Recent changes to SART

SART modified by Wim van Aarle

Wim van Aarle — Fri, 20 Dec 2013 14:47:52 -0000

--- v3
+++ v4
@@ -1,31 +1,21 @@
-========================
 # SART

-This is a CPU implementation of the SART algorithm for 2D data sets.  It takes projection data and an initial reconstruction as input, and returns the reconstruction after a specified number of SART iterations.  Each iteration of SART consists of an FP and BP of one single projection direction.  The order of the projections can be specified.
+This is a CPU implementation of the Simultaneous Algebraic Reconstruction Technique (SART) for 2D data sets.  It takes projection data and an initial reconstruction as input, and returns the reconstruction after a specified number of SART iterations.  Each iteration of SART consists of an FP and BP of one single projection direction.  The order of the projections can be specified.

 Supported geometries: parallel, fanflat, fanflat_vec, matrix.

-## Configuration options:
-
-* **cfg.ProjectorId** (required)
-  The astra_mex_projector ID of the projector.
-* **cfg.ProjectionDataId** (required)
-  The astra_mex_data2d ID of the projection data.
-* **cfg.ReconstructionDataId** (required)
-  The astra_mex_data2d ID of the reconstruction data. The content of this when starting SART is used as the initial reconstruction.
-* **cfg.option.SinogramMaskId** (optional)
-  If specified, the astra_mex_data2d ID of a projection-data-sized volume to be used as a [mask](Masks).
-* **cfg.option.ReconstructionMaskId** (optional)
-  If specified, the astra_mex_data2d ID of a volume-data-sized volume to be used as a [mask](Masks).
-* **cfg.option.MinConstraint** (optional)
-  If specified, all values below MinConstraint will be set to MinConstraint. This can, for example, be used to enforce non-negative reconstructions.
-* **cfg.option.MaxConstraint** (optional)
-  If specified, all values above MaxConstraint will be set to MaxConstraint.
-* **cfg.option.ProjectionOrder** (optional, default = 'random')
-  This specifies the order in which the projections are used.  Possible values are: 'random' (default), 'sequential', and 'custom'.  If 'custom' is specified, the option.ProjectionOrderList is required.
-* **cfg.option.ProjectionOrderList** (required if option.ProjectionOrder = 'custom', ignored otherwise)
-  A matlab vector containing the custom order in which the projections are used.
-
+## Configuration options
+name                               | type      | description
+------------------------------------|-----------|-----------------------------------------------------
+**cfg.ProjectorId**                | required  | The astra_mex_projector ID of the projector.
+**cfg.ProjectionDataId**           | required  | The astra_mex_data2d ID of the projection data
+**cfg.ReconstructionDataId**       | required  | The astra_mex_data2d ID of the reconstruction data. The content of this when starting SART is used as the initial reconstruction.
+**cfg.option.SinogramMaskId**      | optional  | If specified, the astra_mex_data2d ID of a projection-data-sized volume to be used as a [mask](Masks).
+**cfg.option.ReconstructionMaskId** | optional | If specified, the astra_mex_data2d ID of a volume-data-sized volume to be used as a [mask](Masks).
+**cfg.option.MinConstraint**       | optional  | If specified, all values below MinConstraint will be set to MinConstraint. This can, for example, be used to enforce non-negative reconstructions.
+**cfg.option.MaxConstraint**       | optional  | If specified, all values above MaxConstraint will be set to MaxConstraint.
+**cfg.option.ProjectionOrder**         | optional  | This specifies the order in which the projections are used.  Possible values are: 'random' (default), 'sequential', and 'custom'.  If 'custom' is specified, the option.ProjectionOrderList is required.
+**cfg.option.ProjectionOrderList**     | optional  | Required if option.ProjectionOrder = 'custom', ignored otherwise.  A matlab vector containing the custom order in which the projections are used.

