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em2d doxygen warnings #363

Closed drussel closed 11 years ago

drussel commented 11 years ago 
/Users/drussel/src/imp/debug/include/IMP/em2d/RelativePositionMover.h:32: Warning: unexpected end of comment block while parsing the argument of command param
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:109: Warning: argument 'Radius' of command @param is not found in the argument list of IMP::em2d::apply_circular_mask(const cv::Mat &mat, cv::Mat &result, int radius, double value=0.0)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:109: Warning: The following parameters of IMP::em2d::apply_circular_mask(const cv::Mat &mat, cv::Mat &result, int radius, double value=0.0) are not documented:
  parameter 'mat'
  parameter 'result'
  parameter 'radius'
  parameter 'value'
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:204: Warning: The following parameters of IMP::em2d::apply_diffusion_filter(const cv::Mat &m, cv::Mat &result, double beta, double pixelsize, unsigned int time_steps) are not documented:
  parameter 'm'
  parameter 'result'
  parameter 'pixelsize'
  parameter 'time_steps'
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:96: Warning: argument 'value' of command @param is not found in the argument list of IMP::em2d::apply_mask(const cv::Mat &m, cv::Mat &result, const cvIntMat &mask, double val)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:96: Warning: The following parameters of IMP::em2d::apply_mask(const cv::Mat &m, cv::Mat &result, const cvIntMat &mask, double val) are not documented:
  parameter 'val'
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:352: Warning: argument 'threshold.' of command @param is not found in the argument list of IMP::em2d::apply_threshold(cv::Mat &m, cv::Mat &result, double threshold=0.0)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:352: Warning: The following parameters of IMP::em2d::apply_threshold(cv::Mat &m, cv::Mat &result, double threshold=0.0) are not documented:
  parameter 'm'
  parameter 'result'
  parameter 'threshold'
/Users/drussel/src/imp/debug/include/IMP/em2d/hierarchical_clustering.h:208: Warning: argument 'Function' of command @param is not found in the argument list of IMP::em2d::do_hierarchical_agglomerative_clustering(const FloatsList &distances)
/Users/drussel/src/imp/debug/include/IMP/em2d/hierarchical_clustering.h:208: Warning: argument 'a' of command @param is not found in the argument list of IMP::em2d::do_hierarchical_agglomerative_clustering(const FloatsList &distances)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:184: Warning: argument 'result' of command @param is not found in the argument list of IMP::em2d::do_labeling(const cvIntMat &m, cvIntMat &mat_to_label)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:184: Warning: argument 'labels' of command @param is not found in the argument list of IMP::em2d::do_labeling(const cvIntMat &m, cvIntMat &mat_to_label)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:184: Warning: The following parameters of IMP::em2d::do_labeling(const cvIntMat &m, cvIntMat &mat_to_label) are not documented:
  parameter 'mat_to_label'
/Users/drussel/src/imp/debug/include/IMP/em2d/project.h:153: Warning: argument 'clear_matrix_before' of command @param is not found in the argument list of IMP::em2d::do_project_particles(const ParticlesTemp &ps, cv::Mat &m2, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const ProjectingOptions &options, MasksManagerPtr masks)
/Users/drussel/src/imp/debug/include/IMP/em2d/project.h:153: Warning: The following parameters of IMP::em2d::do_project_particles(const ParticlesTemp &ps, cv::Mat &m2, const algebra::Rotation3D &R, const algebra::Vector3D &translation, const ProjectingOptions &options, MasksManagerPtr masks) are not documented:
  parameter 'm2'
  parameter 'options'
  parameter 'masks'
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:139: Warning: The following parameters of IMP::em2d::do_remove_small_objects(cvIntMat &m, double percentage, int background=0, int foreground=1) are not documented:
  parameter 'foreground'
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:313: Warning: argument 'm' of command @param is not found in the argument list of IMP::em2d::do_resample_polar(const cv::Mat &input, cv::Mat &resampled, const PolarResamplingParameters &polar_params)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:313: Warning: argument 'result' of command @param is not found in the argument list of IMP::em2d::do_resample_polar(const cv::Mat &input, cv::Mat &resampled, const PolarResamplingParameters &polar_params)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:313: Warning: argument 'polar' of command @param is not found in the argument list of IMP::em2d::do_resample_polar(const cv::Mat &input, cv::Mat &resampled, const PolarResamplingParameters &polar_params)
