From 95b658e873839cd2a85e333fe65c1cd282a3c41a Mon Sep 17 00:00:00 2001
From: "ogueler@idiap.ch" <ogueler@vws110.idiap.ch>
Date: Wed, 20 Sep 2023 01:07:24 +0200
Subject: [PATCH] fixed formatting
---
src/ptbench/engine/visualizer.py | 21 ++++++++++++--------
src/ptbench/scripts/calculate_road.py | 8 ++++----
src/ptbench/scripts/comparevis.py | 4 ++++
src/ptbench/scripts/evaluate_saliencymaps.py | 8 ++++----
src/ptbench/scripts/evaluatevis.py | 4 ++++
src/ptbench/scripts/generate_saliencymaps.py | 9 +++++----
src/ptbench/scripts/visualize.py | 10 +++++-----
src/ptbench/utils/cam_utils.py | 4 ++++
tests/test_11k.py | 1 -
tests/test_11k_RS.py | 1 -
tests/test_11k_v2.py | 1 -
tests/test_11k_v2_RS.py | 1 -
tests/test_cam_utils.py | 1 -
tests/test_comparevis.py | 1 -
tests/test_visualizer.py | 4 +++-
15 files changed, 46 insertions(+), 32 deletions(-)
diff --git a/src/ptbench/engine/visualizer.py b/src/ptbench/engine/visualizer.py
index b149f3ea..593b19dc 100644
--- a/src/ptbench/engine/visualizer.py
+++ b/src/ptbench/engine/visualizer.py
@@ -115,7 +115,10 @@ def run(
for samples in tqdm(data_loader, desc="batches", leave=False, disable=None):
includes_bboxes = True
- if samples[1]["label"].item() == 0 or "radsign_bboxes" not in samples[1]:
+ if (
+ samples[1]["label"].item() == 0
+ or "radsign_bboxes" not in samples[1]
+ ):
includes_bboxes = False
else:
gt_bboxes = samples[1]["radsign_bboxes"]
@@ -124,10 +127,14 @@ def run(
names = samples[1]["name"]
- if visualize_groundtruth and not includes_bboxes and samples[1]["label"].item() == 1:
- logger.warning(
- f'Sample "{names[0]}" does not have bounding box information. No ground truth bounding boxes can be visualized.'
- )
+ if (
+ visualize_groundtruth
+ and not includes_bboxes
+ and samples[1]["label"].item() == 1
+ ):
+ logger.warning(
+ f'Sample "{names[0]}" does not have bounding box information. No ground truth bounding boxes can be visualized.'
+ )
for target_class in target_classes:
input_base_path = (
@@ -152,9 +159,7 @@ def run(
# Draw bounding boxes on the image
if visualize_groundtruth and includes_bboxes:
- img_with_boxes = draw_boxes_on_image(
- img_with_boxes, gt_bboxes
- )
+ img_with_boxes = draw_boxes_on_image(img_with_boxes, gt_bboxes)
# show_cam_on_image expects the img to be between [0, 1]
rgb_img = img_with_boxes / 255.0
diff --git a/src/ptbench/scripts/calculate_road.py b/src/ptbench/scripts/calculate_road.py
index 708e7254..2265ce9c 100644
--- a/src/ptbench/scripts/calculate_road.py
+++ b/src/ptbench/scripts/calculate_road.py
@@ -300,8 +300,8 @@ def calculate_road(
"""
from ..engine.device import DeviceManager
- from .utils import save_sh_command
from ..engine.road_calculator import run
+ from .utils import save_sh_command
save_sh_command(output_folder / "command.sh")
@@ -311,8 +311,8 @@ def calculate_road(
datamodule.set_chunk_size(batch_size, 1)
datamodule.drop_incomplete_batch = False
- #datamodule.cache_samples = cache_samples
- #datamodule.parallel = parallel
+ # datamodule.cache_samples = cache_samples
+ # datamodule.parallel = parallel
datamodule.model_transforms = model.model_transforms
datamodule.prepare_data()
@@ -349,7 +349,7 @@ def calculate_road(
csv_files, csv_writers = prepare_csv_writers(
output_folder, vis_type, k, num_classes=0
)
-
+
logger.info(f"Calculating ROAD scores for '{k}' set...")
run(
diff --git a/src/ptbench/scripts/comparevis.py b/src/ptbench/scripts/comparevis.py
index 08eebc12..cdec4ad7 100644
--- a/src/ptbench/scripts/comparevis.py
+++ b/src/ptbench/scripts/comparevis.py
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
import os
import click
diff --git a/src/ptbench/scripts/evaluate_saliencymaps.py b/src/ptbench/scripts/evaluate_saliencymaps.py
index e9cc72a9..6f931231 100644
--- a/src/ptbench/scripts/evaluate_saliencymaps.py
+++ b/src/ptbench/scripts/evaluate_saliencymaps.py
@@ -89,7 +89,7 @@ def prepare_csv_writers(input_folder, dataset_split):
"-i",
help="Path to the folder containing the saliency maps for a specific visualization type.",
required=True,
- type=click.Path(
+ type=click.Path(
file_okay=False,
dir_okay=True,
writable=True,
@@ -112,15 +112,15 @@ def evaluate_saliencymaps(
Calculates them for each target class and split of the dataset.
