Special if case for `acq-coilQaSagLarge_SNR_T0000` is overwritten

[jcohenadad]

https://github.com/spinal-cord-7t/coil-qc-code/blob/a8dee4de63f4acffcf0294b6114a5bc13df914f0/data_processing-phantom.ipynb#L312-L315

The variable data declared in the if case for acq-coilQaSagLarge_SNR_T0000 gets overwritten later. Any comment/justification that I should be aware of before addressing this issue @evaalonsoortiz ?

[evaalonsoortiz]

I'm retracing my steps here for something I was trying to debug a few weeks ago, so I may be forgetting something ... But from what I recall, reassigning "data" seemed to fix a problem I was having (see below). I don't know why it works, but it does.

Here's what happens if I do the following:

if file_name=="acq-coilQaSagLarge_SNR_T0000":
            data=map.get_fdata()[round(map.get_fdata().shape[0]/2),125:385,round(map.get_fdata().shape[2]/2)]
else:    
            data=map.get_fdata()[round(map.get_fdata().shape[0]/2),:,round(map.get_fdata().shape[2]/2)]

The range along the x-axis isn't showing data from 125-385 as requested.

For some reason re-assigning the data using:

if file_name=="acq-coilQaSagLarge_SNR_T0000":
            data=map.get_fdata()[round(map.get_fdata().shape[0]/2),125:385,round(map.get_fdata().shape[2]/2)]          
data=map.get_fdata()[round(map.get_fdata().shape[0]/2),:,round(map.get_fdata().shape[2]/2)]`

results in somehow showing the data in the proper range along the x-axis:

[jcohenadad]

Because you are first creating a vector of shape=260, and then you are further cropping that vector when displaying it: https://github.com/spinal-cord-7t/coil-qc-code/blob/a8dee4de63f4acffcf0294b6114a5bc13df914f0/data_processing-phantom.ipynb#L325

The solution is to either not crop the vector (ie: drop the if case at line 312) or drop the cropping of the plot (line 325)

Note: these bugs are much easier to debug when running a script and using the debugger from an IDE vs. within a jupyter notebook 😉

[evaalonsoortiz]

Ah! This is where my lack of python experience gets me into trouble. I did not realize that plt.xlim(125, 385) was cropping anything, I assumed it was only labelling ticks with a range of 125 to 385.

You mean an IDE with a python script? I would need a crash course on making the most of that, my experience as a former matlab enthusiast has not been good. I don't find it user friendly at all, but it could be because I don't know how to make the most of it.

[jcohenadad]

You mean an IDE with a python script?

Yes, this is what I meant. Learning Python after having been myself a Matlab-addict, I could not program without an IDE. Examples of IDE that I've used: PyCharm and VScode. It is pretty straightforward to use and the debugger is similar to that of Matlab.

[evaalonsoortiz]

This problem has been addressed given that the code now plots the data stored in a CSV file (see https://github.com/spinal-cord-7t/coil-qc-code/blob/d2bc792c5388e0d31b4008ca177741a2d7a0f590/data_processing-phantom.ipynb#L442 and below).

If I can get a thumbs up, I'll close the issue.