Collaboration diagram for Generic stimfit classes and functions:

Classes
class	Channel
	A Channel contains several data Sections representing observations of the same physical quantity. More...
class	Recording
	Represents the data within a file. More...
class	Section
	Represents a continuously sampled sweep of data points. More...
struct	stfnum::parInfo
	Information about parameters used in storedFunc. More...
class	stfnum::Table
	A table used for printing information. More...
struct	stfnum::storedFunc
	Function used for least-squares fitting. More...
class	stf::wxProgressInfo
	Progress Info interface adapter; maps to wxProgressDialog. More...
struct	stf::UserInput
	Represents user input from dialogs that can be used in plugins. More...
struct	stf::Plugin
	User-defined plugin. More...
struct	stf::Extension
	User-defined Python extension. More...
struct	stf::ifstreamMan
	Resource manager for ifstream objects. More...
struct	stf::ofstreamMan
	Resource manager for ofstream objects. More...
class	stf::Event
	Describes the attributes of an event. More...
struct	stf::PyMarker
	A marker that can be set from Python. More...
struct	stf::SectionAttributes
struct	stf::SectionPointer

Typedefs
typedef boost::function< double(double, const Vector_double &)>	stfnum::Func
	A function taking a double and a vector and returning a double.
typedef boost::function< Vector_double(double, const Vector_double &)>	stfnum::Jac
	The jacobian of a stfnum::Func.
typedef boost::function< double(double, double, double, double, double)>	stfnum::Scale
	Scaling function for fit parameters.
typedef boost::function< Table(const Vector_double &, const std::vector< stfnum::parInfo >, double)>	stfnum::Output
	Print the output of a fit into a stfnum::Table.
typedef boost::function< void(const Vector_double &, double, double, double, double, double, Vector_double &)>	stfnum::Init
	Initialising function for the parameters in stfnum::Func to start a fit.
typedef boost::function< Recording(const Recording &, const Vector_double &, std::map< std::string, double > &)>	stf::PluginFunc
	Get a Recording, do something with it, return the new Recording.

Enumerations
enum	stfnum::direction { stfnum::up , stfnum::down , stfnum::both , stfnum::undefined_direction }
	The direction of peak calculations. More...
enum	stfnum::baseline_method { stfnum::mean_sd = 0 , stfnum::median_iqr = 1 }
	Methods for Baseline computation. More...
enum	stf::cursor_type { stf::measure_cursor , stf::peak_cursor , stf::base_cursor , stf::decay_cursor , stf::latency_cursor , stf::zoom_cursor , stf::event_cursor , stf::annotation_cursor , stf::undefined_cursor }
	Mouse cursor types. More...
enum	stf::zoom_channels { stf::zoomch1 , stf::zoomch2 , stf::zoomboth }
	Determines which channels to scale. More...
enum	stf::latency_mode { stf::manualMode = 0 , stf::peakMode = 1 , stf::riseMode = 2 , stf::halfMode = 3 , stf::footMode = 4 , stf::undefinedMode }
	Latency cursor settings. More...
enum	stf::latency_window_mode { stf::defaultMode = 0 , stf::windowMode = 1 }
	Latency window settings. More...
enum	stf::extraction_mode { stf::criterion , stf::correlation , stf::deconvolution }
	Deconvolution. More...

Functions
	Channel::Channel (void)
	Default constructor.
	Channel::Channel (const Section &c_Section)
	Constructor.
	Channel::Channel (const std::deque< Section > &SectionList)
	Constructor.
	Channel::Channel (std::size_t c_n_sections, std::size_t section_size=0)
	Constructor.
	Channel::~Channel ()
	Destructor.
