STYLE: Ensure line breaks at the end of all files (#717)
* Add line breaks at the end of all files * Handle last line in VS Code settings
This commit is contained in:
Fernando Pérez-García
GitHub
Родитель
2edbdc8d64
Коммит
6aab3b1f93
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@ -54,4 +54,3 @@ jobs:
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- name: Perform CodeQL Analysis
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uses: github/codeql-action/analyze@v1
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@ -17,4 +17,4 @@
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<component name="TestRunnerService">
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<option name="PROJECT_TEST_RUNNER" value="pytest" />
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</component>
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</module>
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</module>
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@ -16,4 +16,4 @@
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<option name="WRAP_LONG_LINES" value="true" />
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</codeStyleSettings>
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</code_scheme>
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</component>
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</component>
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@ -2,4 +2,4 @@
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<state>
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<option name="USE_PER_PROJECT_SETTINGS" value="true" />
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</state>
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</component>
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</component>
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@ -4,4 +4,4 @@
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<option name="notice" value="------------------------------------------------------------------------------------------ Copyright (c) Microsoft Corporation. All rights reserved. Licensed under the MIT License (MIT). See LICENSE in the repo root for license information. ------------------------------------------------------------------------------------------" />
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<option name="myName" value="MIT license" />
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</copyright>
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</component>
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</component>
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@ -4,4 +4,4 @@
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<element module="All" copyright="MIT license" />
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</module2copyright>
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</settings>
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</component>
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</component>
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@ -41,4 +41,4 @@
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</inspection_tool>
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<inspection_tool class="Pylint" enabled="true" level="WARNING" enabled_by_default="true" />
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</profile>
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</component>
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</component>
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@ -5,4 +5,4 @@
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<module fileurl="file://$PROJECT_DIR$/.idea/InnerEye-DeepLearning.iml" filepath="$PROJECT_DIR$/.idea/InnerEye-DeepLearning.iml" />
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</modules>
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</component>
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</project>
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</project>
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@ -4,4 +4,4 @@
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<option name="PY_SCI_VIEW" value="true" />
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<option name="PY_SCI_VIEW_SUGGESTED" value="true" />
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</component>
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</project>
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</project>
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@ -20,4 +20,4 @@
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<option name="INPUT_FILE" value="" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -20,4 +20,4 @@
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<option name="INPUT_FILE" value="" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -21,4 +21,4 @@
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<option name="INPUT_FILE" value="" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -21,4 +21,4 @@
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<option name="INPUT_FILE" value="" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -20,4 +20,4 @@
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<option name="INPUT_FILE" value="" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -20,4 +20,4 @@
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<option name="INPUT_FILE" value="" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -20,4 +20,4 @@
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<option name="INPUT_FILE" value="" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -20,4 +20,4 @@
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<option name="INPUT_FILE" value="" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -16,4 +16,4 @@
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<option name="_new_targetType" value=""PATH"" />
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<method v="2" />
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</configuration>
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</component>
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</component>
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@ -5,4 +5,4 @@
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<mapping directory="$PROJECT_DIR$/fastMRI" vcs="Git" />
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<mapping directory="$PROJECT_DIR$/hi-ml" vcs="Git" />
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</component>
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</project>
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</project>
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@ -5,5 +5,7 @@
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],
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"python.testing.unittestEnabled": false,
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"python.testing.pytestEnabled": true,
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"files.trimTrailingWhitespace": true
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"files.trimTrailingWhitespace": true,
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"files.trimFinalNewlines": true,
