diff --git a/.github/workflows/test-inference-pipeline.yml b/.github/workflows/test-inference-pipeline.yml index a288130..43fce31 100644 --- a/.github/workflows/test-inference-pipeline.yml +++ b/.github/workflows/test-inference-pipeline.yml @@ -47,7 +47,7 @@ jobs: - name: Run inference for deepFCD run: | - conda run -n deepFCD ./app/inference.py ${CI_TESTING_PATIENT_ID} t1.nii.gz flair.nii.gz ~/io cuda 1 1 + ./app/inference.py ${CI_TESTING_PATIENT_ID} t1.nii.gz flair.nii.gz ~/io cuda 1 1 env: CI_TESTING_PATIENT_ID: "sub-00055" CI_TESTING_GT: "./tests/segmentations/sub-00055/sub-00055_label_dilated_final.nii.gz" diff --git a/app/inference.py b/app/inference.py index 155bcbd..b13d4f8 100755 --- a/app/inference.py +++ b/app/inference.py @@ -1,4 +1,4 @@ -#!/usr/bin/env python3 +#!/usr/bin/env conda run -n deepFCD python3 import logging import multiprocessing @@ -128,7 +128,7 @@ # seed = options['seed'] options["dropout_mc"] = True options["batch_size"] = 350000 -options["mini_batch_size"] = 2048 +options["mini_batch_size"] = 8192 # 1536 uses 3700MiB of GPU VRAM; 8192:18888MiB options["load_checkpoint_1"] = True options["load_checkpoint_2"] = True