1 ## SimuPBI_circle_func: function that launches the phase-contrast simulation of a single wire, of a material defined by the user.
2 # In this file, I detailed all the input and output arguments, followed by one or several examples (one line beginning with a %)
3 ## Author: Loriane Weber <loriane.weber@creatis.insa-lyon.fr>
7 ## SimuPBI_3WirePhant_func('Analytical', 2, 'test', [0 0.1 0.5], 19, 2.7, 300, 180, 1, 0, '', 'gaussian', 35)
9 ## Please note that dir_out, noise_type, noise_amount are optional arguments.
11 ################################################
12 ############### INPUT parameters ###############
13 ################################################
15 ######### Parameter related to the computation - and names of the result #########
17 ## 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') ?)
18 ## use the strings 'Radon' OR 'Analytical'
19 ## be careful, octave is case-sensitive.
23 ## oversamp: is a number that defines the oversampling of the projections in the real domain.
24 ## use the number 2 or 4 only
28 ## basename_output: is a string that contains the basename of the resulting files.
29 ## use a string, of your choice.
30 %basename_output = 'Test'
32 ######### Parameter related to the physics #########
34 ## dist is a vector, which contains the propagation distances, expressed in meters.
35 ## use a vector, beggining and ending with a square bracket; the distances should be separated by a space. Use a point as decimal mark.
36 % dist = [0 0.01 0.1 0.20 0.50]
38 ## energy refers to the energy of the incoming X-ray beam, expressed in keV.
39 ## use a float (if decimal, the decimal mark should be a point).
40 # in the following example, the energy is set to 19 keV and 17.5 keV.
44 ## ps refers to the physical pixel size of the detector, expressed in microns.
45 ## use a float (if decimal, the decimal mark should be a point).
46 # in the following example, the pixel size is set to 1 um and 3.5 um.
50 ## nbproj refers to the number of (equally-angled) projections simulated.
54 ## range_angle refers to the angular range of the tomography (either 180 or 360 degrees).
59 ## 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.
60 ## should be equal to 0 or 1
64 ## model_Fresnel refers to the Fresnel propagation model. Use 1 if you want to simulate propagation with the fresnel model, or 0 otherwise.
65 ## should be equal to 0 or 1
70 ############# Parameters related to the object #############
71 ## in this case, the obejct is a three wire phantom, described in [Frachon, Weber et al., PMB, 2016].
72 ## height of the object. If height == 1, the simulation is computed in 1D. If height >=2 , the simulation turns into 2D.
75 ################################
76 ############# OPTIONAL Parameters
77 ################################
79 ## dir_out is a string referring to the output directory
80 ## By default, the output directory is the working directory. default value is ''.
81 % dir_out='/mntdirect/_users/lweber/Matlab/SimulationsPBI/Results_Circle'
84 ## noise_type is a string, referring to the type of noise you want to add to the simulated projections.
85 ## Use 'gaussian' for addition of gaussian noise, 'poisson' for generation of Poisson noise, or '' for no noise.
86 ## the default value is '' (no noise)
87 % noise_type='gaussian'
90 ## noise_amount is a number (integer or float) referring to the amount of noise. It is defined depending on the type of noise:
91 ## For additive Gaussian noise, noise_amount is the Peak-to-Peak Signal-to-Noise Ratio (PPSNR), expressed in dB.
92 ## The default value for additive gaussian noise is 35 dB (noise_amount = 35).
95 ## For Poisson noise, noise_amount refer to the percentage of noise.
96 ## The default value is 5% (noise_amount=0.05).
98 ## !! note that poisson noise is here not implemented yet
100 #######################################################
101 ############### End of INPUT parameters ###############
102 #######################################################
104 #################################################
105 ############### OUTPUT parameters ###############
106 #################################################
108 ## None, files are directly save in the output directory (variable out_dir)
110 ########################################################
111 ############### End of OUTPUT parameters ###############
112 ########################################################