Welcome to the official documentation for ShapeAXI. Dive into the cutting-edge framework designed for comprehensive shape analysis.
ShapeAXI is a state-of-the-art shape analysis framework that harnesses a multi-view approach. This approach is adept at capturing 3D objects from a variety of viewpoints and analyzing them through 2D Convolutional Neural Networks (CNNs).
(python 3.8 or 3.9 are required, no other versions)
pip install shapeaxi
For this installation, we are going to use a variable, {YOURVERSION}, because this installation is specific to each computer configuration. First, you can run this line to print the content of the variable {YOURVERSION} that we will use :
python -c "import sys; import torch; pyt_version_str=torch.__version__.split('+')[0].replace('.', ''); version_str=''.join([f'py3{sys.version_info.minor}_cu', torch.version.cuda.replace('.', ''), f'_pyt{pyt_version_str}']); print(version_str)"
It will print something like this : py39_cu117_pyt201.
pip install --no-index --no-cache-dir pytorch3d -f https://dl.fbaipublicfiles.com/pytorch3d/packaging/wheels/{YOURVERSION}/download.html
Finally, check the installation,
pip show pytorch3d
In this package you have the possibility of running four different models :
To use ShapeAXI, execute the saxi_folds.py script with several options:
usage: shapeaxi [-h] [--csv CSV] [--csv_train CSV_TRAIN] [--csv_test CSV_TEST] [--folds FOLDS] [--valid_split VALID_SPLIT] [--group_by GROUP_BY] --nn
{SaxiClassification,SaxiRegression,SaxiSegmentation,SaxiIcoClassification,SaxiIcoClassification_fs,SaxiRing,SaxiRingTeeth} [--model MODEL] [--train_sphere_samples TRAIN_SPHERE_SAMPLES]
[--surf_column SURF_COLUMN] [--class_column CLASS_COLUMN] [--scale_factor SCALE_FACTOR] [--column_scale_factor COLUMN_SCALE_FACTOR] [--profiler PROFILER]
[--compute_scale_factor COMPUTE_SCALE_FACTOR] [--compute_features COMPUTE_FEATURES] [--mount_point MOUNT_POINT] [--num_workers NUM_WORKERS] [--base_encoder BASE_ENCODER]
[--base_encoder_params BASE_ENCODER_PARAMS] [--hidden_dim HIDDEN_DIM] [--radius RADIUS] [--image_size IMAGE_SIZE] [--lr LR] [--epochs EPOCHS] [--batch_size BATCH_SIZE]
[--patience PATIENCE] [--log_every_n_steps LOG_EVERY_N_STEPS] [--tb_dir TB_DIR] [--tb_name TB_NAME] [--neptune_project NEPTUNE_PROJECT] [--neptune_tags NEPTUNE_TAGS]
[--path_ico_right PATH_ICO_RIGHT] [--path_ico_left PATH_ICO_LEFT] [--layer LAYER] [--fs_path FS_PATH] [--num_images NUM_IMAGES] [--ico_lvl ICO_LVL]
[--crown_segmentation CROWN_SEGMENTATION] [--fdi FDI] [--csv_true_column CSV_TRUE_COLUMN] [--csv_tag_column CSV_TAG_COLUMN] [--csv_prediction_column CSV_PREDICTION_COLUMN]
[--eval_metric {F1,AUC}] [--target_layer TARGET_LAYER] [--fps FPS] [--out OUT]
Automatically train and evaluate a N fold cross-validation model for Shape Analysis Explainability and Interpretability
optional arguments:
-h, --help show this help message and exit
Split:
--csv CSV CSV with columns surf,class
--csv_train CSV_TRAIN
CSV with column surf
--csv_test CSV_TEST CSV with column surf
--folds FOLDS Number of folds
--valid_split VALID_SPLIT
Split float [0-1]
--group_by GROUP_BY GroupBy criteria in the CSV. For example, SubjectID in case the same subjects has multiple timepoints/data points and the subject must belong to the same data split
Train:
--nn {SaxiClassification,SaxiRegression,SaxiSegmentation,SaxiIcoClassification,SaxiIcoClassification_fs,SaxiRing,SaxiRingTeeth}
Neural network name : SaxiClassification, SaxiRegression, SaxiSegmentation, SaxiIcoClassification, SaxiIcoClassification_fs, SaxiRing, SaxiRingTeeth
--model MODEL Model to continue training
--train_sphere_samples TRAIN_SPHERE_SAMPLES
Number of samples for the training sphere
--surf_column SURF_COLUMN
Surface column name
--class_column CLASS_COLUMN
Class column name
--scale_factor SCALE_FACTOR
Scale factor for the shapes
--column_scale_factor COLUMN_SCALE_FACTOR
Specify the name if there already is a column with scale factor in the input file
--profiler PROFILER Profiler
--compute_scale_factor COMPUTE_SCALE_FACTOR
Compute a global scale factor for all shapes in the population.
