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Stimfit
0.13.15
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Stimfit
0.13.15
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The stimfit namespace. More...
Classes | |
| struct | parInfo |
| Information about parameters used in storedFunc. More... | |
| struct | storedFunc |
| Function used for least-squares fitting. More... | |
| class | wxProgressInfo |
| Progress Info interface adapter; maps to wxProgressDialog. More... | |
| class | Table |
| A table used for printing information. More... | |
| struct | UserInput |
| Represents user input from dialogs that can be used in plugins. More... | |
| struct | Plugin |
| User-defined plugin. More... | |
| struct | Extension |
| User-defined Python extension. More... | |
| struct | ifstreamMan |
| Resource manager for ifstream objects. More... | |
| struct | ofstreamMan |
| Resource manager for ofstream objects. More... | |
| class | Event |
| Describes the attributes of an event. More... | |
| struct | PyMarker |
| A marker that can be set from Python. More... | |
| struct | SectionAttributes |
| struct | SectionPointer |
Typedefs | |
| typedef boost::function < double(double, const Vector_double &)> | Func |
| A function taking a double and a vector and returning a double. | |
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typedef boost::function < Vector_double(double, const Vector_double &)> | Jac |
| The jacobian of a stf::Func. | |
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typedef boost::function < double(double, double, double, double, double)> | Scale |
| Scaling function for fit parameters. | |
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typedef boost::function< Table(const Vector_double &, const std::vector< stf::parInfo > , double)> | Output |
| Print the output of a fit into a stf::Table. | |
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typedef boost::function< void(const Vector_double &, double, double, double, double, double, Vector_double &)> | Init |
| Initialising function for the parameters in stf::Func to start a fit. | |
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typedef boost::function < Recording(const Recording &, const Vector_double &, std::map< std::string, double > &)> | PluginFunc |
| Get a Recording, do something with it, return the new Recording. | |
Enumerations | |
| enum | cursor_type { measure_cursor, peak_cursor, base_cursor, decay_cursor, latency_cursor, zoom_cursor, event_cursor, undefined_cursor } |
| Mouse cursor types. More... | |
| enum | direction { up, down, both, undefined_direction } |
| The direction of peak calculations. More... | |
| enum | zoom_channels { zoomch1, zoomch2, zoomboth } |
| Determines which channels to scale. More... | |
| enum | latency_mode { manualMode = 0, peakMode = 1, riseMode = 2, halfMode = 3, footMode = 4, undefinedMode } |
| Latency cursor settings. More... | |
| enum | latency_window_mode { defaultMode = 0, windowMode = 1 } |
| Latency window settings. More... | |
| enum | extraction_mode { criterion, correlation, deconvolution } |
| Deconvolution. More... | |
Functions | |
| template<typename T > | |
| T | linFit (const std::vector< T > &x, const std::vector< T > &y, T &m, T &c) |
| Performs a linear fit. | |
| double StfDll | lmFit (const Vector_double &data, double dt, const stf::storedFunc &fitFunc, const Vector_double &opts, bool use_scaling, Vector_double &p, std::string &info, int &warning) |
| Uses the Levenberg-Marquardt algorithm to perform a non-linear least-squares fit. | |
| double | flin (double x, const Vector_double &p) |
| Linear function. | |
| void | flin_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit) |
| Dummy function to be passed to stf::storedFunc for linear functions. | |
| stf::storedFunc | initLinFunc () |
| initializes a linear function | |
| Vector_double | get_scale (Vector_double &data, double oldx) |
| Compute and perform normalisation. | |
| Vector_double | LM_default_opts () |
| Return default LM options. | |
| double | base (double &var, const std::vector< double > &data, std::size_t llb, std::size_t ulb) |
| Calculate the average of all sampling points between and including llb and ulb. | |
| double | peak (const std::vector< double > &data, double base, std::size_t llp, std::size_t ulp, int pM, stf::direction, double &maxT) |
| Find the peak value of data between llp and ulp. | |
| double | threshold (const std::vector< double > &data, std::size_t llp, std::size_t ulp, double slope, double &thrT, std::size_t windowLength) |
