DM4 File format

Collaboration diagram for DM4 File format:

Classes
struct	DM4head
struct	DM4dataHead

Functions
DataType	datatypeDM4 (int nType)
void	FREADTagValueDM4 (double *fieldValue, int numberType, int n, FILE *fimg, bool swap)
double	readTagDM4 (FILE *fimg, DM4head *header, int parentId, int &nodeId, bool isLE, bool swap)
int	parentDM4 (MetaData &MD, int nodeId, int depth=1)
size_t	gotoTagDM4 (MetaData &MD, int &nodeId, const std::string &tagsList)
void	printDM4node (const MetaData &MD, size_t id)
void	printDM4 (const MetaData &MD)
int	readDM4 (size_t img_select, bool isStack=false)
int	writeDM4 (size_t img_select, bool isStack=false, int mode=WRITE_OVERWRITE)
int	ImageBase::readDM4 (size_t img_select, bool isStack=false)
int	ImageBase::writeDM4 (size_t img_select, bool isStack=false, int mode=WRITE_OVERWRITE)

Detailed Description

Function Documentation

datatypeDM4()

DataType datatypeDM4

(

int

nType

)

DM4 Determine DM4 datatype

Definition at line 71 of file rwDM4.cpp.

{
    DataType datatype;

    switch(nType)
    {
    case 2:      // (02h =  2  i2* signed    (short)
        datatype = DT_Short;
        break;
    case 3:          // 03h =  3  i4* signed    (long)
        datatype = DT_Int;
        break;
    case 4:       //  04h =  4  i2* unsigned  (ushort) or unicode string
        datatype = DT_UShort;
        break;
    case 5:        //  05h =  5  i4* unsigned  (ulong)
        datatype = DT_UInt;
        break;
    case 6:        //  06h =  6  f4*           (float)
        datatype = DT_Float;
        break;
    case 7:        //  07h =  7  f8*           (double)
        datatype = DT_Double;
        break;
    case 8:        //  08h =  8  i1            (boolean)
        datatype = DT_Bool;
        break;
    case 9:        //  0ah = 10  i1
        datatype = DT_SChar;
        break;
    case 10:        //  0ah = 10  i1
        datatype = DT_SChar;
        break;
    case 11:        //  0ah = 10  i1
        datatype = DT_ULong;
        break;
    case 12:        //  0ah = 10  i1
        datatype = DT_Long;
        break;
    default:
        datatype = DT_Unknown;
        break;
    }
    return datatype;
}

FREADTagValueDM4()

void FREADTagValueDM4	(	double *	fieldValue,
		int	numberType,
		int	n,
		FILE *	fimg,
		bool	swap
	)

DM4 Low level reader

Definition at line 120 of file rwDM4.cpp.

{
    DataType datatype = datatypeDM4(numberType);
    size_t datatypesize=gettypesize(datatype);

    xmippFREAD(fieldValue, datatypesize, n, fimg, swap);

    switch(numberType)
    {
    case 2:      // (02h =  2  i2* signed    (short)
        {
            short* sValue = (short*) fieldValue;
            *fieldValue = (double) *sValue;
            break;
        }
    case 3:          // 03h =  3  i4* signed    (long)
        {
            int* iValue = (int*) fieldValue;
            *fieldValue = (double) *iValue;
            break;
        }
    case 4:       //  04h =  4  i2* unsigned  (ushort) or unicode string
        {
            unsigned short* usValue = (unsigned short*) fieldValue;
            *fieldValue = (double) *usValue;
            break;
        }
    case 5:        //  05h =  5  i4* unsigned  (ulong)
        {
            unsigned int* uiValue = (unsigned int*) fieldValue;
            *fieldValue = (double) *uiValue;
            break;
        }
    case 6:        //  06h =  6  f4*           (float)
        {
            float* fValue = (float*) fieldValue;
            *fieldValue = (double) *fValue;
            break;
        }
    case 7:        //  07h =  7  f8*           (double)
        {
            //            double* caca = (double*) fieldValue;
            break;
        }
    case 8:        //  08h =  8  i1            (boolean)
        {
            bool* bValue = (bool*) fieldValue;
            *fieldValue = (double) *bValue;
            break;
        }
    case 9:        //  0ah = 10  i1
    case 10:        //  0ah = 10  i1
        {
            char* cValue = (char*) fieldValue;
            *fieldValue = (double) *cValue;
            break;
        }
    case 11:        //  0ah = 10  i1
    {
        unsigned long* cValue = (unsigned long*) fieldValue;
        *fieldValue = (double) *cValue;
        break;
    }
    case 12:        //  0ah = 10  i1
    {
        long* cValue = (long*) fieldValue;
        *fieldValue = (double) *cValue;
        break;
    }
    default:
    {
        break;
    }
    }
}

gotoTagDM4()

size_t gotoTagDM4	(	MetaData &	MD,
		int &	nodeId,
		const std::string &	tagsList
	)

DM4 Go to tag

Definition at line 393 of file rwDM4.cpp.