"""
- from .utils import save_sh_command
from ..engine.saliencymap_evaluator import run
+ from .utils import save_sh_command
save_sh_command(input_folder / "command.sh")
datamodule.set_chunk_size(1, 1)
datamodule.drop_incomplete_batch = False
- #datamodule.cache_samples = cache_samples
- #datamodule.parallel = parallel
+ # datamodule.cache_samples = cache_samples
+ # datamodule.parallel = parallel
datamodule.model_transforms = model.model_transforms
datamodule.prepare_data()
diff --git a/src/ptbench/scripts/evaluatevis.py b/src/ptbench/scripts/evaluatevis.py
index e98dcad9..ff67b702 100644
--- a/src/ptbench/scripts/evaluatevis.py
+++ b/src/ptbench/scripts/evaluatevis.py
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
import click
from clapper.click import verbosity_option
diff --git a/src/ptbench/scripts/generate_saliencymaps.py b/src/ptbench/scripts/generate_saliencymaps.py
index 411ac0d7..0b741d30 100644
--- a/src/ptbench/scripts/generate_saliencymaps.py
+++ b/src/ptbench/scripts/generate_saliencymaps.py
@@ -2,9 +2,10 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-import click
import pathlib
+import click
+
from clapper.click import ConfigCommand, ResourceOption, verbosity_option
from clapper.logging import setup
from pytorch_grad_cam import (
@@ -229,8 +230,8 @@ def generate_saliencymaps(
on visualization technique and model."""
from ..engine.device import DeviceManager
- from .utils import save_sh_command
from ..engine.saliencymap_generator import run
+ from .utils import save_sh_command
save_sh_command(output_folder / "command.sh")
@@ -240,8 +241,8 @@ def generate_saliencymaps(
datamodule.set_chunk_size(batch_size, 1)
datamodule.drop_incomplete_batch = False
- #datamodule.cache_samples = cache_samples
- #datamodule.parallel = parallel
+ # datamodule.cache_samples = cache_samples
+ # datamodule.parallel = parallel
datamodule.model_transforms = model.model_transforms
datamodule.prepare_data()
diff --git a/src/ptbench/scripts/visualize.py b/src/ptbench/scripts/visualize.py
index 96bf4b04..e26a2d46 100644
--- a/src/ptbench/scripts/visualize.py
+++ b/src/ptbench/scripts/visualize.py
@@ -45,7 +45,7 @@ logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
"-i",
help="Path to the folder containing the saliency maps for a specific visualization type.",
required=True,
- type=click.Path(
+ type=click.Path(
file_okay=False,
dir_okay=True,
writable=True,
@@ -117,15 +117,15 @@ def visualize(
) -> None:
"""Generates heatmaps for input CXRs based on existing saliency maps."""
- from .utils import save_sh_command
from ..engine.visualizer import run
+ from .utils import save_sh_command
save_sh_command(input_folder / "command.sh")
datamodule.set_chunk_size(1, 1)
datamodule.drop_incomplete_batch = False
- #datamodule.cache_samples = cache_samples
- #datamodule.parallel = parallel
+ # datamodule.cache_samples = cache_samples
+ # datamodule.parallel = parallel
datamodule.model_transforms = model.model_transforms
datamodule.prepare_data()
@@ -152,4 +152,4 @@ def visualize(
else:
logger.warning(
'No "datadir" found in dataset. No visualizations can be generated.'
- )
\ No newline at end of file
+ )
diff --git a/src/ptbench/utils/cam_utils.py b/src/ptbench/utils/cam_utils.py
index 15699342..f379e644 100644
--- a/src/ptbench/utils/cam_utils.py
+++ b/src/ptbench/utils/cam_utils.py
@@ -1,3 +1,7 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
+
import glob
import os
import shutil
diff --git a/tests/test_11k.py b/tests/test_11k.py
index 2bba74dc..2812c0fd 100644
--- a/tests/test_11k.py
+++ b/tests/test_11k.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for TBX11K simplified dataset split 1."""
import pytest
diff --git a/tests/test_11k_RS.py b/tests/test_11k_RS.py
index 601bbc46..1433b130 100644
--- a/tests/test_11k_RS.py
+++ b/tests/test_11k_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Extended TBX11K simplified dataset split 1."""
import pytest
diff --git a/tests/test_11k_v2.py b/tests/test_11k_v2.py
index 12662886..01e1f37f 100644
--- a/tests/test_11k_v2.py
+++ b/tests/test_11k_v2.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for TBX11K simplified dataset split 2."""
import pytest
diff --git a/tests/test_11k_v2_RS.py b/tests/test_11k_v2_RS.py
index c6ac2464..a58e6abb 100644
--- a/tests/test_11k_v2_RS.py
+++ b/tests/test_11k_v2_RS.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for Extended TBX11K simplified dataset split 2."""
import pytest
diff --git a/tests/test_cam_utils.py b/tests/test_cam_utils.py
index 328be392..5e4198fd 100644
--- a/tests/test_cam_utils.py
+++ b/tests/test_cam_utils.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the cam_utils script."""
import cv2
diff --git a/tests/test_comparevis.py b/tests/test_comparevis.py
index 4540ea50..b1d8933f 100644
--- a/tests/test_comparevis.py
+++ b/tests/test_comparevis.py
@@ -1,7 +1,6 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-
"""Tests for the comparevis script."""
import shutil
diff --git a/tests/test_visualizer.py b/tests/test_visualizer.py
index 1341df98..46d5c7ea 100644
--- a/tests/test_visualizer.py
+++ b/tests/test_visualizer.py
@@ -1,5 +1,7 @@
+# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
+#
+# SPDX-License-Identifier: GPL-3.0-or-later
import numpy as np
-import pytest
from ptbench.engine.visualizer import (
_compute_avg_saliency_focus,
--
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