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Particle Identification and Tracking
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Namespace for utilities and helper functions. More...
Classes | |
| class | Accum_case |
| A class to hold a stack of accum objects for handing into a hash_case. More... | |
| class | Attr_list_hdf |
| Wraps the attribute functionality of hdf objects. More... | |
| class | CL_parse |
| A class to wrap the parsing of the command line to extract the input file, output file and parameter file. More... | |
| class | Counted_vector |
| A class for computing many averages in parallel. More... | |
| class | Data_map |
| class to handle translation from D_TYPE to column position for flat data structures. More... | |
| struct | Data_store |
| A struct to hold the data_map and raw data for input and output wrappers. More... | |
| class | Ll_range_error |
| Exception class derived from the standard range_error class to indicate when a linked list has stepped over it's range. More... | |
| class | Null_field |
| Exception to report when a function that should return valid pointer from an object, but the field is NULL in the object. More... | |
| class | Filter |
| ABC for filter objects. More... | |
| class | Filter_trivial |
| a trivial filter class that does nothing More... | |
| class | Filter_ers |
| A basic filter, does rg (top), shift (top) and eccentricity (top) cuts. More... | |
| class | Filter_ersI |
| A basic filter, does rg (top), shift (top), eccentricity (top), and I (bottom) cuts. More... | |
| class | Generic_wrapper |
| An interface for extracting data from the internal data structures. More... | |
| class | Generic_wrapper_read |
| Abstract base class to provide an interface for reading data out of Generic_wrapper objects. More... | |
| class | Generic_wrapper_hdf |
| generic_wrapper for writing to hdf files More... | |
| class | Histogram |
| Base class for historgram objects. More... | |
| class | Histogram2D |
| Implements a 2D histogram. More... | |
| class | Md_store |
| A class to hold meta data. More... | |
| class | ND_Array |
| A N-D array. More... | |
| class | Read_config |
| class for reading configuration from xml files. More... | |
| class | SQL_handler |
| Class to wrap around the sqlite3 interface to deal with making connections to data basese, cleaning up after them etc. More... | |
| class | Tuple |
| Class for carrying around the posistion and velocity vectors. More... | |
| class | Wrapper_in |
| A mostly abstract base class for input wrappers. More... | |
| class | Wrapper_i_dummy |
| Wrapper class for testing purposes. More... | |
| class | Wrapper_i_file |
| Wrapper class for dealing with data from a text file. More... | |
| class | Wrapper_i_generic |
| Wrapper class for eating data from arbitrary sources. More... | |
| class | Wrapper_i_hdf |
| Wrapper class for eating data from hdf files, take 2. More... | |
| class | Wrapper_i_jb_binary |
| Wrapper class for dealing with data from Justin's simulations. More... | |
| class | Wrapper_out |
| ABC for output wrappers. More... | |
| class | wrapper_o_file |
| wrapper_o class for dealing with writing data to a file. More... | |
| class | Wrapper_o_hdf |
| Wrapper class for dealing with output to matlab. More... | |
| class | Wrapper_o_hdf_group |
| Wrapper class for dealing with output to matlab. More... | |
Typedefs | |
| typedef enum utilities::W_TYPE | W_TYPE |
| Enumeration for wrapper types. More... | |
| typedef enum utilities::D_TYPE | D_TYPE |
| Enumeration for data types (where type is the physical meaning of the data). More... | |
| typedef enum utilities::V_TYPE | V_TYPE |
| Enumeration for the type of value the data is (ie float, int,complex) More... | |
| typedef enum utilities::FILT_TYPE | FILT_TYPE |
