diff --git a/.gitignore b/.gitignore index bf6a22fc6..960cd008f 100644 --- a/.gitignore +++ b/.gitignore @@ -1,4 +1,7 @@ *.sw[a-z] *.patch _build +html +xml *.pt +.DS_store diff --git a/alg/teca_2d_component_area.h b/alg/teca_2d_component_area.h index 5a9d57e6a..48b19e4b2 100644 --- a/alg/teca_2d_component_area.h +++ b/alg/teca_2d_component_area.h @@ -44,6 +44,22 @@ stored in the output dataset metadata in the following keys: background_id - the label used for cells outside of the segmentation, i.e. the background. This can be used to skip processing of the background when desirable. + +@rst +.. table:: Algorithm Properties + + +----------------------------+------------------------------------------------------------+ + | Property | Description | + +============================+============================================================+ + | component_variable | the component variable name containing the region labels. | + +----------------------------+------------------------------------------------------------+ + | contiguous_component_ids | the label used for cells inside the segmentation. | + +----------------------------+------------------------------------------------------------+ + | background_id | | the label used for cells outside of the segmentation, | + | | | i.e. the background. This can be used to skip processing | + | | | of the background when desirable. | + +----------------------------+------------------------------------------------------------+ +@endrst */ class teca_2d_component_area : public teca_algorithm { @@ -57,18 +73,23 @@ class teca_2d_component_area : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the name of the input array + // The component variable name containing the region labels. TECA_ALGORITHM_PROPERTY(std::string, component_variable) - // set this only if you know for certain that label ids are contiguous and - // start at 0. this enables use of a faster implementation. + /** @fn set_contiguous_component_ids + * @attention set this only if you know for certain that label ids + * are contiguous and start at 0. this enables use of a + * faster implementation. + */ TECA_ALGORITHM_PROPERTY(int, contiguous_component_ids) - - // set this to override the component label used for background. By default - // this is set to -1 to indicate that the value should be obtained from the - // metadata key `background_id`. Note that TECA's connected component - // labeler uses the id 0 for the background and passes this in a metadata - // key and as a result no action is required. + + /** @fn set_background_id + * @note By default this is set to -1 to indicate that the value should + * be obtained from the metadata key `background_id`. + * TECA's connected component labeler uses the id 0 for the + * background and passes this in a metadata key and as a result + * no action is required. + */ TECA_ALGORITHM_PROPERTY(long, background_id) protected: diff --git a/alg/teca_bayesian_ar_detect.h b/alg/teca_bayesian_ar_detect.h index c2805cf99..3e00155bf 100644 --- a/alg/teca_bayesian_ar_detect.h +++ b/alg/teca_bayesian_ar_detect.h @@ -49,28 +49,53 @@ class teca_bayesian_ar_detect : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the name of the input array + /** @anchor ivt_variable + * @name ivt_variable + * Set the name of the input array + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, ivt_variable) - // set the names of columns in the parameter table. + /** @anchor min_ivt_variable + * @name min_ivt_variable + * Set the name of the min IVT column in the parameter table. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, min_ivt_variable) + ///@} + + /** @anchor min_component_area_variable + * @name min_component_area_variable + * Set the name of the component area column in the parameter table. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, min_component_area_variable) + ///@} + + /** @anchor hwhm_latitude_variable + * @name hwhm_latitude_variable + * Set the name of the HWHM lattitude column in the parameter table. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, hwhm_latitude_variable) + ///@} - // flag indicating verbose terminal output is desired. - // default is 0 TECA_ALGORITHM_PROPERTY(int, verbose) - // set/get the number of threads in the pool. setting - // to -1 results in a thread per core factoring in all MPI - // ranks running on the node. the default is -1. + /** set the number of threads in the pool. setting + * to -1 results in a thread per core factoring in all MPI + * ranks running on the node. the default is -1. + */ void set_thread_pool_size(int n_threads); + + /** get the number of threads in the pool. the default is -1. */ unsigned int get_thread_pool_size() const noexcept; - // override the input connections because we are going to - // take the first input and use it to generate metadata. - // the second input then becomes the only one the pipeline - // knows about. + /** override the input connections because we are going to + * take the first input and use it to generate metadata. + * the second input then becomes the only one the pipeline + * knows about. + */ void set_input_connection(unsigned int id, const teca_algorithm_output_port &port) override; diff --git a/alg/teca_binary_segmentation.h b/alg/teca_binary_segmentation.h index 983a497fb..eb255eb78 100644 --- a/alg/teca_binary_segmentation.h +++ b/alg/teca_binary_segmentation.h @@ -30,24 +30,65 @@ class teca_binary_segmentation : public teca_algorithm TECA_ALGORITHM_CLASS_NAME(teca_binary_segmentation) ~teca_binary_segmentation(); - // set the name of the output array to store the resulting segmentation in + /** @anchor segmentation_variable + * @name segmentation_variable + * Set the name of the output array to store the resulting segmentation in. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, segmentation_variable) + ///@} // set extra metadata for the segmentation variable + /** @anchor segmentation_variable_attributes + * @name segmentation_variable_attributes + * Set extra metadata for the segmentation variable. + */ + ///@{ TECA_ALGORITHM_PROPERTY(teca_metadata, segmentation_variable_attributes) + ///@} - // set the name of the input array to segment + /** @anchor threshold_variable + * @name threshold_variable + * Set the name of the input array to segment. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, threshold_variable) + ///@} - // Set the threshold range. The defaults are (-infinity, infinity]. + /** @anchor low_threshold_value + * @name low_threshold_value + * Sets the low threshold value. default is -infinity. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, low_threshold_value) + ///@} + /** @anchor high_threshold_value + * @name high_threshold_value + * Sets the high threshold value. default is infinity. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, high_threshold_value) - - // Set the threshold mode. In BY_PERCENTILE mode low and high thresholds - // define the percentiles (0 to 100) between which data is in the - // segmentation. default is BY_VALUE. - enum {BY_VALUE=0, BY_PERCENTILE=1}; + ///@} + + /** list threshold modes. In BY_PERCENTILE mode low and high thresholds + * define the percentiles (0 to 100) between which data is in the + * segmentation. + */ + enum + { + /** 0 */ + BY_VALUE=0, + /** 1 */ + BY_PERCENTILE=1 + }; + + /** @anchor threshold_mode + * @name threshold_mode + * Set the threshold mode. default is BY_VALUE + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, threshold_mode); + ///@} void set_threshold_by_percentile() { set_threshold_mode(BY_PERCENTILE); } void set_threshold_by_value() { set_threshold_mode(BY_VALUE); } diff --git a/alg/teca_cartesian_mesh_regrid.h b/alg/teca_cartesian_mesh_regrid.h index f9ae85da2..1a52a15a6 100644 --- a/alg/teca_cartesian_mesh_regrid.h +++ b/alg/teca_cartesian_mesh_regrid.h @@ -37,21 +37,45 @@ class teca_cartesian_mesh_regrid : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the list of arrays to move from the source - // to the target + /** @anchor arrays + * @name arrays + * Set the list of arrays to move from the source to the target. + */ + ///@{ TECA_ALGORITHM_VECTOR_PROPERTY(std::string, array) - - // set the input connection from which metadata such as arrays - // and time steps are taken from. + ///@} + + /** @anchor target_input + * @name target_input + * Set the input connection from which metadata such as arrays + * and time steps are taken from. + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, target_input) - - // set the interpolation mode used in transfering - // data between meshes of differing resolution. - // in nearest mode value at the nearest grid point - // is used, in linear mode bi/tri linear interpolation - // is used. - enum {nearest=0, linear=1}; + ///@} + + /** list the interpolation modes used in transfering + * data between meshes of differing resolution. + * In nearest mode value at the nearest grid point + * is used, in linear mode bi/tri linear interpolation + * is used. + */ + enum + { + /** 0 */ + nearest=0, + /** 1 */ + linear=1 + }; + + /** @anchor interpolation_mode + * @name interpolation_mode + * Set the interpolation_mode mode. default is nearest + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, interpolation_mode) + ///@} + void set_interpolation_mode_nearest(){ interpolation_mode = nearest; } void set_interpolation_mode_linear(){ interpolation_mode = linear; } diff --git a/alg/teca_cartesian_mesh_source.h b/alg/teca_cartesian_mesh_source.h index 168c85a94..c2652e58d 100644 --- a/alg/teca_cartesian_mesh_source.h +++ b/alg/teca_cartesian_mesh_source.h @@ -54,50 +54,137 @@ class teca_cartesian_mesh_source : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set/get the type code for generated coordinates. - // default is 32 bit floating point. Use - // teca_variant_array_type::get() to get specific type - // codes for C++ POD types NT. + /** @anchor coordinate_type_code + * @name coordinate_type_code + * Set the type code for generated coordinates. + * default is 32 bit floating point. Use + * teca_variant_array_type::get() to get specific type + * codes for C++ POD types NT. + */ + ///@{ TECA_ALGORITHM_PROPERTY(unsigned int, coordinate_type_code) - TECA_ALGORITHM_PROPERTY(unsigned int, field_type_code) + ///@} - // set/get the global index space extent of the data. the extents are - // given by 8 values, 6 spatial plus 2 temporal, in the following order - // [i0 i1 j0 j1 k0 k1 q0 q1] - // this should be the same on all ranks elements. + /** @anchor field_type_code + * @name field_type_code + */ + ///@{ + TECA_ALGORITHM_PROPERTY(unsigned int, field_type_code) + ///@} + + /** @anchor whole_extents + * @name whole_extents + * Set the global index space extent of the data. the extents are + * given by 8 values, 6 spatial plus 2 temporal, in the following order + * [i0 i1 j0 j1 k0 k1 q0 q1] + * this should be the same on all ranks elements. + */ + ///@{ TECA_ALGORITHM_VECTOR_PROPERTY(unsigned long, whole_extent) - - // set/get the global bounds of the data. the bounds are 8 values 6 spatial - // plus 2 temporal in the following order. - // [x0 x1 y0 y1 z0 z1 t0 t1] - // this should be the same on all ranks elements. + ///@} + + /** @anchor bounds + * @name bounds + * Set the global bounds of the data. the bounds are 8 values 6 spatial + * plus 2 temporal in the following order. + * [x0 x1 y0 y1 z0 z1 t0 t1] + * this should be the same on all ranks elements. + */ + ///@{ TECA_ALGORITHM_VECTOR_PROPERTY(double, bound) - - // set the variable to use for the coordinate axes. - // the defaults are: x => lon, y => lat, z = plev, - // t => time + ///@} + + /** @anchor x_axis_variable + * @name x_axis_variable + * Set the variable to use for the x coordinate axis. default is lon + * the defaults are: x => lon, y => lat, z = plev, + * t => time + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, x_axis_variable) + ///@} + + /** @anchor y_axis_variable + * @name y_axis_variable + * Set the variable to use for the y coordinate axis. default is lat + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, y_axis_variable) + ///@} + + /** @anchor z_axis_variable + * @name z_axis_variable + * Set the variable to use for the y coordinate axis. default is plev + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, z_axis_variable) + ///@} + + /** @anchor t_axis_variable + * @name t_axis_variable + * Set the variable to use for the y coordinate axis. default is time + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, t_axis_variable) + ///@} - // set the units of spatial axes. The defaults are: - // degrees_east, degrees_north, and pressure_level + /** @anchor x_axis_units + * @name x_axis_units + * Set the units of the x spatial axis. The default is degrees_east + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, x_axis_units) + ///@} + + /** @anchor y_axis_units + * @name y_axis_units + * Set the units of the y spatial axis. The default is degrees_north + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, y_axis_units) - TECA_ALGORITHM_PROPERTY(std::string, z_axis_units) + ///@} - // number of time steps to generate + /** @anchor z_axis_units + * @name z_axis_units + * Set the units of the z spatial axis. The default is pressure_level + */ + ///@{ + TECA_ALGORITHM_PROPERTY(std::string, z_axis_units) + ///@} + + /** @anchor calendar + * @name calendar + * Set the calendar to generate the number of time steps. + * @note @ref time_units need to be set as well to correctly generate + * the number of time steps + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, calendar) + ///@} + + /** @anchor time_units + * @name time_units + * Set the time units to generate the number of time steps. + * @note @ref calendar need to be set as well to correctly generate + * the number of time steps + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, time_units) - - // set the named callbacks to generate fields on the mesh. A callback - // function must have the signature f(x,y,z,t). + ///@} + + /** @anchor field_generators + * @name field_generators + * Set the named callbacks to generate fields on the mesh. A callback + * function must have the signature f(x,y,z,t). + */ + ///@{ TECA_ALGORITHM_VECTOR_PROPERTY(field_generator_t, field_generator); + ///@} - // set a callback function f(x,y,z,t) that generates a field named name - // x,y,z are coordinate axes in variant arrays, t is the double precision - // time value. + /** set a callback function f(x,y,z,t) that generates a field named name + * x,y,z are coordinate axes in variant arrays, t is the double precision + * time value. + */ void append_field_generator(const std::string &name, const teca_array_attributes &atts, field_generator_callback &callback); diff --git a/alg/teca_component_area_filter.h b/alg/teca_component_area_filter.h index f6c8e5a22..d3dbe84f4 100644 --- a/alg/teca_component_area_filter.h +++ b/alg/teca_component_area_filter.h @@ -49,45 +49,95 @@ class teca_component_area_filter : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the name of the input array containing connected - // component labels + /** @anchor component_variable + * @name component_variable + * Set the name of the input array containing connected + * component labels + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_variable) - - // set the name of the dataset metadata key holding the number of - // components left after the filter is applied + ///@} + + /** @anchor number_of_components_key + * @name number_of_components_key + * Set the name of the dataset metadata key holding the number of + * components left after the filter is applied + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, number_of_components_key) - - // set the name of the dataset metadata key holding connected component - // label ids + ///@} + + /** @anchor component_ids_key + * @name component_ids_key + * Set the name of the dataset metadata key holding connected component + * label ids + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_ids_key) - - // set the name of the dataset metadata key holding connected component - // areas + ///@} + + /** @anchor component_area_key + * @name component_area_key + * Set the name of the dataset metadata key holding connected component + * areas + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_area_key) - - // set this to be the default label id for the filtered out component - // areas. This will typically correspond to the label used for cells - // outside of the segmentation (i.e. in the background). One can use this - // property to override the mask value. The default mask value is '-1' - // which results in aquiring the mask value from input metadata key - // `background_id`. Use -2 to specify no background label. + ///@} + + /** @anchor mask_value + * @name mask_value + * Set this to be the default label id for the filtered out component + * areas. This will typically correspond to the label used for cells + * outside of the segmentation (i.e. in the background). One can use this + * property to override the mask value. The default mask value is '-1' + * which results in aquiring the mask value from input metadata key + * `background_id`. Use -2 to specify no background label. + */ + ///@{ TECA_ALGORITHM_PROPERTY(long, mask_value) + ///@} // set the range identifying values to area filter. // The defaults are (-infinity, infinity]. + /** @anchor low_area_threshold + * @name low_area_threshold + * Set the low area threshold value to area filter. + * default is -infinity. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, low_area_threshold) + ///@} + + /** @anchor high_area_threshold + * @name high_area_threshold + * Set the high area threshold value to area filter. + * default is infinity. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, high_area_threshold) - - // a string to be appended to the name of the output variable. - // setting this to an empty string will result in the masked array - // replacing the input array in the output. default is an empty - // string "" + ///@} + + /** @anchor variable_post_fix + * @name variable_post_fix + * Set a string to be appended to the name of the output variable. + * setting this to an empty string will result in the masked array + * replacing the input array in the output. default is an empty + * string "" + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, variable_post_fix) - - // set this only if you know for certain that label ids - // are contiguous and start at 0. this enables use of a - // faster implementation. + ///@} + + /** @anchor contiguous_component_ids + * @name contiguous_component_ids + * @attention Set this only if you know for certain that label ids + * are contiguous and start at 0. this enables use of a + * faster implementation. + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, contiguous_component_ids) + ///@} protected: teca_component_area_filter(); diff --git a/alg/teca_connected_components.h b/alg/teca_connected_components.h index 0f188f7e0..9a4e29f52 100644 --- a/alg/teca_connected_components.h +++ b/alg/teca_connected_components.h @@ -50,12 +50,22 @@ class teca_connected_components : public teca_algorithm TECA_ALGORITHM_CLASS_NAME(teca_connected_components) ~teca_connected_components(); - // set the input array containing a binary segmentation - // see teca_binary_segmentation + /** @anchor segmentation_variable + * @name segmentation_variable + * Set the input array containing a binary segmentation + * see @ref teca_binary_segmentation + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, segmentation_variable) + ///@} - // set the name of the output array to store the component labels in + /** @anchor component_variable + * @name component_variable + * Set the name of the output array to store the component labels in + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_variable) + ///@} protected: diff --git a/alg/teca_dataset_diff.h b/alg/teca_dataset_diff.h index 9a317441e..e0f02cbf3 100644 --- a/alg/teca_dataset_diff.h +++ b/alg/teca_dataset_diff.h @@ -41,18 +41,30 @@ class teca_dataset_diff : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // Relative tolerance below which two floating-point quantities are - // considered equal (1e-6). The relative difference for a computed - // quantity A and a reference quantity B is - // - // rel_diff = |A - B| / B, B != 0 - // = |A - B| / A, B == 0, A != 0 - // 0 otherwise + /** @anchor tolerance + * @name tolerance + * Set tolerance. Relative tolerance below which two floating-point + * quantities are considered equal (1e-6). The relative difference + * \f$ (d_r) \f$ for a computed quantity A and a reference quantity B is + * + * \f{eqnarray*}{ + * d_r &=& \frac{|A - B|}{B}, B != 0 \\ + * &=& \frac{|A - B|}{A}, B == 0, A != 0 \\ + * &=& 0, otherwise + * \f} + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, tolerance) - - // if set infromation about the test progress is displayed during - // the test. + ///@} + + /** @anchor verbose + * @name verbose + * If set, infromation about the test progress is displayed during + * the test. + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, verbose) + ///@} protected: teca_dataset_diff(); @@ -84,8 +96,9 @@ class teca_dataset_diff : public teca_algorithm // Reporting methods. - // Call this with contextual information when datasets differ. You can use - // printf formatting. + /** Call this with contextual information when datasets differ. You can use + * printf formatting. + */ void datasets_differ(const char* info, ...); private: @@ -101,7 +114,7 @@ class teca_dataset_diff : public teca_algorithm const teca_metadata &request) override; private: - // Tolerance for equality of field values. + /** Tolerance for equality of field values. */ double tolerance; int verbose; }; diff --git a/alg/teca_integrated_vapor_transport.h b/alg/teca_integrated_vapor_transport.h index 923f7d6b9..69d676bd1 100644 --- a/alg/teca_integrated_vapor_transport.h +++ b/alg/teca_integrated_vapor_transport.h @@ -10,14 +10,16 @@ TECA_SHARED_OBJECT_FORWARD_DECL(teca_integrated_vapor_transport) -/// an algorithm that computes integrated vapor transport (IVT) +/// an algorithm that computes integrated vapor transport \f$ (\vec{\text{IVT}}) \f$ /** -Compute integrated vaport transport (IVT) from wind vector and +Compute integrated vaport transport \f$ (\vec{\text{IVT}}) \f$ from wind vector and specific humidity. -IVT = - \frac{1}{g} \int_{p_0}^{p_1} \vec{v} q dp +\f{eqnarray*}{ +\vec{\text{IVT}} = - \frac{1}{g} \int_{p_0}^{p_1} \vec{v}q \,dp +\f} -where q is the specific humidity, and \vec{v} = (u, v) are the +where q is the specific humidity, and \f$ \vec{v} = (u, v) \f$ are the longitudinal and latitudinal components of wind. This calculation is an instance of a vertical reduction where @@ -36,26 +38,51 @@ class teca_integrated_vapor_transport : public teca_vertical_reduction TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the name of the varaiable that contains the longitudinal - // component of the wind vector ("ua") + /** @anchor wind_u_variable + * @name wind_u_variable + * Set the name of the varaiable that contains the longitudinal + * component of the wind vector ("ua") + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, wind_u_variable) - - // set the name of the varaiable that contains the latitudinal - // component of the wind vector ("va") + ///@} + + /** @anchor wind_v_variable + * @name wind_v_variable + * Set the name of the varaiable that contains the latitudinal + * component of the wind vector ("va") + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, wind_v_variable) - - // set the name of the variable that contains the specific - // humidity ("hus") + ///@} + + /** @anchor specific_humidity_variable + * @name specific_humidity_variable + * Set the name of the variable that contains the specific + * humidity ("hus") + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, specific_humidity_variable) - - // set the name of the varaiable that contains the longitudinal - // component of the ivt vector ("ivt_u") + ///@} + + /** @anchor ivt_u_variable + * @name ivt_u_variable + * Set the name of the varaiable that contains the longitudinal + * component of the ivt vector ("ivt_u") + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, ivt_u_variable) - - // set the name of the varaiable that contains the latitudinal - // component of the ivt vector ("ivt_v") + ///@} + + /** @anchor ivt_v_variable + * @name ivt_v_variable + * Set the name of the varaiable that contains the latitudinal + * component of the ivt vector ("ivt_v") + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, ivt_v_variable) + ///@} protected: teca_integrated_vapor_transport(); diff --git a/alg/teca_l2_norm.h b/alg/teca_l2_norm.h index f67e23581..ad394ceaf 100644 --- a/alg/teca_l2_norm.h +++ b/alg/teca_l2_norm.h @@ -27,15 +27,41 @@ class teca_l2_norm : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the arrays that contain the vector components - // to compute norm from + /** @anchor component_0_variable + * @name component_0_variable + * Set the 1st array that contains the vector components + * to compute norm from + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_0_variable) + ///@} + + /** @anchor component_1_variable + * @name component_1_variable + * Set the 2nd array that contains the vector components + * to compute norm from + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_1_variable) + ///@} + + /** @anchor component_2_variable + * @name component_2_variable + * Set the 3rd array that contains the vector components + * to compute norm from + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_2_variable) + ///@} - // set the name of the array to store the result in. - // the default is "l2_norm" + /** @anchor l2_norm_variable + * @name l2_norm_variable + * Set the name of the array to store the result in. + * the default is "l2_norm" + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, l2_norm_variable) + ///@} protected: teca_l2_norm(); diff --git a/alg/teca_latitude_damper.h b/alg/teca_latitude_damper.h index 9cab2b7ff..cb20d4390 100644 --- a/alg/teca_latitude_damper.h +++ b/alg/teca_latitude_damper.h @@ -38,35 +38,57 @@ class teca_latitude_damper : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the center of the Gaussian in units of degress latitude. - // default is 0.0 deg lat + /** @anchor center + * @name center + * Set the center of the Gaussian in units of degress latitude. + * default is \f$ 0.0 ^{\circ} \f$ lat + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, center) - - // set the half width of the Gaussian in units of degrees latitude. - // default is 45.0 deg lat + ///@} + + /** @anchor half_width_at_half_max + * @name half_width_at_half_max + * Set the half width of the Gaussian in units of degrees latitude. + * default is \f$ 45.0 ^{\circ} \f$ lat + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, half_width_at_half_max) + ///@} - // set the names of the arrays that the filter will apply on + /** @anchor damped_variables + * @name damped_variables + * Set the names of the arrays that the filter will apply on + */ + ///@{ TECA_ALGORITHM_VECTOR_PROPERTY(std::string, damped_variable) - - // a string to be appended to the name of each output variable - // setting this to an empty string will result in the damped array - // replacing the input array in the output. default is an empty - // string "" + ///@} + + /** @anchor variable_post_fix + * @name variable_post_fix + * Set a string to be appended to the name of each output variable + * setting this to an empty string will result in the damped array + * replacing the input array in the output. default is an empty + * string "" + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, variable_post_fix) + ///@} protected: teca_latitude_damper(); - // helpers to get parameters defining the Gaussian used by the - // the filter. if the user has not specified a value then the - // request is probed. a return of zero indicates success + /* helpers to get parameters defining the Gaussian used by the + * the filter. if the user has not specified a value then the + * request is probed. a return of zero indicates success + */ int get_sigma(const teca_metadata &request, double &sigma); int get_mu(const teca_metadata &request, double &mu); - // helper to get the list of variables to apply the filter on - // if the user provided none, then the request is probed. a - // return of 0 indicates success + /* helper to get the list of variables to apply the filter on + * if the user provided none, then the request is probed. a + * return of 0 indicates success + */ int get_damped_variables(std::vector &vars); private: diff --git a/alg/teca_tc_candidates.h b/alg/teca_tc_candidates.h index 85b1dcdcb..538c9685a 100644 --- a/alg/teca_tc_candidates.h +++ b/alg/teca_tc_candidates.h @@ -58,53 +58,213 @@ class teca_tc_candidates : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set/get the name of input variables + /** @anchor surface_wind_speed_variable + * @name surface_wind_speed_variable + * Set the name of surface wind speed input variable + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, surface_wind_speed_variable) + ///@} + + /** @anchor vorticity_850mb_variable + * @name vorticity_850mb_variable + * Set the name of vorticity 850mb input variable + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, vorticity_850mb_variable) + ///@} + + /** @anchor sea_level_pressure_variable + * @name sea_level_pressure_variable + * Set the name of sea level pressure input variable + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, sea_level_pressure_variable) + ///@} + + /** @anchor core_temperature_variable + * @name core_temperature_variable + * Set the name of core temperature input variable + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, core_temperature_variable) + ///@} + + /** @anchor thickness_variable + * @name