From 936c402c8bb604b1bf7ba328490eec9b5b06931d Mon Sep 17 00:00:00 2001 From: scap3yvt <149599669+scap3yvt@users.noreply.github.com> Date: Tue, 10 Jun 2025 22:15:17 -0400 Subject: [PATCH 1/3] updated version for release --- GANDLF/version.py | 2 +- samples/config_all_options.yaml | 4 ++-- samples/config_classification.yaml | 4 ++-- samples/config_getting_started_classification_histo2d.yaml | 2 +- samples/config_getting_started_classification_rad3d.yaml | 2 +- samples/config_getting_started_regression_histo2d.yaml | 2 +- samples/config_getting_started_regression_rad3d.yaml | 2 +- samples/config_getting_started_segmentation_histo2d.yaml | 2 +- samples/config_regression.yaml | 4 ++-- samples/config_segmentation_brats.yaml | 4 ++-- samples/config_segmentation_histology.yaml | 4 ++-- testing/config_classification.yaml | 2 +- testing/config_regression.yaml | 2 +- testing/config_segmentation.yaml | 2 +- 14 files changed, 19 insertions(+), 19 deletions(-) diff --git a/GANDLF/version.py b/GANDLF/version.py index 5888063de..6247f9bd5 100644 --- a/GANDLF/version.py +++ b/GANDLF/version.py @@ -2,4 +2,4 @@ # -*- coding: UTF-8 -*- # check GaNDLF wiki for versioning and release guidelines: https://github.com/mlcommons/GaNDLF/wiki -__version__ = "0.1.4-dev" +__version__ = "0.1.4" diff --git a/samples/config_all_options.yaml b/samples/config_all_options.yaml index c832adec2..192148e20 100644 --- a/samples/config_all_options.yaml +++ b/samples/config_all_options.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.4-dev, - maximum: 0.1.4-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.4, + maximum: 0.1.4 # this should NOT be made a variable, but should be tested after every tag is created } ## Choose the model parameters here model: diff --git a/samples/config_classification.yaml b/samples/config_classification.yaml index 8b23f9075..fcc01f70f 100644 --- a/samples/config_classification.yaml +++ b/samples/config_classification.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.4-dev, - maximum: 0.1.4-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.4, + maximum: 0.1.4 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_getting_started_classification_histo2d.yaml b/samples/config_getting_started_classification_histo2d.yaml index 48883e087..f86c17af9 100644 --- a/samples/config_getting_started_classification_histo2d.yaml +++ b/samples/config_getting_started_classification_histo2d.yaml @@ -94,6 +94,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.4-dev + maximum: 0.1.4 minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_classification_rad3d.yaml b/samples/config_getting_started_classification_rad3d.yaml index 3653fa48c..e187f485f 100644 --- a/samples/config_getting_started_classification_rad3d.yaml +++ b/samples/config_getting_started_classification_rad3d.yaml @@ -99,6 +99,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.4-dev + maximum: 0.1.4 minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_regression_histo2d.yaml b/samples/config_getting_started_regression_histo2d.yaml index b540c4791..a211b850e 100644 --- a/samples/config_getting_started_regression_histo2d.yaml +++ b/samples/config_getting_started_regression_histo2d.yaml @@ -59,6 +59,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.4-dev + maximum: 0.1.4 minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_getting_started_regression_rad3d.yaml b/samples/config_getting_started_regression_rad3d.yaml index d3e517877..fa566c47f 100644 --- a/samples/config_getting_started_regression_rad3d.yaml +++ b/samples/config_getting_started_regression_rad3d.yaml @@ -62,6 +62,6 @@ scheduler: track_memory_usage: false verbose: false version: - maximum: 0.1.4-dev + maximum: 0.1.4 minimum: 0.0.14 weighted_loss: false diff --git a/samples/config_getting_started_segmentation_histo2d.yaml b/samples/config_getting_started_segmentation_histo2d.yaml index e1e43226a..79f40e787 100644 --- a/samples/config_getting_started_segmentation_histo2d.yaml +++ b/samples/config_getting_started_segmentation_histo2d.yaml @@ -66,6 +66,6 @@ scheduler: track_memory_usage: false verbose: true version: - maximum: 0.1.4-dev + maximum: 0.1.4 minimum: 0.0.14 weighted_loss: true diff --git a/samples/config_regression.yaml b/samples/config_regression.yaml index 149b01869..f8534d658 100644 --- a/samples/config_regression.yaml +++ b/samples/config_regression.