Contributors: Juan Prieto, Maxime Dumont, Louis Bumbolo, Mathieu Leclerq, Baptiste Baquero
Fly by CNN is an approach to capture 2D views from 3D objects and use the generated images to train deep learning algorithms or make inference once you have a trained model.
It scales the mesh to the unit sphere, then, depending on the type of sampling chosen, it captures views from these view points. There are currently 2 types of sampling, i.e., icosahedron subdivision or following the path of a spiral.
- Icosahedron subdivision: regular subdivision of the sphere.
- Spiral: Smooth path in the sphere that generates a sequence of images.
The easiest way is to use the docker container.
docker pull dcbia/fly-by-cnn:latest
docker run --gpus all -t -i -u $(id -u):$(id -g) --name fly_by_cnn dcbia/fly-by-cnn:latest /bin/bash
Once inside the container you can run to get all the available options.
python /app/fly-by-cnn/src/py/fly_by_features.py --help
- Example: This example will extract the normals and the depth map as a separate component and generate a single 3D image with all the views.
python /app/fly-by-cnn/src/py/fly_by_features.py --surf my_surf.(vtk,.stl,.obj) --subdivision 2 --resolution 512 --out out.nrrd --radius 2 --use_z 1 --split_z 1"
The easiest way to use the docker container. Docker/README.md
Here are the command lines to run the scripts:
Universal Labeling:
Input:
- Dental crown model that contains the teeth of a patient (vtk file)
Output:
- Dental crown model with the universal labels on each tooth (vtk file)
python3 fly-by-cnn/src/py/universal_labeling.py --help
usage: universal_labeling.py [-h] --surf SURF --label_groundtruth
LABEL_GROUNDTRUTH --model_feature MODEL_FEATURE
--model_LU MODEL_LU --out_feature OUT_FEATURE
[--out OUT]
Label the teeth from 2 to 16 or with the universal IDs used by clinicians
optional arguments:
-h, --help show this help message and exit
--surf SURF Input surface mesh to label (default: None)
--out OUT Output model with labels (default: out.vtk)
Label parameters:
--label_groundtruth LABEL_GROUNDTRUTH
directory of the template labels (default: None)
Prediction parameters:
--model_feature MODEL_FEATURE
path of the VGG19 model (default: None)
--model_LU MODEL_LU path of the LowerUpper model (default: None)
--out_feature OUT_FEATURE
out of the feature (default: None)
Merging and Separating:
Inputs:
- Dental crown model that contains the teeth of a patient with the universal labels on each tooth (vtk file)
- The root canal segmentation file (.nii)
Output:
- A merged model with the teeth and roots labeled based on the universal labels and individual teeth and roots (vtk files)
bash fly-by-cnn/src/sh/compute_MergingSeparating.sh --help
Program to run the Merging and Separating algorithm
Syntax: compute_MergingSeparating.sh [--options]
options:
--src_code Path of the source code
--input_file_uid Output directory of the teeth with the universal labels.
--input_file_root Input directory with the root canal segmentation files.
--out_tmp Temporary output folder.
--out_merge Output directory of the merged surfaces.
--out_separate Output directory of the separated surfaces.
ULMS algortihm:
Inputs:
- Dental crown model that contains the teeth of a patient (vtk file)
- The root canal segmentation file (.nii)
Output:
- A merged model with the teeth and roots labeled based on the universal labels and individual teeth and roots (vtk files)
bash fly-by-cnn/src/sh/compute_ULMS.sh --help
Program to run the Universal Labeling Merging and Separated algorithm
Syntax: compute_ULMS.sh [--options]
options:
--src_code Path of the source code
--input_file_surf Input file surface with only the teeth.
--label_GT_dir Folder containing the template for the Upper/Lower classification.
--model_ft Path to the feature model .
--model_LU Path to the LowerUpper classification model.
--out_feature Output of the feature.
--output_dir_uid Output directory of the teeth with the universal labels.
--input_file_root Root canal segmentation file.
--out_tmp Temporary output folder.
--out_merge Output directory of the merged surfaces.
--out_separate Output directory of the separated surfaces.
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