 ## Example
 ~~~~:::matlab

SART modified by Willem Jan Palenstijn

Willem Jan Palenstijn — Fri, 20 Dec 2013 13:02:47 -0000

--- v2
+++ v3
@@ -3,7 +3,7 @@

 This is a CPU implementation of the SART algorithm for 2D data sets.  It takes projection data and an initial reconstruction as input, and returns the reconstruction after a specified number of SART iterations.  Each iteration of SART consists of an FP and BP of one single projection direction.  The order of the projections can be specified.

-Supported geometries: parallel, fanflat, fanflat_vec, sampling_fanflat, matrix.
+Supported geometries: parallel, fanflat, fanflat_vec, matrix.

 ## Configuration options:

SART modified by Wim van Aarle

Wim van Aarle — Fri, 20 Dec 2013 12:33:07 -0000

--- v1
+++ v2
@@ -8,17 +8,17 @@
 ## Configuration options:

 * **cfg.ProjectorId** (required)
-  The astra_mex_projector ID of the projector
+  The astra_mex_projector ID of the projector.
 * **cfg.ProjectionDataId** (required)
-  The astra_mex_data2d ID of the projection data
+  The astra_mex_data2d ID of the projection data.
 * **cfg.ReconstructionDataId** (required)
-  The astra_mex_data2d ID of the reconstruction data. The content of this when starting SIRT_CUDA is used as the initial reconstruction.
+  The astra_mex_data2d ID of the reconstruction data. The content of this when starting SART is used as the initial reconstruction.
 * **cfg.option.SinogramMaskId** (optional)
-  If specified, the astra_mex_data2d ID of a projection-data-sized volume to be used as a mask. It should only have values 0.0 and 1.0. See the section on [Masks] for details.
+  If specified, the astra_mex_data2d ID of a projection-data-sized volume to be used as a [mask](Masks).
 * **cfg.option.ReconstructionMaskId** (optional)
-  If specified, the astra_mex_data2d ID of a volume-data-sized volume to be used as a mask. It should only have values 0.0 and 1.0. See the section on [Masks] for details.
+  If specified, the astra_mex_data2d ID of a volume-data-sized volume to be used as a [mask](Masks).
 * **cfg.option.MinConstraint** (optional)
-  If specified, all values below MinConstraint will be set to MinConstraint. This can be used to enforce non-negative reconstructions, for example.
+  If specified, all values below MinConstraint will be set to MinConstraint. This can, for example, be used to enforce non-negative reconstructions.
 * **cfg.option.MaxConstraint** (optional)
   If specified, all values above MaxConstraint will be set to MaxConstraint.
 * **cfg.option.ProjectionOrder** (optional, default = 'random')
@@ -48,15 +48,15 @@
 cfg.ReconstructionDataId = recon_id;
 cfg.option.ProjectionOrder = 'custom';
 cfg.option.ProjectionOrderList = [0:5:175 1:5:176 2:5:177 3:5:178 4:5:179];
-sirt_id = astra_mex_algorithm('create', cfg);
-astra_mex_algorithm('iterate', sirt_id, 10*180);
+sart_id = astra_mex_algorithm('create', cfg);
+astra_mex_algorithm('iterate', sart_id, 10*180);
 V = astra_mex_data2d('get', recon_id);
 imshow(V, []);

 %% garbage disposal
 astra_mex_data2d('delete', sinogram_id, recon_id);
 astra_mex_projector('delete', proj_id);
-astra_mex_algorithm('delete', sirt_id);
+astra_mex_algorithm('delete', sart_id);
 ~~~~

-Further examples regarding the different projection orders can be found in example_sart_order.m
+Further examples regarding the different projection orders can be found in example_sart_order.m .

SART modified by Wim van Aarle

Wim van Aarle — Fri, 20 Dec 2013 10:42:32 -0000

========================

SART

This is a CPU implementation of the SART algorithm for 2D data sets. It takes projection data and an initial reconstruction as input, and returns the reconstruction after a specified number of SART iterations. Each iteration of SART consists of an FP and BP of one single projection direction. The order of the projections can be specified.

Supported geometries: parallel, fanflat, fanflat_vec, sampling_fanflat, matrix.

Configuration options:

cfg.ProjectorId (required)
The astra_mex_projector ID of the projector
cfg.ProjectionDataId (required)
The astra_mex_data2d ID of the projection data
cfg.ReconstructionDataId (required)
The astra_mex_data2d ID of the reconstruction data. The content of this when starting SIRT_CUDA is used as the initial reconstruction.
cfg.option.SinogramMaskId (optional)
If specified, the astra_mex_data2d ID of a projection-data-sized volume to be used as a mask. It should only have values 0.0 and 1.0. See the section on [Masks] for details.
cfg.option.ReconstructionMaskId (optional)
If specified, the astra_mex_data2d ID of a volume-data-sized volume to be used as a mask. It should only have values 0.0 and 1.0. See the section on [Masks] for details.
cfg.option.MinConstraint (optional)
If specified, all values below MinConstraint will be set to MinConstraint. This can be used to enforce non-negative reconstructions, for example.
cfg.option.MaxConstraint (optional)
If specified, all values above MaxConstraint will be set to MaxConstraint.
cfg.option.ProjectionOrder (optional, default = 'random')
This specifies the order in which the projections are used. Possible values are: 'random' (default), 'sequential', and 'custom'. If 'custom' is specified, the option.ProjectionOrderList is required.
cfg.option.ProjectionOrderList (required if option.ProjectionOrder = 'custom', ignored otherwise)
A matlab vector containing the custom order in which the projections are used.

Example

%% create phantom
V_exact = phantom(256);

%% create geometries and projector
proj_geom = astra_create_proj_geom('parallel', 1.0, 256, linspace2(0,pi,180));
vol_geom = astra_create_vol_geom(256,256);
proj_id = astra_create_projector('linear', proj_geom, vol_geom);

%% create forward projection
[sinogram_id, sinogram] = astra_create_sino(V_exact, proj_id);

%% reconstruct
recon_id = astra_mex_data2d('create', '-vol', vol_geom, 0);
cfg = astra_struct('SART');
cfg.ProjectorId = proj_id;
cfg.ProjectionDataId = sinogram_id;
cfg.ReconstructionDataId = recon_id;
cfg.option.ProjectionOrder = 'custom';
cfg.option.ProjectionOrderList = [0:5:175 1:5:176 2:5:177 3:5:178 4:5:179];
sirt_id = astra_mex_algorithm('create', cfg);
astra_mex_algorithm('iterate', sirt_id, 10*180);
V = astra_mex_data2d('get', recon_id);
imshow(V, []);

%% garbage disposal
astra_mex_data2d('delete', sinogram_id, recon_id);
astra_mex_projector('delete', proj_id);
astra_mex_algorithm('delete', sirt_id);

Further examples regarding the different projection orders can be found in example_sart_order.m