{
    std::string tag;
    std::vector<std::string> vTags;
    splitString(tagsList,",",vTags, false);
    size_t id=0;

    MDValueEQ queryParentId(MDL_DM3_PARENTID,-1), queryTagname(MDL_DM3_TAGNAME,tag);
    MDMultiQuery queries;

    queries.addAndQuery(queryParentId);
    queries.addAndQuery(queryTagname);

    for (size_t n = 0; n < vTags.size(); n++)
    {
        tag = vTags[n];

        queryParentId.setValue(nodeId);
        queryTagname.setValue(tag);
        id = MD.firstObject(queries);
        if (id != BAD_OBJID)
        {
            MD.getValue(MDL_DM3_NODEID, nodeId, id);
        }
    }
    return id;
}

parentDM4()

int parentDM4	(	MetaData &	MD,
		int	nodeId,
		int	depth = 1
	)

DM4 Get DM4 parent

Definition at line 378 of file rwDM4.cpp.

{
    for (int n = 0; n < depth; n++)
    {
        MD.getValue(MDL_DM3_PARENTID, nodeId, MD.firstObject(MDValueEQ(MDL_DM3_NODEID, nodeId)));

        if (nodeId == 0)
            break;
    }
    return nodeId;
}

printDM4()

void printDM4

(

const MetaData &

MD

)

DM4 Print DM4 header

Definition at line 453 of file rwDM4.cpp.

{
    std::vector<size_t> vObjs;
    spaceDM4 = 0;
    MD.findObjects(vObjs,MDValueEQ(MDL_DM3_PARENTID, 0));

    for (size_t i = 0; i < vObjs.size(); i++)
        printDM4node(MD, vObjs[i]);
}

printDM4node()

void printDM4node	(	const MetaData &	MD,
		size_t	id
	)

DM4 Print DM4 node

Definition at line 425 of file rwDM4.cpp.

{
    std::string tag;
    MD.getValue(MDL_DM3_TAGNAME, tag, id);

    int nodeId;
    MD.getValue(MDL_DM3_NODEID, nodeId, id);

    for (int i = 0; i < spaceDM4; i++)
        std::cout << " ";

    std::cout << tag << std::endl;

    std::vector<size_t> vObjs;
    MD.findObjects(vObjs, MDValueEQ(MDL_DM3_PARENTID, nodeId));

    spaceDM4 += 3;

    for (size_t i = 0; i < vObjs.size(); i++)
        printDM4node(MD, vObjs[i]);

    spaceDM4 -= 3;

}

readDM4() [1/2]

int readDM4	(	size_t	img_select,
		bool	isStack = false
	)

DM4 Reader

readDM4() [2/2]

int ImageBase::readDM4 ( size_t  select_img, bool  isStack = false  )

protected

DM4 Reader

Definition at line 466 of file rwDM4.cpp.

{
#undef DEBUG
    //#define DEBUG
#ifdef DEBUG
    printf("DEBUG readDM4: Reading DM4 file\n");
#endif

    DM4head * header = new DM4head;
    int dummy;

    // Check Machine endianness
    bool isLE = IsLittleEndian();

    xmippFREAD(&header->fileVersion, sizeof(int), 1, fimg, isLE);
    xmippFREAD(&dummy, sizeof(long), 1, fimg, isLE);
    xmippFREAD(&header->byteOrder, sizeof(int), 1, fimg, isLE);

    // Set Endianess
    swap = (isLE^header->byteOrder);

    if ( header->fileVersion!=4 )
        REPORT_ERROR(ERR_IO_NOREAD, "readDM4: Input file is not Digital Micrograph 3 format.");

    xmippFREAD(&header->sorted, sizeof(char), 1, fimg, false);
    xmippFREAD(&header->open, sizeof(char), 1, fimg, false);
    xmippFREAD(&header->nTags, sizeof(long), 1, fimg, isLE);

    header->tags.addLabel(MDL_DM3_NODEID);
    header->tags.addLabel(MDL_DM3_PARENTID);
    header->tags.addLabel(MDL_DM3_IDTAG);
    header->tags.addLabel(MDL_DM3_TAGNAME);
    header->tags.addLabel(MDL_DM3_TAGCLASS);
    header->tags.addLabel(MDL_DM3_SIZE);
    header->tags.addLabel(MDL_DM3_NUMBER_TYPE);
    header->tags.addLabel(MDL_DM3_VALUE);

    int nodeID = 0, parentID = 0;

    for (int n=1;n<=header->nTags;n++)
        readTagDM4(fimg, header, parentID, nodeID, isLE, swap);