thickness_variable + * Set the name of thickness input variable + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, thickness_variable) + ///@} - // a candidate is defined as having: - // 1) a local maximum in vorticity above vorticty_850mb_threshold, - // centered on a window of vorticty_850mb_window degrees - // 2) a local minimum in pressure within max_core_radius degrees - // 3) having max pressure delta within max_pressure_radius at - // that location + /** @anchor max_core_radius + * @name max_core_radius + * Set `max_core_radius`. + * + * @note A candidate is defined as having:\n + * 1) a local maximum in vorticity above vorticty_850mb_threshold, + * centered on a window of vorticty_850mb_window degrees\n + * 2) a local minimum in pressure within max_core_radius degrees\n + * 3) having max pressure delta within max_pressure_radius at + * that location + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, max_core_radius) + ///@} + + /** @anchor min_vorticity_850mb + * @name min_vorticity_850mb + * Set `min_vorticity_850mb`. + * + * @note A candidate is defined as having:\n + * 1) a local maximum in vorticity above vorticty_850mb_threshold, + * centered on a window of vorticty_850mb_window degrees\n + * 2) a local minimum in pressure within max_core_radius degrees\n + * 3) having max pressure delta within max_pressure_radius at + * that location + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, min_vorticity_850mb) + ///@} + + /** @anchor vorticity_850mb_window + * @name vorticity_850mb_window + * Set `vorticity_850mb_window`. + * + * @note A candidate is defined as having:\n + * 1) a local maximum in vorticity above vorticty_850mb_threshold, + * centered on a window of vorticty_850mb_window degrees\n + * 2) a local minimum in pressure within max_core_radius degrees\n + * 3) having max pressure delta within max_pressure_radius at + * that location + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, vorticity_850mb_window) + ///@} + + /** @anchor max_pressure_delta + * @name max_pressure_delta + * Set `max_pressure_delta`. + * + * @note A candidate is defined as having:\n + * 1) a local maximum in vorticity above vorticty_850mb_threshold, + * centered on a window of vorticty_850mb_window degrees\n + * 2) a local minimum in pressure within max_core_radius degrees\n + * 3) having max pressure delta within max_pressure_radius at + * that location + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, max_pressure_delta) + ///@} + + /** @anchor max_pressure_radius + * @name max_pressure_radius + * Set `max_pressure_radius`. + * + * @note A candidate is defined as having:\n + * 1) a local maximum in vorticity above vorticty_850mb_threshold, + * centered on a window of vorticty_850mb_window degrees\n + * 2) a local minimum in pressure within max_core_radius degrees\n + * 3) having max pressure delta within max_pressure_radius at + * that location + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, max_pressure_radius) + ///@} - // these criteria are recorded here but only used in the trajectory - // stitching stage. + /** @anchor max_core_temperature_delta + * @name max_core_temperature_delta + * this criteria is recorded here but only used in the trajectory + * stitching stage. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, max_core_temperature_delta) + ///@} + + /** @anchor max_core_temperature_radius + * @name max_core_temperature_radius + * this criteria is recorded here but only used in the trajectory + * stitching stage. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, max_core_temperature_radius) + ///@} + + /** @anchor max_thickness_delta + * @name max_thickness_delta + * this criteria is recorded here but only used in the trajectory + * stitching stage. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, max_thickness_delta) + ///@} + + /** @anchor max_thickness_radius + * @name max_thickness_radius + * this criteria is recorded here but only used in the trajectory + * stitching stage. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, max_thickness_radius) + ///@} - // set/get the bounding box to search for storms - // in units of degreees lat,lon + /** @anchor search_lat_low + * @name search_lat_low + * Set the low lat bounding box to search for storms + * in units of degrees + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, search_lat_low) + ///@} + + /** @anchor search_lat_high + * @name search_lat_high + * Set the high lat bounding box to search for storms + * in units of degrees + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, search_lat_high) + ///@} + + /** @anchor search_lon_low + * @name search_lon_low + * Set the low lon bounding box to search for storms + * in units of degrees + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, search_lon_low) + ///@} + + /** @anchor search_lon_high + * @name search_lon_high + * Set the high lon bounding box to search for storms + * in units of degrees + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, search_lon_high) + ///@} - // set/get the number of iterations to search for the - // storm local minimum. raising this paramter might increase - // detections but the detector will run slowerd. default is - // 50. + /** @anchor minimizer_iterations + * @name minimizer_iterations + * Set the number of iterations to search for the + * storm local minimum. raising this paramter might increase + * detections but the detector will run slowerd. default is + * 50. + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, minimizer_iterations) + ///@} - // send humand readable representation to the - // stream + /** send humand readable representation to the + * stream + */ virtual void to_stream(std::ostream &os) const override; protected: teca_tc_candidates(); - // helper that computes the output extent + /** helper that computes the output extent */ int get_active_extent( p_teca_variant_array lat, p_teca_variant_array lon, diff --git a/alg/teca_tc_trajectory.h b/alg/teca_tc_trajectory.h index 2154cc881..286880737 100644 --- a/alg/teca_tc_trajectory.h +++ b/alg/teca_tc_trajectory.h @@ -46,16 +46,42 @@ class teca_tc_trajectory : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the arrays that contain the vector components - // to compute norm from + /** @anchor max_daily_distance + * @name max_daily_distance + * Set the `max_daily_distance` array that contains the vector + * components to compute norm from + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, max_daily_distance) + ///@} + + /** @anchor min_wind_speed + * @name min_wind_speed + * Set the `min_wind_speed` array that contains the vector + * components to compute norm from + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, min_wind_speed) + ///@} + + /** @anchor min_wind_duration + * @name min_wind_duration + * Set the `min_wind_duration` array that contains the vector + * components to compute norm from + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, min_wind_duration) - - // number of time steps between candidate data - // this is used to detect missing candidate data - // and abort those tracks. default 1 + ///@} + + /** @anchor step_interval + * @name step_interval + * Set the number of time steps between candidate data. + * This is used to detect missing candidate data + * and abort those tracks. default 1 + */ + ///@{ TECA_ALGORITHM_PROPERTY(unsigned long, step_interval) + ///@} protected: teca_tc_trajectory(); diff --git a/alg/teca_tc_wind_radii.h b/alg/teca_tc_wind_radii.h index 6b9befc38..254a73336 100644 --- a/alg/teca_tc_wind_radii.h +++ b/alg/teca_tc_wind_radii.h @@ -35,59 +35,135 @@ class teca_tc_wind_radii : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the name of the column that defines the track ids - // if set the specified column is coppied into the output - // metadata and accessed with the key event_id + /** @anchor storm_id_column + * @name storm_id_column + * Set the name of the column that defines the track ids + * if set the specified column is coppied into the output + * metadata and accessed with the key event_id. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, storm_id_column) - - // set the name of the columns that define the event position - // if set the columns are coppied into the output metadata - // and accessed with the keys storm_x_coordinate, storm_y_coordinate + ///@} + + /** @anchor storm_x_coordinate_column + * @name storm_x_coordinate_column + * Set the name of the `storm_x_coordinate_column` + * column that define the event position. + * If set the column is copied into the output metadata + * and accessed with the key storm_x_coordinate. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, storm_x_coordinate_column) + ///@} + + /** @anchor storm_y_coordinate_column + * @name storm_y_coordinate_column + * Set the name of the `storm_y_coordinate_column` + * column that define the event position. + * If set the column is copied into the output metadata + * and accessed with the key storm_y_coordinate. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, storm_y_coordinate_column) - - // set the name of the column containing peak instantanious - // surface wind speed + ///@} + + /** @anchor storm_wind_speed_column + * @name storm_wind_speed_column + * Set the name of the column containing peak instantanious + * surface wind speed + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, storm_wind_speed_column) - - // set the name of the column that defines the event time - // if set the specified column is coppied into the output - // metadata and accessed with the key event_time + ///@} + + /** @anchor storm_time_column + * @name storm_time_column + * Set the name of the column that defines the event time + * if set the specified column is coppied into the output + * metadata and accessed with the key event_time + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, storm_time_column) + ///@} - // set the name of the wind variable components + /** @anchor wind_u_variable + * @name wind_u_variable + * Set the name of the U wind variable component. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, wind_u_variable) + ///@} + + /** @anchor wind_v_variable + * @name wind_v_variable + * Set the name of the V wind variable component. + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, wind_v_variable) + ///@} - // set the radius in degrees of latitude to sample the wind - // field + /** @anchor search_radius + * @name search_radius + * Set the radius in degrees of latitude to sample the wind field. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, search_radius) - - // set the radius in degrees of latitude beyond which to - // terminate the search for peak wind speed. if the peak - // lies beyond this distance search is terminated and a - // warning is displayed. + ///@} + + /** @anchor core_radius + * @name core_radius + * Set the radius in degrees of latitude beyond which to + * terminate the search for peak wind speed. if the peak + * lies beyond this distance search is terminated and a + * warning is displayed. + */ + ///@{ TECA_ALGORITHM_PROPERTY(double, core_radius) + ///@} - // number of bins to discetize by in the radial direction + /** @anchor number_of_radial_bins + * @name number_of_radial_bins + * Set the number of bins to discetize by in the radial direction. + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, number_of_radial_bins) - - // set the wind speeds (in m/s) to find the radius of. the - // defualt values are the transition speeds of the Saffir-Simpson - // scale. + ///@} + + /** @anchor critical_wind_speeds + * @name critical_wind_speeds + * Set the wind speeds (in m/s) to find the radius of. the + * defualt values are the transition speeds of the Saffir-Simpson + * scale. + */ + ///@{ TECA_ALGORITHM_VECTOR_PROPERTY(double, critical_wind_speed) - - // set the profile type. PROFILE_MAX uses the maximum - // wind speed on each interval of the discretization, while - // PROFILE_AVERAGE uses the average on each interval - enum {PROFILE_MAX = 0, PROFILE_AVERAGE = 1}; + ///@} + + /** Profile types. PROFILE_MAX uses the maximum + * wind speed on each interval of the discretization, while + * PROFILE_AVERAGE uses the average on each interval + */ + enum { + /** 0 */ + PROFILE_MAX = 0, + /** 1 */ + PROFILE_AVERAGE = 1 + }; + + /** @anchor profile_type + * @name profile_type + * Set the profile type. + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, profile_type); + ///@} - // override the input connections because we are going to - // take the first input and use it to generate metadata. - // the second input then becomes the only one the pipeline - // knows about. + /** override the input connections because we are going to + * take the first input and use it to generate metadata. + * the second input then becomes the only one the pipeline + * knows about. + */ void set_input_connection(unsigned int id, const teca_algorithm_output_port &port) override; diff --git a/alg/teca_temporal_average.h b/alg/teca_temporal_average.h index ca00c5c40..ee401f547 100644 --- a/alg/teca_temporal_average.h +++ b/alg/teca_temporal_average.h @@ -29,17 +29,28 @@ class teca_temporal_average : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the number of steps to average. should be odd. + /** @anchor filter_width + * @name filter_width + * Set the number of steps to average. should be odd. + */ + ///@{ TECA_ALGORITHM_PROPERTY(unsigned int, filter_width) + ///@} - - // select the filter stencil, default is backward + /** filter stencil types */ enum { backward, centered, forward }; + + /** @anchor filter_type + * @name filter_type + * Select the filter stencil, default is backward. + */ + ///@{ TECA_ALGORITHM_PROPERTY(int, filter_type) + ///@} protected: teca_temporal_average(); diff --git a/alg/teca_vorticity.h b/alg/teca_vorticity.h index 7ac3226f6..eab2d4f0d 100644 --- a/alg/teca_vorticity.h +++ b/alg/teca_vorticity.h @@ -27,14 +27,32 @@ class teca_vorticity : public teca_algorithm TECA_GET_ALGORITHM_PROPERTIES_DESCRIPTION() TECA_SET_ALGORITHM_PROPERTIES() - // set the arrays that contain the vector components - // to compute vorticity from + /** @anchor component_0_variable + * @name component_0_variable + * Set the 1st array that contains the vector components + * to compute vorticity from + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_0_variable) + ///@} + + /** @anchor component_1_variable + * @name component_1_variable + * Set the 2nd array that contains the vector components + * to compute vorticity from + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, component_1_variable) + ///@} - // set the name of the array to store the result in. - // the default is "vorticity" + /** @anchor vorticity_variable + * @name vorticity_variable + * Set the name of the array to store the result in. + * the default is "vorticity" + */ + ///@{ TECA_ALGORITHM_PROPERTY(std::string, vorticity_variable) + ///@} protected: teca_vorticity(); diff --git a/core/teca_algorithm_fwd.h