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Merge pull request #1 from curtislisle/main
AutoSeg3D
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‎models/a3ds-vertebrae/README.md

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# a3ds-vertebrae @ MHub.ai
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For details on the model or how to run the end-to-end pipeline on your data in a single command, visit [mhub.ai/models/auto3dseg](https://mhub.ai/models/auto3dseg)
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This model segments spinal vertebrae using a segresnet network pre-trained on the totalsegmenter v2.0 dataset. The model was trained by Andras Lasso and is also contained in the MONAIAuto3DSeg extension for 3D Slicer documented here: [https://github.com/lassoan/SlicerMONAIAuto3DSeg] (https://github.com/lassoan/SlicerMONAIAuto3DSeg)
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‎models/a3ds-vertebrae/__init__.py

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‎models/a3ds-vertebrae/config/auto-gen-auto3dseg.json

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{"ContentCreatorName": "Andras Lasso", "ClinicalTrialSeriesID": "AutoSeg3D", "ClinicalTrialTimePointID": "1", "SeriesDescription": "Segmentation", "SeriesNumber": "300", "InstanceNumber": "1", "BodyPartExamined": "Spinal Vertebrae", "segmentAttributes": [[{"LabelID": 1, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "sacrum", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "54735007", "CodeMeaning": "Sacrum"}}, {"LabelID": 2, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_S1", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "65985001", "CodeMeaning": "S1 vertebra"}}, {"LabelID": 3, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_L5", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "49668003", "CodeMeaning": "L5 vertebra"}}, {"LabelID": 4, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_L4", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "11994002", "CodeMeaning": "L4 vertebra"}}, {"LabelID": 5, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_L3", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "36470004", "CodeMeaning": "L3 vertebra"}}, {"LabelID": 6, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_L2", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "14293000", "CodeMeaning": "L2 vertebra"}}, {"LabelID": 7, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_L1", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "66794005", "CodeMeaning": "L1 vertebra"}}, {"LabelID": 8, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T12", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "23215003", "CodeMeaning": "T12 vertebra"}}, {"LabelID": 9, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T11", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "12989004", "CodeMeaning": "T11 vertebra"}}, {"LabelID": 10, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T10", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "7610001", "CodeMeaning": "T10 vertebra"}}, {"LabelID": 11, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T9", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "82687006", "CodeMeaning": "T9 vertebra"}}, {"LabelID": 12, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T8", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "11068009", "CodeMeaning": "T8 vertebra"}}, {"LabelID": 13, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T7", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "62487009", "CodeMeaning": "T7 vertebra"}}, {"LabelID": 14, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T6", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "45296009", "CodeMeaning": "T6 vertebra"}}, {"LabelID": 15, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T5", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "56401006", "CodeMeaning": "T5 vertebra"}}, {"LabelID": 16, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T4", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "73071006", "CodeMeaning": "T4 vertebra"}}, {"LabelID": 17, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T3", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "1626008", "CodeMeaning": "T3 vertebra"}}, {"LabelID": 18, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T2", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "53733008", "CodeMeaning": "T2 vertebra"}}, {"LabelID": 19, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_T1", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "64864005", "CodeMeaning": "T1 vertebra"}}, {"LabelID": 20, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_C7", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "87391001", "CodeMeaning": "C7 vertebra"}}, {"LabelID": 21, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_C6", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "36054005", "CodeMeaning": "C6 vertebra"}}, {"LabelID": 22, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_C5", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "36978003", "CodeMeaning": "C5 vertebra"}}, {"LabelID": 23, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_C4", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "5329002", "CodeMeaning": "C4 vertebra"}}, {"LabelID": 24, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_C3", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "113205007", "CodeMeaning": "C3 vertebra"}}, {"LabelID": 25, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_C2", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "39976000", "CodeMeaning": "C2 vertebra"}}, {"LabelID": 26, "SegmentAlgorithmType": "AUTOMATIC", "SegmentAlgorithmName": "Auto3DSeg-segresnet", "SegmentDescription": "vertebrae_C1", "SegmentedPropertyCategoryCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "123037004", "CodeMeaning": "Anatomical Structure"}, "SegmentedPropertyTypeCodeSequence": {"CodingSchemeDesignator": "SCT", "CodeValue": "14806007", "CodeMeaning": "C1 vertebra"}}]]}

