Definition of multiref_polar_ali_2d_delta differs between util_sparx.cpp/h and libpyUtils2.cpp

[akesandgren]

The definition in libEM/sparx/util_sparx.h says

        static vector<float> multiref_polar_ali_2d_delta(EMData* image, const vector< EMData* >& crefim,
                vector<float> xrng, vector<float> yrng, float step, string mode,
                vector< int >numr, float cnx, float cny, float delta_start, float delta);

while the one in libpyUtils2.cpp says

                .def("multiref_polar_ali_2d_delta", &EMAN::Util::multiref_polar_ali_2d_delta, args("image", "crefim", "xrng", "yrng", "step", "mode", "numr", "cnx", "cny"), "formerly known as apmq\nDetermine shift and rotation between image and many referenceimages (crefim, weights have to be applied) quadratic\ninterpolation")

Note the missing two arguments in the libpyUtils2 definition.

[ghost]

Hi This is inconsequential as “missing” arguments are simply a part of help line. Regards, Pawel

…

On Feb 21, 2019, at 10:58 AM, Åke Sandgren ***@***.***> wrote: The definition in libEM/sparx/util_sparx.h says static vector<float> multiref_polar_ali_2d_delta(EMData* image, const vector< EMData* >& crefim, vector<float> xrng, vector<float> yrng, float step, string mode, vector< int >numr, float cnx, float cny, float delta_start, float delta); while the one in libpyUtils2.cpp says .def("multiref_polar_ali_2d_delta", &EMAN::Util::multiref_polar_ali_2d_delta, args("image", "crefim", "xrng", "yrng", "step", "mode", "numr", "cnx", "cny"), "formerly known as apmq\nDetermine shift and rotation between image and many referenceimages (crefim, weights have to be applied) quadratic\ninterpolation") Note the missing two arguments in the libpyUtils2 definition. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.

[akesandgren]

Well, SPRING's usage of

Util.multiref_polar_ali_2d_delta(align_img, ringref, x_range,
            y_range, translation_step, full_circle_mode, polar_interpolation_parameters, center_x + shift_x,
            center_y + shift_y, each_image.inplane_angle, self.delta_psi)

fails with:

  File "/scratch/ake/easybuild/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/SPRING/0.86.1661-Python-2.7.15/lib/python2.7/site-packages/spring/segment2d/segmentalign2d.py", line 219, in perform_coarse_restrained_alignment
    center_y + shift_y, each_image.inplane_angle, self.delta_psi)
Boost.Python.ArgumentError: Python argument types in
    Util.multiref_polar_ali_2d_delta(EMData, list, numpy.float64, numpy.float64, int, str, list, numpy.float64, numpy.float64, int, float)
did not match C++ signature:
    multiref_polar_ali_2d_delta(EMAN::EMData*, std::vector<EMAN::EMData*, std::allocator<EMAN::EMData*> >, std::vector<float, std::allocator<float> > image, std::vector<float, std::allocator<float> > crefim, float xrng, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > yrng, std::vector<int, std::allocator<int> > step, float mode, float numr, float cnx, float cny)

so there is a problem somewhere. Is the actual problem somewhere else?

[akesandgren]

Ah, there is one type that is wrong, didn't notice the first two times i looked at it.

[ghost]

Hi What is SPRING? Regards, Pawel

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On Feb 21, 2019, at 11:09 AM, Åke Sandgren ***@***.***> wrote: Well, SPRING's usage of Util.multiref_polar_ali_2d_delta(align_img, ringref, x_range, y_range, translation_step, full_circle_mode, polar_interpolation_parameters, center_x + shift_x, center_y + shift_y, each_image.inplane_angle, self.delta_psi) fails with: File "/scratch/ake/easybuild/software/MPI/GCC-CUDA/7.3.0-2.30-9.2.88/OpenMPI/3.1.1/SPRING/0.86.1661-Python-2.7.15/lib/python2.7/site-packages/spring/segment2d/segmentalign2d.py", line 219, in perform_coarse_restrained_alignment center_y + shift_y, each_image.inplane_angle, self.delta_psi) Boost.Python.ArgumentError: Python argument types in Util.multiref_polar_ali_2d_delta(EMData, list, numpy.float64, numpy.float64, int, str, list, numpy.float64, numpy.float64, int, float) did not match C++ signature: multiref_polar_ali_2d_delta(EMAN::EMData*, std::vector<EMAN::EMData*, std::allocator<EMAN::EMData*> >, std::vector<float, std::allocator<float> > image, std::vector<float, std::allocator<float> > crefim, float xrng, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > yrng, std::vector<int, std::allocator<int> > step, float mode, float numr, float cnx, float cny) so there is a problem somewhere. Is the actual problem somewhere else? — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[akesandgren]

http://www.sachse.embl.de/emspring/index.html

[ghost]

In this case it is possible something changed in sparx and spring was not updated. If you have github with eman2 you can look up the history of util_sparx. On the other hand, it is unlikely this particular function was changed recently. Regards, Pawel

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On Feb 21, 2019, at 11:29 AM, Åke Sandgren ***@***.***> wrote: http://www.sachse.embl.de/emspring/index.html — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.

[akesandgren]

Yeah, I'm looking into it.

[shadowwalkersb]

@akesandgren , can we close this issue, if there is no more feedback?

[akesandgren]

Sorry, forgot about this one. I'll close it until I have time to figure it out properly.

[ghost]

Hi I do not know what that is. I would close it. Regards, Pawel

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On May 27, 2019, at 8:29 AM, shadow_walker ***@***.***> wrote: @akesandgren , can we close this issue, if there is no more feedback? — You are receiving this because you commented. Reply to this email directly, view it on GitHub, or mute the thread.