VTK Camera Loader #147

NicerNewerCar · 2023-07-14T13:17:03Z

Adds a new camera loader for VTK cameras
- Defined as a *.json file

{
  "@schema": "https://autoscoperm.slicer.org/vtk-schema-1.0.json",
  "version": 1.0,
  "focal-point": [-7.9999999999999964, -245.50000000000006, -186.65000000000006],
  "camera-position": [104.71926635196253, -255.22259800818924, -179.66771669788898],
  "view-up": [0.0, 1.0, 0.0],
  "view-angle": 30.0,
  "image-width": 1760,
  "image-height": 1760,
}

NicerNewerCar · 2023-08-17T18:35:54Z

Update 8.17.23

It would appear that both of the cameras are not looking at the correct spot, I suspect it has something to do with my Rotation calculations. Note the location of the manipulator in Autoscoper represents the focal point of both cameras. The radiograph images are the directions of the actual cameras within Autoscoper.

Camera Layout	Slicer	Autoscoper

Another 8.17.23 Update

Getting closer, I think there may be another issue with the orientations of the VRGs but that will be fixed by the extension.

NicerNewerCar · 2023-08-18T15:35:41Z

Update 8.18.23

Initially, I had thought that the issue had lied with the VRG gen but upon further inspection, I think the rotations within Autoscoper are just slightly off. As of right now, it is impossible to align the partial volumes with both of the radiographs.
Below is a quick recording of the problem as well as the current calculations being done to compute the rotation for each camera. [From Slicer I am exporting the camera position and the focal point, the view up vector is constant between cameras with the y-axis being the up direction.]

Autoscoper/libautoscoper/src/Camera.cpp

Lines 553 to 558 in e00fee9

    
           Vec3d normal; 
        
           normal.x = focal_point[0] - camera_pos[0]; 
        
           normal.y = focal_point[1] - camera_pos[1]; 
        
           normal.z = focal_point[2] - camera_pos[2]; 
        
           normal = unit(normal); // Normalize the vector

Autoscoper/libautoscoper/src/Camera.cpp

Lines 569 to 582 in e00fee9

    
               Vec3d up(0, 1, 0); 
        
               Vec3d w0(-normal.y, normal.x, 0); 
        
               Vec3d u0 = cross(w0,up); 
        
               double angle_x, angle_y, angle_z; 
        
               angle_z = std::atan(normal.x / -normal.y); 
        
               angle_y = std::atan(std::sqrt(normal.x * normal.x + normal.y * normal.y) / normal.z); 
        
               /*angle_z = std::atan2(normal.y, normal.x); 
        
               angle_y = std::asin(normal.z);*/ 
        
               angle_x = std::atan2( 
        
                 dot(w0,up), 
        
                 dot(u0,up) / std::sqrt(dot(w0,w0)) * std::sqrt(dot(u0,u0)) 
        
               );

NicerNewerCar · 2023-08-28T17:46:00Z

Update 8.28.23

I think I got it now, I ended up adding an implementation of glLookAt, similar to what is described here

Autoscoper/libautoscoper/src/Camera.cpp

Lines 561 to 572 in 35c9100

    
           double* Camera::lookAt(Vec3d eye, Vec3d center, Vec3d up) { 
        
             // Implementation based off of: 
        
             // https://www.khronos.org/opengl/wiki/GluLookAt_code 
        
             Vec3d forward = unit(center - eye); 
        
             Vec3d side = unit(cross(forward, up)); 
        
             up = cross(side, forward); 
        
             double matrix[9]; 
        
             matrix[0] = side.x; matrix[1] = side.y; matrix[2] = side.z; 
        
             matrix[3] = up.x; matrix[4] = up.y; matrix[5] = up.z; 
        
             matrix[6] = -forward.x; matrix[7] = -forward.y; matrix[8] = -forward.z; 
        
             return matrix; 
        
           }

NicerNewerCar · 2023-08-28T19:06:28Z

Rebase with #200 once integrated

amymmorton · 2023-08-29T20:20:26Z

After building PR #53 and PR #147 Anthony and I used the PRE PROC LEFT Hop Knee dicom to run through the vrg gen in SAM.

