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Automatic Ablation Volume Estimation

The following repo includes python code, that enables us to read STL files, results from a 3D light scanner of stones with grooves. The grooves were created using laser cutting technology, and the goal is to measure the volume of the grooves automatically. The repo includes the main script Main.py, which should be executed cell by cell, fine-tuning the parameters, and examine the results at every step. utils.py contain utils function, serving the Main.py script, plane.py calculate the plane equation using the RANSAC method.

Requirements: Open3D, and Pytorch with Cuda to support GPU calculation. In addition, Python standard packages like Numpy, Scipy, Matplotlib.

Oped3d:

conda install -c open3d-admin open3d

PyTorch with GPU:

conda install pytorch torchvision torchaudio cudatoolkit=10.2 -c pytorch

Algorithm

The algorithm includes the following steps (modules or cells in Main.py):

  1. Read STL file (mesh triangulation) and convert it into Point Cloud
  2. Optional Rotation of the point cloud. In our dataset, the planes were aligned with the coordinate system, but if your stone planes aren't aligned with the coordinate system, you should align them, to make the automatic analysis possible. your first need to extract the angels from the detected main plane and then rotate the whole point cloud.
  3. Convert the Point cloud into Voxel Grid and calculate the calibration of Voxel Grid.
  4. Calculate the main plane equation (Ax+By+Cz+D=0). this equation will help us to correct the point cloud z-position. we use the RANSAC method with 1000 iterations.
  5. Identify the grooves and extract the points from the point cloud that contain each groove. we use projection (You can use X-axis or Y-axis projection), and using the maximum height in each interval projection, we can find the beginning and end of the groove. we divide the point cloud and plot the result.
  6. Cutting the edges of the projection, because we want to calculate the volume of the stone, using only the main plane, and we need to delete the rest of the planes.
  7. Calculate the volume of the groove using discrete integral,
  8. Plot grooves and volumes

Example of Results and steps

Stone 3D scan, presented in Point Cloud (mesh triangulation) Image 1

when we transform the format to Voxel Grid, the stone looks as: Image 2

The main plane: Image 3

Then we look at the Y-axis projection to try and find the grooves: Image 4

And after some processing, we find the beginning and the end of the grooves Image 5

We remove the unnecessary planes, using the projection at the orthogonal axis: Image 6

And we can easily segment the groove, in both Point cloud: Image 7

And in Voxel Grid: Image 8

And we get the following segmentation on the stone, that enable us to easily compute the volumes: Image 9

Image 10

Image 11

License

Private Property of Lumenis LTD.

Contact information

Developed by Sharon Haimov, Research Engineer at Lumenis.

Email: [email protected] or [email protected]