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.4-dev, - maximum: 0.1.4-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.4, + maximum: 0.1.4 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_segmentation_brats.yaml b/samples/config_segmentation_brats.yaml index 05e2b4c6c..54cfe0b06 100644 --- a/samples/config_segmentation_brats.yaml +++ b/samples/config_segmentation_brats.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.4-dev, - maximum: 0.1.4-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.4, + maximum: 0.1.4 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/samples/config_segmentation_histology.yaml b/samples/config_segmentation_histology.yaml index 64cb3bd51..b999b5f83 100644 --- a/samples/config_segmentation_histology.yaml +++ b/samples/config_segmentation_histology.yaml @@ -1,8 +1,8 @@ # affix version version: { - minimum: 0.1.4-dev, - maximum: 0.1.4-dev # this should NOT be made a variable, but should be tested after every tag is created + minimum: 0.1.4, + maximum: 0.1.4 # this should NOT be made a variable, but should be tested after every tag is created } # Choose the model parameters here model: diff --git a/testing/config_classification.yaml b/testing/config_classification.yaml index b935f83e4..a11a802f4 100644 --- a/testing/config_classification.yaml +++ b/testing/config_classification.yaml @@ -55,7 +55,7 @@ save_output: false scaling_factor: 1 scheduler: triangle version: - maximum: 0.1.4-dev + maximum: 0.1.4 minimum: 0.0.14 weighted_loss: True diff --git a/testing/config_regression.yaml b/testing/config_regression.yaml index 3784c1c33..209a6656b 100644 --- a/testing/config_regression.yaml +++ b/testing/config_regression.yaml @@ -38,7 +38,7 @@ save_output: false scaling_factor: 1 scheduler: triangle version: - maximum: 0.1.4-dev + maximum: 0.1.4 minimum: 0.0.14 weighted_loss: false diff --git a/testing/config_segmentation.yaml b/testing/config_segmentation.yaml index 8b4726388..8f96b93bf 100644 --- a/testing/config_segmentation.yaml +++ b/testing/config_segmentation.yaml @@ -3,7 +3,7 @@ version: { minimum: 0.0.14, - maximum: 0.1.4-dev + maximum: 0.1.4 } model: { From 046d106c53bdd0d1e60f67f4b4dc15b2e139a817 Mon Sep 17 00:00:00 2001 From: scap3yvt <149599669+scap3yvt@users.noreply.github.com> Date: Wed, 11 Jun 2025 10:49:37 -0400 Subject: [PATCH 2/3] ensure citation reminder does not come up --- GANDLF/metrics/segmentation_panoptica.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/GANDLF/metrics/segmentation_panoptica.py b/GANDLF/metrics/segmentation_panoptica.py index 9c8eb3319..b6e4017e2 100644 --- a/GANDLF/metrics/segmentation_panoptica.py +++ b/GANDLF/metrics/segmentation_panoptica.py @@ -1,5 +1,5 @@ from pathlib import Path -import tempfile +import os, tempfile import numpy as np @@ -25,6 +25,8 @@ def generate_instance_segmentation( dict: The evaluation results. """ + os.environ["PANOPTICA_CITATION_REMINDER"] = "False" + cwd = Path(__file__).parent.absolute() # the parameters dict takes precedence over the panoptica_config_path panoptica_config = parameters.get("panoptica_config", None) From eafd87093ec078bba907401dc6e0821e8a46a2f9 Mon Sep 17 00:00:00 2001 From: scap3yvt <149599669+scap3yvt@users.noreply.github.com> Date: Thu, 12 Jun 2025 10:21:04 -0400 Subject: [PATCH 3/3] updated groups for default --- samples/config_segmentation_metrics_brats_default.yaml | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/samples/config_segmentation_metrics_brats_default.yaml b/samples/config_segmentation_metrics_brats_default.yaml index 9a7d3fdd9..36d93d4e3 100644 --- a/samples/config_segmentation_metrics_brats_default.yaml +++ b/samples/config_segmentation_metrics_brats_default.yaml @@ -144,18 +144,21 @@ panoptica: !Panoptica_Evaluator save_group_times: false segmentation_class_groups: !SegmentationClassGroups groups: - ed: !LabelGroup + snfh: !LabelGroup single_instance: false value_labels: [2] et: !LabelGroup single_instance: false value_labels: [3] - net: !LabelGroup + netc: !LabelGroup single_instance: false value_labels: [1] + rc: !LabelGroup + single_instance: false + value_labels: [4] tc: !LabelMergeGroup single_instance: false - value_labels: [1, 3] + value_labels: [1, 3, 4] wt: !LabelMergeGroup single_instance: false value_labels: [1, 2, 3, 4]