Addnoise app

[lesaintjerome]

Add two CL applications to add noise to a set of projections:

• addpoissonnoise: add Poisson noise based on the ShotNoise filter (adaptation of AddNoise.cxx example).
• addgaussiannoise: simple use of AdditiveGaussianNoiseImageFilter.

[SimonRit]

Thanks @lesaintjerome. I did not feel the need to add these apps but if you think they are helpful, let's move forward with this PR. I'd suggest

• to merge the two applications in a single rtkaddnoise app,
• to add a README.md app and a reference in the corresponding example,
• to clean-up code in other app doing the same thing (rtkdrawgeometricphantom, rtkdrawshepploganphantom, rtkprojectshepploganphantom).
• to add the Python version.

The commit messages need to follow ITK's style (add a ENH: prefix).
@axel-grc can help doing all this, just confirm you agree with my suggestions first.

[lesaintjerome]

Thanks for the feedback. One way to go would be to:

• Amend rtkprojectshepploganphantom with an option "gaussian" or "poisson" + relevant parameter.
• Add a --noise option to rtkprojectgeometricphantom similar to rtkprojectshepploganphantom.
  This way, no new app, but the need is fullfiled.

The command line interface could be something like:
--noise (poisson/gaussian) --noise_paramater (I0 mu_ref/sd)
or
`-addpoissonnoise (I mu_ref) --addgaussiannoise (std)

As for rtkdrawXXX, nothing to change since adding Poisson noise to phantoms would be irrelevant.

What do you think?

[axel-grc]

Thanks @lesaintjerome . I think adding options to the projection apps is the way to go.
For the command line arguments, I would like to have:

• One argument for the noise type --noise (poisson/gaussian)
• One for each parameter --I0 --mu_ref --std.

Do you want me to do a first draft ?

[lesaintjerome]

Hi @axel-grc. Thanks. I suggested the second CL interface -addpoissonnoise (I mu_ref) --addgaussiannoise (std) for 2 reasons:

1. No risk of mixing type and parameters (e.g. --noisetype poisson --sd 10).
2. I guess it could make sense to add both types of noise (model shot noise with Poisson and add detector's electronic noise ??

@SimonRit may have a stronger opinion on that.
And thanks for the proposition of drafting the solution.

[SimonRit]

We just discussed it with @axel-grc and @acoussat. We propose:

• we add a section (C++) / group (Python) with the options to add noise
• we add this section / group to all projection apps: rtkprojections, rtkprojectshepploganphantom, rtkprojectgeometricphantom, rtkforwardprojections, any other?
• it's a good point that we may want to add both Poisson and Gaussian noise. We agreed on the following:

--gaussian: double, standard deviation for the additive Gaussian noise
--poisson: two double, number of photons without object and scaling value of projections for computing Poisson noise

Sounds good to you @lesaintjerome ?

[lesaintjerome]

Brilliant!

[lesaintjerome]

Can I help in anything?

[axel-grc]

I will do a first draft!

[SimonRit]

We will implement something like that in the targeted applications:

ImageType::Pointer output = SetNoiseFromGgo(filter->GetOutput());

[SimonRit]

Superseded by #860