b/core/teca_algorithm_fwd.h index ee0a58b21..294199245 100644 --- a/core/teca_algorithm_fwd.h +++ b/core/teca_algorithm_fwd.h @@ -32,6 +32,7 @@ std::shared_ptr shared_from_this() const \ } #define TECA_ALGORITHM_CLASS_NAME(T) \ +/** returns the string value "T" */ \ const char *get_class_name() const override \ { \ return #T; \ @@ -50,90 +51,102 @@ const char *get_class_name() const override \ // convenience macro to declare standard set_X/get_X methods // where X is the name of a class member. will manage the // algorithm's modified state for the user. -#define TECA_ALGORITHM_PROPERTY(T, NAME) \ - \ -void set_##NAME(const T &v) \ -{ \ - if (this->NAME != v) \ - { \ - this->NAME = v; \ - this->set_modified(); \ - } \ -} \ - \ -const T &get_##NAME() const \ -{ \ - return this->NAME; \ +#define TECA_ALGORITHM_PROPERTY(T, NAME) \ + \ +/** Set the @ref NAME algorithm property */ \ +void set_##NAME(const T &v) \ +{ \ + if (this->NAME != v) \ + { \ + this->NAME = v; \ + this->set_modified(); \ + } \ +} \ + \ +/** Get the @ref NAME algorithm property */ \ +const T &get_##NAME() const \ +{ \ + return this->NAME; \ } // convenience macro to declare standard set_X/get_X methods // where X is the name of a class member. will manage the // algorithm's modified state for the user. -#define TECA_ALGORITHM_VECTOR_PROPERTY(T, NAME) \ - \ -size_t get_number_of_##NAME##s () \ -{ \ - return this->NAME##s.size(); \ -} \ - \ -void append_##NAME(const T &v) \ -{ \ - this->NAME##s.push_back(v); \ - this->set_modified(); \ -} \ - \ -void set_##NAME(size_t i, const T &v) \ -{ \ - if (this->NAME##s[i] != v) \ - { \ - this->NAME##s[i] = v; \ - this->set_modified(); \ - } \ -} \ - \ -void set_##NAME##s(const std::vector &v) \ -{ \ - if (this->NAME##s != v) \ - { \ - this->NAME##s = v; \ - this->set_modified(); \ - } \ -} \ - \ -void set_##NAME##s(const std::initializer_list &&l) \ -{ \ - std::vector v(l); \ - if (this->NAME##s != v) \ - { \ - this->NAME##s = v; \ - this->set_modified(); \ - } \ -} \ - \ -void set_##NAME##s(const const_p_teca_variant_array &v) \ -{ \ - v->get(this->NAME##s); \ - this->set_modified(); \ -} \ - \ -const T &get_##NAME(size_t i) const \ -{ \ - return this->NAME##s[i]; \ -} \ - \ -void get_##NAME##s(std::vector &v) const \ -{ \ - v = this->NAME##s; \ -} \ - \ -void get_##NAME##s(const p_teca_variant_array &v) const \ -{ \ - v->set(this->NAME##s); \ -} \ - \ -void clear_##NAME##s() \ -{ \ - this->NAME##s.clear(); \ +#define TECA_ALGORITHM_VECTOR_PROPERTY(T, NAME) \ + \ +/** get the size of the @ref NAME##s algorithm vector property */ \ +size_t get_number_of_##NAME##s () \ +{ \ + return this->NAME##s.size(); \ +} \ + \ +/** append to the @ref NAME##s algorithm vector property */ \ +void append_##NAME(const T &v) \ +{ \ + this->NAME##s.push_back(v); \ + this->set_modified(); \ +} \ + \ +/** set the i-th element of the @ref NAME##s algorithm vector property */ \ +void set_##NAME(size_t i, const T &v) \ +{ \ + if (this->NAME##s[i] != v) \ + { \ + this->NAME##s[i] = v; \ + this->set_modified(); \ + } \ +} \ + \ +/** set the @ref NAME##s algorithm vector property */ \ +void set_##NAME##s(const std::vector &v) \ +{ \ + if (this->NAME##s != v) \ + { \ + this->NAME##s = v; \ + this->set_modified(); \ + } \ +} \ + \ +/** set the @ref NAME##s algorithm vector property */ \ +void set_##NAME##s(const std::initializer_list &&l) \ +{ \ + std::vector v(l); \ + if (this->NAME##s != v) \ + { \ + this->NAME##s = v; \ + this->set_modified(); \ + } \ +} \ + \ +/** set the @ref NAME##s algorithm vector property */ \ +void set_##NAME##s(const const_p_teca_variant_array &v) \ +{ \ + v->get(this->NAME##s); \ + this->set_modified(); \ +} \ + \ +/** get the i-th element of the @ref NAME##s algorithm vector property */ \ +const T &get_##NAME(size_t i) const \ +{ \ + return this->NAME##s[i]; \ +} \ + \ +/** get the @ref NAME##s algorithm vector property */ \ +void get_##NAME##s(std::vector &v) const \ +{ \ + v = this->NAME##s; \ +} \ + \ +/** set the @ref NAME##s algorithm vector property */ \ +void get_##NAME##s(const p_teca_variant_array &v) const \ +{ \ + v->set(this->NAME##s); \ +} \ + \ +/** clear the @ref NAME##s algorithm vector property */ \ +void clear_##NAME##s() \ +{ \ + this->NAME##s.clear(); \ } diff --git a/doc/doxygen/Doxyfile b/doc/doxygen/Doxyfile new file mode 100644 index 000000000..adcd68786 --- /dev/null +++ b/doc/doxygen/Doxyfile @@ -0,0 +1,2568 @@ +# Doxyfile 1.8.20 + +# This file describes the settings to be used by the documentation system +# doxygen (www.doxygen.org) for a project. +# +# All text after a double hash (##) is considered a comment and is placed in +# front of the TAG it is preceding. +# +# All text after a single hash (#) is considered a comment and will be ignored. +# The format is: +# TAG = value [value, ...] +# For lists, items can also be appended using: +# TAG += value [value, ...] +# Values that contain spaces should be placed between quotes (\" \"). + +#--------------------------------------------------------------------------- +# Project related configuration options +#--------------------------------------------------------------------------- + +# This tag specifies the encoding used for all characters in the configuration +# file that follow. The default is UTF-8 which is also the encoding used for all +# text before the first occurrence of this tag. Doxygen uses libiconv (or the +# iconv built into libc) for the transcoding. See +# https://www.gnu.org/software/libiconv/ for the list of possible encodings. +# The default value is: UTF-8. + +DOXYFILE_ENCODING = UTF-8 + +# The PROJECT_NAME tag is a single word (or a sequence of words surrounded by +# double-quotes, unless you are using Doxywizard) that should identify the +# project for which the documentation is generated. This name is used in the +# title of most generated pages and in a few other places. +# The default value is: My Project. + +PROJECT_NAME = "TECA" + +# The PROJECT_NUMBER tag can be used to enter a project or revision number. This +# could be handy for archiving the generated documentation or if some version +# control system is used. + +PROJECT_NUMBER = + +# Using the PROJECT_BRIEF tag one can provide an optional one line description +# for a project that appears at the top of each page and should give viewer a +# quick idea about the purpose of the project. Keep the description short. + +PROJECT_BRIEF = + +# With the PROJECT_LOGO tag one can specify a logo or an icon that is included +# in the documentation. The maximum height of the logo should not exceed 55 +# pixels and the maximum width should not exceed 200 pixels. Doxygen will copy +# the logo to the output directory. + +PROJECT_LOGO = + +# The OUTPUT_DIRECTORY tag is used to specify the (relative or absolute) path +# into which the generated documentation will be written. If a relative path is +# entered, it will be relative to the location where doxygen was started. If +# left blank the current directory will be used. + +OUTPUT_DIRECTORY = + +# If the CREATE_SUBDIRS tag is set to YES then doxygen will create 4096 sub- +# directories (in 2 levels) under the output directory of each output format and +# will distribute the generated files over these directories. Enabling this +# option can be useful when feeding doxygen a huge amount of source files, where +# putting all generated files in the same directory would otherwise causes +# performance problems for the file system. +# The default value is: NO. + +CREATE_SUBDIRS = NO + +# If the ALLOW_UNICODE_NAMES tag is set to YES, doxygen will allow non-ASCII +# characters to appear in the names of generated files. If set to NO, non-ASCII +# characters will be escaped, for example _xE3_x81_x84 will be used for Unicode +# U+3044. +# The default value is: NO. + +ALLOW_UNICODE_NAMES = NO + +# The OUTPUT_LANGUAGE tag is used to specify the language in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all constant output in the proper language. +# Possible values are: Afrikaans, Arabic, Armenian, Brazilian, Catalan, Chinese, +# Chinese-Traditional, Croatian, Czech, Danish, Dutch, English (United States), +# Esperanto, Farsi (Persian), Finnish, French, German, Greek, Hungarian, +# Indonesian, Italian, Japanese, Japanese-en (Japanese with English messages), +# Korean, Korean-en (Korean with English messages), Latvian, Lithuanian, +# Macedonian, Norwegian, Persian (Farsi), Polish, Portuguese, Romanian, Russian, +# Serbian, Serbian-Cyrillic, Slovak, Slovene, Spanish, Swedish, Turkish, +# Ukrainian and Vietnamese. +# The default value is: English. + +OUTPUT_LANGUAGE = English + +# The OUTPUT_TEXT_DIRECTION tag is used to specify the direction in which all +# documentation generated by doxygen is written. Doxygen will use this +# information to generate all generated output in the proper direction. +# Possible values are: None, LTR, RTL and Context. +# The default value is: None. + +OUTPUT_TEXT_DIRECTION = None + +# If the BRIEF_MEMBER_DESC tag is set to YES, doxygen will include brief member +# descriptions after the members that are listed in the file and class +# documentation (similar to Javadoc). Set to NO to disable this. +# The default value is: YES. + +BRIEF_MEMBER_DESC = YES + +# If the REPEAT_BRIEF tag is set to YES, doxygen will prepend the brief +# description of a member or function before the detailed description +# +# Note: If both HIDE_UNDOC_MEMBERS and BRIEF_MEMBER_DESC are set to NO, the +# brief descriptions will be completely suppressed. +# The default value is: YES. + +REPEAT_BRIEF = YES + +# This tag implements a quasi-intelligent brief description abbreviator that is +# used to form the text in various listings. Each string in this list, if found +# as the leading text of the brief description, will be stripped from the text +# and the result, after processing the whole list, is used as the annotated +# text. Otherwise, the brief description is used as-is. If left blank, the +# following values are used ($name is automatically replaced with the name of +# the entity):The $name class, The $name widget, The $name file, is, provides, +# specifies, contains, represents, a, an and the. + +ABBREVIATE_BRIEF = "The $name class" \ + "The $name widget" \ + "The $name file" \ + is \ + provides \ + specifies \ + contains \ + represents \ + a \ + an \ + the + +# If the ALWAYS_DETAILED_SEC and REPEAT_BRIEF tags are both set to YES then +# doxygen will generate a detailed section even if there is only a brief +# description. +# The default value is: NO. + +ALWAYS_DETAILED_SEC = NO + +# If the INLINE_INHERITED_MEMB tag is set to YES, doxygen will show all +# inherited members of a class in the documentation of that class as if those +# members were ordinary class members. Constructors, destructors and assignment +# operators of the base classes will not be shown. +# The default value is: NO. + +INLINE_INHERITED_MEMB = NO + +# If the FULL_PATH_NAMES tag is set to YES, doxygen will prepend the full path +# before files name in the file list and in the header files. If set to NO the +# shortest path that makes the file name unique will be used +# The default value is: YES. + +FULL_PATH_NAMES = YES + +# The STRIP_FROM_PATH tag can be used to strip a user-defined part of the path. +# Stripping is only done if one of the specified strings matches the left-hand +# part of the path. The tag can be used to show relative paths in the file list. +# If left blank the directory from which doxygen is run is used as the path to +# strip. +# +# Note that you can specify absolute paths here, but also relative paths, which +# will be relative from the directory where doxygen is started. +# This tag requires that the tag FULL_PATH_NAMES is set to YES. + +STRIP_FROM_PATH = + +# The STRIP_FROM_INC_PATH tag can be used to strip a user-defined part of the +# path mentioned in the documentation of a class, which tells the reader which +# header file to include in order to use a class. If left blank only the name of +# the header file containing the class definition is used. Otherwise one should +# specify the list of include paths that are normally passed to the compiler +# using the -I flag. + +STRIP_FROM_INC_PATH = + +# If the SHORT_NAMES tag is set to YES, doxygen will generate much shorter (but +# less readable) file names. This can be useful is your file systems doesn't +# support long names like on DOS, Mac, or CD-ROM. +# The default value is: NO. + +SHORT_NAMES = NO + +# If the JAVADOC_AUTOBRIEF tag is set to YES then doxygen will interpret the +# first line (until the first dot) of a Javadoc-style comment as the brief +# description. If set to NO, the Javadoc-style will behave just like regular Qt- +# style comments (thus requiring an explicit @brief command for a brief +# description.) +# The default value is: NO. + +JAVADOC_AUTOBRIEF = NO + +# If the JAVADOC_BANNER tag is set to YES then doxygen will interpret a line +# such as +# /*************** +# as being the beginning of a Javadoc-style comment "banner". If set to NO, the +# Javadoc-style will behave just like regular comments and it will not be +# interpreted by doxygen. +# The default value is: NO. + +JAVADOC_BANNER = NO + +# If the QT_AUTOBRIEF tag is set to YES then doxygen will interpret the first +# line (until the first dot) of a Qt-style comment as the brief description. If +# set to NO, the Qt-style will behave just like regular Qt-style comments (thus +# requiring an explicit \brief command for a brief description.) +# The default value is: NO. + +QT_AUTOBRIEF = NO + +# The MULTILINE_CPP_IS_BRIEF tag can be set to YES to make doxygen treat a +# multi-line C++ special comment block (i.e. a block of //! or /// comments) as +# a brief description. This used to be the default behavior. The new default is +# to treat a multi-line C++ comment block as a detailed description. Set this +# tag to YES if you prefer the old behavior instead. +# +# Note that setting this tag to YES also means that rational rose comments are +# not recognized any more. +# The default value is: NO. + +MULTILINE_CPP_IS_BRIEF = NO + +# By default Python docstrings are displayed as preformatted text and doxygen's +# special commands cannot be used. By setting PYTHON_DOCSTRING to NO the +# doxygen's special commands can be used and the contents of the docstring +# documentation blocks is shown as doxygen documentation. +# The default value is: YES. + +PYTHON_DOCSTRING = YES + +# If the INHERIT_DOCS tag is set to YES then an undocumented member inherits the +# documentation from any documented member that it re-implements. +# The default value is: YES. + +INHERIT_DOCS = YES + +# If the SEPARATE_MEMBER_PAGES tag is set to YES then doxygen will produce a new +# page for each member. If set to NO, the documentation of a member will be part +# of the file/class/namespace that contains it. +# The default value is: NO. + +SEPARATE_MEMBER_PAGES = NO + +# The TAB_SIZE tag can be used to set the number of