## 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_3WirePhant_func('Analytical', 2, 'test', [0 0.1 0.5], 19, 2.7, 300, 180, 1, 0, '', 'gaussian', 35)

## Please note that dir_out, noise_type, noise_amount are optional arguments.
## This method requires the files 'attenuation.edf', and 'delta_beta_map_1200.edf' in the "images"

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

## vers: is a string that defines the way to compute the projections. (ie: are the projections calculated analytically (vers = 'Analytical') or using the Radon transform (vers = 'Radon') ?)
## use the strings 'Radon' OR 'Analytical'
## be careful, octave is case-sensitive.
%vers = 'Analytical' 
%vers = 'Radon'

## 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 object #############
## in this case, the object is a three wire phantom, described in [Frachon, Weber et al., PMB, 2016]. 
## height of the object. If height == 1, the simulation is computed in 1D. If height >=2 , the simulation turns into 2D.
%height=10;

################################
############# 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_type is a string, referring to the type of noise you want to add to the simulated projections. 
## Use 'gaussian' for addition of gaussian noise, 'poisson' for generation of Poisson noise, or '' for no noise.
## the default value is '' (no noise)
% noise_type='gaussian' 


## noise_amount is a number (integer or float) referring to the amount of noise. It is defined depending on the type of noise:
## For additive Gaussian noise, noise_amount is the Peak-to-Peak Signal-to-Noise Ratio (PPSNR), expressed in dB.
## The default value for additive gaussian noise is 35 dB (noise_amount = 35). 
% noise_amount = 40

## For Poisson noise, noise_amount refer to the percentage of noise. 
## The default value is 5% (noise_amount=0.05). 
% noise_amount = 0.15 
## !! note that poisson noise is here not implemented yet

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

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