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ENH: Initial support of DRR calculation for orientated CT volumes #240

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ENH: Initial support of DRR calculation for orientated CT volumes #240

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74 changes: 56 additions & 18 deletions Docs/user_guide/modules/drr.md
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Original file line number Diff line number Diff line change
Expand Up @@ -50,24 +50,56 @@ based on [plastimatch drr](http://www.plastimatch.org/drr.html) ones.

### Graphical User Interface loadable module (GUI)

![image](https://user-images.githubusercontent.com/3785912/118298680-726b9e80-b4e8-11eb-8a39-c5e607459e62.png)
![image](https://private-user-images.githubusercontent.com/3785912/294439297-c315f0db-9ab7-4a91-9eaa-10a4698d7cd8.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.J_kchHVITj00Qsd6Z84Wujp8kEXvknmQYZ9SoiWgqbA)

Loadable GUI module "DRR Image Computation" uses CLI module's logic and nodes data to calculate
and visualize DRR image. It also shows basic detector elements such as: detector boundary,
detector normal vector, detector view-up vector, detector image origin (0,0) pixel,
image subwindow boundary as markups data on a slice and 3D views.

Markups data is only for WYSIWYG purpose.
This module _partially_ supports calculation of DRR for orientated CT volumes,
if IJKToRASDirection matrix of the volume isn't as below.

| -1 0 0 0 |
| 0 -1 0 0 |
| 0 0 1 0 |
| 0 0 0 1 |

The markups data is only for WYSIWYG purpose.

#### Reference input nodes

![image](https://user-images.githubusercontent.com/3785912/118298709-7e576080-b4e8-11eb-8c2b-b1a4f8222eba.png)
![image](https://private-user-images.githubusercontent.com/3785912/294439383-a0718f87-81bf-4a9f-880b-34876a6152ed.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.ZrUVivDARk6G1kLMgdk36E3r-z0UzOV7SLK2OUBZzbg)

1. **CT volume**: Input CT data
2. **RT beam**: Input RT beam (vtkMRMLRTBeamNode) for source and detector orientation parameters
2. **Camera**: Camera node (vtkMRMLCameraNode) to update if needed beam geometry and transformation
3. **Update beam**: Update beam geometry and transformation using camera node data
4. **Show DRR markups**: Show or hide detector markups
4. **Volume direction to LPS transform matrix**: The matrix widget shows elements of the transformation matrix R
The volume direction to LPS transform matrix _R_
can be applied to the volume, to make IJKToRASDirectionMatrix of the volume a LPS orientated
after hardening the transform.

If IJKToRASDirection matrix _A_ isn't LPS transform

| a11 a12 a13 a14 | | -1 0 0 0 |
_A_ = | a21 a22 a23 a24 | != | 0 -1 0 0 |
| a31 a32 a33 a34 | | 0 0 1 0 |
| a41 a42 a43 a44 | | 0 0 0 1 |

the volume direction to LPS transform matrix _R_ can be applied to the volume,
by clicking on `Apply transform to volume` button, to make
the IJKToRASDirection matrix a LPS orientated after hardening the transform.
the matrix transformation:

| -1 0 0 0 |
_R_ = _A_^-1 * | 0 -1 0 0 |
| 0 0 1 0 |
| 0 0 0 1 |

if matrix _A_ is LPS orientated => matrix _R_ is an identity matrix.

5. **Show DRR markups**: Show or hide detector markups

CT data is represented by vtkMRMLScalarVolumeNode object. RT beam data is
represented by vtkMRMLRTBeamNode object. Camera data is represented by vtkMRMLCameraNode object.
Expand All @@ -76,27 +108,33 @@ represented by vtkMRMLRTBeamNode object. Camera data is represented by vtkMRMLCa

![image](https://user-images.githubusercontent.com/3785912/107616499-40d00680-6c5f-11eb-9d45-c6cccc9e12cd.png)

4. **Isocenter to imager distance**: Distance from isocenter to detector center in mm
5. **Imager resolution (columns, rows)**: Detector resolution in pixels
6. **Imager spacing in mm (columns, rows)**: Detector spacing in mm
7. **Image window parameters**: Use and setup image subwindow or a whole detector
6. **Isocenter to imager distance**: Distance from isocenter to detector center in mm
7. **Imager resolution (columns, rows)**: Detector resolution in pixels
8. **Imager spacing in mm (columns, rows)**: Detector spacing in mm
9. **Image window parameters**: Use and setup image subwindow or a whole detector

#### Image Window Parameters
8. **Columns**: Number of image columns in subwindow
9. **Rows**: Number of image rows in subwindow
10. **Columns**: Number of image columns in subwindow
11. **Rows**: Number of image rows in subwindow

#### Markups perspective projection on the imager plane

![image](https://private-user-images.githubusercontent.com/3785912/294439414-d1bbb6ac-4838-47a7-88fc-9ec76bfe19b2.png?jwt=eyJhbGciOiJIUzI1NiIsInR5cCI6IkpXVCJ9.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.yUYlwYdj9JdqD7CUyS-zFfZ4tV0Yezux__UI35jEUlg)

Calculates projection of fiducial markups points in imager plane.

#### Plastimatch DRR image processing

![image](https://user-images.githubusercontent.com/3785912/107617306-b38db180-6c60-11eb-9dd1-b2751b23a314.png)

10. **Use exponential mapping**: Apply exponential mapping of output values
11. **Autoscale**: Automatically rescale intensity
12. **Invert**: Invert image intensity
13. **Range**: Range intensity in form (min, max)
14. **Reconstruction algorithm**: Type of reconstruction algorithm (Type of exposure algorithm in CLI module)
15. **Hounsfield units conversion**: Type of Hounsfield Units conversion during computation
16. **Threading**: Type of parallelism of computation
17. **Hounsfield units threshold**: HU values below threshold are counted as -1000 (Air value)
12. **Use exponential mapping**: Apply exponential mapping of output values
13. **Autoscale**: Automatically rescale intensity
14. **Invert**: Invert image intensity
15. **Range**: Range intensity in form (min, max)
16. **Reconstruction algorithm**: Type of reconstruction algorithm (Type of exposure algorithm in CLI module)
17. **Hounsfield units conversion**: Type of Hounsfield Units conversion during computation
18. **Threading**: Type of parallelism of computation
19. **Hounsfield units threshold**: HU values below threshold are counted as -1000 (Air value)

#### Plastimatch DRR command arguments (read only)

Expand Down
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