Successful use of all tabs in 53

When loaded with the optimized cams config, I attempted to track both tib and femur.. poor results.

Same with all cameras (optimized and manually placed)

Going to try with wrist data - both vrg/pv gen and see if we do get a good ncc optimizziton

libautoscoper/src/Camera.hpp

libautoscoper/src/Camera.cpp

amymmorton · 2023-09-01T18:41:51Z

The config file generation step in this branch is integral for agreement testing. Would it be possible to push that feature to main?

NicerNewerCar · 2023-09-05T13:08:51Z

The config file generation step in this branch is integral for agreement testing. Would it be possible to push that feature to main?

There is no config generation on this branch, are you referring to BrownBiomechanics/SlicerAutoscoperM#53?

libautoscoper/src/Camera.cpp

Documentation/file-specifications/camera-calibration.md

libautoscoper/src/Camera.cpp

Documentation/file-specifications/camera-calibration.md

* Both loadMayaCam1 & 2 had duplicated code. * Add new helper methods `calculateViewport` and `calculateImagePlane` to remove this duplication. * Simplified some of the math by checking in loadMayaCam1 if z is negative.

Documentation/file-specifications/camera-calibration.md

libautoscoper/src/Camera.cpp

jcfr · 2023-09-25T19:30:28Z

For reference, to review the changes while ignoring the space change, this link can be used. See https://github.com/BrownBiomechanics/Autoscoper/pull/147/files?w=1

…td::remove Fix build error like the following reported when using GCC 9.4.0 on Ubuntu 20.04: /path/to/Autoscoper/libautoscoper/src/Camera.cpp:397:44: error: cannot convert ‘std::__cxx11::basic_string<char>::iterator’ {aka ‘__gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >’} to ‘const char*’ 397 | value.erase(std::remove(value.begin(), value.end(), ']'), value.end()); | ~~~~~~~~~~~^~ | | | std::__cxx11::basic_string<char>::iterator {aka __gnu_cxx::__normal_iterator<char*, std::__cxx11::basic_string<char> >}

Fix the following warning: /path/to/Autoscoper/libautoscoper/src/Camera.cpp: In member function ‘double* xromm::Camera::calculateFocalLength(const double&)’: /path/to/Autoscoper/libautoscoper/src/Camera.cpp:602:12: warning: address of local variable ‘focal_lengths’ returned [-Wreturn-local-addr] 602 | return focal_lengths; | ^~~~~~~~~~~~~ /path/to/Autoscoper/libautoscoper/src/Camera.cpp: In member function ‘double* xromm::Camera::lookAt(Vec3d, Vec3d, Vec3d)’: /path/to/Autoscoper/libautoscoper/src/Camera.cpp:615:12: warning: address of local variable ‘matrix’ returned [-Wreturn-local-addr] 615 | return matrix; | ^~~~~~

Also improve readability by splitting setting of each matrix element on its own line.

…Matrix"

…ction

libautoscoper/src/Camera.cpp

jcfr

After updating the schema URL, this will be ready for integration.

For sake of consistency with how Slicer integrates JsonCpp, we ignore the "jsoncppConfig.cmake" file provided by jsoncpp CMake project and instead set JsonCpp_INCLUDE_DIR and JsonCpp_LIBRARY expected by the "FindJsonCpp" CMake module. To streamline distribution of the standalone Autoscoper executable, update JsonCpp project to statically build the JsonCpp library.

libautoscoper/src/Camera.cpp

NicerNewerCar force-pushed the camera-update branch from c160591 to e0d3fbb Compare July 14, 2023 13:18

NicerNewerCar force-pushed the camera-update branch from e0d3fbb to 54aa0e4 Compare August 14, 2023 17:51

NicerNewerCar mentioned this pull request Aug 17, 2023

Virtual Radiograph Generation Module BrownBiomechanics/SlicerAutoscoperM#53

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NicerNewerCar force-pushed the camera-update branch 2 times, most recently from 89045a1 to e00fee9 Compare August 18, 2023 15:28