//#define DEBUG
#ifdef DEBUG

    header->tags.write("images.txt");
    printDM4(header->tags);
#endif


    //std::vector<size_t> vIm;
    //header->tags.findObjects(vIm, );

    header->nIm = 0;
    std::vector<DM4dataHead> dataHeaders;
    DM4dataHead dhRef;

    std::vector<double> vValue;
    int iValue;

    //Initialize query for later use
    MDValueEQ queryNodeId(MDL_DM3_NODEID, -1);

    std::vector<size_t> objIdsDataType;
    header->tags.findObjects(objIdsDataType, MDValueEQ(MDL_DM3_TAGNAME,(String)"DataType"));

    for (size_t objId : objIdsDataType)
        // Read all the image headers
        //for (int n = 0; n < vIm.size(); n++)
    {
        //header->tags.goToObject(vIm[n]);
        header->tags.getValue(MDL_DM3_VALUE, vValue, objId);

        if (vValue[0] != 23) //avoid thumb images
        {
            dataHeaders.push_back(dhRef);

            parentID = parentDM4(header->tags, objId, 2);

            size_t id;
            nodeID = parentID;
            id = gotoTagDM4(header->tags, nodeID, "ImageData,Data");
            header->tags.getValue(MDL_DM3_NUMBER_TYPE, iValue, id);
            dataHeaders[header->nIm].dataType = (short int) iValue;

            header->tags.getValue(MDL_DM3_VALUE, vValue, id);
            dataHeaders[header->nIm].headerSize = (size_t) vValue[0];

            nodeID = parentID;
            id = gotoTagDM4(header->tags, nodeID, "ImageData,Dimensions");

            int nDims;
            header->tags.getValue(MDL_DM3_SIZE, nDims, id);

            nodeID++;
            queryNodeId.setValue(nodeID);
            id = header->tags.firstObject(queryNodeId);
            header->tags.getValue(MDL_DM3_VALUE, vValue, id);
            dataHeaders[header->nIm].imageWidth = (int) vValue[0];

            nodeID++;
            queryNodeId.setValue(nodeID);
            id = header->tags.firstObject(queryNodeId);
            header->tags.getValue(MDL_DM3_VALUE, vValue, id);
            dataHeaders[header->nIm].imageHeight = (int) vValue[0];

            if (nDims ==3 )
            {
                nodeID++;
                queryNodeId.setValue(nodeID);
                id = header->tags.firstObject(queryNodeId);
                header->tags.getValue(MDL_DM3_VALUE, vValue, id);
                dataHeaders[header->nIm].imageDepth = (int) vValue[0];
            } else
                dataHeaders[header->nIm].imageDepth = 1;

            nodeID++;
            queryNodeId.setValue(nodeID);
            id = header->tags.firstObject(queryNodeId);
            header->tags.getValue(MDL_DM3_VALUE, vValue, id);
            dataHeaders[header->nIm].dataTypeSize = (short int) vValue[0];

            nodeID = parentID;
            id = gotoTagDM4(header->tags, nodeID, "ImageTags,Acquisition,Frame,CCD,Pixel Size (um)");
            //            header->tags.nextObject();
            if (id != BAD_OBJID)
            {
                header->tags.getValue(MDL_DM3_VALUE, vValue, id);
                dataHeaders[header->nIm].pixelHeight = vValue[0]*1e4;
                dataHeaders[header->nIm].pixelWidth  = vValue[1]*1e4;
            }

            //TODO: Do I have to include FLIP?!?!? which? vertical or horizontal?
            header->nIm++;
        }

    }

    if (dataHeaders.size() == 0)
        REPORT_ERROR(ERR_IMG_NOREAD,formatString("readDM4: Image information not found in file %s",filename.c_str()));

    int _xDim,_yDim, _zDim;
    size_t _nDim;
    _xDim = dataHeaders[0].imageWidth;
    _yDim = dataHeaders[0].imageHeight;
    _zDim = 1;
    _nDim = dataHeaders[0].imageDepth;
    //_nDim = header->nIm;

