C++ (Cpp) FileName::getFileFormat Examples

Example #1

File: metadata_table.cpp Project: dtegunov/vlion

int MetaDataTable::read(const FileName &filename, const std::string &name, std::vector<EMDLabel> *desiredLabels)
{

    // Clear current table
    clear();

    std::ifstream in(filename.data(), std::ios_base::in);
    if (in.fail())
        REPORT_ERROR( (std::string) "MetaDataTable::read: File " + filename + " does not exists" );

    FileName ext = filename.getFileFormat();
    if (ext =="star")
    {
        //REPORT_ERROR("readSTAR not implemented yet...");
        return readStar(in, name, desiredLabels);
    }
    else
    {
        REPORT_ERROR("MetaDataTable::read ERROR: metadatatable should have .star extension");
    }

    in.close();

}

Example #2

File: micrograph.cpp Project: josegutab/scipion

/* Produce all images ------------------------------------------------------ */
void Micrograph::produce_all_images(int label, double minCost,
                                    const FileName &fn_rootIn, const FileName &fn_image, double ang,
                                    double tilt, double psi, bool rmStack)
{
    MetaData SF;
    Image<double> I;
    Micrograph *M;

    // Set Source image
    if (fn_image == "")
        M = this;
    else
    {
        M = new Micrograph;
        M->open_micrograph(fn_image/*, swapbyte*/);
        M->set_window_size(X_window_size, Y_window_size);
        M->set_transmitance_flag(compute_transmitance);
        M->set_inverse_flag(compute_inverse);
    }

    // Set scale for particles
    int MXdim, MYdim, thisXdim, thisYdim;
    M->size(MXdim, MYdim);
    this->size(thisXdim, thisYdim);
    double scaleX = (double) MXdim / thisXdim;
    double scaleY = (double) MYdim / thisYdim;

    // Compute max and minimum if compute_transmitance
    // or compute_inverse flags are ON
    double Dmax=0., Dmin=0.;
    if (compute_transmitance || compute_inverse)
    {
        (*this).computeDoubleMinMax(Dmin, Dmax);

        if (compute_transmitance)
        {
            if (Dmin > 1)
                Dmin = log10(Dmin);
            if (Dmax > 1)
                Dmax = log10(Dmax);
        }
    }
    // Scissor all particles
    if (ang != 0)
        std::cout << "Angle from Y axis to tilt axis " << ang << std::endl
        << "   applying appropriate rotation\n";
    int nmax = ParticleNo();
    FileName fn_aux;
    FileName _ext = fn_rootIn.getFileFormat();
    FileName fn_out;
    FileName fn_root = fn_rootIn.removeFileFormat().removeLastExtension();
    if (fn_rootIn.hasStackExtension())
        fn_out=fn_root.addExtension(_ext);
    else
    	fn_out=fn_rootIn.addExtension("stk");

    if (rmStack)
        fn_out.deleteFile();
    size_t ii = 0;
    size_t id;
    for (int n = 0; n < nmax; n++)
        if (coords[n].valid && coords[n].cost > minCost && coords[n].label == label)
        {
            fn_aux.compose(++ii, fn_out);
            id = SF.addObject();
            // If the ctfRow was set, copy the info to images metadata
            if (ctfRow.containsLabel(MDL_CTF_DEFOCUSU))
                SF.setRow(ctfRow, id);
            SF.setValue(MDL_IMAGE, fn_aux, id);
            SF.setValue(MDL_MICROGRAPH, M->fn_micrograph, id);
            SF.setValue(MDL_XCOOR, coords[n].X, id);
            SF.setValue(MDL_YCOOR, coords[n].Y, id);
            bool t = M->scissor(coords[n], I(), Dmin, Dmax, scaleX, scaleY);
            if (!t)
            {
                std::cout << "Particle " << fn_aux
                << " is very near the border, "
                << "corresponding image is set to blank\n";
                SF.setValue(MDL_ENABLED, -1, id);
            }
            else
                SF.setValue(MDL_ENABLED, 1, id);
            //  if (ang!=0) I().rotate(-ang);
            I.write(fn_out, ii, true, WRITE_APPEND);
        }
    SF.write(fn_out.withoutExtension() + ".xmd");


    // Free source image??
    if (fn_image != "")
    {
        M->close_micrograph();
        delete M;
    }
}