diff --git a/doc/api.rst b/doc/api.rst index 201bcf562df09c76e6f66c923c63c119447b0152..39b4d40f6218f6100b7f7ab50fb826aaf32e541a 100644 --- a/doc/api.rst +++ b/doc/api.rst @@ -42,9 +42,12 @@ CNN and other models implemented. mednet.models.pasa mednet.models.alexnet mednet.models.densenet - mednet.models.normalizer mednet.models.logistic_regression + mednet.models.loss_weights mednet.models.mlp + mednet.models.normalizer + mednet.models.separate + mednet.models.transforms mednet.models.typing @@ -58,11 +61,12 @@ Functions to actuate on the data. .. autosummary:: :toctree: api/engine - mednet.engine.device mednet.engine.callbacks - mednet.engine.trainer - mednet.engine.predictor + mednet.engine.device mednet.engine.evaluator + mednet.engine.loggers + mednet.engine.predictor + mednet.engine.trainer .. _mednet.api.saliency: @@ -75,9 +79,11 @@ Engines to generate and analyze saliency mapping techniques. .. autosummary:: :toctree: api/saliency - mednet.engine.saliency.generator mednet.engine.saliency.completeness + mednet.engine.saliency.evaluator + mednet.engine.saliency.generator mednet.engine.saliency.interpretability + mednet.engine.saliency.viewer .. _mednet.api.utils: diff --git a/doc/catalog.json b/doc/catalog.json index c837093f96ae2e8cd85cbfa6af52af7100e7e7f3..529a23b480af03f8020f89720ff522d6d9f14d7f 100644 --- a/doc/catalog.json +++ b/doc/catalog.json @@ -14,6 +14,15 @@ "environment": "lightning" } }, + "tensorboardx": { + "versions": { + "stable": "https://tensorboardx.readthedocs.io/en/stable/", + "latest": "https://tensorboardx.readthedocs.io/en/latest/" + }, + "sources": { + "readthedocs": "tensorboardx" + } + }, "tabulate": { "versions": { "latest": "https://tabulate.readthedocs.io/en/latest/", diff --git a/doc/conf.py b/doc/conf.py index 1411e92d8303f385882966b713d2b95e1d0970d1..7cf72ca51fb2b9e6d4f22c2cd8143d63f32893da 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -123,6 +123,7 @@ auto_intersphinx_packages = [ "torch", "torchvision", "lightning", + "tensorboardx", ("clapper", "latest"), ("python", "3"), ] diff --git a/src/mednet/engine/saliency/viewer.py b/src/mednet/engine/saliency/viewer.py index fc03073a94044b78e707f328ab3b5c1a04990143..866f5073ff204b87618aab8f1be49c2d925aa416 100644 --- a/src/mednet/engine/saliency/viewer.py +++ b/src/mednet/engine/saliency/viewer.py @@ -214,7 +214,7 @@ def run( If set, imprint ground truth labels over the original image and saliency maps. threshold : float - The pixel values above ``threshold``% of max value are kept in the + The pixel values above ``threshold`` % of max value are kept in the original saliency map. Everything else is set to zero. The value proposed on [SCORECAM-2020]_ is 0.2. Use this value if unsure. """