tumourkit.research_pipe

Pipeline to ease experiment replication.

This program is free software: you can redistribute it and/or modify it under the terms of the GNU Affero General Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Affero General Public License for more details.

You should have received a copy of the GNU Affero General Public License along with this program. If not, see <https://www.gnu.org/licenses/>.

Contact information: joseperez2000@hotmail.es

Functions

`evaluate_hovernet_with_shape`	Performs evaluation of Hovernet outputs with the specified shape.
`hovernet_preproc_with_shape`	Converts the Hovernet gson format to the rest of formats.
`infer_hovernet_with_shape`	Performs inference with the specified Hovernet model shape.
`main`
`run_early_topo`	It tests the hypothesis that we can use the neural persistence as an early stopping criterion.
`run_postprocessing_with_shape`	Performs post-processing after Hovernet training with the specified shape.
`run_preprocessing`	Runs the preprocessing steps.
`run_scaling`	Runs the scaling experiment for Hovernet.
`run_void`	Runs the training of GNN models without prior and morphological features.
`run_xgb`	Runs the XGBoost training and evaluation.
`train_hovernet_with_shape`	Performs Hovernet preprocessing and training with the specified shape.