gingerbread package

Subpackages

• gingerbread.analytics package
  • Submodules
  • gingerbread.analytics.analytics_module module
    • Analytics
      • Analytics.concat_results()
      • Analytics.convert_class_to_binary()
      • Analytics.get_units()
      • Analytics.lesion_count()
      • Analytics.lesion_volume_ml()
      • Analytics.multiclass_tester()
      • Analytics.run_classification_analytics()
      • Analytics.run_general_analytics()
      • Analytics.segmentation_analysis()
      • Analytics.total_lesion_ml()
  • Module contents
• gingerbread.central_processing_handler package
  • Subpackages
    • gingerbread.central_processing_handler.config package
      • Submodules
      • gingerbread.central_processing_handler.config.config module
      • gingerbread.central_processing_handler.config.exceptions module
      • Module contents
    • gingerbread.central_processing_handler.sql package
      • Module contents
    • gingerbread.central_processing_handler.utils package
      • Submodules
      • gingerbread.central_processing_handler.utils.db_helpers module
      • gingerbread.central_processing_handler.utils.helpers module
      • Module contents
  • Submodules
  • gingerbread.central_processing_handler.central_processing_handler module
    • CentralProcessingHandler
      • CentralProcessingHandler.generate_analytics()
      • CentralProcessingHandler.init_model_from_mq()
      • CentralProcessingHandler.invalidate_cache()
      • CentralProcessingHandler.kill_models()
      • CentralProcessingHandler.start_processing()
  • Module contents
• gingerbread.config package
  • Submodules
  • gingerbread.config.config module
    • BaseModel
      • BaseModel.Config
    • ModelInput
      • ModelInput.model
  • Module contents
• gingerbread.models package
  • Submodules
  • gingerbread.models.config module
  • gingerbread.models.mock_model module
    • MockModel
      • MockModel.forward()
      • MockModel.load_state_dict()
  • Module contents
• gingerbread.neotemplate package
  • Submodules
  • gingerbread.neotemplate.base_central_processing module
    • CPNeoTemplate
      • CPNeoTemplate.check_version()
      • CPNeoTemplate.load_from_checkpoint()
      • CPNeoTemplate.postprocess()
      • CPNeoTemplate.predict_step()
      • CPNeoTemplate.preprocess()
      • CPNeoTemplate.save_checkpoint()
      • CPNeoTemplate.save_hyperparams()
  • Module contents
• gingerbread.realtime package
  • Submodules
  • gingerbread.realtime.realtime module
    • RealTimeModule
      • RealTimeModule.call_process()
      • RealTimeModule.get_img_and_spacing()
      • RealTimeModule.mrsl_convert()
      • RealTimeModule.send_to_analytics()
  • gingerbread.realtime.realtime_trigger module
    • callback()
    • run()
  • Module contents
• gingerbread.rest package
  • Submodules
  • gingerbread.rest.rest module
    • check_connection()
    • extract()
    • run()
  • Module contents
• gingerbread.system_conf package
  • Submodules
  • gingerbread.system_conf.systemconf module
  • Module contents
• gingerbread.user_package_files package
  • Subpackages
    • gingerbread.user_package_files.models package
      • Submodules
      • gingerbread.user_package_files.models.config module
      • gingerbread.user_package_files.models.mock_model module
      • Module contents
  • Submodules
  • gingerbread.user_package_files.central_processing module
    • CentralProcessing
      • CentralProcessing.postprocess()
      • CentralProcessing.predict_step()
      • CentralProcessing.preprocess()
  • Module contents
• gingerbread.utils package
  • Submodules
  • gingerbread.utils.helpers module
    • timer()
  • Module contents

Submodules

gingerbread.data_download module

class gingerbread.data_download.MedqueryDataDownloader

Bases: object

MedqueryDataDownloader class for connecting to MedQuery and downloading data.

mq

pymedquery instance

Type:

pymq.PyMedQuery

download_data(project_id: str, get_affines: bool = False, get_all: bool = True, include_mask: bool = False, batch_size: int = 20) → NoReturn

Download data from MedQuery and save it to disk.

Note

Instanciate the class and use this method to download data from MedQuery and save it to disk. For more information about data extraction from MedQuery, see {INSERT LINK HERE}.

Parameters:

• project_id (str) – Project ID

• get_affines (bool, optional) – Get affines, by default False

• get_all (bool, optional) – Get all, by default True

• include_mask (bool, optional) – Include mask, by default False

• batch_size (int, optional) – Batch size, by default 20

Return type:

None

hdf5_to_nifti_all(hdf5_path: str, output_dir: str) → NoReturn

Convert hdf5 file to nifti file.

Parameters:

• hdf5_path (str) – Path to hdf5 file

• output_dir (str) – Path to output directory

Return type:

None

Attention

This method assumed that the hdf5 file contains affine matrices and data. If this is not the case, the method will not work.

hdf5_to_nifti_single(hdf5_path: str, output_dir: str, series_uid: str) → NoReturn

Convert single series to nifti file.

Parameters:

• hdf5_path (str) – Path to hdf5 file

• output_dir (str) – Path to output directory

• series_uid (str) – Series UID

Return type:

None

Attention

This method assumed that the hdf5 file contains affine matrices and data. If this is not the case, the method will not work.

Module contents