Section &	Channel::operator[] (std::size_t at_)
	Unchecked access to a section (read and write)
const Section &	Channel::operator[] (std::size_t at_) const
	Unchecked access to a section (read-only)
const std::string &	Channel::GetChannelName () const
	Retrieves the channel name.
const std::string &	Channel::GetYUnits () const
	Retrieves the y units string.
size_t	Channel::size () const
	Retrieves the size of the section array.
const Section &	Channel::at (std::size_t at_) const
	Range-checked access to a section (read-only).
Section &	Channel::at (std::size_t at_)
	Range-checked access to a section (read and write).
const std::deque< Section > &	Channel::get () const
	Low-level access to the section array (read-only).
std::deque< Section > &	Channel::get ()
	Low-level access to the section array (read and write).
void	Channel::SetChannelName (const std::string &value)
	Sets the channel name.
void	Channel::SetYUnits (const std::string &value)
	Sets the y units string.
void	Channel::InsertSection (const Section &c_Section, std::size_t pos)
	Inserts a section at the given position, overwriting anything that's currently stored at that position.
void	Channel::resize (std::size_t newSize)
	Resize the section array.
void	Channel::reserve (std::size_t resSize)
	Reserve memory for a number of sections.
	Recording::Recording ()
	Default constuctor.
	Recording::Recording (const Channel &c_Channel)
	Constructor.
	Recording::Recording (const std::deque< Channel > &ChannelList)
	Constructor.
	Recording::Recording (std::size_t c_n_channels, std::size_t c_n_sections=0, std::size_t c_n_points=0)
	Constructor.
virtual	Recording::~Recording ()
	Destructor.
std::size_t	Recording::GetChannelSize (std::size_t n_channel) const
	Retrieves the number of sections in a channel.
const std::deque< Channel > &	Recording::get () const
	Retrieves the channels (read-only).
std::deque< Channel > &	Recording::get ()
	Retrieves the channels (read and write).
const std::string &	Recording::GetFileDescription () const
	Retrieves the file description.
const std::string &	Recording::GetGlobalSectionDescription () const
	Retrieves the common section description.
const std::string &	Recording::GetScaling () const
	Retrieves the scaling as a string.
struct tm	Recording::GetDateTime () const
	Retrieves the date of recording as a string.
const std::string &	Recording::GetComment () const
	Retrieves a comment string.
const std::string &	Recording::GetXUnits () const
	Retrieves the x units.
std::size_t	Recording::size () const
	Retrieves the size of the channel array.
double	Recording::GetXScale () const
	Retrieves the x scaling (sampling interval).
double	Recording::GetSR () const
	Retrieves the sampling rate ( 1 / x-scale )
std::size_t	Recording::GetCurChIndex () const
	Retrieves the index of the current channel.
std::size_t	Recording::GetSecChIndex () const
	Retrieves the index of the second channel.
std::size_t	Recording::GetCurSecIndex () const
	Retrieves the index of the current section.
const std::vector< std::size_t > &	Recording::GetSelectedSections () const
	Retrieves the indices of the selected sections (read-only).
std::vector< std::size_t > &	Recording::GetSelectedSectionsW ()
	Retrieves the indices of the selected sections (read and write).
const Vector_double &	Recording::GetSelectBase () const
	Retrieves the stored baseline values of the selected sections (read-only).
Vector_double &	Recording::GetSelectBaseW ()
	Retrieves the stored baseline values of the selected sections (read and write).
const Section &	Recording::cursec () const
	Retrieves the currently accessed section in the active channel (read-only)
Section &	Recording::cursec ()
	Retrieves the currently accessed section in the active channel (read and write)
const Section &	Recording::secsec () const
	Retrieves the currently accessed section in the second (reference) channel (read-only)
const Channel &	Recording::curch () const
	Retrieves the active channel (read-only)
Channel &	Recording::curch ()
	Retrieves active channel (read and write)
const Channel &	Recording::secch () const
	Retrieves the second (reference) channel (read-only)
const Channel &	Recording::at (std::size_t n_c) const
	Range-checked access to a channel (read-only).
