diff --git a/.gitattributes b/.gitattributes index 136bd36a2..c4e41703f 100644 --- a/.gitattributes +++ b/.gitattributes @@ -1,18 +1,22 @@ *.tar filter=lfs diff=lfs merge=lfs -text *.nii filter=lfs diff=lfs merge=lfs -text -*.nii.gz filter=lfs diff=lfs merge=lfs -text *.pth.tar filter=lfs diff=lfs merge=lfs -text *.h5 filter=lfs diff=lfs merge=lfs -text *.npy filter=lfs diff=lfs merge=lfs -text *.png filter=lfs diff=lfs merge=lfs -text +*.npz filter=lfs diff=lfs merge=lfs -text +*.dcm filter=lfs diff=lfs merge=lfs -text +*.zip filter=lfs diff=lfs merge=lfs -text +*.jpg filter=lfs diff=lfs merge=lfs -text +*.tiff filter=lfs diff=lfs merge=lfs -text * text=auto *.tar binary *.nii binary *.nii.gz binary *.pth.tar binary *.npy binary -*.npz filter=lfs diff=lfs merge=lfs -text -*.dcm filter=lfs diff=lfs merge=lfs -text -*.zip filter=lfs diff=lfs merge=lfs -text -*.jpg filter=lfs diff=lfs merge=lfs -text -*.tiff filter=lfs diff=lfs merge=lfs -text +*.npz binary +*.dcm binary +*.zip binary +*.jpg binary +*.tiff binary diff --git a/CHANGELOG.md b/CHANGELOG.md index d4d409219..d1b65e3e1 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -72,6 +72,7 @@ gets uploaded to AzureML, by skipping all test folders. - ([#596](https://github.com/microsoft/InnerEye-DeepLearning/pull/596)) Add `cudatoolkit=11.1` specification to environment.yml. - ([#615](https://github.com/microsoft/InnerEye-DeepLearning/pull/615)) Minor changes to checkpoint download from AzureML. - ([#605](https://github.com/microsoft/InnerEye-DeepLearning/pull/605)) Make build jobs deterministic for regression testing. +- ([#632](https://github.com/microsoft/InnerEye-DeepLearning/pull/632)) Nifti test data is no longer stored in Git LFS ### Fixed - ([#606](https://github.com/microsoft/InnerEye-DeepLearning/pull/606)) Bug fix: registered models do not include the hi-ml submodule diff --git a/RegressionTestResults/PR_BasicModel2Epochs/OUTPUT/best_validation_epoch/Test/005/background.nii.gz 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a/Tests/ML/test_data/train_and_test_data/id2_region.nii.gz b/Tests/ML/test_data/train_and_test_data/id2_region.nii.gz index be4022fb1..5a66e052a 100644 Binary files a/Tests/ML/test_data/train_and_test_data/id2_region.nii.gz and b/Tests/ML/test_data/train_and_test_data/id2_region.nii.gz differ diff --git a/Tests/ML/test_data/train_and_test_data/scalar_epoch_metrics.csv b/Tests/ML/test_data/train_and_test_data/scalar_epoch_metrics.csv index 57f34d5a0..9c9a781c8 100644 --- a/Tests/ML/test_data/train_and_test_data/scalar_epoch_metrics.csv +++ b/Tests/ML/test_data/train_and_test_data/scalar_epoch_metrics.csv @@ -1,5 +1,5 @@ -loss,cross_entropy,accuracy_at_threshold_05,seconds_per_batch,seconds_per_epoch,learning_rate,area_under_roc_curve,area_under_pr_curve,accuracy_at_optimal_threshold,false_positive_rate_at_optimal_threshold,false_negative_rate_at_optimal_threshold,optimal_threshold,subject_count,epoch,cross_validation_split_index -0.7016490995883942,0.7016490697860718,0.375,0.02346169948577881,0.06398129463195801,0.0001,0.8125,0.85,0.6666666865348816,0.0,0.5,0.5281670689582825,6.0,1,-1 -0.702895998954773,0.7028960287570953,0.375,0.019975781440734863,0.05499887466430664,9.999712322065557e-05,0.5625,0.6458333333333333,0.6666666865348816,0.0,0.5,0.5280245542526245,6.0,2,-1 -0.7125596106052399,0.712559700012207,0.25,0.02925896644592285,0.07402157783508301,9.999306876841536e-05,0.875,0.875,0.6666666865348816,0.0,0.5,0.5277201533317566,6.0,3,-1 -0.7119755446910858,0.711975485086441,0.25,0.025499820709228516,0.0679938793182373,9.998613801725043e-05,0.875,0.875,0.6666666865348816,0.0,0.5,0.5274553894996643,6.0,4,-1 +loss,cross_entropy,accuracy_at_threshold_05,seconds_per_batch,seconds_per_epoch,learning_rate,area_under_roc_curve,area_under_pr_curve,accuracy_at_optimal_threshold,false_positive_rate_at_optimal_threshold,false_negative_rate_at_optimal_threshold,optimal_threshold,subject_count,epoch,cross_validation_split_index +0.7016490995883942,0.7016490697860718,0.375,0.02346169948577881,0.06398129463195801,0.0001,0.8125,0.85,0.6666666865348816,0.0,0.5,0.5281670689582825,6.0,1,-1 +0.702895998954773,0.7028960287570953,0.375,0.019975781440734863,0.05499887466430664,9.999712322065557e-05,0.5625,0.6458333333333333,0.6666666865348816,0.0,0.5,0.5280245542526245,6.0,2,-1 +0.7125596106052399,0.712559700012207,0.25,0.02925896644592285,0.07402157783508301,9.999306876841536e-05,0.875,0.875,0.6666666865348816,0.0,0.5,0.5277201533317566,6.0,3,-1 +0.7119755446910858,0.711975485086441,0.25,0.025499820709228516,0.0679938793182373,9.998613801725043e-05,0.875,0.875,0.6666666865348816,0.0,0.5,0.5274553894996643,6.0,4,-1 diff --git a/Tests/ML/test_data/train_and_test_data/scalar_prediction_target_metrics.csv b/Tests/ML/test_data/train_and_test_data/scalar_prediction_target_metrics.csv index 0b237f448..03606d911 100644 --- a/Tests/ML/test_data/train_and_test_data/scalar_prediction_target_metrics.csv +++ b/Tests/ML/test_data/train_and_test_data/scalar_prediction_target_metrics.csv @@ -1,25 +1,25 @@ -prediction_target,epoch,subject,model_output,label,cross_validation_split_index,data_split -Default,1,S4,0.5216594338417053,0.0,-1,Train -Default,1,S5,0.5216594338417053,1.0,-1,Train -Default,1,S6,0.5216594338417053,0.0,-1,Train -Default,1,S7,0.5216594338417053,0.0,-1,Train -Default,1,S8,0.5213258266448975,0.0,-1,Train -Default,1,S1,0.5281670689582825,1.0,-1,Train -Default,2,S1,0.5280245542526245,1.0,-1,Train -Default,2,S4,0.521056056022644,0.0,-1,Train -Default,2,S7,0.521056056022644,0.0,-1,Train -Default,2,S6,0.521056056022644,0.0,-1,Train -Default,2,S8,0.5207627415657043,0.0,-1,Train -Default,2,S5,0.5207627415657043,1.0,-1,Train -Default,3,S5,0.5205143690109253,1.0,-1,Train -Default,3,S8,0.5205143690109253,0.0,-1,Train -Default,3,S1,0.5277201533317566,1.0,-1,Train -Default,3,S7,0.5205143690109253,0.0,-1,Train -Default,3,S4,0.5202868580818176,0.0,-1,Train -Default,3,S6,0.5202868580818176,0.0,-1,Train -Default,4,S1,0.5274553894996643,1.0,-1,Train -Default,4,S8,0.520030677318573,0.0,-1,Train -Default,4,S5,0.520030677318573,1.0,-1,Train -Default,4,S4,0.520030677318573,0.0,-1,Train -Default,4,S7,0.5197962522506714,0.0,-1,Train -Default,4,S6,0.5197962522506714,0.0,-1,Train +prediction_target,epoch,subject,model_output,label,cross_validation_split_index,data_split +Default,1,S4,0.5216594338417053,0.0,-1,Train +Default,1,S5,0.5216594338417053,1.0,-1,Train +Default,1,S6,0.5216594338417053,0.0,-1,Train +Default,1,S7,0.5216594338417053,0.0,-1,Train +Default,1,S8,0.5213258266448975,0.0,-1,Train +Default,1,S1,0.5281670689582825,1.0,-1,Train +Default,2,S1,0.5280245542526245,1.0,-1,Train +Default,2,S4,0.521056056022644,0.0,-1,Train +Default,2,S7,0.521056056022644,0.0,-1,Train +Default,2,S6,0.521056056022644,0.0,-1,Train +Default,2,S8,0.5207627415657043,0.0,-1,Train +Default,2,S5,0.5207627415657043,1.0,-1,Train +Default,3,S5,0.5205143690109253,1.0,-1,Train +Default,3,S8,0.5205143690109253,0.0,-1,Train +Default,3,S1,0.5277201533317566,1.0,-1,Train +Default,3,S7,0.5205143690109253,0.0,-1,Train +Default,3,S4,0.5202868580818176,0.0,-1,Train +Default,3,S6,0.5202868580818176,0.0,-1,Train +Default,4,S1,0.5274553894996643,1.0,-1,Train +Default,4,S8,0.520030677318573,0.0,-1,Train +Default,4,S5,0.520030677318573,1.0,-1,Train +Default,4,S4,0.520030677318573,0.0,-1,Train +Default,4,S7,0.5197962522506714,0.0,-1,Train +Default,4,S6,0.5197962522506714,0.0,-1,Train