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"files.insertFinalNewline": true
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}
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@ -26,4 +26,4 @@
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<ExcludeFolder>GeoPol.xml</ExcludeFolder>
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<ExcludeFolder>*.nii.gz</ExcludeFolder>
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</Component>
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</GeoPol_Folders>
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</GeoPol_Folders>
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@ -1 +1 @@
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The InnerEye-DataQuality code has been moved here: [https://github.com/microsoft/InnerEye-DeepLearning/tree/1606729c7a16e1bfeb269694314212b6e2737939/InnerEye-DataQuality](https://github.com/microsoft/InnerEye-DeepLearning/tree/1606729c7a16e1bfeb269694314212b6e2737939/InnerEye-DataQuality)
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The InnerEye-DataQuality code has been moved here: [https://github.com/microsoft/InnerEye-DeepLearning/tree/1606729c7a16e1bfeb269694314212b6e2737939/InnerEye-DataQuality](https://github.com/microsoft/InnerEye-DeepLearning/tree/1606729c7a16e1bfeb269694314212b6e2737939/InnerEye-DataQuality)
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@ -49,4 +49,3 @@ class DummyClassification(ScalarModelBase):
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# Use a local import so that we don't need to import pytorch when creating configs in the runner
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from Tests.ML.models.architectures.DummyScalarModel import DummyScalarModel
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return DummyScalarModel(self.expected_image_size_zyx)
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@ -165,4 +165,3 @@ class BiTResNetV2(nn.Module):
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x = self.conv_stack(x)
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x = self.linear(x)
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return x
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@ -280,4 +280,4 @@
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}
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@ -163,4 +163,4 @@
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}
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@ -162,4 +162,4 @@
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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}
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@ -1 +1 @@
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{"model_name": "BasicModel2Epochs", "checkpoint_paths": ["checkpoints/last.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.segmentation.BasicModel2Epochs"}
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{"model_name": "BasicModel2Epochs", "checkpoint_paths": ["checkpoints/last.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.segmentation.BasicModel2Epochs"}
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@ -1 +1 @@
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There were not enough data points for any statistically meaningful comparisons.
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There were not enough data points for any statistically meaningful comparisons.
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@ -998,4 +998,4 @@ epoch,subject,prediction_target,model_output,label,data_split,cross_validation_s
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1,003469-OD,Default,0.482178,0,Train,0
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1,001578-OS,Default,0.487305,1,Train,0
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1,003327-OD,Default,0.477539,1,Train,0
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1,002457-OS,Default,0.466064,0,Train,0
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1,002457-OS,Default,0.466064,0,Train,0
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@ -998,4 +998,4 @@ epoch,subject,prediction_target,model_output,label,data_split,cross_validation_s
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1,003423-OS,Default,0.330811,1,Val,0
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1,003476-OD,Default,0.313477,1,Val,0
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1,003505-OS,Default,0.322266,1,Val,0
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1,003516-OD,Default,0.295898,1,Val,0
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1,003516-OD,Default,0.295898,1,Val,0
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@ -998,4 +998,4 @@ epoch,subject,prediction_target,model_output,label,data_split,cross_validation_s
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1,001436-OD,Default,0.553223,1,Train,1
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1,001255-OS,Default,0.553223,1,Train,1
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1,003059-OS,Default,0.539062,1,Train,1
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1,002407-OD,Default,0.532715,0,Train,1
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1,002407-OD,Default,0.532715,0,Train,1
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@ -998,4 +998,4 @@ epoch,subject,prediction_target,model_output,label,data_split,cross_validation_s
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1,003423-OD,Default,0.422363,1,Val,1
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1,003476-OS,Default,0.388184,1,Val,1
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1,003485-OS,Default,0.418945,1,Val,1
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1,003502-OS,Default,0.399170,1,Val,1
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1,003502-OS,Default,0.399170,1,Val,1
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@ -1 +1 @@
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{"model_name": "GlaucomaPublic", "checkpoint_paths": ["checkpoints/OTHER_RUNS/1/last.ckpt", "checkpoints/last.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.classification.GlaucomaPublic"}
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{"model_name": "GlaucomaPublic", "checkpoint_paths": ["checkpoints/OTHER_RUNS/1/last.ckpt", "checkpoints/last.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.classification.GlaucomaPublic"}
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@ -1 +1 @@
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{"model_name": "HelloContainer", "checkpoint_paths": ["checkpoints/last.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.other.HelloContainer"}
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{"model_name": "HelloContainer", "checkpoint_paths": ["checkpoints/last.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.other.HelloContainer"}
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@ -1 +1 @@
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0.012701375409960747
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0.012701375409960747
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@ -1 +1 @@
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There were not enough data points for any statistically meaningful comparisons.