Channel &	Recording::at (std::size_t n_c)
	Range-checked access to a channel (read and write).
void	Recording::SetFileDescription (const std::string &value)
	Sets the file description.
void	Recording::SetGlobalSectionDescription (const std::string &value)
	Sets the common section description.
void	Recording::SetScaling (const std::string &value)
	Sets the scaling as a string.
int	Recording::SetTime (const std::string &value)
	Sets the time of recording as a string.
int	Recording::SetTime (int hour, int minute, int sec)
int	Recording::SetDate (const std::string &value)
	Sets the date of recording as a string.
int	Recording::SetDate (int year, int month, int mday)
void	Recording::SetDateTime (const struct tm &value)
	Sets the date and time of recording as struct tm.
void	Recording::SetDateTime (int year, int month, int mday, int hour, int minute, int sec)
void	Recording::SetComment (const std::string &value)
	Sets a comment string.
void	Recording::SetGlobalYUnits (std::size_t n_channel, const std::string &value)
	Sets the y units for a channel.
void	Recording::SetXUnits (const std::string &value)
	Sets the x units.
void	Recording::SetXScale (double value)
	Sets the x scaling.
void	Recording::SetCurChIndex (std::size_t value)
	Sets the index of the current channel.
void	Recording::SetSecChIndex (std::size_t value)
	Sets the index of the second channel.
void	Recording::SetCurSecIndex (std::size_t value)
	Sets the index of the current section.
virtual void	Recording::resize (std::size_t c_n_channels)
	Resize the Recording to a new number of channels.
virtual void	Recording::InsertChannel (Channel &c_Channel, std::size_t pos)
	Insert a Channel at a given position.
void	Recording::CopyAttributes (const Recording &c_Recording)
	Copy descriptive attributes from another Recording to this Recording.
void	Recording::MakeAverage (Section &AverageReturn, Section &SigReturn, std::size_t channel, const std::vector< std::size_t > &section_index, bool isSig, const std::vector< int > &shift) const
	Calculates an average of several traces.
void	Recording::AddRec (const Recording &toAdd)
	Add a Recording at the end of this Recording.
void	Recording::SelectTrace (std::size_t sectionToSelect, std::ptrdiff_t base_start, std::ptrdiff_t base_end)
	Selects a section.
bool	Recording::UnselectTrace (std::size_t sectionToUnselect)
	Unselects a section if it was selected before.
Channel &	Recording::operator[] (std::size_t at)
	Unchecked channel access (read and write)
const Channel &	Recording::operator[] (std::size_t at) const
	Unchecked channel access (read-only)
std::string	Recording::GetEventDescription (int type)
	Get Description of Event Type.
void	Recording::SetEventDescription (int type, const char *Description)
	Set Description of Event Type.
void	Recording::InitSectionMarkerList (size_t n)
	Initialize List of Section Markers.
int	Recording::GetSectionType (size_t section_number)
	Get Type of Section.
void	Recording::SetSectionType (size_t section_number, int type)
	Set Type of Section.
	Section::Section ()
	Default constructor.
	Section::Section (const Vector_double &valA, const std::string &label="\0")
	Constructor.
	Section::Section (std::size_t size, const std::string &label="\0")
	Yet another constructor.
	Section::~Section ()
	Destructor.
double &	Section::operator[] (std::size_t at)
	Unchecked access. Returns a non-const reference.
double	Section::operator[] (std::size_t at) const
	Unchecked access. Returns a copy.
double	Section::at (std::size_t at_) const
	Range-checked access. Returns a copy.
double &	Section::at (std::size_t at_)
	Range-checked access. Returns a non-const reference.
const Vector_double &	Section::get () const
	Low-level access to the valarray (read-only).
