From 91f618666ff694687809bdfb2f5a8feaa7744d1f Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Mon, 29 Jan 2024 12:45:21 +0100
Subject: [PATCH] [experiment] Add saliency to experiment script
By default, performs sal gen and sal view. Default parameters
are used for now. Steps requiring databases with human annotations
are not yet included in the experiment script.
---
src/mednet/scripts/experiment.py | 33 +++++++++++++++++++++++++++++++-
1 file changed, 32 insertions(+), 1 deletion(-)
diff --git a/src/mednet/scripts/experiment.py b/src/mednet/scripts/experiment.py
index 38d88fd9..275bc8b8 100644
--- a/src/mednet/scripts/experiment.py
+++ b/src/mednet/scripts/experiment.py
@@ -67,7 +67,6 @@ def experiment(
save_sh_command(output_folder / "command.sh")
- # training
logger.info("Started training")
from .train import train
@@ -139,3 +138,35 @@ def experiment(
)
logger.info("Ended evaluating")
+
+ logger.info("Started generating saliencies")
+
+ from .saliency.generate import generate
+
+ saliencies_gen_folder = output_folder / "gradcam" / "saliencies"
+
+ ctx.invoke(
+ generate,
+ model=model,
+ datamodule=datamodule,
+ weight=train_output_folder,
+ output_folder=saliencies_gen_folder,
+ )
+
+ logger.info("Ended generating saliencies")
+
+ logger.info("Started viewing saliencies")
+
+ from .saliency.view import view
+
+ saliencies_view_folder = output_folder / "gradcam" / "visualizations"
+
+ ctx.invoke(
+ view,
+ model=model,
+ datamodule=datamodule,
+ input_folder=saliencies_gen_folder,
+ output_folder=saliencies_view_folder,
+ )
+
+ logger.info("Ended viewing saliencies")
--
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