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There were not enough data points for any statistically meaningful comparisons.
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@ -1 +1 @@
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There were not enough data points for any statistically meaningful comparisons.
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There were not enough data points for any statistically meaningful comparisons.
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@ -1 +1 @@
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There were not enough data points for any statistically meaningful comparisons.
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There were not enough data points for any statistically meaningful comparisons.
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@ -6,4 +6,4 @@ No outliers found
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=== METRIC: HausdorffDistance_mm ===
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No outliers found
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No outliers found
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@ -1 +1 @@
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{"model_name": "BasicModelForEnsembleTest", "checkpoint_paths": ["checkpoints/OTHER_RUNS/1/last.ckpt", "checkpoints/last.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.segmentation.BasicModel2Epochs"}
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{"model_name": "BasicModelForEnsembleTest", "checkpoint_paths": ["checkpoints/OTHER_RUNS/1/last.ckpt", "checkpoints/last.ckpt"], "model_configs_namespace": "InnerEye.ML.configs.segmentation.BasicModel2Epochs"}
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@ -38,4 +38,4 @@ We prefer all communications to be in English.
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Microsoft follows the principle of [Coordinated Vulnerability Disclosure](https://www.microsoft.com/en-us/msrc/cvd).
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<!-- END MICROSOFT SECURITY.MD BLOCK -->
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<!-- END MICROSOFT SECURITY.MD BLOCK -->
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@ -55,4 +55,4 @@ Patient Structure seriesId
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prostate 6fa04f324339c532a7c06877d1129bfacd7504d9c0bf6277a393915e73e41d66 5a6ba8fe-65bc-43ec-b1fc-682c8c37e40c 1.0 0.0 0.0 0.0
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seminalvesicles 6fa04f324339c532a7c06877d1129bfacd7504d9c0bf6277a393915e73e41d66 5a6ba8fe-65bc-43ec-b1fc-682c8c37e40c 1.0 0.0 0.0 0.0
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SELECT * FROM ROOT as r WHERE true AND (r.InstitutionId = "641eda02-90c3-45ed-b8b1-2651b6a5da6c" OR r.InstitutionId = "5a6ba8fe-65bc-43ec-b1fc-682c8c37e40c") AND (STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"9e84c7f5b030cc48e867430e762e1bb7e756051e27468b4fa6a0472292bb59eb") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"4af0d32eb2c7b4d253b98530b8c6f5aac10602d51ff4097ab3c932331cf0d2a5") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"d41cb61517793f87f97d5d6c0cee9f91df94169c29701c10190723ff8ede419a") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"5f1573dbbf6a8335bcf8bf5eed74e9157d4e7ee9dae8d679d4d4d7118510d741") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"991648f92b04f05e316fe7c99b1aa748c2d556b1e873591ae9b9bbd2c319254a") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"1deef6a1145f76617016a3e26288b009028e411ae4a236043afe7aa8cfbff6b4") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"f040ac05a1eeee9a064662adda21f703d7ba969b7dfc2787248b2c596ccf59a7") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"4b6610b5b249fbc149eb0a47abe97d08df6b26b76ffcf59431271d057f722d14") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"776d594c55725ad79bf59df2e3e9b6e6ded64cd37a1df45b03847c1e54828246") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"6fa04f324339c532a7c06877d1129bfacd7504d9c0bf6277a393915e73e41d66"))
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SELECT * FROM ROOT as r WHERE true AND (r.InstitutionId = "641eda02-90c3-45ed-b8b1-2651b6a5da6c" OR r.InstitutionId = "5a6ba8fe-65bc-43ec-b1fc-682c8c37e40c") AND (STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"9e84c7f5b030cc48e867430e762e1bb7e756051e27468b4fa6a0472292bb59eb") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"4af0d32eb2c7b4d253b98530b8c6f5aac10602d51ff4097ab3c932331cf0d2a5") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"d41cb61517793f87f97d5d6c0cee9f91df94169c29701c10190723ff8ede419a") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"5f1573dbbf6a8335bcf8bf5eed74e9157d4e7ee9dae8d679d4d4d7118510d741") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"991648f92b04f05e316fe7c99b1aa748c2d556b1e873591ae9b9bbd2c319254a") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"1deef6a1145f76617016a3e26288b009028e411ae4a236043afe7aa8cfbff6b4") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"f040ac05a1eeee9a064662adda21f703d7ba969b7dfc2787248b2c596ccf59a7") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"4b6610b5b249fbc149eb0a47abe97d08df6b26b76ffcf59431271d057f722d14") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"776d594c55725ad79bf59df2e3e9b6e6ded64cd37a1df45b03847c1e54828246") OR STARTSWITH(r.VersionedDicomImageSeries.Latest.Series.InstanceUID,"6fa04f324339c532a7c06877d1129bfacd7504d9c0bf6277a393915e73e41d66"))
