FileConversion.cpp

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/* ImLib3D
 * Copyright (c) 2001, ULP-IPB Strasbourg.
 *
 * This program is free software; you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation; either version 2 of the License, or (at
 * your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful, but
 * WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
 * General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program; if not, write to the Free Software
 * Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
 */

#include<ImLib3D/FileConversion.hpp>
#include<ImLib3D/Transformation.hpp>

void
IP3D::ReadFromFileBruker(const string &fname,int imageNumber,Image3Dlinear<short int> &res)
{
    typedef Image3Dlinear<short int> ImType;
    // this is a horrible hack that works for me...
    string prefix=fname+SPrintf("/%d",imageNumber)+"/pdata/1/";
    string info;
    Read(prefix+"d3proc",info,true);
    uint pos;
    pos=info.find("##$IM_SIX=")+10;
    printf("pos:%d\n",(int)pos);
    int six=LongInt(info.substr(pos,info.size()-pos));
    pos=info.find("##$IM_SIY=")+10;
    int siy=LongInt(info.substr(pos,info.size()-pos));
    pos=info.find("##$IM_SIZ=")+10;
    int siz=LongInt(info.substr(pos,info.size()-pos));
    printf("CReadFromFileBruker:: XZY: %d %d %d\n",six,siy,siz);
    int dataSize;
    ImType::value_type *data=(ImType::value_type *)Read(prefix+"2dseq",&dataSize,true);
    if(dataSize!=six*siy*siz*(int)sizeof(ImType::value_type))
    {ThrowError("CReadFromFileBruker: bad file size");}
    IP3D::ImageFromRawData(data,Size3D(six,siz,siy),"XZY",res,true);
    delete [] data;
    if(six==siy && six==siz)
    {// guess this is a 3D aquisition !! :-(
        IP3D::SwapAxes(res,"XZ",res);
        IP3D::SwapAxes(res,"YZ",res);
//      CFlip    ::Apply(res,"Z" ,res);
    }
    else
    {
        // flip in y direction
        IP3D::Flip(res,"Y",res);
    }
}

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