spaces in a tab. Doxygen +# uses this value to replace tabs by spaces in code fragments. +# Minimum value: 1, maximum value: 16, default value: 4. + +TAB_SIZE = 4 + +# This tag can be used to specify a number of aliases that act as commands in +# the documentation. An alias has the form: +# name=value +# For example adding +# "sideeffect=@par Side Effects:\n" +# will allow you to put the command \sideeffect (or @sideeffect) in the +# documentation, which will result in a user-defined paragraph with heading +# "Side Effects:". You can put \n's in the value part of an alias to insert +# newlines (in the resulting output). You can put ^^ in the value part of an +# alias to insert a newline as if a physical newline was in the original file. +# When you need a literal { or } or , in the value part of an alias you have to +# escape them by means of a backslash (\), this can lead to conflicts with the +# commands \{ and \} for these it is advised to use the version @{ and @} or use +# a double escape (\\{ and \\}) + +ALIASES = + +# Set the OPTIMIZE_OUTPUT_FOR_C tag to YES if your project consists of C sources +# only. Doxygen will then generate output that is more tailored for C. For +# instance, some of the names that are used will be different. The list of all +# members will be omitted, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_FOR_C = NO + +# Set the OPTIMIZE_OUTPUT_JAVA tag to YES if your project consists of Java or +# Python sources only. Doxygen will then generate output that is more tailored +# for that language. For instance, namespaces will be presented as packages, +# qualified scopes will look different, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_JAVA = NO + +# Set the OPTIMIZE_FOR_FORTRAN tag to YES if your project consists of Fortran +# sources. Doxygen will then generate output that is tailored for Fortran. +# The default value is: NO. + +OPTIMIZE_FOR_FORTRAN = NO + +# Set the OPTIMIZE_OUTPUT_VHDL tag to YES if your project consists of VHDL +# sources. Doxygen will then generate output that is tailored for VHDL. +# The default value is: NO. + +OPTIMIZE_OUTPUT_VHDL = NO + +# Set the OPTIMIZE_OUTPUT_SLICE tag to YES if your project consists of Slice +# sources only. Doxygen will then generate output that is more tailored for that +# language. For instance, namespaces will be presented as modules, types will be +# separated into more groups, etc. +# The default value is: NO. + +OPTIMIZE_OUTPUT_SLICE = NO + +# Doxygen selects the parser to use depending on the extension of the files it +# parses. With this tag you can assign which parser to use for a given +# extension. Doxygen has a built-in mapping, but you can override or extend it +# using this tag. The format is ext=language, where ext is a file extension, and +# language is one of the parsers supported by doxygen: IDL, Java, JavaScript, +# Csharp (C#), C, C++, D, PHP, md (Markdown), Objective-C, Python, Slice, VHDL, +# Fortran (fixed format Fortran: FortranFixed, free formatted Fortran: +# FortranFree, unknown formatted Fortran: Fortran. In the later case the parser +# tries to guess whether the code is fixed or free formatted code, this is the +# default for Fortran type files). For instance to make doxygen treat .inc files +# as Fortran files (default is PHP), and .f files as C (default is Fortran), +# use: inc=Fortran f=C. +# +# Note: For files without extension you can use no_extension as a placeholder. +# +# Note that for custom extensions you also need to set FILE_PATTERNS otherwise +# the files are not read by doxygen. + +EXTENSION_MAPPING = + +# If the MARKDOWN_SUPPORT tag is enabled then doxygen pre-processes all comments +# according to the Markdown format, which allows for more readable +# documentation. See https://daringfireball.net/projects/markdown/ for details. +# The output of markdown processing is further processed by doxygen, so you can +# mix doxygen, HTML, and XML commands with Markdown formatting. Disable only in +# case of backward compatibilities issues. +# The default value is: YES. + +MARKDOWN_SUPPORT = YES + +# When the TOC_INCLUDE_HEADINGS tag is set to a non-zero value, all headings up +# to that level are automatically included in the table of contents, even if +# they do not have an id attribute. +# Note: This feature currently applies only to Markdown headings. +# Minimum value: 0, maximum value: 99, default value: 5. +# This tag requires that the tag MARKDOWN_SUPPORT is set to YES. + +TOC_INCLUDE_HEADINGS = 5 + +# When enabled doxygen tries to link words that correspond to documented +# classes, or namespaces to their corresponding documentation. Such a link can +# be prevented in individual cases by putting a % sign in front of the word or +# globally by setting AUTOLINK_SUPPORT to NO. +# The default value is: YES. + +AUTOLINK_SUPPORT = YES + +# If you use STL classes (i.e. std::string, std::vector, etc.) but do not want +# to include (a tag file for) the STL sources as input, then you should set this +# tag to YES in order to let doxygen match functions declarations and +# definitions whose arguments contain STL classes (e.g. func(std::string); +# versus func(std::string) {}). This also make the inheritance and collaboration +# diagrams that involve STL classes more complete and accurate. +# The default value is: NO. + +BUILTIN_STL_SUPPORT = NO + +# If you use Microsoft's C++/CLI language, you should set this option to YES to +# enable parsing support. +# The default value is: NO. + +CPP_CLI_SUPPORT = NO + +# Set the SIP_SUPPORT tag to YES if your project consists of sip (see: +# https://www.riverbankcomputing.com/software/sip/intro) sources only. Doxygen +# will parse them like normal C++ but will assume all classes use public instead +# of private inheritance when no explicit protection keyword is present. +# The default value is: NO. + +SIP_SUPPORT = NO + +# For Microsoft's IDL there are propget and propput attributes to indicate +# getter and setter methods for a property. Setting this option to YES will make +# doxygen to replace the get and set methods by a property in the documentation. +# This will only work if the methods are indeed getting or setting a simple +# type. If this is not the case, or you want to show the methods anyway, you +# should set this option to NO. +# The default value is: YES. + +IDL_PROPERTY_SUPPORT = YES + +# If member grouping is used in the documentation and the DISTRIBUTE_GROUP_DOC +# tag is set to YES then doxygen will reuse the documentation of the first +# member in the group (if any) for the other members of the group. By default +# all members of a group must be documented explicitly. +# The default value is: NO. + +DISTRIBUTE_GROUP_DOC = NO + +# If one adds a struct or class to a group and this option is enabled, then also +# any nested class or struct is added to the same group. By default this option +# is disabled and one has to add nested compounds explicitly via \ingroup. +# The default value is: NO. + +GROUP_NESTED_COMPOUNDS = NO + +# Set the SUBGROUPING tag to YES to allow class member groups of the same type +# (for instance a group of public functions) to be put as a subgroup of that +# type (e.g. under the Public Functions section). Set it to NO to prevent +# subgrouping. Alternatively, this can be done per class using the +# \nosubgrouping command. +# The default value is: YES. + +SUBGROUPING = YES + +# When the INLINE_GROUPED_CLASSES tag is set to YES, classes, structs and unions +# are shown inside the group in which they are included (e.g. using \ingroup) +# instead of on a separate page (for HTML and Man pages) or section (for LaTeX +# and RTF). +# +# Note that this feature does not work in combination with +# SEPARATE_MEMBER_PAGES. +# The default value is: NO. + +INLINE_GROUPED_CLASSES = NO + +# When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions +# with only public data fields or simple typedef fields will be shown inline in +# the documentation of the scope in which they are defined (i.e. file, +# namespace, or group documentation), provided this scope is documented. If set +# to NO, structs, classes, and unions are shown on a separate page (for HTML and +# Man pages) or section (for LaTeX and RTF). +# The default value is: NO. + +INLINE_SIMPLE_STRUCTS = NO + +# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or +# enum is documented as struct, union, or enum with the name of the typedef. So +# typedef struct TypeS {} TypeT, will appear in the documentation as a struct +# with name TypeT. When disabled the typedef will appear as a member of a file, +# namespace, or class. And the struct will be named TypeS. This can typically be +# useful for C code in case the coding convention dictates that all compound +# types are typedef'ed and only the typedef is referenced, never the tag name. +# The default value is: NO. + +TYPEDEF_HIDES_STRUCT = NO + +# The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This +# cache is used to resolve symbols given their name and scope. Since this can be +# an expensive process and often the same symbol appears multiple times in the +# code, doxygen keeps a cache of pre-resolved symbols. If the cache is too small +# doxygen will become slower. If the cache is too large, memory is wasted. The +# cache size is given by this formula: 2^(16+LOOKUP_CACHE_SIZE). The valid range +# is 0..9, the default is 0, corresponding to a cache size of 2^16=65536 +# symbols. At the end of a run doxygen will report the cache usage and suggest +# the optimal cache size from a speed point of view. +# Minimum value: 0, maximum value: 9, default value: 0. + +LOOKUP_CACHE_SIZE = 0 + +# The NUM_PROC_THREADS specifies the number threads doxygen is allowed to use +# during processing. When set to 0 doxygen will based this on the number of +# cores available in the system. You can set it explicitly to a value larger +# than 0 to get more control over the balance between CPU load and processing +# speed. At this moment only the input processing can be done using multiple +# threads. Since this is still an experimental feature the default is set to 1, +# which efficively disables parallel processing. Please report any issues you +# encounter. Generating dot graphs in parallel is controlled by the +# DOT_NUM_THREADS setting. +# Minimum value: 0, maximum value: 32, default value: 1. + +NUM_PROC_THREADS = 1 + +#--------------------------------------------------------------------------- +# Build related configuration options +#--------------------------------------------------------------------------- + +# If the EXTRACT_ALL tag is set to YES, doxygen will assume all entities in +# documentation are documented, even if no documentation was available. Private +# class members and static file members will be hidden unless the +# EXTRACT_PRIVATE respectively EXTRACT_STATIC tags are set to YES. +# Note: This will also disable the warnings about undocumented members that are +# normally produced when WARNINGS is set to YES. +# The default value is: NO. + +EXTRACT_ALL = NO +#EXTRACT_ALL = YES + +# If the EXTRACT_PRIVATE tag is set to YES, all private members of a class will +# be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIVATE = NO + +# If the EXTRACT_PRIV_VIRTUAL tag is set to YES, documented private virtual +# methods of a class will be included in the documentation. +# The default value is: NO. + +EXTRACT_PRIV_VIRTUAL = NO + +# If the EXTRACT_PACKAGE tag is set to YES, all members with package or internal +# scope will be included in the documentation. +# The default value is: NO. + +EXTRACT_PACKAGE = NO + +# If the EXTRACT_STATIC tag is set to YES, all static members of a file will be +# included in the documentation. +# The default value is: NO. + +EXTRACT_STATIC = NO + +# If the EXTRACT_LOCAL_CLASSES tag is set to YES, classes (and structs) defined +# locally in source files will be included in the documentation. If set to NO, +# only classes defined in header files are included. Does not have any effect +# for Java sources. +# The default value is: YES. + +EXTRACT_LOCAL_CLASSES = YES + +# This flag is only useful for Objective-C code. If set to YES, local methods, +# which are defined in the implementation section but not in the interface are +# included in the documentation. If set to NO, only methods in the interface are +# included. +# The default value is: NO. + +EXTRACT_LOCAL_METHODS = NO + +# If this flag is set to YES, the members of anonymous namespaces will be +# extracted and appear in the documentation as a namespace called +# 'anonymous_namespace{file}', where file will be replaced with the base name of +# the file that contains the anonymous namespace. By default anonymous namespace +# are hidden. +# The default value is: NO. + +EXTRACT_ANON_NSPACES = NO + +# If the HIDE_UNDOC_MEMBERS tag is set to YES, doxygen will hide all +# undocumented members inside documented classes or files. If set to NO these +# members will be included in the various overviews, but no documentation +# section is generated. This option has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_MEMBERS = NO + +# If the HIDE_UNDOC_CLASSES tag is set to YES, doxygen will hide all +# undocumented classes that are normally visible in the class hierarchy. If set +# to NO, these classes will be included in the various overviews. This option +# has no effect if EXTRACT_ALL is enabled. +# The default value is: NO. + +HIDE_UNDOC_CLASSES = NO + +# If the HIDE_FRIEND_COMPOUNDS tag is set to YES, doxygen will hide all friend +# declarations. If set to NO, these declarations will be included in the +# documentation. +# The default value is: NO. + +HIDE_FRIEND_COMPOUNDS = NO + +# If the HIDE_IN_BODY_DOCS tag is set to YES, doxygen will hide any +# documentation blocks found inside the body of a function. If set to NO, these +# blocks will be appended to the function's detailed documentation block. +# The default value is: NO. + +HIDE_IN_BODY_DOCS = NO + +# The INTERNAL_DOCS tag determines if documentation that is typed after a +# \internal command is included. If the tag is set to NO then the documentation +# will be excluded. Set it to YES to include the internal documentation. +# The default value is: NO. + +INTERNAL_DOCS = NO + +# If the CASE_SENSE_NAMES tag is set to NO then doxygen will only generate file +# names in lower-case letters. If set to YES, upper-case letters are also +# allowed. This is useful if you have classes or files whose names only differ +# in case and if your file system supports case sensitive file names. Windows +# (including Cygwin) and Mac users are advised to set this option to NO. +# The default value is: system dependent. + +CASE_SENSE_NAMES = NO + +# If the HIDE_SCOPE_NAMES tag is set to NO then doxygen will show members with +# their full class and namespace scopes in the documentation. If set to YES, the +# scope will be hidden. +# The default value is: NO. + +HIDE_SCOPE_NAMES = NO + +# If the HIDE_COMPOUND_REFERENCE