‎models/a3ds-vertebrae/config/default.yml

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general:
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data_base_dir: /app/data
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version: 1.0
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description: "Default configuration for MONAIAuto3dSeg (dicom in, dicom out)"
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execute:
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- DicomImporter
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- NiftiConverter
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- A3DS_Vertebrae_Runner
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- DsegConverter
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- DataOrganizer
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modules:
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DicomImporter:
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source_dir: input_data
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import_dir: sorted_data
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sort_data: True
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meta:
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mod: '%Modality'
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DsegConverter:
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model_name: a3ds-vertebrae
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body_part_examined: VERTEBRA
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source_segs: nifti:mod=seg
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json_config_path: /app/models/a3ds-vertebrae/config/auto-gen-auto3dseg.json
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skip_empty_slices: True
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DataOrganizer:
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targets:
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- dicomseg:mod=seg-->[i:sid]/a3ds-vertebrae.seg.dcm

‎models/a3ds-vertebrae/config/slicer.yml

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general:
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data_base_dir: /app/data
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version: 1.0
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description: Auto3dSeg segmentation default (dicom to dicom)
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execute:
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- FileStructureImporter
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- NrrdConverter
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- A3DS_Vertebrae_Runner
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- JsonSegExporter
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- DataOrganizer
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modules:
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FileStructureImporter:
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structures:
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- image.nrrd@instance@nrrd:mod=ct
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JsonSegExporter:
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segment_id_meta_key: roi
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targets:
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- nrrd:mod=seg-->[basename]
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DataOrganizer:
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targets:
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- nrrd:mod=seg-->[basename]
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- json:mod=seg-->segdef.json

‎models/a3ds-vertebrae/dockerfiles/Dockerfile

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FROM mhubai/base:latest
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# load prerequisites
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RUN echo "loading prerequisite libraries"
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RUN pip3 install "monai-weekly[nibabel,tqdm]"
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RUN echo 'model defined remotely again ....'
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# Import the MHub model definiton
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# *** hardcoding for now
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ARG MHUB_MODELS_REPO="https://github.com/curtislisle/mhub_models"
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RUN buildutils/import_mhub_model.sh a3ds-vertebrae ${MHUB_MODELS_REPO}
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# pull the weights for the segresnet model trained on the abdominal total
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# segmentator data model from the MONAIAuto3DSeg Slicer extension repository
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ENV WEIGHTS_DIR="/root/.cache/torch/hub/checkpoints/"
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ENV MODEL_NAME="vertebrae-3mm-v2.0.1.zip"
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ENV WEIGHTS_URL_PREFIX="https://github.com/lassoan/SlicerMONAIAuto3DSeg/releases/download/Models/"
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ENV WEIGHTS_URL=${WEIGHTS_URL_PREFIX}\/${MODEL_NAME}
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RUN echo "weights:" ${WEIGHTS_URL}
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# download the weights
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# *** NOTE: this should be replaced with a call to buildutils/download_weights.sh
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RUN wget --directory-prefix ${WEIGHTS_DIR} ${WEIGHTS_URL}
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# the weights come bundled in a zip file, so unzip
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ENV WEIGHTS_ARCHIVE = ${WEIGHTS_DIR}\/${MODEL_NAME}
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ENV CURRENT_DIR=`pwd`
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WORKDIR ${WEIGHTS_DIR}
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RUN unzip ${MODEL_NAME}
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# Default run script
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#ENTRYPOINT ["python3", "-m", "mhubio.run"]
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#CMD ["--config", "/app/models/a3ds-vertebrae/config/default.yml"]
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ENTRYPOINT ["/bin/bash"]

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