## SimuPBI_circle_func: function that launches the phase-contrast simulation of a single wire, of a material defined by the user.
# In this file, I detailed all the input and output arguments, followed by one or several examples (one line beginning with a %)
## Author: Loriane Weber <loriane.weber@creatis.insa-lyon.fr>
## Created: 2016-02-11

## Example of use :
## SimuPBI_unknown_1D('star', 2, [0 0.1 0.5], 26, 2.7, 300, 180, 1, 1, '/users/lweber/Matlab/SimulationsPBI/mu_star.edf', '/users/lweber/Matlab/SimulationsPBI/delta_star.edf', '', 'gaussian', 35)

## Please note that dir_out, noise_type, noise_amount are optional arguments.

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############### INPUT parameters ############### 
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######### Parameter related to the computation - and names of the result #########

## vers does not exist anymore; the projections are calculated using the Radon transform

## oversamp: is a number that defines the oversampling of the projections in the real domain.
## use the number 2 or 4 only
%oversamp = 2
%oversamp = 4

## basename_output: is a string that contains the basename of the resulting files.
## use a string, of your choice. 
%basename_output = 'Test'

######### Parameter related to the physics #########

## dist is a vector, which contains the propagation distances, expressed in meters. 
## use a vector, beggining and ending with a square bracket; the distances should be separated by a space. Use a point as decimal mark.
% dist = [0 0.01 0.1 0.20 0.50] 

## energy refers to the energy of the incoming X-ray beam, expressed in keV. 
## use a float (if decimal, the decimal mark should be a point).
# in the following example, the energy is set to 19 keV and 17.5 keV.
% energy = 19 
% energy = 17.5

## ps refers to the physical pixel size of the detector, expressed in microns. 
## use a float (if decimal, the decimal mark should be a point).
# in the following example, the pixel size is set to 1 um and 3.5 um.
% ps = 1
% ps= 3.5

## nbproj refers to the number of (equally-angled) projections simulated. 
## use an integer
%nbProj=360

## range_angle refers to the angular range of the tomography (either 180 or 360 degrees).
## use 180 or 360.
% range_angle = 180 
% range_angle = 360 

## model_ctf refers to the Contrast Transfer Function propagation model. use 1 if you want to simulate propagation with the CTF model, or 0 otherwise.
## should be equal to 0 or 1 
% model_ctf = 1
% model_ctf = 0

## model_Fresnel refers to the Fresnel propagation model. Use 1 if you want to simulate propagation with the fresnel model, or 0 otherwise.
## should be equal to 0 or 1 
% model_Fresnel = 1
% model_Fresnel = 0


############# Parameters related to the circle #############

## attenuation map (in cm^-1)
%attenuation_file='mu_star.edf'

## Refractive index decrement map (delta)
%phase_file='delta_star.edf'

################################
############# OPTIONAL Parameters
################################

## dir_out is a string referring to the output directory
## By default, the output directory is the working directory. default value is ''. 
% dir_out='/mntdirect/_users/lweber/Matlab/SimulationsPBI/Results_Circle' 


## Noise-related part
## Noise addition to the simulated data? 
## Use noise='gaussian' (addition of gaussian noise) or noise='poisson' ( generation of Poisson noise) or '' (no noise is added).

%noise_type='gaussian' 
% default value is '' (no noise)

## Amount of noise
## If 'gaussian' (additive noise), please specify the Peak-to-peak Signe-to-noise ratio (PPSNR, in dB)
% noise_amount=40;
%default value is 35 dB
## if 'poisson', please specify the amount of noise 
%noise_amount=0.05; 
% default value is 5%. 

%noise=0; % O (no noise) or 1 (noise)
%PPSNR=24; % noise, in dB

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############### End of INPUT parameters ############### 
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#################################################
############### OUTPUT parameters ############### 
#################################################

## None, files are directly save in the output directory (variable out_dir)

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############### End of OUTPUT parameters ############### 
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