tag is set to NO (default) then doxygen will +# append additional text to a page's title, such as Class Reference. If set to +# YES the compound reference will be hidden. +# The default value is: NO. + +HIDE_COMPOUND_REFERENCE= NO + +# If the SHOW_INCLUDE_FILES tag is set to YES then doxygen will put a list of +# the files that are included by a file in the documentation of that file. +# The default value is: YES. + +SHOW_INCLUDE_FILES = YES + +# If the SHOW_GROUPED_MEMB_INC tag is set to YES then Doxygen will add for each +# grouped member an include statement to the documentation, telling the reader +# which file to include in order to use the member. +# The default value is: NO. + +SHOW_GROUPED_MEMB_INC = NO + +# If the FORCE_LOCAL_INCLUDES tag is set to YES then doxygen will list include +# files with double quotes in the documentation rather than with sharp brackets. +# The default value is: NO. + +FORCE_LOCAL_INCLUDES = NO + +# If the INLINE_INFO tag is set to YES then a tag [inline] is inserted in the +# documentation for inline members. +# The default value is: YES. + +INLINE_INFO = YES + +# If the SORT_MEMBER_DOCS tag is set to YES then doxygen will sort the +# (detailed) documentation of file and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. +# The default value is: YES. + +SORT_MEMBER_DOCS = YES + +# If the SORT_BRIEF_DOCS tag is set to YES then doxygen will sort the brief +# descriptions of file, namespace and class members alphabetically by member +# name. If set to NO, the members will appear in declaration order. Note that +# this will also influence the order of the classes in the class list. +# The default value is: NO. + +SORT_BRIEF_DOCS = NO + +# If the SORT_MEMBERS_CTORS_1ST tag is set to YES then doxygen will sort the +# (brief and detailed) documentation of class members so that constructors and +# destructors are listed first. If set to NO the constructors will appear in the +# respective orders defined by SORT_BRIEF_DOCS and SORT_MEMBER_DOCS. +# Note: If SORT_BRIEF_DOCS is set to NO this option is ignored for sorting brief +# member documentation. +# Note: If SORT_MEMBER_DOCS is set to NO this option is ignored for sorting +# detailed member documentation. +# The default value is: NO. + +SORT_MEMBERS_CTORS_1ST = NO + +# If the SORT_GROUP_NAMES tag is set to YES then doxygen will sort the hierarchy +# of group names into alphabetical order. If set to NO the group names will +# appear in their defined order. +# The default value is: NO. + +SORT_GROUP_NAMES = NO + +# If the SORT_BY_SCOPE_NAME tag is set to YES, the class list will be sorted by +# fully-qualified names, including namespaces. If set to NO, the class list will +# be sorted only by class name, not including the namespace part. +# Note: This option is not very useful if HIDE_SCOPE_NAMES is set to YES. +# Note: This option applies only to the class list, not to the alphabetical +# list. +# The default value is: NO. + +SORT_BY_SCOPE_NAME = NO + +# If the STRICT_PROTO_MATCHING option is enabled and doxygen fails to do proper +# type resolution of all parameters of a function it will reject a match between +# the prototype and the implementation of a member function even if there is +# only one candidate or it is obvious which candidate to choose by doing a +# simple string match. By disabling STRICT_PROTO_MATCHING doxygen will still +# accept a match between prototype and implementation in such cases. +# The default value is: NO. + +STRICT_PROTO_MATCHING = NO + +# The GENERATE_TODOLIST tag can be used to enable (YES) or disable (NO) the todo +# list. This list is created by putting \todo commands in the documentation. +# The default value is: YES. + +GENERATE_TODOLIST = YES + +# The GENERATE_TESTLIST tag can be used to enable (YES) or disable (NO) the test +# list. This list is created by putting \test commands in the documentation. +# The default value is: YES. + +GENERATE_TESTLIST = YES + +# The GENERATE_BUGLIST tag can be used to enable (YES) or disable (NO) the bug +# list. This list is created by putting \bug commands in the documentation. +# The default value is: YES. + +GENERATE_BUGLIST = YES + +# The GENERATE_DEPRECATEDLIST tag can be used to enable (YES) or disable (NO) +# the deprecated list. This list is created by putting \deprecated commands in +# the documentation. +# The default value is: YES. + +GENERATE_DEPRECATEDLIST= YES + +# The ENABLED_SECTIONS tag can be used to enable conditional documentation +# sections, marked by \if ... \endif and \cond +# ... \endcond blocks. + +ENABLED_SECTIONS = + +# The MAX_INITIALIZER_LINES tag determines the maximum number of lines that the +# initial value of a variable or macro / define can have for it to appear in the +# documentation. If the initializer consists of more lines than specified here +# it will be hidden. Use a value of 0 to hide initializers completely. The +# appearance of the value of individual variables and macros / defines can be +# controlled using \showinitializer or \hideinitializer command in the +# documentation regardless of this setting. +# Minimum value: 0, maximum value: 10000, default value: 30. + +MAX_INITIALIZER_LINES = 30 + +# Set the SHOW_USED_FILES tag to NO to disable the list of files generated at +# the bottom of the documentation of classes and structs. If set to YES, the +# list will mention the files that were used to generate the documentation. +# The default value is: YES. + +SHOW_USED_FILES = YES + +# Set the SHOW_FILES tag to NO to disable the generation of the Files page. This +# will remove the Files entry from the Quick Index and from the Folder Tree View +# (if specified). +# The default value is: YES. + +SHOW_FILES = YES + +# Set the SHOW_NAMESPACES tag to NO to disable the generation of the Namespaces +# page. This will remove the Namespaces entry from the Quick Index and from the +# Folder Tree View (if specified). +# The default value is: YES. + +SHOW_NAMESPACES = YES + +# The FILE_VERSION_FILTER tag can be used to specify a program or script that +# doxygen should invoke to get the current version for each file (typically from +# the version control system). Doxygen will invoke the program by executing (via +# popen()) the command command input-file, where command is the value of the +# FILE_VERSION_FILTER tag, and input-file is the name of an input file provided +# by doxygen. Whatever the program writes to standard output is used as the file +# version. For an example see the documentation. + +FILE_VERSION_FILTER = + +# The LAYOUT_FILE tag can be used to specify a layout file which will be parsed +# by doxygen. The layout file controls the global structure of the generated +# output files in an output format independent way. To create the layout file +# that represents doxygen's defaults, run doxygen with the -l option. You can +# optionally specify a file name after the option, if omitted DoxygenLayout.xml +# will be used as the name of the layout file. +# +# Note that if you run doxygen from a directory containing a file called +# DoxygenLayout.xml, doxygen will parse it automatically even if the LAYOUT_FILE +# tag is left empty. + +LAYOUT_FILE = + +# The CITE_BIB_FILES tag can be used to specify one or more bib files containing +# the reference definitions. This must be a list of .bib files. The .bib +# extension is automatically appended if omitted. This requires the bibtex tool +# to be installed. See also https://en.wikipedia.org/wiki/BibTeX for more info. +# For LaTeX the style of the bibliography can be controlled using +# LATEX_BIB_STYLE. To use this feature you need bibtex and perl available in the +# search path. See also \cite for info how to create references. + +CITE_BIB_FILES = + +#--------------------------------------------------------------------------- +# Configuration options related to warning and progress messages +#--------------------------------------------------------------------------- + +# The QUIET tag can be used to turn on/off the messages that are generated to +# standard output by doxygen. If QUIET is set to YES this implies that the +# messages are off. +# The default value is: NO. + +QUIET = NO + +# The WARNINGS tag can be used to turn on/off the warning messages that are +# generated to standard error (stderr) by doxygen. If WARNINGS is set to YES +# this implies that the warnings are on. +# +# Tip: Turn warnings on while writing the documentation. +# The default value is: YES. + +WARNINGS = YES + +# If the WARN_IF_UNDOCUMENTED tag is set to YES then doxygen will generate +# warnings for undocumented members. If EXTRACT_ALL is set to YES then this flag +# will automatically be disabled. +# The default value is: YES. + +WARN_IF_UNDOCUMENTED = YES + +# If the WARN_IF_DOC_ERROR tag is set to YES, doxygen will generate warnings for +# potential errors in the documentation, such as not documenting some parameters +# in a documented function, or documenting parameters that don't exist or using +# markup commands wrongly. +# The default value is: YES. + +WARN_IF_DOC_ERROR = YES + +# This WARN_NO_PARAMDOC option can be enabled to get warnings for functions that +# are documented, but have no documentation for their parameters or return +# value. If set to NO, doxygen will only warn about wrong or incomplete +# parameter documentation, but not about the absence of documentation. If +# EXTRACT_ALL is set to YES then this flag will automatically be disabled. +# The default value is: NO. + +WARN_NO_PARAMDOC = NO + +# If the WARN_AS_ERROR tag is set to YES then doxygen will immediately stop when +# a warning is encountered. +# The default value is: NO. + +WARN_AS_ERROR = NO + +# The WARN_FORMAT tag determines the format of the warning messages that doxygen +# can produce. The string should contain the $file, $line, and $text tags, which +# will be replaced by the file and line number from which the warning originated +# and the warning text. Optionally the format may contain $version, which will +# be replaced by the version of the file (if it could be obtained via +# FILE_VERSION_FILTER) +# The default value is: $file:$line: $text. + +WARN_FORMAT = "$file:$line: $text" + +# The WARN_LOGFILE tag can be used to specify a file to which warning and error +# messages should be written. If left blank the output is written to standard +# error (stderr). + +WARN_LOGFILE = + +#--------------------------------------------------------------------------- +# Configuration options related to the input files +#--------------------------------------------------------------------------- + +# The INPUT tag is used to specify the files and/or directories that contain +# documented source files. You may enter file names like myfile.cpp or +# directories like /usr/src/myproject. Separate the files or directories with +# spaces. See also FILE_PATTERNS and EXTENSION_MAPPING +# Note: If this tag is empty the current directory is searched. + +INPUT = ../../alg/teca_2d_component_area.h \ + ../../alg/teca_bayesian_ar_detect.h \ + ../../alg/teca_binary_segmentation.h \ + ../../alg/teca_cartesian_mesh_regrid.h \ + ../../alg/teca_cartesian_mesh_source.h \ + ../../alg/teca_component_area_filter.h \ + ../../alg/teca_connected_components.h \ + ../../alg/teca_dataset_diff.h \ + ../../alg/teca_deeplab_ar_detect.py \ + ../../alg/teca_integrated_vapor_transport.h \ + ../../alg/teca_l2_norm.h \ + ../../alg/teca_latitude_damper.h \ + ../../alg/teca_normalize_coordinates.h \ + ../../alg/teca_table_reduce.h \ + ../../alg/teca_tc_candidates.h \ + ../../alg/teca_tc_trajectory.h \ + ../../alg/teca_tc_wind_radii.h \ + ../../alg/teca_temporal_average.h \ + ../../alg/teca_temporal_reduction.py \ + ../../alg/teca_vorticity.h +#INPUT = ../../alg/teca_2d_component_area.h +#INPUT = ../.. +#INPUT = + +# This tag can be used to specify the character encoding of the source files +# that doxygen parses. Internally doxygen uses the UTF-8 encoding. Doxygen uses +# libiconv (or the iconv built into libc) for the transcoding. See the libiconv +# documentation (see: https://www.gnu.org/software/libiconv/) for the list of +# possible encodings. +# The default value is: UTF-8. + +INPUT_ENCODING = UTF-8 + +# If the value of the INPUT tag contains directories, you can use the +# FILE_PATTERNS tag to specify one or more wildcard patterns (like *.cpp and +# *.h) to filter out the source-files in the directories. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# read by doxygen. +# +# If left blank the following patterns are tested:*.c, *.cc, *.cxx, *.cpp, +# *.c++, *.java, *.ii, *.ixx, *.ipp, *.i++, *.inl, *.idl, *.ddl, *.odl, *.h, +# *.hh, *.hxx, *.hpp, *.h++, *.cs, *.d, *.php, *.php4, *.php5, *.phtml, *.inc, +# *.m, *.markdown, *.md, *.mm, *.dox (to be provided as doxygen C comment), +# *.doc (to be provided as doxygen C comment), *.txt (to be provided as doxygen +# C comment), *.py, *.pyw, *.f90, *.f95, *.f03, *.f08, *.f18, *.f, *.for, *.vhd, +# *.vhdl, *.ucf, *.qsf and *.ice. + +FILE_PATTERNS = *.c \ + *.cc \ + *.cxx \ + *.cpp \ + *.c++ \ + *.h \ + *.hh \ + *.hxx \ + *.hpp \ + *.h++ \ + *.py + +# The RECURSIVE tag can be used to specify whether or not subdirectories should +# be searched for input files as well. +# The default value is: NO. + +RECURSIVE = YES + +# The EXCLUDE tag can be used to specify files and/or directories that should be +# excluded from the INPUT source files. This way you can easily exclude a +# subdirectory from a directory tree whose root is specified with the INPUT tag. +# +# Note that relative paths are relative to the directory from which doxygen is +# run. + +EXCLUDE = + +# The EXCLUDE_SYMLINKS tag can be used to select whether or not files or +# directories that are symbolic links (a Unix file system feature) are excluded +# from the input. +# The default value is: NO. + +EXCLUDE_SYMLINKS = NO + +# If the value of the INPUT tag contains directories, you can use the +# EXCLUDE_PATTERNS tag to specify one or more wildcard patterns to exclude +# certain files from those directories. +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories for example use the pattern */test/* + +EXCLUDE_PATTERNS = + +# The EXCLUDE_SYMBOLS tag can be used to specify one or more symbol names +# (namespaces, classes, functions, etc.) that should be excluded from the +# output. The symbol name can be a fully qualified name, a word, or if the +# wildcard * is used, a substring. Examples: ANamespace, AClass, +# AClass::ANamespace, ANamespace::*Test +# +# Note that the wildcards are matched against the file with absolute path, so to +# exclude all test directories use the pattern */test/* + +EXCLUDE_SYMBOLS = + +# The EXAMPLE_PATH tag can be used to specify one or more files or directories +# that contain example code fragments that are included (see the \include +# command). + +EXAMPLE_PATH = + +# If the value of the EXAMPLE_PATH tag contains directories, you can use the +# EXAMPLE_PATTERNS tag to specify one or more wildcard pattern (like *.cpp and +# *.h) to filter out the source-files in the directories. If left blank all +# files are included. + +EXAMPLE_PATTERNS = * + +# If the EXAMPLE_RECURSIVE tag is set to YES then subdirectories will be +# searched for input files to be used with the \include or \dontinclude commands +# irrespective of the value of the RECURSIVE tag. +# The default value is: NO. + +EXAMPLE_RECURSIVE = NO + +# The IMAGE_PATH tag can be used to specify one or more files or directories +# that contain images that are to be included in the documentation (see the +# \image command). + +IMAGE_PATH = + +# The INPUT_FILTER tag can be used to specify a program that doxygen should +# invoke to filter for each input file. Doxygen will invoke the filter program +# by executing (via popen()) the command: +# +# +# +# where is the value of the INPUT_FILTER tag, and is the +# name of an input file. Doxygen will then use the output that the filter +# program writes to standard output. If FILTER_PATTERNS is specified, this tag +# will be ignored. +# +# Note that the filter must not add or remove lines; it is applied before the +# code is scanned, but not when the output code is generated. If lines are added +# or removed, the anchors will not be placed correctly. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +INPUT_FILTER = + +# The FILTER_PATTERNS tag can be used to specify filters on a per file pattern +# basis. Doxygen will compare the file name with each pattern and apply the +# filter if there is a match. The filters are a list of the form: pattern=filter +# (like *.cpp=my_cpp_filter). See INPUT_FILTER for further information on how +# filters are used. If the FILTER_PATTERNS tag is empty or if none of the +# patterns match the file name, INPUT_FILTER is applied. +# +# Note that for custom extensions or not directly supported extensions you also +# need to set EXTENSION_MAPPING for the extension otherwise the files are not +# properly processed by doxygen. + +FILTER_PATTERNS = + +# If the FILTER_SOURCE_FILES tag is set to YES, the input filter (if set using +# INPUT_FILTER) will also be used to filter the input files that are used for +# producing the source files to browse (i.e. when SOURCE_BROWSER is set to YES). +# The default value is: NO. + +FILTER_SOURCE_FILES = NO + +# The FILTER_SOURCE_PATTERNS tag can be used to specify source filters per file +# pattern. A pattern will override the setting for FILTER_PATTERN (if any) and +# it is also possible to disable source filtering for a specific pattern using +# *.ext= (so without naming a filter). +# This tag requires that the tag FILTER_SOURCE_FILES is set to YES. + +FILTER_SOURCE_PATTERNS = + +# If the USE_MDFILE_AS_MAINPAGE tag refers to the name of a markdown file that +# is part of the input, its contents will be placed on the main page +# (index.html). This can be useful if you have a project on for instance GitHub +# and want to reuse the introduction page also for the doxygen output. + +USE_MDFILE_AS_MAINPAGE = + +#--------------------------------------------------------------------------- +# Configuration options related to source browsing +#--------------------------------------------------------------------------- + +# If the SOURCE_BROWSER tag is set to YES then a list of source files will be +# generated. Documented entities will be cross-referenced with these sources. +# +# Note: To get rid of all source code in the generated output, make sure that +# also VERBATIM_HEADERS is set to NO. +# The default value is: NO. + +SOURCE_BROWSER = NO + +# Setting the INLINE_SOURCES tag to YES will include the body of functions, +# classes and enums directly into the documentation. +# The default value is: NO. + +INLINE_SOURCES = NO + +# Setting the STRIP_CODE_COMMENTS tag to YES will instruct doxygen to hide any +# special comment blocks from generated source code fragments. Normal C, C++ and +# Fortran comments will always remain visible. +# The default value is: YES. + +STRIP_CODE_COMMENTS = YES + +# If the REFERENCED_BY_RELATION tag is set to YES then for each documented +# entity all documented functions referencing it will be listed. +# The default value is: NO. + +REFERENCED_BY_RELATION = NO + +# If the REFERENCES_RELATION tag is set to YES then for each documented function +# all documented entities called/used by that function will be listed. +# The default value is: NO. + +REFERENCES_RELATION = NO + +# If the REFERENCES_LINK_SOURCE tag is set to YES and SOURCE_BROWSER tag is set +# to YES then the hyperlinks from functions in REFERENCES_RELATION and +# REFERENCED_BY_RELATION lists will link to the source code. Otherwise they will +# link to the documentation. +# The default value is: YES. + +REFERENCES_LINK_SOURCE = YES + +# If SOURCE_TOOLTIPS is enabled (the default) then hovering a hyperlink in the +# source code will show a tooltip with additional information such as prototype, +# brief description and links to the definition and documentation. Since this +# will make the HTML file larger and loading of large files a bit slower, you +# can opt to disable this feature. +# The default value is: YES. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +SOURCE_TOOLTIPS = YES + +# If the USE_HTAGS tag is set to YES then the references to source code will +# point to the HTML generated by the htags(1) tool instead of doxygen built-in +# source browser. The htags tool is part of GNU's global source tagging system +# (see https://www.gnu.org/software/global/global.html). You will need version +# 4.8.6 or higher. +# +# To use it do the following: +# - Install the latest version of global +# - Enable SOURCE_BROWSER and USE_HTAGS in the configuration file +# - Make sure the INPUT points to the root of the source tree +# - Run doxygen as normal +# +# Doxygen will invoke htags (and that will in turn invoke gtags), so these +# tools must be available from the command line (i.e. in the search path). +# +# The result: instead of the source browser generated by doxygen, the links to +# source code will now point to the output of htags. +# The default value is: NO. +# This tag requires that the tag SOURCE_BROWSER is set to YES. + +USE_HTAGS = NO + +# If the VERBATIM_HEADERS tag is set the YES then doxygen will generate a +# verbatim copy of the header file for each class for which an include is +# specified. Set to NO to disable this. +# See also: Section \class. +# The default value is: YES. + +VERBATIM_HEADERS = YES + +#--------------------------------------------------------------------------- +# Configuration options related to the alphabetical class index +#--------------------------------------------------------------------------- + +# If the ALPHABETICAL_INDEX tag is set to YES, an alphabetical index of all +# compounds will be generated. Enable this if the project contains a lot of +# classes, structs, unions or interfaces. +# The default value is: YES. + +ALPHABETICAL_INDEX = YES + +# The COLS_IN_ALPHA_INDEX tag can be used to specify the number of columns in +# which the alphabetical index list will be split. +# Minimum value: 1, maximum value: 20, default value: 5. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +COLS_IN_ALPHA_INDEX = 5 + +# In case all classes in a project start with a common prefix, all classes will +# be put under the same header in the alphabetical index. The IGNORE_PREFIX tag +# can be used to specify a prefix (or a list of prefixes) that should be ignored +# while generating the index headers. +# This tag requires that the tag ALPHABETICAL_INDEX is set to YES. + +IGNORE_PREFIX = + +#--------------------------------------------------------------------------- +# Configuration options related to the HTML output +#--------------------------------------------------------------------------- + +# If the GENERATE_HTML tag is set to YES, doxygen will generate HTML output +# The default value is: YES. + +GENERATE_HTML = YES + +# The HTML_OUTPUT tag is used to specify where the HTML docs will be put. If a +# relative path is entered the value of OUTPUT_DIRECTORY will be put in front of +# it. +# The default directory is: html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_OUTPUT = html + +# The HTML_FILE_EXTENSION tag can be used to specify the file extension for each +# generated HTML page (for example: .htm, .php, .asp). +# The default value is: .html. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FILE_EXTENSION = .html + +# The HTML_HEADER tag can be used to specify a user-defined HTML header file for +# each generated HTML page. If the tag is left blank doxygen will generate a +# standard header. +# +# To get valid HTML the header file that includes any scripts and style sheets +# that doxygen needs, which is dependent on the configuration options used (e.g. +# the setting GENERATE_TREEVIEW). It is highly recommended to start with a +# default header using +# doxygen -w html new_header.html new_footer.html new_stylesheet.css +# YourConfigFile +# and then modify the file new_header.html. See also section "Doxygen usage" +# for information on how to generate the default header that doxygen normally +# uses. +# Note: The header is subject to change so you typically have to regenerate the +# default header when upgrading to a newer version of doxygen. For a description +# of the possible markers and block names see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_HEADER = + +# The HTML_FOOTER tag can be used to specify a user-defined HTML footer for each +# generated HTML page. If the tag is left blank doxygen will generate a standard +# footer. See HTML_HEADER for more information on how to generate a default +# footer and what special commands can be used inside the footer. See also +# section "Doxygen usage" for information on how to generate the default footer +# that doxygen normally uses. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FOOTER = + +# The HTML_STYLESHEET tag can be used to specify a user-defined cascading style +# sheet that is used by each HTML page. It can be used to fine-tune the look of +# the HTML output. If left blank doxygen will generate a default style sheet. +# See also section "Doxygen usage" for information on how to generate the style +# sheet that doxygen normally uses. +# Note: It is recommended to use HTML_EXTRA_STYLESHEET instead of this tag, as +# it is more robust and this tag (HTML_STYLESHEET) will in the future become +# obsolete. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_STYLESHEET = + +# The HTML_EXTRA_STYLESHEET tag can be used to specify additional user-defined +# cascading style sheets that are included after the standard style sheets +# created by doxygen. Using this option one can overrule certain style aspects. +# This is preferred over using HTML_STYLESHEET since it does not replace the +# standard style sheet and is therefore more robust against future updates. +# Doxygen will copy the style sheet files to the output directory. +# Note: The order of the extra style sheet files is of importance (e.g. the last +# style sheet in the list overrules the setting of the previous ones in the +# list). For an example see the documentation. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_STYLESHEET = + +# The HTML_EXTRA_FILES tag can be used to specify one or more extra images or +# other source files which should be copied to the HTML output directory. Note +# that these files will be copied to the base HTML output directory. Use the +# $relpath^ marker in the HTML_HEADER and/or HTML_FOOTER files to load these +# files. In the HTML_STYLESHEET file, use the file name only. Also note that the +# files will be copied as-is; there are no commands or markers available. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_EXTRA_FILES = + +# The HTML_COLORSTYLE_HUE tag controls the color of the HTML output. Doxygen +# will adjust the colors in the style sheet and background images according to +# this color. Hue is specified as an angle on a colorwheel, see +# https://en.wikipedia.org/wiki/Hue for more information. For instance the value +# 0 represents red, 60 is yellow, 120 is green, 180 is cyan, 240 is blue, 300 +# purple, and 360 is red again. +# Minimum value: 0, maximum value: 359, default value: 220. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_HUE = 220 + +# The HTML_COLORSTYLE_SAT tag controls the purity (or saturation) of the colors +# in the HTML output. For a value of 0 the output will use grayscales only. A +# value of 255 will produce the most vivid colors. +# Minimum value: 0, maximum value: 255, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_SAT = 100 + +# The HTML_COLORSTYLE_GAMMA tag controls the gamma correction applied to the +# luminance component of the colors in the HTML output. Values below 100 +# gradually make the output lighter, whereas values above 100 make the output +# darker. The value divided by 100 is the actual gamma applied, so 80 represents +# a gamma of 0.8, The value 220 represents a gamma of 2.2, and 100 does not +# change the gamma. +# Minimum value: 40, maximum value: 240, default value: 80. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_COLORSTYLE_GAMMA = 80 + +# If the HTML_TIMESTAMP tag is set to YES then the footer of each generated HTML +# page will contain the date and time when the page was generated. Setting this +# to YES can help to show when doxygen was last run and thus if the +# documentation is up to date. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_TIMESTAMP = NO + +# If the HTML_DYNAMIC_MENUS tag is set to YES then the generated HTML +# documentation will contain a main index with vertical navigation menus that +# are dynamically created via JavaScript. If disabled, the navigation index will +# consists of multiple levels of tabs that are statically embedded in every HTML +# page. Disable this option to support browsers that do not have JavaScript, +# like the Qt help browser. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_MENUS = YES + +# If the HTML_DYNAMIC_SECTIONS tag is set to YES then the generated HTML +# documentation will contain sections that can be hidden and shown after the +# page has loaded. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_DYNAMIC_SECTIONS = NO + +# With HTML_INDEX_NUM_ENTRIES one can control the preferred number of entries +# shown in the various tree structured indices initially; the user can expand +# and collapse entries dynamically later on. Doxygen will expand the tree to +# such a level that at most the specified number of entries are visible (unless +# a fully collapsed tree already exceeds this amount). So setting the number of +# entries 1 will produce a full collapsed tree by default. 0 is a special value +# representing an infinite number of entries and will result in a full expanded +# tree by default. +# Minimum value: 0, maximum value: 9999, default value: 100. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_INDEX_NUM_ENTRIES = 100 + +# If the GENERATE_DOCSET tag is set to YES, additional index files will be +# generated that can be used as input for Apple's Xcode 3 integrated development +# environment (see: https://developer.apple.com/xcode/), introduced with OSX +# 10.5 (Leopard). To create a documentation set, doxygen will generate a +# Makefile in the HTML output directory. Running make will produce the docset in +# that directory and running make install will install the docset in +# ~/Library/Developer/Shared/Documentation/DocSets so that Xcode will find it at +# startup. See https://developer.apple.com/library/archive/featuredarticles/Doxy +# genXcode/_index.html for more information. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_DOCSET = NO + +# This tag determines the name of the docset feed. A documentation feed provides +# an umbrella under which multiple documentation sets from a single provider +# (such as a company or product suite) can be grouped. +# The default value is: Doxygen generated docs. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_FEEDNAME = "Doxygen generated docs" + +# This tag specifies a string that should uniquely identify the documentation +# set bundle. This should be a reverse domain-name style string, e.g. +# com.mycompany.MyDocSet. Doxygen will append .docset to the name. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_BUNDLE_ID = org.doxygen.Project + +# The DOCSET_PUBLISHER_ID tag specifies a string that should uniquely identify +# the documentation publisher. This should be a reverse domain-name style +# string, e.g. com.mycompany.MyDocSet.documentation. +# The default value is: org.doxygen.Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_ID = org.doxygen.Publisher + +# The DOCSET_PUBLISHER_NAME tag identifies the documentation publisher. +# The default value is: Publisher. +# This tag requires that the tag GENERATE_DOCSET is set to YES. + +DOCSET_PUBLISHER_NAME = Publisher + +# If the GENERATE_HTMLHELP tag is set to YES then doxygen generates three +# additional HTML index files: index.hhp, index.hhc, and index.hhk. The +# index.hhp is a project file that can be read by Microsoft's HTML Help Workshop +# (see: https://www.microsoft.com/en-us/download/details.aspx?id=21138) on +# Windows. +# +# The HTML Help Workshop contains a compiler that can convert all HTML output +# generated by doxygen into a single compiled HTML file (.chm). Compiled HTML +# files are now used as the Windows 98 help format, and will replace the old +# Windows help format (.hlp) on all Windows platforms in the future. Compressed +# HTML files also contain an index, a table of contents, and you can search for +# words in the documentation. The HTML workshop also contains a viewer for +# compressed HTML files. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_HTMLHELP = NO + +# The CHM_FILE tag can be used to specify the file name of the resulting .chm +# file. You can add a path in front of the file if the result should not be +# written to the html output directory. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_FILE = + +# The HHC_LOCATION tag can be used to specify the location (absolute path +# including file name) of the HTML help compiler (hhc.exe). If non-empty, +# doxygen will try to run the HTML help compiler on the generated index.hhp. +# The file has to be specified with full path. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +HHC_LOCATION = + +# The GENERATE_CHI flag controls if a separate .chi index file is generated +# (YES) or that it should be included in the main .chm file (NO). +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +GENERATE_CHI = NO + +# The CHM_INDEX_ENCODING is used to encode HtmlHelp index (hhk), content (hhc) +# and project file content. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +CHM_INDEX_ENCODING = + +# The BINARY_TOC flag controls whether a binary table of contents is generated +# (YES) or a normal table of contents (NO) in the .chm file. Furthermore it +# enables the Previous and Next buttons. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +BINARY_TOC = NO + +# The TOC_EXPAND flag can be set to YES to add extra items for group members to +# the table of contents of the HTML help documentation and to the tree view. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTMLHELP is set to YES. + +TOC_EXPAND = NO + +# If the GENERATE_QHP tag is set to YES and both QHP_NAMESPACE and +# QHP_VIRTUAL_FOLDER are set, an additional index file will be generated that +# can be used as input for Qt's qhelpgenerator to generate a Qt Compressed Help +# (.qch) of the generated HTML documentation. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_QHP = NO + +# If the QHG_LOCATION tag is specified, the QCH_FILE tag can be used to specify +# the file name of the resulting .qch file. The path specified is relative to +# the HTML output folder. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QCH_FILE = + +# The QHP_NAMESPACE tag specifies the namespace to use when generating Qt Help +# Project output. For more information please see Qt Help Project / Namespace +# (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#namespace). +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_NAMESPACE = org.doxygen.Project + +# The QHP_VIRTUAL_FOLDER tag specifies the namespace to use when generating Qt +# Help Project output. For more information please see Qt Help Project / Virtual +# Folders (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#virtual- +# folders). +# The default value is: doc. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_VIRTUAL_FOLDER = doc + +# If the QHP_CUST_FILTER_NAME tag is set, it specifies the name of a custom +# filter to add. For more information please see Qt Help Project / Custom +# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_NAME = + +# The QHP_CUST_FILTER_ATTRS tag specifies the list of the attributes of the +# custom filter to add. For more information please see Qt Help Project / Custom +# Filters (see: https://doc.qt.io/archives/qt-4.8/qthelpproject.html#custom- +# filters). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_CUST_FILTER_ATTRS = + +# The QHP_SECT_FILTER_ATTRS tag specifies the list of the attributes this +# project's filter section matches. Qt Help Project / Filter Attributes (see: +# https://doc.qt.io/archives/qt-4.8/qthelpproject.html#filter-attributes). +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHP_SECT_FILTER_ATTRS = + +# The QHG_LOCATION tag can be used to specify the location of Qt's +# qhelpgenerator. If non-empty doxygen will try to run qhelpgenerator on the +# generated .qhp file. +# This tag requires that the tag GENERATE_QHP is set to YES. + +QHG_LOCATION = + +# If the GENERATE_ECLIPSEHELP tag is set to YES, additional index files will be +# generated, together with the HTML files, they form an Eclipse help plugin. To +# install this plugin and make it available under the help contents menu in +# Eclipse, the contents of the directory containing the HTML and XML files needs +# to be copied into the plugins directory of eclipse. The name of the directory +# within the plugins directory should be the same as the ECLIPSE_DOC_ID value. +# After copying Eclipse needs to be restarted before the help appears. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_ECLIPSEHELP = NO + +# A unique identifier for the Eclipse help plugin. When installing the plugin +# the directory name containing the HTML and XML files should also have this +# name. Each documentation set should have its own identifier. +# The default value is: org.doxygen.Project. +# This tag requires that the tag GENERATE_ECLIPSEHELP is set to YES. + +ECLIPSE_DOC_ID = org.doxygen.Project + +# If you want full control over the layout of the generated HTML pages it might +# be necessary to disable the index and replace it with your own. The +# DISABLE_INDEX tag can be used to turn on/off the condensed index (tabs) at top +# of each HTML page. A value of NO enables the index and the value YES disables +# it. Since the tabs in the index contain the same information as the navigation +# tree, you can set this option to YES if you also set GENERATE_TREEVIEW to YES. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +DISABLE_INDEX = NO + +# The GENERATE_TREEVIEW tag is used to specify whether a tree-like index +# structure should be generated to display hierarchical information. If the tag +# value is set to YES, a side panel will be generated containing a tree-like +# index structure (just like the one that is generated for HTML Help). For this +# to work a browser that supports JavaScript, DHTML, CSS and frames is required +# (i.e. any modern browser). Windows users are probably better off using the +# HTML help feature. Via custom style sheets (see HTML_EXTRA_STYLESHEET) one can +# further fine-tune the look of the index. As an example, the default style +# sheet generated by doxygen has an example that shows how to put an image at +# the root of the tree instead of the PROJECT_NAME. Since the tree basically has +# the same information as the tab index, you could consider setting +# DISABLE_INDEX to YES when enabling this option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +GENERATE_TREEVIEW = NO + +# The ENUM_VALUES_PER_LINE tag can be used to set the number of enum values that +# doxygen will group on one line in the generated HTML documentation. +# +# Note that a value of 0 will completely suppress the enum values from appearing +# in the overview section. +# Minimum value: 0, maximum value: 20, default value: 4. +# This tag requires that the tag GENERATE_HTML is set to YES. + +ENUM_VALUES_PER_LINE = 4 + +# If the treeview is enabled (see GENERATE_TREEVIEW) then this tag can be used +# to set the initial width (in pixels) of the frame in which the tree is shown. +# Minimum value: 0, maximum value: 1500, default value: 250. +# This tag requires that the tag GENERATE_HTML is set to YES. + +TREEVIEW_WIDTH = 250 + +# If the EXT_LINKS_IN_WINDOW option is set to YES, doxygen will open links to +# external symbols imported via tag files in a separate window. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +EXT_LINKS_IN_WINDOW = NO + +# If the HTML_FORMULA_FORMAT option is set to svg, doxygen will use the pdf2svg +# tool (see https://github.com/dawbarton/pdf2svg) or inkscape (see +# https://inkscape.org) to generate formulas as SVG images instead of PNGs for +# the HTML output. These images will generally look nicer at scaled resolutions. +# Possible values are: png (the default) and svg (looks nicer but requires the +# pdf2svg or inkscape tool). +# The default value is: png. +# This tag requires that the tag GENERATE_HTML is set to YES. + +HTML_FORMULA_FORMAT = png + +# Use this tag to change the font size of LaTeX formulas included as images in +# the HTML documentation. When you change the font size after a successful +# doxygen run you need to manually remove any form_*.png images from the HTML +# output directory to force them to be regenerated. +# Minimum value: 8, maximum value: 50, default value: 10. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_FONTSIZE = 10 + +# Use the FORMULA_TRANSPARENT tag to determine whether or not the images +# generated for formulas are transparent PNGs. Transparent PNGs are not +# supported properly for IE 6.0, but are supported on all modern browsers. +# +# Note that when changing this option you need to delete any form_*.png files in +# the HTML output directory before the changes have effect. +# The default value is: YES. +# This tag requires that the tag GENERATE_HTML is set to YES. + +FORMULA_TRANSPARENT = YES + +# The FORMULA_MACROFILE can contain LaTeX \newcommand and \renewcommand commands +# to create new LaTeX commands to be used in formulas as building blocks. See +# the section "Including formulas" for details. + +FORMULA_MACROFILE = + +# Enable the USE_MATHJAX option to render LaTeX formulas using MathJax (see +# https://www.mathjax.org) which uses client side JavaScript for the rendering +# instead of using pre-rendered bitmaps. Use this if you do not have LaTeX +# installed or if you want to formulas look prettier in the HTML output. When +# enabled you may also need to install MathJax separately and configure the path +# to it using the MATHJAX_RELPATH option. +# The default value is: NO. +# This tag requires that the tag GENERATE_HTML is set to YES. + +#USE_MATHJAX = NO +USE_MATHJAX = YES + +# When MathJax is enabled you can set the default output format to be used for +# the MathJax output. See the MathJax site (see: +# http://docs.mathjax.org/en/latest/output.html) for more details. +# Possible values are: HTML-CSS (which is slower, but has the best +# compatibility), NativeMML (i.e. MathML) and SVG. +# The default value is: HTML-CSS. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_FORMAT = HTML-CSS + +# When MathJax is enabled you need to specify the location relative to the HTML +# output directory using the MATHJAX_RELPATH option. The destination directory +# should contain the MathJax.js script. For instance, if the mathjax directory +# is located at the same level as the HTML output directory, then +# MATHJAX_RELPATH should be ../mathjax. The default value points to the MathJax +# Content Delivery Network so you can quickly see the result without installing +# MathJax. However, it is strongly recommended to install a local copy of +# MathJax from https://www.mathjax.org before deployment. +# The default value is: https://cdn.jsdelivr.net/npm/mathjax@2. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_RELPATH = https://cdn.jsdelivr.net/npm/mathjax@2 + +# The MATHJAX_EXTENSIONS tag can be used to specify one or more MathJax +# extension names that should be enabled during MathJax rendering. For example +# MATHJAX_EXTENSIONS = TeX/AMSmath TeX/AMSsymbols +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_EXTENSIONS = + +# The MATHJAX_CODEFILE tag can be used to specify a file with javascript pieces +# of code that will be used on startup of the MathJax code. See the MathJax site +# (see: http://docs.mathjax.org/en/latest/output.html) for more details. For an +# example see the documentation. +# This tag requires that the tag USE_MATHJAX is set to YES. + +MATHJAX_CODEFILE = + +# When the SEARCHENGINE tag is enabled doxygen will generate a search box for +# the HTML output. The underlying search engine uses javascript and DHTML and +# should work on any modern browser. Note that when using HTML help +# (GENERATE_HTMLHELP), Qt help (GENERATE_QHP), or docsets (GENERATE_DOCSET) +# there is already a search function so this one should typically be disabled. +# For large projects the javascript based search engine can be slow, then +# enabling SERVER_BASED_SEARCH may provide a better solution. It is possible to +# search using the keyboard; to jump to the search box use + S +# (what the is depends on the OS and browser, but it is typically +# , /