Vector_double &	Section::get_w ()
	Low-level access to the valarray (read and write).
void	Section::resize (std::size_t new_size)
	Resize the Section to a new number of data points; deletes all previously stored data when gcc is used.
size_t	Section::size () const
	Retrieve the number of data points.
void	Section::SetXScale (double value)
	Sets the x scaling.
double	Section::GetXScale () const
	Retrieves the x scaling.
const std::string &	Section::GetSectionDescription () const
	Retrieves a section description.
void	Section::SetSectionDescription (const std::string &value)
	Sets a section description.
std::size_t	Section::GetSectionSize ()
	Range-checked access. Returns a non-const reference.
void	Section::AddAnnotation (Annotation annotation)
void	Section::MoveAnnotation (size_t index, int new_position)
void	Section::RemoveAnnotation (size_t index)
void	Section::EraseAllAnnotations ()
std::vector< Annotation >	Section::GetAnnotationList ()
std::size_t	Section::GetFirstAnnotationPosition ()
std::size_t	Section::GetLastAnnotationPosition ()
template<typename T>
T	stfnum::linFit (const std::vector< T > &x, const std::vector< T > &y, T &m, T &c)
	Performs a linear fit.
double StfnumDll	stfnum::lmFit (const Vector_double &data, double dt, const stfnum::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	stfnum::flin (double x, const Vector_double &p)
	Linear function.
void	stfnum::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 stfnum::storedFunc for linear functions.
StfnumDll stfnum::storedFunc	stfnum::initLinFunc ()
	initializes a linear function
Vector_double	stfnum::get_scale (Vector_double &data, double oldx)
	Compute and perform normalisation.
StfnumDll Vector_double	stfnum::LM_default_opts ()
	Return default LM options.
StfnumDll double	stfnum::fexp (double x, const Vector_double &p)
	Sum of n exponential functions.
Vector_double	stfnum::fexp_jac (double x, const Vector_double &p)
	Computes the Jacobian of stfnum::fexp().
void	stfnum::fexp_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit)
	Initialises parameters for fitting stfnum::fexp() to data.
void	stfnum::fexp_init2 (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit)
	Yet another initialiser for fitting stfnum::fexp() to data.
StfnumDll double	stfnum::fexpde (double x, const Vector_double &p)
	Monoexponential function with delay.
void	stfnum::fexpde_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit)
	Initialises parameters for fitting stfnum::fexpde() to data.
StfnumDll double	stfnum::fexpbde (double x, const Vector_double &p)
	Biexponential function with delay.
double	stfnum::fexptde (double x, const Vector_double &p)
	Triexponential function with delay.
void	stfnum::fexpbde_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit)
	Initialises parameters for fitting stfnum::fexpde() to data.
void	stfnum::fexptde_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit)
	Initialises parameters for fitting stfnum::fexpde() to data.
StfnumDll double	stfnum::falpha (double x, const Vector_double &p)
	Alpha function.
Vector_double	stfnum::falpha_jac (double x, const Vector_double &p)
	Computes the Jacobian of stfnum::falpha().
StfnumDll double	stfnum::fHH (double x, const Vector_double &p)
	Hodgkin-Huxley sodium conductance function.
StfnumDll double	stfnum::fgauss (double x, const Vector_double &p)
	Computes the sum of an arbitrary number of Gaussians.
Vector_double	stfnum::fgauss_jac (double x, const Vector_double &p)
	Computes the Jacobian of a sum of Gaussians.
StfnumDll double	stfnum::fgnabiexp (double x, const Vector_double &p)
	power of 1 sodium conductance function.
