Add the readme (README_SimuPBI_3WiresPhant_func.txt), and make some minor changes...

diff --git a/README_SimuPBI_3WiresPhant_func.txt b/README_SimuPBI_3WiresPhant_func.txt
new file mode 100644 (file)
index 0000000..b669791
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+++ b/README_SimuPBI_3WiresPhant_func.txt
@@ -0,0 +1,113 @@
+## 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.
+
+################################################
+############### INPUT parameters ############### 
+################################################
+
+######### 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 obejct 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
+
+#######################################################
+############### End of INPUT parameters ############### 
+#######################################################
+
+#################################################
+############### OUTPUT parameters ############### 
+#################################################
+
+## None, files are directly save in the output directory (variable out_dir)
+
+########################################################
+############### End of OUTPUT parameters ############### 
+########################################################
+

diff --git a/SimuPBI_3WiresPhant_func.m b/SimuPBI_3WiresPhant_func.m
index 094fce7e467021e02eb5f5cd1e670599c25bb34b..65b550ff0084a76b1b299495d63b7af294b1e371 100644 (file)
--- a/SimuPBI_3WiresPhant_func.m
+++ b/SimuPBI_3WiresPhant_func.m
@@ -67,8 +67,15 @@ addpath(genpath('octave_packages'))
 %range_angle=180; 
 
 ## Which model do you want to use for the propagation? use 1 or 0
-%model_ctf=0;
-%model_Fresnel=1;
+## 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