| Find the value within data between llp and ulp at which slope is exceeded. | |
| double | risetime (const std::vector< double > &data, double base, double ampl, double left, double right, double frac, std::size_t &tLoId, std::size_t &tHiId, double &tLoReal) |
| Find 20 to 80% rise time of an event in data. | |
| double | risetime2 (const std::vector< double > &data, double base, double ampl, double left, double right, double frac, double &innerTLoReal, double &innerTHiReal, double &outerTLoReal, double &outerTHiReal) |
| Find 20 to 80% rise time of an event in data. | |
| double | t_half (const std::vector< double > &data, double base, double ampl, double left, double right, double center, std::size_t &t50LeftId, std::size_t &t50RightId, double &t50LeftReal) |
| Find the full width at half-maximal amplitude of an event within data. | |
| double | maxRise (const std::vector< double > &data, double left, double right, double &maxRiseT, double &maxRiseY, std::size_t windowLength) |
| Find the maximal slope during the rising phase of an event within data. | |
| double | maxDecay (const std::vector< double > &data, double left, double right, double &maxDecayT, double &maxDecayY, std::size_t windowLength) |
| Find the maximal slope during the decaying phase of an event within data. | |
| double | fexp (double x, const Vector_double &p) |
| Sum of n exponential functions. | |
| Vector_double | fexp_jac (double x, const Vector_double &p) |
| Computes the Jacobian of stf::fexp(). | |
| void | fexp_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit) |
| Initialises parameters for fitting stf::fexp() to data. | |
| void | fexp_init2 (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit) |
| Yet another initialiser for fitting stf::fexp() to data. | |
| double | fexpde (double x, const Vector_double &p) |
| Monoexponential function with delay. | |
| void | fexpde_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit) |
| Initialises parameters for fitting stf::fexpde() to data. | |
| double | fexpbde (double x, const Vector_double &p) |
| Biexponential function with delay. | |
| void | fexpbde_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit) |
| Initialises parameters for fitting stf::fexpde() to data. | |
| double | falpha (double x, const Vector_double &p) |
| Alpha function. | |
| Vector_double | falpha_jac (double x, const Vector_double &p) |
| Computes the Jacobian of stf::falpha(). | |
| double | fHH (double x, const Vector_double &p) |
| Hodgkin-Huxley sodium conductance function. | |
| double | fgauss (double x, const Vector_double &p) |
| Computes the sum of an arbitrary number of Gaussians. | |
| Vector_double | fgauss_jac (double x, const Vector_double &p) |
| Computes the Jacobian of a sum of Gaussians. | |
| double | fgnabiexp (double x, const Vector_double &p) |
| power of 1 sodium conductance function. | |
| Vector_double | fgnabiexp_jac (double x, const Vector_double &p) |
| Computes the Jacobian of stf::fgnabiexp(). | |
| void | falpha_init (const Vector_double &data, double base, double peak, double RTLoHI, double HalfWidth, double dt, Vector_double &pInit) |
| Initialises parameters for fitting stf::falpha() to data. | |
| void | fgauss_init (const Vector_double &data, double base, double peak, double RTLoHI, double HalfWidth, double dt, Vector_double &pInit) |
| Initialises parameters for fitting stf::fgauss() to data. | |
| void | fHH_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit) |
| Initialises parameters for fitting stf::falpha() to data. | |
| void | fgnabiexp_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit) |
| Initialises parameters for fitting stf::falpha() to data. | |
| double | xscale (double param, double xscale, double xoff, double yscale, double yoff) |
| Scales a parameter that linearly depends on x. | |
| double | xunscale (double param, double xscale, double xoff, double yscale, double yoff) |
| Unscales a parameter that linearly depends on x. | |
| double | yscale (double param, double xscale, double xoff, double yscale, double yoff) |
| Scales a parameter that linearly depends on y. | |
| double | yscaleoffset (double param, double xscale, double xoff, double yscale, double yoff) |
| Scales a parameter that linearly depends on y and adds an offset. | |
| double | yunscale (double param, double xscale, double xoff, double yscale, double yoff) |
| Unscales a parameter that linearly depends on y. | |
| double | yunscaleoffset (double param, double xscale, double xoff, double yscale, double yoff) |
