From 143cf210a3a2c406bbd91809439b98d8431a356c Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Wed, 7 Feb 2024 17:10:17 +0100
Subject: [PATCH] [saliency.interpretability] Apply model transforms to
datamodule
---
src/mednet/scripts/saliency/interpretability.py | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/mednet/scripts/saliency/interpretability.py b/src/mednet/scripts/saliency/interpretability.py
index 0d1b84f7..14a99040 100644
--- a/src/mednet/scripts/saliency/interpretability.py
+++ b/src/mednet/scripts/saliency/interpretability.py
@@ -23,10 +23,19 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
.. code:: sh
- mednet saliency interpretability -vv tbx11k-v1-healthy-vs-atb --input-folder=parent-folder/saliencies/ --output-json=path/to/interpretability-scores.json
+ mednet saliency interpretability -vv pasa tbx11k-v1-healthy-vs-atb --input-folder=parent-folder/saliencies/ --output-json=path/to/interpretability-scores.json
""",
)
+@click.option(
+ "--model",
+ "-m",
+ help="""A lightning module instance implementing the network architecture
+ (not the weights, necessarily) to be used for inference. Currently, only
+ supports pasa and densenet models.""",
+ required=True,
+ cls=ResourceOption,
+)
@click.option(
"--datamodule",
"-d",
@@ -78,6 +87,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
)
@verbosity_option(logger=logger, cls=ResourceOption, expose_value=False)
def interpretability(
+ model,
datamodule,
input_folder,
target_label,
@@ -114,7 +124,7 @@ def interpretability(
from ...engine.saliency.interpretability import run
- datamodule.model_transforms = []
+ datamodule.model_transforms = model.transforms
datamodule.prepare_data()
datamodule.setup(stage="predict")
--
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