    // Map the parameters
    if (select_img >  _nDim)
        REPORT_ERROR(ERR_INDEX_OUTOFBOUNDS, formatString("readDM4: Image number %lu exceeds stack size %lu", select_img, _nDim));
    else if (select_img == ALL_IMAGES)
    {
//        // Check images dimensions. Need to be the same
//        for (size_t i = 1; i < _nDim ; i++)
//        {
//            if (dataHeaders[0].imageHeight != dataHeaders[i].imageHeight || \
//                dataHeaders[0].imageWidth != dataHeaders[i].imageWidth  || \
//                dataHeaders[0].dataType != dataHeaders[i].dataType)
//                REPORT_ERROR(ERR_IMG_NOREAD, "readDM4: images in DM4 file with different \
//                             dimensions and data types are not currently supported. Try to read them individually.");
//        }
//        //FIXME: Code is not totally implemented to load automatically multiple images if they have same size.
//        //if (_nDim > 1)
//        //    REPORT_ERROR(ERR_IO_NOREAD, "readDM4: Reading multiple \
//                         images at once in DM4 file are not currently supported. Try to read them individually.");
    }
    else
        _nDim = 1;

    setDimensions(_xDim, _yDim, _zDim, _nDim);

    size_t   imgStart = IMG_INDEX(select_img);
    size_t   imgEnd = (select_img != ALL_IMAGES) ? imgStart + 1 : _nDim;

    DataType datatype = datatypeDM4(dataHeaders[0].dataType);

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

    if (dataMode == HEADER) // Stop reading if not necessary
    {
        delete header;
        return 0;
    }

    MD.clear();
    for (size_t i = 0; i < imgEnd-imgStart; i++)
        MD.push_back(std::unique_ptr<MDRowVec>(new MDRowVec(MDL::emptyHeaderVec())));
    offset = dataHeaders[0].headerSize;
    delete header;

    if( dataMode < DATA )
        return 0;

#undef DEBUG
#ifdef DEBUG

    MDMainHeader.write(std::cerr);
    MD.write(std::cerr);
#endif

    size_t pad = 0;
    readData(fimg, select_img, datatype, pad);

    return(0);
}

readTagDM4()

double readTagDM4	(	FILE *	fimg,
		DM4head *	header,
		int	parentId,
		int &	nodeId,
		bool	isLE,
		bool	swap
	)

DM4 Tag reader

Definition at line 199 of file rwDM4.cpp.

{
    /* Header Tag ============================================================== */
    unsigned char cdTag;
    unsigned short int ltName;

    xmippFREAD(&cdTag,sizeof (unsigned char),1,fimg,false); // Identification tag: 20 = tag dir,  21 = tag
    xmippFREAD(&ltName,sizeof(unsigned short int), 1,fimg,isLE); // Length of the tag name
    int idTag = int(cdTag);

    std::string stagName;

    if (ltName > 0)
    {
        char * tagName =  new char[ltName+1];
        xmippFREAD(tagName,1,ltName,fimg,false); // Tag name
        tagName[ltName] = '\0';
        stagName = tagName;
        delete [] tagName;
    }

    /*total bytes in tag/tag directory including all sub-directories
     * (new for DM4). Actually, we don't use it*/
    fseek(fimg, 8, SEEK_CUR);

    size_t id = header->tags.addObject();

    nodeId++;
    header->tags.setValue(MDL_DM3_NODEID, nodeId, id);
    header->tags.setValue(MDL_DM3_PARENTID, parentId, id);
    header->tags.setValue(MDL_DM3_IDTAG, idTag, id);
    header->tags.setValue(MDL_DM3_TAGNAME, stagName, id);

    /* Reading tags ===================================================================*/
    if (idTag == 20)  // Tag directory
    {
        unsigned char dummy;
        int nTags;
        xmippFREAD(&dummy,sizeof(unsigned char),1,fimg,false); // 1 = sorted (normally = 1)
        xmippFREAD(&dummy,sizeof(unsigned char),1,fimg,false); //  0 = closed, 1 = open (normally = 0)

        xmippFREAD(&nTags,sizeof(long),1,fimg,isLE);             //  number of tags in tag directory


        header->tags.setValue(MDL_DM3_TAGCLASS,(std::string) "Dir", id);
        header->tags.setValue(MDL_DM3_SIZE, nTags, id);

        parentId = nodeId;
        for (int n=1;n<=nTags;n++) // Rest of directories
        {
            readTagDM4(fimg, header, parentId, nodeId, isLE, swap);
        }
        return 0;
    }
    else if (idTag == 21)    // Tag
    {
        unsigned int nnum;
        char buf[4]; // to read %%%% symbols

        xmippFREAD(&buf,1,4,fimg,false); // To read %%%% symbols
        xmippFREAD(&nnum,sizeof(long),1,fimg,isLE); // Size of info array

        size_t * info;
        info = new size_t[nnum];
        xmippFREAD(info,sizeof(long),nnum,fimg,isLE); // Reading of Info