| Enumeration for keeping track of which filter type a filter is, useful for checking to make sure that the factory behaved properly. More... | |
| typedef Tuple< int, 2 > | Tuplei |
| typedef Tuple< float, 2 > | Tuplef |
| typedef enum utilities::F_TYPE | F_TYPE |
| Enumeration for functions that maps to the tables in the database. More... | |
Enumerations | |
| enum | W_TYPE { W_MATLAB = 0, W_TEXT, W_NING, W_HDF } |
| Enumeration for wrapper types. More... | |
| enum | D_TYPE { D_INDEX =0, D_XPOS =1, D_YPOS =2, D_FRAME =3, D_I =4, D_R2 =5, D_E =6, D_NEXT_INDX =7, D_PREV_INDX =8, D_DX =9, D_DY =10, D_ORGX =11, D_ORGY =12, D_ZPOS =13, D_TRACKID =14, D_S_ORDER_PARAMETER =15, D_MULT =16, D_N_SIZE =17, D_SENTRY } |
| Enumeration for data types (where type is the physical meaning of the data). More... | |
| enum | V_TYPE { V_ERROR = -1, V_UINT = 0, V_INT =1, V_FLOAT =2, V_COMPLEX =3, V_STRING =4, V_BOOL =5, V_TIME =6, V_GUID =7 } |
| Enumeration for the type of value the data is (ie float, int,complex) More... | |
| enum | FILT_TYPE { FILT_TRIV = 0, FILT_ERS, FILT_ERSImin } |
| Enumeration for keeping track of which filter type a filter is, useful for checking to make sure that the factory behaved properly. More... | |
| enum | F_TYPE { F_NOFUNCTION = 0, F_IDEN = 1, F_IDEN_AVG = 2, F_GOFR = 3, F_GOFR3D = 4, F_GOFR_BY_PLANE = 5, F_LINK3D = 6, F_MSD = 7, F_PHI6 = 8, F_TRACK_STATS = 9, F_TRACKING = 10, F_VANHOVE = 11, F_MSD_SWEEP = 12 } |
| Enumeration for functions that maps to the tables in the database. More... | |
Functions | |
| std::string | DT2str_s (D_TYPE in) |
| Helper functions to convert D_TYPEs in to short name strings. More... | |
| D_TYPE | str2DT_s (std::string in) |
| Helper functions to convert short name strings in to D_TYPEs. More... | |
| V_TYPE | v_type (D_TYPE in) |
| Helper function to map between D_TYPE and V_TYPE. More... | |
| std::string | format_dset_name (D_TYPE type, int comp_num) |
| Helper function to format dset names with computation numbers attached. More... | |
| std::string | format_name (const std::string &name,int comp_num) |
| Helper function to format computation numbers on to strings. More... | |
| V_TYPE | str2VT_s (const std::string &type_str) |
| Helper function to make string in to V_TYPE. More... | |
| V_TYPE | str2VT_s (const char *const in) |
| Helper function to make string in to V_TYPE. More... | |
| std::string | VT2str_s (V_TYPE) |
| Helper function to make v_types to strings. More... | |
| template<typename _CharT , class _Traits > | |
| std::basic_ostream< _CharT, _Traits > & | operator<< (std::basic_ostream< _CharT, _Traits > &__os, const Data_map &in) |
| prints out the data_map to cout lifted almost whole cloth from c++/4.3/complex More... | |
| Filter * | filter_factory (const Md_store &filter_prams) |
| Guesses which filter to generate from the parameters it is given in the Md_store object. More... | |
| Md_store | extract_prams (const std::string &fname, int comp_num, const std::vector< std::string > &pram_list) |
| Extracts filter parameters from a data file. More... | |
| std::string | ftype_to_str (F_TYPE f) |
| template<typename _CharT , class _Traits , class T , int length> | |
| std::basic_ostream< _CharT, _Traits > & | operator<< (std::basic_ostream< _CharT, _Traits > &__os, const Tuple< T, length > &in) |
| prints out the tuple to cout lifted almost whole cloth from c++/4.3/complex More... | |
Variables | |
| const int | format_padding_ = 7 |
Namespace for utilities and helper functions.
| typedef enum utilities::D_TYPE utilities::D_TYPE |
Enumeration for data types (where type is the physical meaning of the data).
If you add to this you MUST update the count below this, add the D_TYPE to the V_TYPE conversion function, and D2Str function.
| typedef enum utilities::F_TYPE utilities::F_TYPE |
Enumeration for functions that maps to the tables in the database.
