Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
Merge pull request #14 from dkazanc/typecheck
new interface to create Objects and Sinograms.
- Loading branch information
Showing
20 changed files
with
1,576 additions
and
1,312 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Large diffs are not rendered by default.
Oops, something went wrong.
Large diffs are not rendered by default.
Oops, something went wrong.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,87 @@ | ||
| #!/usr/bin/env python3 | ||
| # -*- coding: utf-8 -*- | ||
| """ | ||
| GPLv3 license (ASTRA toolbox) | ||
| Note that the TomoPhantom package is released under Apache License, Version 2.0 | ||
| Script to generate 2D/3D analytical phantoms and their sinograms | ||
| If one needs to modify/add phantoms, please edit Phantom2DLibrary.dat or | ||
| Phantom3DLibrary.dat | ||
| >>>> Prerequisites: ASTRA toolbox, if one needs to do reconstruction <<<<< | ||
| Main difference from DemoModel.py is that we extract all parameters from the | ||
| library file using Python and then pass it to the Object function instead of model | ||
| Run demo from the folder "Demos" | ||
| @author: Daniil Kazantsev | ||
| """ | ||
| import numpy as np | ||
| import matplotlib.pyplot as plt | ||
| from tomophantom import TomoP2D | ||
| from astraOP import AstraTools | ||
| from libraryToDict import modelfile2Dtolist | ||
|
|
||
| #%% | ||
| model = 11 | ||
| N_size = 512 | ||
| #specify a full path to the parameters file | ||
| pathTP = '../../functions/models/Phantom2DLibrary.dat' | ||
| objlist = modelfile2Dtolist(pathTP, model) # extract parameters using Python | ||
| #This will generate a N_size x N_size phantom (2D) | ||
| phantom_2D = TomoP2D.Object(N_size, objlist) | ||
|
|
||
| plt.close('all') | ||
| plt.figure(1) | ||
| plt.rcParams.update({'font.size': 21}) | ||
| plt.imshow(phantom_2D, vmin=0, vmax=1, cmap="BuPu") | ||
| plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical') | ||
| plt.title('{}''{}'.format('2D Phantom using model no.',model)) | ||
| #%% | ||
| # create sinogram analytically | ||
| angles_num = int(0.5*np.pi*N_size); # angles number | ||
| angles = np.linspace(0,180,angles_num,dtype='float32') | ||
| angles_rad = angles*(np.pi/180) | ||
| P = int(np.sqrt(2)*N_size) #detectors | ||
|
|
||
| sino_an = TomoP2D.ObjectSino(N_size, P, angles, objlist) | ||
|
|
||
| plt.figure(2) | ||
| plt.rcParams.update({'font.size': 21}) | ||
| plt.imshow(sino_an, cmap="BuPu") | ||
| plt.colorbar(ticks=[0, 150, 250], orientation='vertical') | ||
| plt.title('{}''{}'.format('Analytical sinogram of model no.',model)) | ||
| #%% | ||
| Atools = AstraTools(P, angles_rad, N_size, 'cpu') # initiate a class object | ||
| sino_num_ASTRA = Atools.forwproj(phantom_2D) # generate numerical sino (Ax) | ||
| #x = Atools.backproj(sino_an) # generate backprojection (A'b) | ||
|
|
||
| plt.figure(3) | ||
| plt.subplot(121) | ||
| plt.imshow(sino_an,cmap="BuPu") | ||
| plt.title('Analytical sinogram') | ||
| plt.subplot(122) | ||
| plt.imshow(sino_num_ASTRA,cmap="BuPu") | ||
| plt.title('Numerical sinogram') | ||
| plt.show() | ||
| #%% | ||
| print ("Reconstructing analytical sinogram using FBP (astra TB)...") | ||
| FBPrec1 = Atools.fbp2D(sino_an) | ||
| plt.figure(4) | ||
| plt.imshow(FBPrec1, vmin=0, vmax=1, cmap="BuPu") | ||
| plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical') | ||
| plt.title('FBP Reconstructed Phantom (analyt)') | ||
| #%% | ||
| print ("Reconstructing numerical sinogram using FBP (astra TB)...") | ||
| FBPrec2 = Atools.fbp2D(sino_num_ASTRA) | ||
| plt.figure(5) | ||
| plt.imshow(FBPrec2, vmin=0, vmax=1, cmap="BuPu") | ||
| plt.colorbar(ticks=[0, 0.5, 1], orientation='vertical') | ||
| plt.title('FBP Reconstructed Phantom (numeric)') | ||
| #%% | ||
| plt.figure(6) | ||
| plt.imshow(abs(FBPrec1-FBPrec2), vmin=0, vmax=0.05, cmap="BuPu") | ||
| plt.colorbar(ticks=[0, 0.02, 0.05], orientation='vertical') | ||
| plt.title('FBP rec differences') | ||
| rmse2 = np.linalg.norm(FBPrec1 - FBPrec2)/np.linalg.norm(FBPrec2) | ||
| #%% |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Oops, something went wrong.