| Unscales a parameter that linearly depends on y and removes the offset. | |
| std::vector< stf::parInfo > | getParInfoExp (int n_exp) |
| Creates stf::parInfo structs for n-exponential functions. | |
| stf::Table | outputWTau (const Vector_double &p, const std::vector< stf::parInfo > &parsInfo, double chisqr) |
| Calculates a weighted time constant. | |
| std::size_t | whereis (const Vector_double &data, double value) |
| Finds the index of data where value is encountered for the first time. | |
| std::vector< stf::storedFunc > | GetFuncLib () |
| Returns the library of functions for non-linear regression. | |
| Vector_double | nojac (double x, const Vector_double &p) |
| Dummy function, serves as a placeholder to initialize functions without a Jacobian. | |
| double | noscale (double param, double xscale, double xoff, double yscale, double yoff) |
| Dummy function, serves as a placeholder to initialize parameters without a scaling function. | |
| Table | defaultOutput (const Vector_double &pars, const std::vector< parInfo > &parsInfo, double chisqr) |
| Default fit output function, constructing a stf::Table from the parameters, their description and chisqr. | |
| template<typename T > | |
| T | SQR (T a) |
| Calculates the square of a number. | |
| Vector_double | filter (const Vector_double &toFilter, std::size_t filter_start, std::size_t filter_end, const Vector_double &a, int SR, stf::Func func, bool inverse=false) |
| Convolves a data set with a filter function. | |
| std::map< double, int > | histogram (const Vector_double &data, int nbins=-1) |
| Computes a histogram. | |
| StfDll Vector_double | deconvolve (const Vector_double &data, const Vector_double &templ, int SR, double hipass, double lopass, stfio::ProgressInfo &progDlg) |
| Deconvolves a template from a signal. | |
| template<class T > | |
| std::vector< T > | cubicSpline (const std::vector< T > &y, T oldF, T newF) |
| Interpolates a dataset using cubic splines. | |
| template<class T > | |
| std::vector< T > | diff (const std::vector< T > &input, T x_scale) |
| Differentiate data. | |
| double | integrate_simpson (const Vector_double &input, std::size_t a, std::size_t b, double x_scale) |
| Integration using Simpson's rule. | |
| double | integrate_trapezium (const Vector_double &input, std::size_t a, std::size_t b, double x_scale) |
| Integration using the trapezium rule. | |
| int | linsolv (int m, int n, int nrhs, Vector_double &A, Vector_double &B) |
| Solves a linear equation system using LAPACK. | |
| Vector_double | quad (const Vector_double &data, std::size_t begin, std::size_t end) |
| Solve quadratic equations for 3 adjacent sampling points. | |
| StfDll Vector_double | detectionCriterion (const Vector_double &data, const Vector_double &templ, stfio::ProgressInfo &progDlg) |
| Computes the event detection criterion according to Clements & Bekkers (1997). | |
| StfDll std::vector< int > | peakIndices (const Vector_double &data, double threshold, int minDistance) |
| Searches for positive-going peaks. | |
| StfDll Vector_double | linCorr (const Vector_double &va1, const Vector_double &va2, stfio::ProgressInfo &progDlg) |
| Computes the linear correlation between two arrays. | |
| double | fgaussColqu (double x, const Vector_double &p) |
| Computes a Gaussian that can be used as a filter kernel. | |
| double | fboltz (double x, const Vector_double &p) |
| Computes a Boltzmann function. | |
| double | fbessel (double x, int n) |
| Computes a Bessel polynomial. | |
| double | fbessel4 (double x, const Vector_double &p) |
| Computes a 4th-order Bessel polynomial that can be used as a filter kernel. | |
| int | fac (int arg) |
| Computes the faculty of an integer. | |
| int | pow2 (int arg) |
| Computes \( 2^{arg} \). Uses the bitwise-shift operator (<<). | |
| std::string | wx2std (const wxString &wxs) |
| wxString | std2wx (const std::string &sst) |
| wxString | sectionToString (const Section §ion) |
| Converts a Section to a wxString. | |
| wxString | CreatePreview (const wxString &fName) |
| Creates a preview of a text file. | |
| wxString | noPath (const wxString &fName) |
| Strips the directory off a full path name, returns only the filename. | |
| int | round (double toRound) |
| Does what it says. | |
Variables | |
| const double | PI = 3.14159265358979323846 |
| Add decimals if you are not satisfied. | |
The stimfit namespace.
All essential core functions and classes are in this namespace. Its purpose is to reduce name mangling problems.
1.7.6.1
