TIA File format

Collaboration diagram for TIA File format:

Classes
struct	TIAhead
struct	TIAdataHead

Functions
int	readTIA (int img_select, bool isStack=false)
int	writeTIA (int img_select, bool isStack=false, int mode=WRITE_OVERWRITE)
int	ImageBase::readTIA (int img_select, bool isStack=false)
int	ImageBase::writeTIA (int img_select, bool isStack=false, int mode=WRITE_OVERWRITE)

Detailed Description

Function Documentation

readTIA() [1/2]

int readTIA	(	int	img_select,
		bool	isStack = false
	)

TIA Reader

readTIA() [2/2]

int ImageBase::readTIA ( int  select_img, bool  isStack = false  )

protected

TIA Reader

Definition at line 79 of file rwTIA.cpp.

{
    TIAhead * header = new TIAhead;

    xmippFREAD(&header->endianess, sizeof(short int), 1, fimg, swap );

    // Set Endianess
    if (header->endianess == 18761)
        swap = 0;
    else
        swap = 1;
    if (IsBigEndian())
        swap = !swap;

    xmippFREAD(&header->SeriesID, sizeof(short int), 1, fimg, swap );
    xmippFREAD(&header->SeriesVersion, sizeof(short int), 1, fimg, swap);
    xmippFREAD(&header->DATA_TYPE_ID, sizeof(int), 1, fimg, swap);
    xmippFREAD(&header->TagTypeID, sizeof(int), 1, fimg, swap );
    xmippFREAD(&header->TotalNumberElements, sizeof(int), 1, fimg, swap );
    xmippFREAD(&header->NUMBER_IMAGES, sizeof(int), 1, fimg, swap );
    xmippFREAD(&header->OFFSET_ARRAY_OFFSET, sizeof(int), 1, fimg, swap );
    xmippFREAD(&header->numberdimensions, sizeof(int), 1, fimg, swap );

    // Check data type
    if (header->DATA_TYPE_ID != 16674)
        REPORT_ERROR(ERR_TYPE_INCORRECT, "ERROR: readTIA only processes images in real space");

    fseek(fimg, header->OFFSET_ARRAY_OFFSET, SEEK_SET);
    header->pDATA_OFFSET = (int *) askMemory(header->NUMBER_IMAGES * sizeof(int));
    xmippFREAD(header->pDATA_OFFSET, sizeof(int), header->NUMBER_IMAGES, fimg, swap);

    TIAdataHead* dataHeaders = new TIAdataHead [header->NUMBER_IMAGES];

    // Read all the image headers
    for (int i = 0; i < header->NUMBER_IMAGES; i++)
    {
        fseek(fimg, header->pDATA_OFFSET[i], SEEK_SET);
        xmippFREAD(&(dataHeaders[i].CalibrationOffsetX), sizeof(double), 1, fimg, swap);
        xmippFREAD(&dataHeaders[i].PIXEL_WIDTH, sizeof(double), 1, fimg, swap);
        xmippFREAD(&dataHeaders[i].CalibrationElementX, sizeof(int), 1, fimg, swap);
        xmippFREAD(&dataHeaders[i].CalibrationOffsetY, sizeof(double), 1, fimg, swap);
        xmippFREAD(&dataHeaders[i].PIXEL_HEIGHT, sizeof(double), 1, fimg, swap);
        xmippFREAD(&dataHeaders[i].CalibrationElementY, sizeof(int), 1, fimg, swap);
        xmippFREAD(&dataHeaders[i].DATA_TYPE, sizeof(short int), 1, fimg, swap);
        xmippFREAD(&dataHeaders[i].IMAGE_WIDTH, sizeof(int), 1, fimg, swap);
        xmippFREAD(&dataHeaders[i].IMAGE_HEIGHT, sizeof(int), 1, fimg, swap);
    }

    int _xDim,_yDim;
    size_t _nDim;

    size_t   imgStart = IMG_INDEX(select_img);
    size_t   imgEnd = (select_img != ALL_IMAGES) ? imgStart + 1 : header->NUMBER_IMAGES;