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:313: Warning: The following parameters of IMP::em2d::do_resample_polar(const cv::Mat &input, cv::Mat &resampled, const PolarResamplingParameters &polar_params) are not documented:
  parameter 'input'
  parameter 'resampled'
  parameter 'polar_params'
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:195: Warning: The following parameters of IMP::em2d::do_segmentation(const cv::Mat &m, cv::Mat &result, const SegmentationParameters &params) are not documented:
  parameter 'params'
/Users/drussel/src/imp/debug/include/IMP/em2d/project.h:212: Warning: The following parameters of IMP::em2d::get_enclosing_image_size(const ParticlesTemp &ps, double pixel_size, unsigned int slack) are not documented:
  parameter 'ps'
  parameter 'pixel_size'
/Users/drussel/src/imp/debug/include/IMP/em2d/image_processing.h:271: Warning: argument 'vector' of command @param is not found in the argument list of IMP::em2d::get_histogram(const cv::Mat &m, int bins)
/Users/drussel/src/imp/debug/include/IMP/em2d/project.h:138: Warning: The following parameters of IMP::em2d::get_projection(em2d::Image *img, const ParticlesTemp &ps, const RegistrationResult &reg, const ProjectingOptions &options, MasksManagerPtr masks=MasksManagerPtr(), String name="") are not documented:
  parameter 'options'
  parameter 'name'
/Users/drussel/src/imp/debug/include/IMP/em2d/project.h:126: Warning: The following parameters of IMP::em2d::get_projections(const ParticlesTemp &ps, const RegistrationResults &registration_values, int rows, int cols, const ProjectingOptions &options, Strings names=Strings()) are not documented:
  parameter 'ps'
  parameter 'rows'
  parameter 'cols'
  parameter 'options'
  parameter 'names'
/Users/drussel/src/imp/debug/include/IMP/em2d/align2D.h:79: Warning: argument 'M1' of command @param is not found in the argument list of IMP::em2d::get_rotational_alignment_no_preprocessing(const cv::Mat &POLAR1, const cv::Mat &POLAR2)
/Users/drussel/src/imp/debug/include/IMP/em2d/align2D.h:79: Warning: argument 'M2' of command @param is not found in the argument list of IMP::em2d::get_rotational_alignment_no_preprocessing(const cv::Mat &POLAR1, const cv::Mat &POLAR2)
/Users/drussel/src/imp/debug/include/IMP/em2d/align2D.h:79: Warning: The following parameters of IMP::em2d::get_rotational_alignment_no_preprocessing(const cv::Mat &POLAR1, const cv::Mat &POLAR2) are not documented:
  parameter 'POLAR1'
  parameter 'POLAR2'
/Users/drussel/src/imp/debug/include/IMP/em2d/domino_particle_states.h:42: Warning: The following parameters of IMP::em2d::GridStates::GridStates(const algebra::Vector3Ds &positions, const algebra::Rotation3Ds &orientations, const String &name="GridStates") are not documented:
  parameter 'name'
/Users/drussel/src/imp/debug/include/IMP/em2d/ProjectionMask.h:181: Warning: argument 'params' of command @param is not found in the argument list of IMP::em2d::MasksManager::create_mask(double radius, double mass)
/Users/drussel/src/imp/debug/include/IMP/em2d/ProjectionFinder.h:86: Warning: argument 'resolution' of command @param is not found in the argument list of IMP::em2d::ProjectionFinder::setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
/Users/drussel/src/imp/debug/include/IMP/em2d/ProjectionFinder.h:86: Warning: argument 'coarse_registration_method' of command @param is not found in the argument list of IMP::em2d::ProjectionFinder::setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
/Users/drussel/src/imp/debug/include/IMP/em2d/ProjectionFinder.h:86: Warning: argument 'optimization' of command @param is not found in the argument list of IMP::em2d::ProjectionFinder::setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
/Users/drussel/src/imp/debug/include/IMP/em2d/ProjectionFinder.h:86: Warning: argument 'simplex_initial_length' of command @param is not found in the argument list of IMP::em2d::ProjectionFinder::setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
/Users/drussel/src/imp/debug/include/IMP/em2d/ProjectionFinder.h:86: Warning: argument 'Value' of command @param is not found in the argument list of IMP::em2d::ProjectionFinder::setup(ScoreFunction *score_function, const Em2DRestraintParameters &params)
/Users/drussel/src/imp/debug/include/IMP/em2d/ProjectionFinder.h:86: Warning: The following parameters of IMP::em2d::ProjectionFinder::setup(ScoreFunction *score_function, const Em2DRestraintParameters &params) are not documented:
  parameter 'score_function'
  parameter 'params'
/Users/drussel/src/imp/debug/include/IMP/em2d/ProjectionMask.h:61: Warning: argument 'weight' of command @param is not found in the argument list of IMP::em2d::ProjectionMask::apply(cv::Mat &m, const algebra::Vector2D &v)