The values of the enumeration need to stay synced with the values of func_names table in the database. This should be replaced with something more flexible eventually.
| typedef enum utilities::FILT_TYPE utilities::FILT_TYPE |
Enumeration for keeping track of which filter type a filter is, useful for checking to make sure that the factory behaved properly.
| typedef Tuple<float,2> utilities::Tuplef |
| typedef Tuple<int,2> utilities::Tuplei |
| typedef enum utilities::V_TYPE utilities::V_TYPE |
Enumeration for the type of value the data is (ie float, int,complex)
| typedef enum utilities::W_TYPE utilities::W_TYPE |
| enum utilities::D_TYPE |
Enumeration for data types (where type is the physical meaning of the data).
If you add to this you MUST update the count below this, add the D_TYPE to the V_TYPE conversion function, and D2Str function.
| Enumerator | |
|---|---|
| D_INDEX | |
| D_XPOS | |
| D_YPOS | |
| D_FRAME | |
| D_I | |
| D_R2 | |
| D_E | |
| D_NEXT_INDX | |
| D_PREV_INDX | |
| D_DX | |
| D_DY | |
| D_ORGX | |
| D_ORGY | |
| D_ZPOS | |
| D_TRACKID | |
| D_S_ORDER_PARAMETER | |
| D_MULT | |
| D_N_SIZE | |
| D_SENTRY | |
| enum utilities::F_TYPE |
Enumeration for functions that maps to the tables in the database.
The values of the enumeration need to stay synced with the values of func_names table in the database. This should be replaced with something more flexible eventually.
| Enumerator | |
|---|---|
| F_NOFUNCTION | |
| F_IDEN | |
| F_IDEN_AVG | |
| F_GOFR | |
| F_GOFR3D | |
| F_GOFR_BY_PLANE | |
| F_LINK3D | |
| F_MSD | |
| F_PHI6 | |
| F_TRACK_STATS | |
| F_TRACKING | |
| F_VANHOVE | |
| F_MSD_SWEEP | |
| enum utilities::FILT_TYPE |
| enum utilities::V_TYPE |
| enum utilities::W_TYPE |
Enumeration for wrapper types.
I do not think that this is used by anything
| Enumerator | |
|---|---|
| W_MATLAB | |
| W_TEXT | |
| W_NING | |
| W_HDF | |
| std::string utilities::DT2str_s | ( | D_TYPE | in) |
Helper functions to convert D_TYPEs in to short name strings.
References D_DX, D_DY, D_E, D_FRAME, D_I, D_INDEX, D_MULT, D_N_SIZE, D_NEXT_INDX, D_ORGX, D_ORGY, D_PREV_INDX, D_R2, D_S_ORDER_PARAMETER, D_TRACKID, D_XPOS, D_YPOS, and D_ZPOS.
Referenced by format_dset_name(), utilities::Wrapper_i_hdf::get_value(), and utilities::Wrapper_i_generic::get_value().
| Md_store utilities::extract_prams | ( | const std::string & | fname, |
| int | comp_num, | ||
| const std::vector< std::string > & | pram_list | ||
| ) |
Extracts filter parameters from a data file.
Extracts the parameters asked for. This functionality should be folded into the wrapper class.
References utilities::Md_store::add_element(), utilities::Attr_list_hdf::contains_attr(), D_XPOS, format_dset_name(), utilities::Attr_list_hdf::get_type(), utilities::Attr_list_hdf::get_value(), V_BOOL, V_COMPLEX, V_ERROR, V_FLOAT, V_GUID, V_INT, V_STRING, V_TIME, V_UINT, and VT2str_s().
Referenced by main().
Guesses which filter to generate from the parameters it is given in the Md_store object.
The returned object needs to be cleaned up.
References utilities::Md_store::contains_key(), utilities::Filter_ers::init(), and utilities::Filter_ersI::init().
Referenced by main().
| std::string utilities::format_dset_name | ( | D_TYPE | type, |
| int | comp_num | ||
| ) |
Helper function to format dset names with computation numbers attached.
References DT2str_s(), and format_name().
Referenced by extract_prams(), utilities::Wrapper_o_hdf::initialize_wrapper(), local_add_meta(), utilities::Wrapper_i_hdf::priv_init(), and utilities::Wrapper_o_hdf_group::Wrapper_o_hdf_group().
| std::string utilities::format_name | ( | const std::string & | name, |
| int | comp_num | ||
| ) |
Helper function to format computation numbers on to strings.
References format_padding_.