NicerNewerCar force-pushed the camera-update branch 2 times, most recently from aa7857d to 35c9100 Compare August 28, 2023 17:43

NicerNewerCar changed the title ~~WIP: Camera update for Multi-modality support~~ VTK Camera Loader Aug 28, 2023

NicerNewerCar force-pushed the camera-update branch from 35c9100 to 7795207 Compare August 28, 2023 18:05

NicerNewerCar marked this pull request as ready for review August 28, 2023 18:06

NicerNewerCar requested a review from jcfr August 28, 2023 18:06

NicerNewerCar force-pushed the camera-update branch 3 times, most recently from 524190a to b25162e Compare August 29, 2023 14:05

NicerNewerCar linked an issue Aug 29, 2023 that may be closed by this pull request

Converting between VTK cameras and Autoscoper cameras #197

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NicerNewerCar force-pushed the camera-update branch from 01e4e93 to 41d76ea Compare August 30, 2023 13:20

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NicerNewerCar force-pushed the camera-update branch 2 times, most recently from 9f0dda0 to 8ffae49 Compare September 13, 2023 18:16

NicerNewerCar requested a review from jcfr September 13, 2023 18:17

jcfr reviewed Sep 13, 2023

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STYLE: Refactor mayacam readers

5d98799

* Both loadMayaCam1 & 2 had duplicated code. * Add new helper methods `calculateViewport` and `calculateImagePlane` to remove this duplication. * Simplified some of the math by checking in loadMayaCam1 if z is negative.

NicerNewerCar force-pushed the camera-update branch 2 times, most recently from cfb2260 to 3f724c9 Compare September 25, 2023 13:25

jcfr reviewed Sep 25, 2023

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libautoscoper/src/Camera.cpp Show resolved Hide resolved

DOC: Fix incorrect statements in the camera calibration file specs

c2a92f5

NicerNewerCar force-pushed the camera-update branch 2 times, most recently from 58323c3 to 38cc22c Compare September 25, 2023 15:50

NicerNewerCar requested a review from jcfr September 25, 2023 15:50

jcfr force-pushed the camera-update branch 2 times, most recently from 5f46175 to 0762d92 Compare September 25, 2023 20:48

NicerNewerCar and others added 7 commits September 25, 2023 17:06

ENH: Add VTKCam Reader

3e72db1

COMP: Fix constness of "lookAt" function

16f08df

Also improve readability by splitting setting of each matrix element on its own line.

STYLE: Improve name consistency renaming "lookAt" to "calculateLookAt…

d670c36

…Matrix"

COMP: Remove unused and undefined Camera::calculateRotationMatrix fun…

df41ba2

…ction

ENH: Add Schema for vtkCamera JSON file

fcfad15

jcfr force-pushed the camera-update branch from 0762d92 to 062a702 Compare September 25, 2023 21:08

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NicerNewerCar and others added 3 commits September 26, 2023 09:20

ENH: Refactor VTK Cam loader for JSON files

eb8f561

STYLE: Consistently indent Camera.cpp

0c11207

NicerNewerCar force-pushed the camera-update branch from f6deb01 to 0c11207 Compare September 26, 2023 13:20

NicerNewerCar merged commit 97c8deb into BrownBiomechanics:main Sep 26, 2023
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ENH: Update Autoscoper with various enhancements and fixes BrownBiomechanics/SlicerAutoscoperM#67

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VTK Camera Loader #147

VTK Camera Loader #147

NicerNewerCar commented Jul 14, 2023 •

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VTK Camera Loader #147

VTK Camera Loader #147

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NicerNewerCar commented Jul 14, 2023 • edited Loading

NicerNewerCar commented Aug 17, 2023 • edited Loading

Update 8.17.23

Another 8.17.23 Update

NicerNewerCar commented Aug 18, 2023

Update 8.18.23

NicerNewerCar commented Aug 28, 2023

Update 8.28.23

NicerNewerCar commented Aug 28, 2023

amymmorton commented Aug 29, 2023

amymmorton commented Sep 1, 2023

NicerNewerCar commented Sep 5, 2023

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