/Users/drussel/src/imp/debug/include/IMP/em2d/domino_particle_states.h:78: Warning: unexpected end of comment block while parsing the argument of command param
/Users/drussel/src/imp/debug/include/IMP/em2d/domino_particle_states.h:89: Warning: argument 'Projections' of command @param is not found in the argument list of IMP::em2d::ProjectionStates::ProjectionStates(const algebra::Vector3Ds &positions, const algebra::Rotation3Ds &orientations, const Images &projections, const String &name="ProjectionStates")
/Users/drussel/src/imp/debug/include/IMP/em2d/domino_particle_states.h:89: Warning: The following parameters of IMP::em2d::ProjectionStates::ProjectionStates(const algebra::Vector3Ds &positions, const algebra::Rotation3Ds &orientations, const Images &projections, const String &name="ProjectionStates") are not documented:
  parameter 'projections'
  parameter 'name'
/Users/drussel/src/imp/debug/lib/IMP/em2d/buildxlinks.py:17: Warning: unexpected end of comment block while parsing the argument of command param
/Users/drussel/src/imp/debug/lib/IMP/em2d/buildxlinks.py:44: Warning: unexpected end of comment block while parsing the argument of command param
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:81: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.do_sampling(self,mode='assignments_heap_container',params=None) are not documented:
  parameter 'params'
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:126: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.get_assignments_with_heap(self,vertex,k=0) are not documented:
  parameter 'k'
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:58: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.set_complementarity_restraint(self,name1,name2,rname,max_sep_distance,max_penetration,weight,max_score=10000000000.0) are not documented:
  parameter 'rname'
  parameter 'max_sep_distance'
  parameter 'max_penetration'
  parameter 'weight'
  parameter 'max_score'
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:143: Warning: argument 'fn_pdb_native' of command @param is not found in the argument list of IMP.em2d.DominoModel.DominoModel::set_native_assembly_for_benchmark(self,params)
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:143: Warning: argument 'anchored' of command @param is not found in the argument list of IMP.em2d.DominoModel.DominoModel::set_native_assembly_for_benchmark(self,params)
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:143: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.set_native_assembly_for_benchmark(self,params) are not documented:
  parameter 'params'
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:248: Warning: argument 'Name' of command @param is not found in the argument list of IMP.em2d.DominoModel.DominoModel::set_not_optimized(self,name)
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:248: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.set_not_optimized(self,name) are not documented:
  parameter 'name'
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:277: Warning: argument 'weight.' of command @param is not found in the argument list of IMP.em2d.DominoModel.DominoModel::set_pair_score_restraint(self,name1,name2,restraint_name,distance=10,weight=1.0,n_pairs=1,stddev=2,max_score=None)
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:277: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.set_pair_score_restraint(self,name1,name2,restraint_name,distance=10,weight=1.0,n_pairs=1,stddev=2,max_score=None) are not documented:
  parameter 'weight'
  parameter 'n_pairs'
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:48: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.set_xlink_restraint(self,id1,chain1,residue1,id2,chain2,residue2,distance,weight,stddev,max_score=False) are not documented:
  parameter 'chain1'
  parameter 'chain2'
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:305: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.write_pdb_for_configuration(self,n,fn_pdb) are not documented:
  parameter 'fn_pdb'
/Users/drussel/src/imp/debug/lib/IMP/em2d/DominoModel.py:283: Warning: The following parameters of IMP::em2d.DominoModel.DominoModel.write_solutions_database(self,fn_database,max_number=None) are not documented:
  parameter 'fn_database'
/Users/drussel/src/imp/debug/lib/IMP/em2d/solutions_io.py:88: Warning: The following parameters of IMP::em2d.solutions_io.ResultsDB.get_solutions(self,fields=False,max_number=None,orderby=False) are not documented:
  parameter 'max_number'
  parameter 'orderby'
drussel commented 11 years ago 
/Users/drussel/src/imp/debug/include/IMP/em2d/filenames_manipulation.h:23: Warning: argument 'List' of command @param is not found in the argument list of read_selection_file(String fn)