question regarding passing rate calculation

[Alexander S]

Dear all,

If I could clarify the passing rate calculation with your help, I would appreciate much.

From what I can see in the code, passing rate is defined as  (all_values <1) / (all_values). But it means that background values , i.e. values that are not included in the irradiation field, are also included in the calculation ?

So if I have a very large background, and my irradiation field is small compared with the whole picture, I would inherently have high passing rate nevertheless? Because background values always have 0 gamma ?

Sorry if my question is unclear, in that case I would try to illustrate my question with the pictures.

Thanks,

Alex

[Simon Biggs]

Hi Alex,

For future readers, the reference you're referring to is https://docs.pymedphys.com/howto/gamma/effect-of-noise.html

Regarding the passing rate calculation, the key is actually the following parameter:

'lower_percent_dose_cutoff': 20,

which was defined at the beginning of the notebook. This makes it so that only the values where the reference dose is larger than that percentage have their gamma calculated. All other points end up having their result set to np.nan

lower_dose_cutoff = lower_percent_dose_cutoff / 100 * global_normalisation

reference_dose_above_threshold = dose_reference >= lower_dose_cutoff

reference_points_to_calc = reference_dose_above_threshold

From:

https://github.com/pymedphys/pymedphys/blob/0fdc8ee4a7e6e01437d359773f38df88010b41f8/pymedphys/_gamma/implementation/shell.py#L255

https://github.com/pymedphys/pymedphys/blob/0fdc8ee4a7e6e01437d359773f38df88010b41f8/pymedphys/_gamma/implementation/shell.py#L267

https://github.com/pymedphys/pymedphys/blob/0fdc8ee4a7e6e01437d359773f38df88010b41f8/pymedphys/_gamma/implementation/shell.py#L274

Then, in order to calculate the passing rate, all np.nan values are filtered out using ~np.isnan(gamma):

valid_gamma_no_noise = gamma_no_noise[~np.isnan(gamma_no_noise)]
no_noise_passing = 100 * np.round(np.sum(valid_gamma_no_noise <= 1) / len(valid_gamma_no_noise), 4)

This therefore only calculates the passing rate over the range of doses where the reference dose is larger than the "lower_percent_dose_cutoff"

Cheers,

Simon

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[Aleksandras]

Hi Simon,

Crystal clear, thanks!

A.

[Simon Biggs]

My pleasure :)

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