--compute_features COMPUTE_FEATURES
Compute features for the shapes in the population.
--mount_point MOUNT_POINT
Dataset mount directory
--num_workers NUM_WORKERS
Number of workers for loading
--base_encoder BASE_ENCODER
Base encoder for the feature extraction
--base_encoder_params BASE_ENCODER_PARAMS
Base encoder parameters that are passed to build the feature extraction
--hidden_dim HIDDEN_DIM
Hidden dimension for features output. Should match with output of base_encoder. Default value is 512
--radius RADIUS Radius of icosphere
--image_size IMAGE_SIZE
Image resolution size
--lr LR Learning rate
--epochs EPOCHS Max number of epochs
--batch_size BATCH_SIZE
Batch size
--patience PATIENCE Patience for early stopping
--log_every_n_steps LOG_EVERY_N_STEPS
Log every n steps
--tb_dir TB_DIR Tensorboard output dir
--tb_name TB_NAME Tensorboard experiment name
--neptune_project NEPTUNE_PROJECT
Neptune project
--neptune_tags NEPTUNE_TAGS
Neptune tags
--path_ico_right PATH_ICO_RIGHT
Path to ico right (default: ../3DObject/sphere_f327680_v163842.vtk)
--path_ico_left PATH_ICO_LEFT
Path to ico left (default: ../3DObject/sphere_f327680_v163842.vtk)
--layer LAYER Layer, choose between 'Att','IcoConv2D','IcoConv1D','IcoLinear' (default: IcoConv2D)
--fs_path FS_PATH Path to freesurfer folder
--num_images NUM_IMAGES
Number of images to use for the training
--ico_lvl ICO_LVL Ico level, minimum level is 1 (default: 2)
Prediction group:
--crown_segmentation CROWN_SEGMENTATION
Isolation of each different tooth in a specific vtk file
--fdi FDI numbering system. 0: universal numbering; 1: FDI world dental Federation notation
Test group:
--csv_true_column CSV_TRUE_COLUMN
Which column to do the stats on
--csv_tag_column CSV_TAG_COLUMN
Which column has the actual names
--csv_prediction_column CSV_PREDICTION_COLUMN
csv true class
--eval_metric {F1,AUC}
Score you want to choose for picking the best model : F1 or AUC
Explainability group:
--target_layer TARGET_LAYER
Target layer for explainability
--fps FPS Frames per second
Output:
--out OUT Output
The first step of the code is to compute a global scale factor for all shapes in the population.
If you want to do this, add --compute_scale_factor 1.
Moreover, if you already has a column with scale_factor in your csv file, specify it with --column_scale_factor name_of_your_column.
Otherwise, if you do not want to compute a global scale factor, do not specify anything and it will skip this part.
No matter which model you choose you must specify your input.
You can choose between --csv input or both --csv_first_train and --csv_first_test. If you specify one csv file as input, ShapeAXI will split the dataset between train and test (80% and 20% but you can specify the split using --valid_split if you want 85% and 15% for example).
Otherwise, if you specify csv_train and csv_test, it will skip this first split.
Now, ShapeAXI uses the train set and split it between : train, test and valid dataset for each folder.
ShapeAXI will train, test and evaluate one model for each folder.
Here, an example of the content of you csv files :
| surf | class |
|---|---|
| path/to/shape1.vtk | class1 |
| path/to/shape2.stl | class2 |
| path/to/shape3.vtk | class1 |
| ... | ... |
surf: This column holds the file paths to the 3D shape objects. The tool supports the formats .vtk and .stl.
class: This column indicates the class of the 3D object.
For this step, there are one training, validation and testing dataset for each fold. You can choose for the training : batch size, maximum number of epochs, model you want.
If you want, you can specify --csv_train, --csv_test and --csv_valid for each fold.
Finally, ShapeAXI will test the different models after their training. It will test them during the evaluation part.
During this process, ShapeAXI will pick the best model from all the different folders depending on F1 score or AUC score.
You can choose the evaluation metric with the option --eval_metric F1 or --eval_metric AUC.
