From 2e63e8ce023a08c1c05e6fb27fdbacc5f954a02a Mon Sep 17 00:00:00 2001
From: Lea Vauchier <lea.vauchier@ign.fr>
Date: Thu, 18 Apr 2024 16:52:44 +0200
Subject: [PATCH] Add workflow to run prediction on lidar-prod optimization
 dataset

---
 .../predict-for-lidar-prod-optimization.yml   | 104 ++++++++++++++++++
 CHANGELOG.md                                  |   3 +
 2 files changed, 107 insertions(+)
 create mode 100644 .github/workflows/predict-for-lidar-prod-optimization.yml

diff --git a/.github/workflows/predict-for-lidar-prod-optimization.yml b/.github/workflows/predict-for-lidar-prod-optimization.yml
new file mode 100644
index 00000000..1f7f95d0
--- /dev/null
+++ b/.github/workflows/predict-for-lidar-prod-optimization.yml
@@ -0,0 +1,104 @@
+# Workflow name
+name: "Prediction on lidar-prod optimization dataset"
+
+on:
+  # Run workflow on user request
+  workflow_dispatch:
+    inputs:
+      user:
+        description: |
+          Username :
+          Utilisé pour générer un chemin standard pour les sorties dans le
+          dossier IA du store (projet-LHD/IA/MYRIA3D-SHARED-WORKSPACE/$USER/$SAMPLING_NAME/)
+        required: true
+      sampling_name:
+        description: |
+          Sampling name :
+          Nom du dataset sur lequel le modèle a été entraîné.
+          Utilisé pour générer un chemin standard pour les sorties dans le
+          dossier IA du store (projet-LHD/IA/MYRIA3D-SHARED-WORKSPACE/$USER/$SAMPLING_NAME/)
+          Eg. YYYYMMDD_MonBeauDataset
+        required: true
+      model_id:
+        description: |
+          Identifiant du modèle :
+          Il correspond au nom du fichier checkpoint à utiliser pour les prédictions (sans l'extension .qckpt !)
+          ($MODEL_ID.ckpt doit exister dans projet-LHD/IA/MYRIA3D-SHARED-WORKSPACE/$USER/$SAMPLING_NAME/)
+          Il est aussi utilisé pour générer le dossier de sortie
+          (projet-LHD/IA/LIDAR-PROD-OPTIMIZATION/$SAMPLING_NAME/$MODEL_ID)
+          Exemple : YYYMMDD_MonBeauSampling_epochXXX_Myria3Dx.y.z
+        required: true
+      predict_config_name:
+        description: |
+          Nom du fichier de config de myria3d (fichier .yaml) à utiliser pour la prédiction
+          (doit exister dans projet-LHD/IA/MYRIA3D-SHARED-WORKSPACE/$USER/$SAMPLING_NAME/)
+          Exemple: YYYMMDD_MonBeauSampling_epochXXX_Myria3Dx.y.z_predict_config_Vx.y.z.yaml
+        required: true
+
+jobs:
+  predict-validation-dataset:
+    runs-on: self-hosted
+    env:
+      OUTPUT_DIR: /var/data/LIDAR-PROD-OPTIMIZATION/${{ github.event.inputs.sampling_name }}/${{ github.event.inputs.model_id }}/
+      DATA: /var/data/LIDAR-PROD-OPTIMIZATION/20221018_lidar-prod-optimization-on-151-proto/Comparison/
+      CONFIG_DIR: /var/data/MYRIA3D-SHARED-WORKSPACE/${{ github.event.inputs.user }}/${{ github.event.inputs.sampling_name }}/
+      BATCH_SIZE: 1
+
+    steps:
+      - name: Log configuration
+        run: |
+          echo "Run prediction on lidar-prod optimization datasets (val and test)"
+          echo "Sampling name: ${{ github.event.inputs.sampling_name }}"
+          echo "User name: ${{ github.event.inputs.user }}"
+          echo "Checkpoint name: ${{ github.event.inputs.model_id }}"
+          echo "Prediction config name: ${{ github.event.inputs.predict_config_name }}"
+          echo "Output_dir: ${{env.OUTPUT_DIR}}"
+          echo "Data: ${{env.DATA}}"
+          echo "Config files dir: ${{env.CONFIG_DIR}}"
+
+      - name: Checkout branch
+        uses: actions/checkout@v4
+
+      # See https://github.com/marketplace/actions/setup-micromamba
+      - name: setup-micromamba
+        uses: mamba-org/setup-micromamba@v1.8.1
+        with:
+          environment-file: environment.yml
+          environment-name: myria3d # activate the environment
+          cache-environment-key: environment-myria3d-predict-validation-dataset # create cache for this pipeline only
+          # Do not restore downloads as they are already stored by micromamba
+          # cache-downloads-key: downloads-myria3d-predict-validation-dataset
+          generate-run-shell: true
+          download-micromamba: false
+          micromamba-binary-path: /var/data/.local/bin/micromamba
+          micromamba-root-path: /var/data/micromamba
+
+      - name: Run prediction on validation dataset
+        shell: micromamba-shell {0}
+        run: >
+          python run.py
+          --config-path ${{env.CONFIG_DIR}}
+          --config-name ${{ github.event.inputs.predict_config_name }}
+          task.task_name=predict
+          predict.src_las=${{env.DATA}}/val/*.laz
+          predict.ckpt_path=${{env.CONFIG_DIR}}${{ github.event.inputs.model_id }}.ckpt
+          predict.output_dir=${{env.OUTPUT_DIR}}/preds-valset/
+          predict.interpolator.probas_to_save=[building]
+          predict.gpus=0
+          datamodule.batch_size=${{env.BATCH_SIZE}}
+          datamodule.tile_width=1000
+
+      - name: Run prediction on test dataset
+        shell: micromamba-shell {0}
+        run: >
+          python run.py
+          --config-path ${{env.CONFIG_DIR}}
+          --config-name ${{ github.event.inputs.predict_config_name }}
+          task.task_name=predict
+          predict.src_las=${{env.DATA}}/test/*.laz
+          predict.ckpt_path=${{env.CONFIG_DIR}}${{ github.event.inputs.model_id }}
+          predict.output_dir=${{env.OUTPUT_DIR}}/preds-testset/
+          predict.interpolator.probas_to_save=[building]
+          predict.gpus=0
+          datamodule.batch_size=${{env.BATCH_SIZE}}
+          datamodule.tile_width=1000
diff --git a/CHANGELOG.md b/CHANGELOG.md
index 8e793776..24613047 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -1,5 +1,8 @@
 # CHANGELOG
 
+- Add a github action workflow to run a trained model on the lidar-prod thresholds optimisation dataset
+(in order to automate thresholds optimization)
+
 ### 3.8.4
 - fix: move IoU appropriately to fix wrong device error created by a breaking change in torch when using DDP.