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Fix for dense parameter selection in the study (#17)
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‎.github/workflows/build.yml‎

Lines changed: 23 additions & 17 deletions
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@@ -66,8 +66,6 @@ jobs:
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strategy:
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matrix:
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include:
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- os: ubuntu-22.04
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python-version: "3.8"
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- os: ubuntu-22.04
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python-version: "3.9"
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- os: ubuntu-22.04
@@ -76,8 +74,8 @@ jobs:
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python-version: "3.11"
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- os: ubuntu-22.04
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python-version: "3.12"
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- os: ubuntu-24.04
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python-version: "3.8"
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- os: ubuntu-22.04
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python-version: "3.13"
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- os: ubuntu-24.04
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python-version: "3.9"
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- os: ubuntu-24.04
@@ -86,28 +84,28 @@ jobs:
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python-version: "3.11"
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- os: ubuntu-24.04
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python-version: "3.12"
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- os: windows-2019
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python-version: "3.8"
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- os: windows-2019
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- os: ubuntu-24.04
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python-version: "3.13"
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- os: windows-2022
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python-version: "3.9"
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- os: windows-2019
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- os: windows-2022
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python-version: "3.10"
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- os: windows-2019
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- os: windows-2022
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python-version: "3.11"
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- os: windows-2019
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python-version: "3.12"
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- os: windows-2022
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python-version: "3.8"
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python-version: "3.12"
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- os: windows-2022
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python-version: "3.13"
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- os: windows-2025
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python-version: "3.9"
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- os: windows-2022
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- os: windows-2025
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python-version: "3.10"
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- os: windows-2022
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- os: windows-2025
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python-version: "3.11"
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- os: windows-2022
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- os: windows-2025
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python-version: "3.12"
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- os: macos-13
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python-version: "3.8"
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- os: windows-2025
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python-version: "3.13"
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- os: macos-13
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python-version: "3.9"
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- os: macos-13
@@ -120,10 +118,18 @@ jobs:
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python-version: "3.10"
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- os: macos-14
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python-version: "3.11"
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- os: macos-14
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python-version: "3.12"
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- os: macos-14
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python-version: "3.13"
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- os: macos-15
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python-version: "3.10"
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- os: macos-15
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python-version: "3.11"
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- os: macos-15
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python-version: "3.12"
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- os: macos-15
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python-version: "3.13"
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steps:
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- name: Set up Python ${{ matrix.python-version }}

‎README.md‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1,7 +1,7 @@
11
# Segmentation validation and metrics computation backend for Raidionics related publications
22

