_XYpoint_name_1.py and *2.py. When I tried running SL3DTFM_postFEniCS.m I got the following error where the script couldn't find inpaint_nans.m.

I see that inpaint_nans.m is provided so I added a 3 to inpaint_nans on line 74 of funCalculateTractions.m and got the following error

Is this an issue with inpaint_nans3.m or how I'm running the code? The .py files are save in the same directory as the _fenicsOut files. Right now I'm just processing the provided example_data