Port saliency map generation/analysis to new name

doc/api.rst

@@ -65,7 +65,7 @@ Functions to actuate on the data.
    mednet.engine.evaluator
 
 
-.. _ptbench.api.saliency:
+.. _mednet.api.saliency:
 
 Saliency Map Generation and Analysis
 ------------------------------------
@@ -75,9 +75,9 @@ Engines to generate and analyze saliency mapping techniques.
 .. autosummary::
    :toctree: api/saliency
 
-   ptbench.engine.saliency.generator
-   ptbench.engine.saliency.completeness
-   ptbench.engine.saliency.interpretability
+   mednet.engine.saliency.generator
+   mednet.engine.saliency.completeness
+   mednet.engine.saliency.interpretability
 
 
 .. _mednet.api.utils:

src/ptbench/scripts/saliency/completeness.py → src/mednet/scripts/saliency/completeness.py

@@ -17,7 +17,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
 
 @click.command(
-    entry_point_group="ptbench.config",
+    entry_point_group="mednet.config",
     cls=ConfigCommand,
     epilog="""Examples:
 
@@ -25,7 +25,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
    .. code:: sh
 
-      ptbench saliency completeness -vv pasa tbx11k-v1-healthy-vs-atb --device="cuda" --weight=path/to/model-at-lowest-validation-loss.ckpt --output-json=path/to/completeness-scores.json
+      mednet saliency completeness -vv pasa tbx11k-v1-healthy-vs-atb --device="cuda" --weight=path/to/model-at-lowest-validation-loss.ckpt --output-json=path/to/completeness-scores.json
 
 """,
 )

src/ptbench/scripts/saliency/evaluate.py → src/mednet/scripts/saliency/evaluate.py

@@ -20,7 +20,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
 
 @click.command(
-    entry_point_group="ptbench.config",
+    entry_point_group="mednet.config",
     cls=ConfigCommand,
     epilog="""Examples:
 
@@ -28,7 +28,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
    .. code:: sh
 
-      ptbench saliency evaluate -vv -e gradcam path/to/gradcam-completeness.json path/to/gradcam-interpretability.json -e gradcam++ path/to/gradcam++-completeness.json path/to/gradcam++-interpretability.json
+      mednet saliency evaluate -vv -e gradcam path/to/gradcam-completeness.json path/to/gradcam-interpretability.json -e gradcam++ path/to/gradcam++-completeness.json path/to/gradcam++-interpretability.json
 """,
 )
 @click.option(
@@ -37,9 +37,9 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
     required=True,
     multiple=True,
     help=f"ENTRY is a triplet containing the algorithm name, the path to the "
-    f"scores issued from the completness analysis (``ptbench "
-    f"saliency-completness``) and scores issued from the interpretability "
-    f"analysis (``ptbench saliency-interpretability``), both in JSON format. "
+    f"scores issued from the completness analysis (``mednet "
+    f"saliency completness``) and scores issued from the interpretability "
+    f"analysis (``mednet saliency interpretability``), both in JSON format. "
     f"Paths to score files must exist before the program is called. Valid values "
     f"for saliency map algorithms are "
     f"{'|'.join(typing.get_args(SaliencyMapAlgorithm))}",

src/ptbench/scripts/saliency/generate.py → src/mednet/scripts/saliency/generate.py

@@ -17,7 +17,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
 
 @click.command(
-    entry_point_group="ptbench.config",
+    entry_point_group="mednet.config",
     cls=ConfigCommand,
     epilog="""Examples:
 
@@ -27,7 +27,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
    .. code:: sh
 
-      ptbench saliency generate -vv densenet tbx11k-v1-healthy-vs-atb --weight=path/to/model-at-lowest-validation-loss.ckpt --output-folder=path/to/output
+      mednet saliency generate -vv densenet tbx11k-v1-healthy-vs-atb --weight=path/to/model-at-lowest-validation-loss.ckpt --output-folder=path/to/output
 
 """,
 )

src/ptbench/scripts/saliency/interpretability.py → src/mednet/scripts/saliency/interpretability.py

@@ -15,7 +15,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
 
 @click.command(
-    entry_point_group="ptbench.config",
+    entry_point_group="mednet.config",
     cls=ConfigCommand,
     epilog="""Examples:
 
@@ -23,7 +23,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
    .. code:: sh
 
-      ptbench saliency interpretability -vv tbx11k-v1-healthy-vs-atb --input-folder=parent-folder/saliencies/ --output-json=path/to/interpretability-scores.json
+      mednet saliency interpretability -vv tbx11k-v1-healthy-vs-atb --input-folder=parent-folder/saliencies/ --output-json=path/to/interpretability-scores.json
 
 """,
 )
@@ -41,7 +41,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
     "--input-folder",
     "-i",
     help="""Path where to load saliency maps from.  You can generate saliency
-    maps with ``ptbench generate-saliencymaps``.""",
+    maps with ``mednet saliency generate``.""",
     required=True,
     type=click.Path(
         exists=True,

src/ptbench/scripts/saliency/view.py → src/mednet/scripts/saliency/view.py

@@ -14,7 +14,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
 
 @click.command(
-    entry_point_group="ptbench.config",
+    entry_point_group="mednet.config",
     cls=ConfigCommand,
     epilog="""Examples:
 
@@ -22,7 +22,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
 
    .. code:: sh
 
-      ptbench saliency view -vv pasa tbx11k-v1-healthy-vs-atb --input-folder=parent_folder/gradcam/ --output-folder=path/to/visualizations
+      mednet saliency view -vv pasa tbx11k-v1-healthy-vs-atb --input-folder=parent_folder/gradcam/ --output-folder=path/to/visualizations
 """,
 )
 @click.option(

tests/test_cli.py

@@ -155,25 +155,25 @@ def test_evaluate_help():
 
 
 def test_saliency_generate_help():
-    from ptbench.scripts.saliency.generate import generate
+    from mednet.scripts.saliency.generate import generate
 
     _check_help(generate)
 
 
 def test_saliency_completeness_help():
-    from ptbench.scripts.saliency.completeness import completeness
+    from mednet.scripts.saliency.completeness import completeness
 
     _check_help(completeness)
 
 
 def test_saliency_view_help():
-    from ptbench.scripts.saliency.view import view
+    from mednet.scripts.saliency.view import view
 
     _check_help(view)
 
 
 def test_saliency_evaluate_help():
-    from ptbench.scripts.saliency.evaluate import evaluate
+    from mednet.scripts.saliency.evaluate import evaluate
 
     _check_help(evaluate)
 
@@ -440,7 +440,7 @@ def test_evaluate_pasa_montgomery(temporary_basedir):
 # def test_evaluatevis(temporary_basedir):
 #     import pandas as pd
 
-#     from ptbench.scripts.evaluatevis import evaluatevis
+#     from mednet.scripts.evaluatevis import evaluatevis
 
 #     runner = CliRunner()
 

tests/test_saliencymap_evaluator.py

@@ -3,8 +3,8 @@
 # SPDX-License-Identifier: GPL-3.0-or-later
 import numpy as np
 
-from ptbench.config.data.tbx11k.datamodule import BoundingBox, BoundingBoxes
-from ptbench.engine.saliency.interpretability import (
+from mednet.config.data.tbx11k.datamodule import BoundingBox, BoundingBoxes
+from mednet.engine.saliency.interpretability import (
     _compute_avg_saliency_focus,
     _compute_binary_mask,
     _compute_max_iou_and_ioda,