Referenced by utilities::Wrapper_o_hdf::add_meta_data_comp(), format_dset_name(), main(), tracking::Accum_chi4_self::out_to_wrapper(), tracking::Corr_pair_diffusion::out_to_wrapper(), tracking::Corr_case::out_to_wrapper(), tracking::TA_vanHove::output_to_wrapper(), tracking::TA_disp::output_to_wrapper(), tracking::TA_theta_rlim::output_to_wrapper(), tracking::TA_msd::output_to_wrapper(), and tracking::Track_shelf::output_to_wrapper().
| std::string utilities::ftype_to_str | ( | F_TYPE | f) |
References F_GOFR, F_GOFR3D, F_GOFR_BY_PLANE, F_IDEN, F_IDEN_AVG, F_LINK3D, F_MSD, F_MSD_SWEEP, F_NOFUNCTION, F_PHI6, F_TRACK_STATS, F_TRACKING, and F_VANHOVE.
| std::basic_ostream<_CharT, _Traits>& utilities::operator<< | ( | std::basic_ostream< _CharT, _Traits > & | __os, |
| const Data_map & | in | ||
| ) |
prints out the data_map to cout lifted almost whole cloth from c++/4.3/complex
References D_SENTRY.
| std::basic_ostream<_CharT, _Traits>& utilities::operator<< | ( | std::basic_ostream< _CharT, _Traits > & | __os, |
| const Tuple< T, length > & | in | ||
| ) |
prints out the tuple to cout lifted almost whole cloth from c++/4.3/complex
| D_TYPE utilities::str2DT_s | ( | std::string | in) |
Helper functions to convert short name strings in to D_TYPEs.
References D_TRACKID.
| V_TYPE utilities::str2VT_s | ( | const std::string & | type_str) |
Helper function to make string in to V_TYPE.
References V_BOOL, V_ERROR, V_FLOAT, V_GUID, V_INT, V_STRING, V_TIME, and V_UINT.
Referenced by utilities::Md_store::add_element(), and str2VT_s().
| V_TYPE utilities::str2VT_s | ( | const char *const | in) |
Helper function to make string in to V_TYPE.
References str2VT_s().
| V_TYPE utilities::v_type | ( | D_TYPE | in) |
Helper function to map between D_TYPE and V_TYPE.
References D_DX, D_DY, D_E, D_FRAME, D_I, D_INDEX, D_MULT, D_N_SIZE, D_NEXT_INDX, D_ORGX, D_ORGY, D_PREV_INDX, D_R2, D_S_ORDER_PARAMETER, D_TRACKID, D_XPOS, D_YPOS, D_ZPOS, V_COMPLEX, V_ERROR, V_FLOAT, and V_INT.
Referenced by utilities::Wrapper_i_generic::add_float_data(), utilities::Wrapper_i_generic::add_int_data(), tracking::particle_base::get_value(), utilities::Wrapper_i_hdf::get_value(), utilities::Wrapper_i_generic::get_value(), tracking::particle_track::get_value(), utilities::Wrapper_i_generic::open_frame(), utilities::Wrapper_i_hdf::priv_init(), utilities::Wrapper_i_generic::setup(), utilities::Wrapper_o_hdf_group::store_particle(), utilities::Wrapper_o_hdf_group::Wrapper_o_hdf_group(), and utilities::Wrapper_o_hdf_group::write_to_disk().
| std::string utilities::VT2str_s | ( | V_TYPE | type) |
Helper function to make v_types to strings.
References V_BOOL, V_COMPLEX, V_ERROR, V_FLOAT, V_GUID, V_INT, V_STRING, V_TIME, and V_UINT.
Referenced by utilities::Wrapper_o_hdf::add_meta_data_list(), extract_prams(), utilities::Md_store::get_value(), main(), utilities::Wrapper_i_generic::open_frame(), utilities::Md_store::print(), utilities::Wrapper_i_hdf::priv_init(), utilities::Wrapper_i_generic::setup(), utilities::Wrapper_o_hdf_group::store_particle(), and utilities::Wrapper_o_hdf_group::Wrapper_o_hdf_group().
| const int utilities::format_padding_ = 7 |
Referenced by format_name().
1.8.4