print_header() goes to terminal when on Juypter Notebook

DANAJK commented 3 years ago

When using a Jupyter notebook, print_header() sends its output to a terminal window, not into the notebook.

Also, the method returns the NIfTI header and this should perhaps be reflected in the name of the method?

KrisThielemans commented 3 years ago

change to get_nifti_header

evgueni-ovtchinnikov commented 3 years ago

@DANAJK which notebook please?

DANAJK commented 3 years ago

If you add it to the sirf_registration notebook, you will see that nothing gets output. e.g. flo.print_header()

evgueni-ovtchinnikov commented 3 years ago

@DANAJK @KrisThielemans Python print_header calls (via C interface) C++ print_headers, which calls dump_headers:

/// Dump info of multiple nifti images
template<class dataType>
void NiftiImageData<dataType>::dump_headers(const std::vector<const NiftiImageData<dataType>*> &ims)
{
    std::cout << "\nPrinting info for " << ims.size() << " nifti image(s):\n";
    dump_nifti_element(ims, "analyze_75_orient", &nifti_image::analyze75_orient);
    dump_nifti_element(ims, "analyze75_orient",  &nifti_image::analyze75_orient);
    dump_nifti_element(ims, "byteorder",         &nifti_image::byteorder);
    dump_nifti_element(ims, "cal_max",           &nifti_image::cal_max);
    dump_nifti_element(ims, "cal_min",           &nifti_image::cal_min);
    dump_nifti_element(ims, "datatype",          &nifti_image::datatype);
    dump_nifti_element(ims, "dt",                &nifti_image::dt);
    dump_nifti_element(ims, "du",                &nifti_image::du);
    dump_nifti_element(ims, "dv",                &nifti_image::dv);
    dump_nifti_element(ims, "dw",                &nifti_image::dw);
    dump_nifti_element(ims, "dx",                &nifti_image::dx);
    dump_nifti_element(ims, "dy",                &nifti_image::dy);
    dump_nifti_element(ims, "dz",                &nifti_image::dz);
    dump_nifti_element(ims, "ext_list",          &nifti_image::ext_list);
    dump_nifti_element(ims, "freq_dim",          &nifti_image::freq_dim);
    dump_nifti_element(ims, "iname_offset",      &nifti_image::iname_offset);
    dump_nifti_element(ims, "intent_code",       &nifti_image::intent_code);
    dump_nifti_element(ims, "intent_p1",         &nifti_image::intent_p1);
    dump_nifti_element(ims, "intent_p2",         &nifti_image::intent_p2);
    dump_nifti_element(ims, "intent_p3",         &nifti_image::intent_p3);
    dump_nifti_element(ims, "nbyper",            &nifti_image::nbyper);
    dump_nifti_element(ims, "ndim",              &nifti_image::ndim);
    dump_nifti_element(ims, "nifti_type",        &nifti_image::nifti_type);
    dump_nifti_element(ims, "num_ext",           &nifti_image::num_ext);
    dump_nifti_element(ims, "nvox",              &nifti_image::nvox);
    dump_nifti_element(ims, "nx",                &nifti_image::nx);
    dump_nifti_element(ims, "ny",                &nifti_image::ny);
    dump_nifti_element(ims, "nz",                &nifti_image::nz);
    dump_nifti_element(ims, "nt",                &nifti_image::nt);
    dump_nifti_element(ims, "nu",                &nifti_image::nu);
    dump_nifti_element(ims, "nv",                &nifti_image::nv);
    dump_nifti_element(ims, "nw",                &nifti_image::nw);
    dump_nifti_element(ims, "phase_dim",         &nifti_image::phase_dim);
    dump_nifti_element(ims, "qfac",              &nifti_image::qfac);
    dump_nifti_element(ims, "qform_code",        &nifti_image::qform_code);
    dump_nifti_element(ims, "qoffset_x",         &nifti_image::qoffset_x);
    dump_nifti_element(ims, "qoffset_y",         &nifti_image::qoffset_y);
    dump_nifti_element(ims, "qoffset_z",         &nifti_image::qoffset_z);
    dump_nifti_element(ims, "quatern_b",         &nifti_image::quatern_b);
    dump_nifti_element(ims, "quatern_c",         &nifti_image::quatern_c);
    dump_nifti_element(ims, "quatern_d",         &nifti_image::quatern_d);
    dump_nifti_element(ims, "scl_inter",         &nifti_image::scl_inter);
    dump_nifti_element(ims, "scl_slope",         &nifti_image::scl_slope);
    dump_nifti_element(ims, "sform_code",        &nifti_image::sform_code);
    dump_nifti_element(ims, "slice_code",        &nifti_image::slice_code);
    dump_nifti_element(ims, "slice_dim",         &nifti_image::slice_dim);
    dump_nifti_element(ims, "slice_duration",    &nifti_image::slice_duration);
    dump_nifti_element(ims, "slice_end",         &nifti_image::slice_end);
    dump_nifti_element(ims, "slice_start",       &nifti_image::slice_start);
    dump_nifti_element(ims, "swapsize",          &nifti_image::swapsize);
    dump_nifti_element(ims, "time_units",        &nifti_image::time_units);
    dump_nifti_element(ims, "toffset",           &nifti_image::toffset);
    dump_nifti_element(ims, "xyz_units",         &nifti_image::xyz_units);
    dump_nifti_element(ims, "dim",               &nifti_image::dim,    8);
    dump_nifti_element(ims, "pixdim",            &nifti_image::pixdim, 8);

