TubeTK/Design Discussions

Introduction

Tubetk has adopted MIDAS to store testing and algorithm validation dataset. For this purpose, we have created a dedicated tubetk MIDAS community

In the tubetk community, we have two main types of folders

1. Input data folder: Where all input data for testing will be stored
2. Baseline dataset folder: These are individual folders that will be used to store the baseline images for regression tests in tubetk

How to add a new tubetk test

1. If the input data is not already in Midas,
   1. Upload the data to the "Data" folder
   2. Download the key file (*.md5) and store it in the MIDAS_KEYS directory at the top level of tubetk source code tree
2. Add baseline dataset for the new test ( if your test is a regression testing )
   1. Upload the dataset to the appropriate CLI or module folder. If your test is part of a new "module" or CLI, create a new a folder in MIDAS and then upload the dataset
   2. Download the key file (*.md5) for the baseline image and store it in the MIDAS_KEYS directory.
3. Modify cmake list files in the Testing directory to "add" unit tests to use the data from MIDAS.
   1. Use MIDAS_FETCH_ONLY macro, if you would like to fetch the dataset but not use it directly in the test
   2. Use MIDAS_DIRECTORY, if you would like to specify a whole directory as an input command line argument to your test

Examples:

Test using a data store in MIDAS

MIDAS_ADD_TEST( ${PROJECT_NAME}MIDAS-Test4
           ${PROJ_EXE}
            MIDAS{SyntheticTubePlusSurfaceImage_oriented.mha.md5}
            ${TEMP}/SyntheticTubePlusSurfaceEEDFilterResultImage_oriented.mha )

Test with a directory as input argument: DICOMSeries

MIDAS_ADD_TEST( ${PROJECT_NAME}MIDAS-Test1
            ${PROJ_EXE}
              -i
              -r
              -a Test1 001
              -w
              -o ${TEMP}
              -b DSC_
              MIDAS_DIRECTORY{DICOMSeries} )

Test that demonstrates fetch only option: tubeEdgeEnhancingAnisotropicDiffusionMIDAS-Test1

MIDAS_ADD_TEST( ${PROJECT_NAME}MIDAS-Test1
           ${PROJ_EXE}
              MIDAS{CroppedWholeLungCTScan.mhd.md5}
              ${TEMP}/itkAnisotropicEdgeEnhancingDiffusionImageFilterTest.mha
              MIDAS_FETCH_ONLY{CroppedWholeLungCTScan.raw.md5}
             )

MIDAS macro

The following are the essential midas macros for setting up a test using data stored in midas.

1. MIDAS_ADD_TEST
2. MIDAS_TGZ
3. MIDAS_FETCH ONLY
4. MIDAS_DIRECTORY