Your best model will then be tested on the first test dataset of the first split.
ShapeAXI will produce :
shapeaxi --csv your_data.csv --nn SaxiClassification --epochs 40 --folds 5 --mount_point /path/to/your/data/directory --out /path/to/your/output_directory --compute_scale_factor 1 --surf_column surf --class_column class --batch_size 8
For this model, you have to specify the path to your right vtk hemisphere data and same for the left one.
shapeaxi --csv your_data.csv --nn SaxiIcoClassification --epochs 30 --folds 3 --mount_point /path/to/your/data/directory --out /path/to/your/output_directory --path_ico_left /path/to/vtk/left/hemisphere --path_ico_right /path/to/vtk/right/hemisphere --class_column ASD_administered
shapeaxi --csv your_data.csv --nn SaxiClassification --epochs 40 --folds 5 --mount_point /path/to/your/data/directory --surf_column surf --class_column class --batch_size 8 --compute_scale_factor 1 --out /path/to/your/output_directory
shapeaxi --csv your_data.csv --nn SaxiSegmentation --epochs 40 --folds 5 --mount_point /path/to/your/data/directory --out /path/to/your/output_directory --eval_metric AUC
This model creates two networks for each hemisphere of the brain and uses the output surfaces from Freesurfer. If you want to use this model with other data use the next model.
shapeaxi --csv your_data.csv --nn SaxiRing --epochs 40 --folds 5 --mount_point /path/to/your/data/directory --surf_column surf --class_column class --batch_size 8 --fs_path /path/to/directory/subjects --out /path/to/your/output_directory
shapeaxi --csv your_data.csv --nn SaxiRingTeeth --epochs 40 --folds 5 --mount_point /path/to/your/data/directory --surf_column surf --class_column class --batch_size 8 --out /path/to/your/output_directory
ShapeAXI has been rigorously tested across multiple domains. Below is a summary of our key experiments:
In ShapeAXI, we prioritize transparency and understanding. The explainability feature of our framework offers heat-maps which grant insights into its classification rationale.
https://github.com/DCBIA-OrthoLab/ShapeAXI/assets/7086191/120b0095-5f2d-4f0d-b650-a0587a33e067
https://github.com/DCBIA-OrthoLab/ShapeAXI/assets/7086191/2c635250-624f-4cce-b150-4d5507b398b4
We welcome community contributions to ShapeAXI. For those keen on enhancing this tool, please adhere to the steps below:
git checkout -b feature/YourFeature).git commit -am 'Add some feature').git push origin feature/YourFeature).For a comprehensive understanding of our contribution process, consult our Contribution Guidelines.
Of course! Here are some general FAQ entries tailored for a tool/framework like ShapeAXI:
One of the application on this tool is to be able to run a prediction using a pretrained model on your own data.
If you want, you can have access to this package documentation called dentalmodelseg :
Answer: ShapeAXI is an innovative shape analysis framework that employs a multi-view approach, rendering 3D objects from varied perspectives and analyzing them using 2D Convolutional Neural Networks (CNNs).
Answer: Detailed installation and setup instructions can be found in the 'Installation' section of our documentation. Simply follow the steps mentioned, and you should have ShapeAXI up and running in no time.
Answer: Absolutely! ShapeAXI is designed to be versatile. You can use it on a wide variety of shape datasets. Ensure your data is in the required format as outlined in the 'Usage' section.
Answer: ShapeAXI offers a unique approach to explainability, providing heat-maps for each class across every shape. These visualizations provide insights into the underlying object characteristics and the classification rationale.
Answer: Like all models and frameworks, ShapeAXI has its constraints. It is optimized for the datasets and tasks it has been trained and tested on. While it offers versatility across a range of datasets, results may vary based on the quality and type of data. We continually work on refining and improving ShapeAXI to overcome any limitations.
Answer: We welcome contributions! Please refer to the 'Contribute' section of our documentation for guidelines on how you can contribute.
Answer: For technical support or any questions, please create a new issue in our GitHub repository.
Answer: Yes, we plan on continuously improving and expanding ShapeAXI based on user feedback, new research, and technological advancements. Stay tuned to our repository for updates.
ShapeAXI is under the APACHE 2.0 license.
ShapeAXI Team: For further details, inquiries, or suggestions, feel free to contact us.
FAQs
Shape Analysis Exploration and Interpretability
We found that shapeaxi demonstrated a healthy version release cadence and project activity because the last version was released less than a year ago. It has 3 open source maintainers collaborating on the project.
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