    std::vector<std::shared_ptr<const nifti_image> > images;
    for(unsigned i=0;i<ims.size();i++)
        images.push_back(ims[i]->get_raw_nifti_sptr());

    // Print transformation matrices
    std::vector<AffineTransformation<float> > qto_ijk_vec, qto_xyz_vec, sto_ijk_vec, sto_xyz_vec;
    for(unsigned j=0; j<images.size(); j++) {
        qto_ijk_vec.push_back(images[j]->qto_ijk.m);
        qto_xyz_vec.push_back(images[j]->qto_xyz.m);
        sto_ijk_vec.push_back(images[j]->sto_ijk.m);
        sto_xyz_vec.push_back(images[j]->sto_xyz.m);
    }
    std::cout << "\t" << std::left << std::setw(19) << "qto_ijk:" << "\n";
    AffineTransformation<float>::print(qto_ijk_vec);
    std::cout << "\t" << std::left << std::setw(19) << "qto_xyz:" << "\n";
    AffineTransformation<float>::print(qto_xyz_vec);
    std::cout << "\t" << std::left << std::setw(19) << "sto_ijk:" << "\n";
    AffineTransformation<float>::print(sto_ijk_vec);
    std::cout << "\t" << std::left << std::setw(19) << "sto_xyz:" << "\n";
    AffineTransformation<float>::print(sto_xyz_vec);

    // Print original datatype
    std::string original_datatype = "orig_datatype: ";
    std::cout << "\t" << std::left << std::setw(19) << original_datatype;
    for(unsigned i=0; i<ims.size(); i++)
        std::cout << std::setw(19) << ims[i]->get_original_datatype();

    // Print min
    std::string min_header = "min: ";
    std::cout << "\n\t" << std::left << std::setw(19) << min_header;
    for(unsigned i=0; i<ims.size(); i++)
        std::cout << std::setw(19) << ims[i]->get_min();

    // Print max
    std::cout << "\n\t" << std::left << std::setw(19) << "max: ";
    for(unsigned i=0; i<ims.size(); i++)
        std::cout << std::setw(19) << ims[i]->get_max();

    // Print mean
    std::cout << "\n\t" << std::left << std::setw(19) << "mean: ";
    for(unsigned i=0; i<ims.size(); i++)
        std::cout << std::setw(19) << ims[i]->get_mean();

    // Print if image contains nans
    std::cout << "\n\t" << std::left << std::setw(19) << "contains nans?: ";
    for(unsigned i=0; i<ims.size(); i++)
        std::cout << std::setw(19) << ims[i]->get_contains_nans();

    std::cout << "\n\n";
}

The naming and the amount of printed data suggests that Richard needed this print purely for debugging - do we really need to dump all this data on the notebook user? I rather doubt.

KrisThielemans commented 3 years ago

The naming and the amount of printed data suggests that Richard needed this print purely for debugging - do we really need to dump all this data on the notebook user? I rather doubt.

A continuing problem with nifti (or any other fileformat) is if the header is correct etc. so yes, debugging, useful.

What about

keeping print_header() but let it do std::cout << get_nifti_header_info() << std::endl which would do the hard work

using std::stringstream like

std::string get_nifti_header_info()
{
std::stringstream stream;
stream << whatever;
return stream.str();
}

replacing all std::cout with stream.

Python/MATLAB would only wrap get_nifti_header_info()

seems easy enough. Of course, I guess we don't need this for 3.1, but I'll let @DANAJK decide on that.

SyneRBI / SIRF

print_header() goes to terminal when on Juypter Notebook #905