        /* Tag classification  =======================================*/

        if (nnum == 1)   // Single entry tag
        {
            header->tags.setValue(MDL_DM3_TAGCLASS,(std::string) "Single", id);

            double tagValue = 0;

            FREADTagValueDM4(&tagValue,info[0],1,fimg,swap);

            std::vector<double> vtagValue(1);
            vtagValue.assign(1,tagValue);

            header->tags.setValue(MDL_DM3_NUMBER_TYPE, (int) info[0], id);
            header->tags.setValue(MDL_DM3_VALUE, vtagValue, id);
            delete []info;
            return tagValue;
        }
        else if(nnum == 3 && info[0]==20)   // Tag array
        {
            /*nnum = 3
            info(0) = 20
            info(1) = number type for all values
            info(2) = info(nnum) = size of array*/

            header->tags.setValue(MDL_DM3_TAGCLASS,(std::string) "Array", id);

            header->tags.setValue(MDL_DM3_NUMBER_TYPE, (int)info[1], id);
            header->tags.setValue(MDL_DM3_SIZE, (int) info[nnum-1], id);
            std::vector<double> vtagValue(1);
            vtagValue.assign(1,(double) ftell(fimg));

            header->tags.setValue(MDL_DM3_VALUE, vtagValue, id);

            // Jump the array values
            int k;
            if(info[1] == 2 || info[1] == 4)
                k = 2;
            else if(info[1] == 3 || info[1] == 5 || info[1] == 6)
                k = 4;
            else if(info[1] == 10 )
                k = 1;
            else
                REPORT_ERROR(ERR_ARG_INCORRECT,formatString("unsupported value info[1]=%d, read at %d",info[1],ftell(fimg)));

            fseek( fimg, ftell(fimg)+(info[nnum-1])*k , SEEK_SET );
            delete []info;
            return 0;
        }
        else if (info[0]==20 && info[1] == 15)    // Tag Group array
        {
            /*nnum = size of array
                     info(0) = 20 (array)
                     info(1) = 15 (group)
                     info(2) = 0 (always 0)
                     info(3) = number of values in group
                     info(2*i+3) = number type for value i
                     info(nnum) = size of info array*/

            header->tags.setValue(MDL_DM3_TAGCLASS, (std::string) "GroupArray", id);
            header->tags.setValue(MDL_DM3_SIZE, (int)info[3], id);
            int nBytes=0, k;
            double fieldValue;
            for (int n=1;n<=info[3];n++)
            {
                fieldValue=0;
                FREADTagValueDM4(&fieldValue,info[3+2*n],1,fimg,swap);

                if(info[3+2*n] == 2 || info[3+2*n] == 4)
                    k = 2;
                else if(info[3+2*n] == 3 || info[3+2*n] == 5)
                    k = 4;
                else if(info[3+2*n] == 10 )
                    k = 1;
                nBytes+=k;
            }

            // Jump the array values
            fseek( fimg, ftell(fimg)+(info[nnum-1]-1)*nBytes , SEEK_SET );
            delete []info;
            return 0;
        }
        else if (info[0] == 15)    // Tag Group  (struct)
        {
            /* info[1] = length group name (always =0)
                    info[2] = number of entries in group */
            /*nnum = size of info array
            info(1) = 0fh
            info(3) = number of values in group
            info(2*i+3) = number type for value i
            Other info entries are always zero*/

            header->tags.setValue(MDL_DM3_TAGCLASS, (std::string) "Group", id);
            header->tags.setValue(MDL_DM3_SIZE,(int) info[2], id);
            std::vector<double> vtagValue((int)info[2]);
            for (int n=1;n<=info[2];n++)
            {
                double fieldValue=0;
                FREADTagValueDM4(&fieldValue,info[2+2*n],1,fimg,swap);
                vtagValue.assign(n,fieldValue);
            }
            header->tags.setValue(MDL_DM3_VALUE, vtagValue, id);
            delete []info;
            return 0;
        }
        delete []info;
    }
    return 0;
}

writeDM4() [1/2]

int writeDM4	(	size_t	img_select,
		bool	isStack = false,
		int	mode = WRITE_OVERWRITE
	)

DM4 Writer

writeDM4() [2/2]

int ImageBase::writeDM4 ( size_t  img_select, bool  isStack = false, int  mode = WRITE_OVERWRITE  )

protected

DM4 Writer

Definition at line 676 of file rwDM4.cpp.

{
    REPORT_ERROR(ERR_IO_NOWRITE, "ERROR: writeDM4 is not implemented.");
}