    if (select_img >  header->NUMBER_IMAGES)
        REPORT_ERROR(ERR_INDEX_OUTOFBOUNDS, formatString("readTIA: Image number %lu exceeds stack size %lu", select_img, header->NUMBER_IMAGES));
    else if (select_img == ALL_IMAGES)
    {
        for (int i = 1; i < header->NUMBER_IMAGES; i++)    // Check images dimensions. Need to be the same
        {
            if (dataHeaders[0].IMAGE_HEIGHT != dataHeaders[i].IMAGE_HEIGHT || \
                dataHeaders[0].IMAGE_WIDTH != dataHeaders[i].IMAGE_WIDTH  || \
                dataHeaders[0].DATA_TYPE != dataHeaders[i].DATA_TYPE)
                REPORT_ERROR(ERR_IMG_NOREAD, "readTIA: images in TIA file with different dimensions and data types are not supported");
        }
        _xDim = dataHeaders[0].IMAGE_WIDTH;
        _yDim = dataHeaders[0].IMAGE_HEIGHT;
        _nDim = (size_t) header->NUMBER_IMAGES;
    }
    else
    {
        _xDim = dataHeaders[imgStart].IMAGE_WIDTH;
        _yDim = dataHeaders[imgStart].IMAGE_HEIGHT;
        _nDim = 1;
    }

    // Map the parameters
    setDimensions(_xDim, _yDim, 1, _nDim);

    DataType datatype;
    //    dataHeaders[0].isSigned = false;
    int tiaDT;
    tiaDT = dataHeaders[imgStart].DATA_TYPE;
    offset = header->pDATA_OFFSET[imgStart] + TIAdataSIZE;

    switch ( tiaDT )
    {
    case 1:
        datatype = DT_UChar;
        break;
    case 2:
        datatype = DT_UShort;
        //        datatype = DT_Short;
        break;
    case 3:
        datatype = DT_UInt;
        break;
    case 4:
        datatype = DT_SChar;
        break;
    case 5:
        datatype = DT_Short;
        //        dataHeaders[0].isSigned = true;
        break;
    case 6:
        datatype = DT_Int;
        break;
    case 7:
        datatype = DT_Float;
        break;
    case 8:
        datatype = DT_Double;
        break;
    case 9:
        datatype = DT_CFloat;
        break;
    case 10:
        datatype = DT_CDouble;
        break;
    default:
        datatype = DT_Unknown;
       (void)datatype; // to suppress dead assignment warning
        break;
    }

    MDMainHeader.setValue(MDL_SAMPLINGRATE_X,(double)dataHeaders[0].PIXEL_WIDTH);
    MDMainHeader.setValue(MDL_SAMPLINGRATE_Y,(double)dataHeaders[0].PIXEL_HEIGHT);
    MDMainHeader.setValue(MDL_DATATYPE,(int)datatype);

    if (dataMode == HEADER || (dataMode == _HEADER_ALL && _nDim > 1)) // Stop reading if not necessary
    {
        delete header;
        delete[] dataHeaders;
        return 0;
    }

    MD.clear();
    for (size_t i = 0; i < imgEnd-imgStart; i++)
        MD.push_back(std::unique_ptr<MDRowVec>(new MDRowVec(MDL::emptyHeaderVec())));

    double aux;
    for ( size_t i = 0; i < imgEnd - imgStart; ++i )
    {
        if (dataMode == _HEADER_ALL || dataMode == _DATA_ALL)
        {
            if(MDMainHeader.getValue(MDL_SAMPLINGRATE_X,aux))
            {
                MD[i]->setValue(MDL_SHIFT_X, dataHeaders[i].CalibrationOffsetX/aux);
                aux = ROUND(dataHeaders[i].CalibrationElementX - \
                            dataHeaders[i].CalibrationOffsetX/aux - _xDim/2);
                MD[i]->setValue(MDL_ORIGIN_X, aux);
            }
            if(MDMainHeader.getValue(MDL_SAMPLINGRATE_Y,aux))
            {
                MD[i]->setValue(MDL_SHIFT_Y, dataHeaders[i].CalibrationOffsetY/aux);
                aux = ROUND(dataHeaders[i].CalibrationElementY - \
                            dataHeaders[i].CalibrationOffsetY/aux -_yDim/2);
                MD[i]->setValue(MDL_ORIGIN_Y, aux);
            }
        }
    }

    delete header;
    delete[] dataHeaders;

    if( dataMode < DATA )
        return 0;

    size_t pad = TIAdataSIZE;
    readData(fimg, select_img, datatype, pad);

    return(0);
}

writeTIA() [1/2]

int writeTIA	(	int	img_select,
		bool	isStack = false,
		int	mode = WRITE_OVERWRITE
	)

TIA Writer

writeTIA() [2/2]

int ImageBase::writeTIA ( int  img_select, bool  isStack = false, int  mode = WRITE_OVERWRITE  )

protected

TIA Writer

Definition at line 253 of file rwTIA.cpp.

{
    REPORT_ERROR(ERR_IMG_NOWRITE, "ERROR: writeTIA is not implemented.");
}