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@ -53,4 +53,4 @@ Patient Structure
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411 bladder 1.0 0.0 0.0 0.0
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femur_r 1.0 0.0 0.0 0.0
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prostate 1.0 0.0 0.0 0.0
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seminalvesicles 1.0 0.0 0.0 0.0
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seminalvesicles 1.0 0.0 0.0 0.0
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@ -4,4 +4,4 @@ S1,green,1_green.png,
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S2,blue,1_blue.png,2|3
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S2,green,1_green.png,
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S3,blue,1_blue.png,3
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S3,green,1_green.png,
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S3,green,1_green.png,
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@ -25,4 +25,4 @@
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3250.00005,VST 7,25,Bar,category_1,category_B,233,0,0,84,img_8,5,0
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3250.00005,VST 8,25,Bar,category_1,category_B,218,0,0,84,img_9,6,0
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3250.00005,VST 9,25,Bar,category_1,category_B,221,0,0,84,img_10,7,0
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3250.00005,VST 10,25,Bar,category_1,category_B,238,0,0.02,84,img_11,8,0
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3250.00005,VST 10,25,Bar,category_1,category_B,238,0,0.02,84,img_11,8,0
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@ -1,4 +1,3 @@
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1,2,crop_sizes
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[ 37 37 37],[ 37 37 37],"[55, 55, 55]"
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[ 37 37 37],[ 37 37 37],"[55, 55, 55]"
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@ -42,4 +42,3 @@ def test_set_temperature() -> None:
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assert after_ece.item() < before_ece.item()
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assert np.isclose(optimal_temperature, 1.44, rtol=0.1)
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assert model.temperature.requires_grad is False
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@ -252,4 +252,3 @@ class Container2(LightningContainer):
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# These arguments will be passed through to the Lightning trainer.
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return {"gradient_clip_val": 1, "limit_train_batches": 10}
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```
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@ -25,4 +25,4 @@ workspace specified in the parameters.
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The model is expected to be in the format above, i.e. contained in a subfolder called `name_version` of the path in `--path` parameter. The model will be automatically given the next available `id` once uploaded to the workspace. For example, if `my_model:100` already exists then it will be called `my_model:101`.
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Once in place you may want to run inference on the model with partial test data, i.e. test data from patients for whom
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some of the labels are missing. Normally inference on partial test data would raise an exception. To allow inference to continue over partial test data add the flag `--allow_incomplete_labels` to your inference call, for example `python InnerEye/ML/runner.py --allow_incomplete_labels --no-train --azureml --model=<model_name> --run_recovery_id=<recovery_id>`
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some of the labels are missing. Normally inference on partial test data would raise an exception. To allow inference to continue over partial test data add the flag `--allow_incomplete_labels` to your inference call, for example `python InnerEye/ML/runner.py --allow_incomplete_labels --no-train --azureml --model=<model_name> --run_recovery_id=<recovery_id>`
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@ -196,4 +196,4 @@ or for a local run
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```
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python ML/runner.py --model=CXRImageClassifier --local_weights_path={LOCAL_PATH_TO_YOUR_SSL_CHECKPOINT}
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```
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```
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