update API

[casperdcl]

• use 'image_to_parametric_files' instead of 'image_to_parametric'
• add the use of a mask file, can automate the mask file selection according to the current image file organisation
• change 'user_inputs', split linear_phase_start/end for logan_ref, logan_ref_k2p, mrtm, mrtm_k2p
• use 'models' (list of 'model's) instead of 'model'

closes JJiao#2

[casperdcl]

not sure about this @JJiao...

• why try to do multiple models in one function? Why not just call the function multiple times (once per model)?
• linear_phase_(start|end)_(l|l2|m|m2) seems very clunky (again, old API seems much cleaner)

[casperdcl]

maybe better to do this? That way we have both versions...

def kinetic_modelS(modelS=[...], **kwargs):
    resultS = []
    for model in modelS:
        resultS.append(kinetic_model(**kwargs))
    return resultS

kinetic_modelS vs kinetic_model:

• pro: easier to select multiple models
• con: lots of kwargs are unrelated to the selected models, so very confusing, hard to explain, error-prone (e.g. model=['srtmb_basis'], linear_phase_start_l=... doesn't make sense)

Overall I think the con is much bigger than the pro.

[JJiao]

Sure! Let's use 'kinetic_modelS'

[JJiao]

Hi Casper, I'm away this week, do you want to have a quick chat next week about this?

…

On Tue, 31 May 2022, 12:02 Casper da Costa-Luis, ***@***.***> wrote: ***@***.**** commented on this pull request. ------------------------------ In niftypad/api/__init__.py <#6 (comment)>: > @@ -7,15 +7,23 @@ log = logging.getLogger(__name__) -def kinetic_model(src, dst=None, params=None, model='srtmb_basis', input_interp_method='linear', - w=None, r1=1, k2p=0.000250, beta_lim=None, n_beta=40, linear_phase_start=500, - linear_phase_end=None, km_outputs=None, thr=0.1, fig=False): +# def kinetic_model(src, dst=None, params=None, model='srtmb_basis', input_interp_method='linear', +# w=None, r1=1, k2p=0.000250, beta_lim=None, n_beta=40, linear_phase_start=500, +# linear_phase_end=None, km_outputs=None, thr=0.1, fig=False): + +def kinetic_models(src, dst=None, params=None, models=['srtmb_basis','logan_ref'], input_interp_method='linear', not sure about this @JJiao <https://github.com/JJiao>... - why try to do multiple models in one function? Why not just call the function multiple times (once per model)? - linear_phase_(start|end)_(l|l2|m|m2) seems very clunky (again, old API seems much cleaner) — Reply to this email directly, view it on GitHub <#6 (review)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AA4XHECFJ27S63ENXDA7BCDVMXWUXANCNFSM5XNBERCQ> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[casperdcl]

I don't have push access to https://github.com/JJiao/NiftyPAD/tree/patch-3, so merged manually in e3f6221 instead

[casperdcl]

released in https://github.com/AMYPAD/NiftyPAD/releases/tag/v2.0.0