AddingANewDataType.md

This document contains developer documentation for BioImage Suite Web.

---

Adding a New Data Object Type in BisWeb (JavaScript/Python/C++)

List of Steps

We will use the Surface class as an example. Basically there are 3-4 steps for each language

1. Create an implementation for the data object type
2. Register it with the serialization/deserialization layers
3. Add code to data object factories to create an object of this type.
4. In JS and Python: Modify the wrapper generation code to account for this type.

C++

1. Implement the C++ version in src/cpp (see bisSurface.h, bisSurface.cpp). The class must derive (directly or indirectly) from bisDataObject. It must implement the four abstract methods in this namely:

    virtual unsigned char* serialize();
    virtual void serializeInPlace(unsigned char* output)=0;
    virtual int deSerialize(unsigned char* pointer)=0;
    virtual long getRawSize()=0;
   

2. Declare a magic code (for serialization/deserialization purposes in bisDataTypes.h). This must be unique

    /** Magic number for collection object=20006 for serialization */
    const int s_surface=20007;
   

   Also add a function in bisExportedFunction.cpp that defines the magic type (and its corresponding declartion in bisExportedFunction.h)

    BISEXPORT int getSurfaceMagicCode();
    int getSurfaceMagicCode() { return bisDataTypes::s_surface; }
   

3. Modify bisDataObjectFactory::desrializeSimpleDataObjectTemplate (in bisDataObjectFactory) to create a an object of this type

    if (magic_type==bisDataTypes::s_surface)   {
      std::shared_ptr<bisSurface> obj(new bisSurface(name));
      if (obj->deSerialize(pointer))
         return obj;
    }
   

JS

1. Create a class in js/dataobjects to implement this. In this case, this is the file bisweb_surface.js. This should implement the following functions (at a bare minimum) (see bisweb_dataobject.js)

    getObject
    getDescription()
    computeHash()
    getMemorySize()
    load()
    save()
    serializeToDictionary()
    parseFromDictionary()
    serializeWASM()
    getWASMNumberOfBytes();
    deserializeWASM()
    compareWithOther()
   

2. Add and export a function in core/bis_wasmutils.js to return the magic code

    var get_surface_magic_code=function(Module) { return Module._getSurfaceMagicCode(); };
   

   Also add code in core/bis_wrapperutils.js deserializeAndDeleteObject to deserialize this object e.g.

    if (datatype==='bisSurface' || datatype==='surface' || datatype==='Surface') {
      let output=new BisWebSurface();
      output.deserializeWasmAndDelete(Module,ptr);
      return output;
    }
   

3. Add code in dataobjects/bisweb_dataobjectcollection.js to instantiate an object of this class (in functions parseObject and loadObject)

4. Modify the wrapper generator script compiletools/bis_create_wrappers.js to create info about the name 'bisSurface' (used in the C++ code headers) to denote this class. (This also applies to python)

Python

1. Create a class bisSurface (for now in biswebpython/core/bis_objects.py). This should implement at a mimimum: getRawSize() serializeWasm() deserializeWasm() load() save() getDescription()

2. Modify the file biswebpython/core/bis_wasmutils.py to:

   • add a function getSurfaceMagicCode()
   • modify the getNameFromMagicCode() function to handle surfaces
   • modify the deserialize_object() function to handle surfaces

3. Modify the function loadSingleInput in biswebpython/core/bis_basemodule.py to load surfaces

   Also modify the function processTestResult in biswebpython/core/bis_commandline.py to compare surfaces

4. Modify the wrapper generator script compiletools/bis_create_wrappers.js to create info about the name 'bisSurface' (used in the C++ code headers) to denote this class. (This also applies to JS)