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[![License](https://img.shields.io/badge/License-BSD%202--Clause-orange.svg)](https://opensource.org/licenses/BSD-2-Clause)
4-
[![](https://img.shields.io/badge/python-3.8|3.9|3.10|3.11|3.12-blue.svg)](https://www.python.org/downloads/)
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[![](https://img.shields.io/badge/python-3.9|3.10|3.11|3.12|3.13-blue.svg)](https://www.python.org/downloads/)
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[![Paper](https://zenodo.org/badge/DOI/10.3389/fneur.2022.932219.svg)](https://www.frontiersin.org/articles/10.3389/fneur.2022.932219/full)
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[![codecov](https://codecov.io/gh/dbouget/validation_metrics_computation/branch/master/graph/badge.svg?token=ZSPQVR7RKX)](https://codecov.io/gh/dbouget/validation_metrics_computation)
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[![Open In Colab](https://colab.research.google.com/assets/colab-badge.svg)](https://colab.research.google.com/gist/dbouget/491b0d34e3df00e730cd7fe7a8989202/compute_validation_example.ipynb)
@@ -15,6 +15,8 @@ the only hard requirement is the expected folder structure to use as input.
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## [Installation](https://github.com/dbouget/validation_metrics_computation#installation)
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1717
```
18+
pip install raidionicsval
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or
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pip install git+https://github.com/dbouget/validation_metrics_computation.git
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```
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‎pyproject.toml‎

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Original file line numberDiff line numberDiff line change
@@ -4,11 +4,11 @@ build-backend = "setuptools.build_meta"
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[project]
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name = "raidionicsval"
7-
version = "1.1.0"
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version = "1.1.1"
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description = "Raidionics backend for running validation and metrics computation"
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readme = "README.md"
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license = { text = "BSD-2-Clause" }
11-
requires-python = ">=3.8"
11+
requires-python = ">=3.9"
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authors = [{ name = "David Bouget", email = "david.bouget@sintef.no" }]
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dependencies = [

‎raidionicsval/Studies/AbstractStudy.py‎

Lines changed: 3 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -379,7 +379,7 @@ def compute_and_plot_metric_over_metric_categories(self, class_name: str, metric
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cat_optimal_results = total_optimal_results.loc[total_optimal_results[metric2] <= cutoff]
380380
optimal_results_per_cutoff['<=' + str(cutoff)] = cat_optimal_results
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else:
382-
cat_optimal_results = total_optimal_results.loc[metric2_cutoffs[c-1] < total_optimal_results[metric2] <= cutoff]
382+
cat_optimal_results = total_optimal_results.loc[(total_optimal_results[metric2] > metric2_cutoffs[c-1]) & (total_optimal_results[metric2] <= cutoff)]
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optimal_results_per_cutoff[']' + str(metric2_cutoffs[c-1]) + ',' + str(cutoff) + ']'] = cat_optimal_results
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cat_optimal_results = total_optimal_results.loc[total_optimal_results[metric2] > metric2_cutoffs[-1]]
385385
optimal_results_per_cutoff['>' + str(metric2_cutoffs[-1])] = cat_optimal_results
@@ -738,7 +738,7 @@ def compute_and_plot_metric_over_metric_cascading_categories(self, class_name: s
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cat_optimal_results = total_optimal_results.loc[total_optimal_results[metric2] <= cutoff]
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new_data_per_complete_selection[metric2 + '<=' + str(cutoff)] = cat_optimal_results
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else:
741-
cat_optimal_results = total_optimal_results.loc[metric2_cutoffs[c-1] < total_optimal_results[metric2] <= cutoff]
741+
cat_optimal_results = total_optimal_results.loc[(total_optimal_results[metric2] > metric2_cutoffs[c-1]) & (total_optimal_results[metric2] <= cutoff)]
742742
new_data_per_complete_selection[metric2 + ']' + str(metric2_cutoffs[c-1]) + ',' + str(cutoff) + ']'] = cat_optimal_results
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cat_optimal_results = total_optimal_results.loc[total_optimal_results[metric2] > metric2_cutoffs[-1]]
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new_data_per_complete_selection[metric2 + '>' + str(metric2_cutoffs[-1])] = cat_optimal_results
@@ -750,8 +750,7 @@ def compute_and_plot_metric_over_metric_cascading_categories(self, class_name: s
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cat_optimal_results = results_pool.loc[results_pool[metric2] <= cutoff]
751751
new_data_per_complete_selection[sel + ';' + metric2 + '<=' + str(cutoff)] = cat_optimal_results
752752
else:
753-
cat_optimal_results = results_pool.loc[
754-
metric2_cutoffs[c - 1] < results_pool[metric2] <= cutoff]
753+
cat_optimal_results = results_pool.loc[(results_pool[metric2] > metric2_cutoffs[c - 1]) & (results_pool[metric2] <= cutoff)]
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new_data_per_complete_selection[sel + ';' + metric2 +
756755
']' + str(metric2_cutoffs[c - 1]) + ',' + str(cutoff) + ']'] = cat_optimal_results
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cat_optimal_results = results_pool.loc[

‎tests/generic_tests/test_studies_pipeline.py‎

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Original file line numberDiff line numberDiff line change
@@ -7,7 +7,7 @@
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import traceback
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10-
def test_validation_pipeline_package(test_dir):
10+
def test_studies_pipeline_package(test_dir):
1111
logging.basicConfig()
1212
logging.getLogger().setLevel(logging.DEBUG)
1313
logging.info("Running standard reporting unit test.\n")
@@ -63,7 +63,7 @@ def test_validation_pipeline_package(test_dir):
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val_config.set('Studies', 'extra_parameters_filename', os.path.join(test_dir, 'Patient1',
6464
'Predictions',
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'external_patient_parameters.csv'))
66-
val_config.set('Studies', 'selections_dense', "PiW Dice,GT volume (ml),4,TP")
66+
val_config.set('Studies', 'selections_dense', "PiW Dice,GT volume (ml),2-4-8,TP")
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config_filename = os.path.join(output_folder, 'config.ini')
6868
with open(config_filename, 'w') as outfile:
6969
val_config.write(outfile)
@@ -83,5 +83,4 @@ def test_validation_pipeline_package(test_dir):
8383

8484
logging.info("k-fold cross-validation unit test succeeded.\n")
8585
if os.path.exists(output_folder):
86-
shutil.rmtree(output_folder)
87-
86+
shutil.rmtree(output_folder)

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