Vector_double	stfnum::fgnabiexp_jac (double x, const Vector_double &p)
	Computes the Jacobian of stfnum::fgnabiexp().
void	stfnum::falpha_init (const Vector_double &data, double base, double peak, double RTLoHI, double HalfWidth, double dt, Vector_double &pInit)
	Initialises parameters for fitting stfnum::falpha() to data.
void	stfnum::fgauss_init (const Vector_double &data, double base, double peak, double RTLoHI, double HalfWidth, double dt, Vector_double &pInit)
	Initialises parameters for fitting stfnum::fgauss() to data.
void	stfnum::fHH_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit)
	Initialises parameters for fitting stfnum::falpha() to data.
void	stfnum::fgnabiexp_init (const Vector_double &data, double base, double peak, double RTLoHi, double HalfWidth, double dt, Vector_double &pInit)
	Initialises parameters for fitting stfnum::falpha() to data.
double	stfnum::xscale (double param, double xscale, double xoff, double yscale, double yoff)
	Scales a parameter that linearly depends on x.
double	stfnum::xunscale (double param, double xscale, double xoff, double yscale, double yoff)
	Unscales a parameter that linearly depends on x.
double	stfnum::yscale (double param, double xscale, double xoff, double yscale, double yoff)
	Scales a parameter that linearly depends on y.
double	stfnum::yscaleoffset (double param, double xscale, double xoff, double yscale, double yoff)
	Scales a parameter that linearly depends on y and adds an offset.
double	stfnum::yunscale (double param, double xscale, double xoff, double yscale, double yoff)
	Unscales a parameter that linearly depends on y.
double	stfnum::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< stfnum::parInfo >	stfnum::getParInfoExp (int n_exp)
	Creates stfnum::parInfo structs for n-exponential functions.
stfnum::Table	stfnum::outputWTau (const Vector_double &p, const std::vector< stfnum::parInfo > &parsInfo, double chisqr)
	Calculates a weighted time constant.
std::size_t	stfnum::whereis (const Vector_double &data, double value)
	Finds the index of data where value is encountered for the first time.
StfnumDll std::vector< stfnum::storedFunc >	stfnum::GetFuncLib ()
	Returns the library of functions for non-linear regression.
StfnumDll double	stfnum::base (enum stfnum::baseline_method method, 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.
StfnumDll double	stfnum::peak (const std::vector< double > &data, double base, std::size_t llp, std::size_t ulp, int pM, stfnum::direction, double &maxT)
	Find the peak value of data between llp and ulp.
StfnumDll double	stfnum::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.
StfnumDll double	stfnum::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.
StfnumDll double	stfnum::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.
StfnumDll double	stfnum::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.
StfnumDll double	stfnum::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.
StfnumDll double	stfnum::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.
Vector_double	stfnum::nojac (double x, const Vector_double &p)
	Dummy function, serves as a placeholder to initialize functions without a Jacobian.
double	stfnum::noscale (double param, double xscale, double xoff, double yscale, double yoff)
	Dummy function, serves as a placeholder to initialize parameters without a scaling function.
	stfnum::parInfo::parInfo ()
	Default constructor.
	stfnum::parInfo::parInfo (const std::string &desc_, bool toFit_, bool constrained_=false, double constr_lb_=0, double constr_ub_=0, Scale scale_=noscale, Scale unscale_=noscale)
	Constructor.
	stfnum::Table::Table (std::size_t nRows, std::size_t nCols)
	Constructor.
	stfnum::Table::Table (const std::map< std::string, double > &map)
	Constructor.
double	stfnum::Table::at (std::size_t row, std::size_t col) const
	Range-checked access. Returns a copy. Throws std::out_of_range if out of range.
double &	stfnum::Table::at (std::size_t row, std::size_t col)
	Range-checked access. Returns a reference. Throws std::out_of_range if out of range.
bool	stfnum::Table::IsEmpty (std::size_t row, std::size_t col) const
	Check whether a cell is empty.
void	stfnum::Table::SetEmpty (std::size_t row, std::size_t col, bool value=true)
	Empties or un-empties a cell.
void	stfnum::Table::SetRowLabel (std::size_t row, const std::string &label)
	Sets the label of a row.
void	stfnum::Table::SetColLabel (std::size_t col, const std::string &label)
	Sets the label of a column.
const std::string &	stfnum::Table::GetRowLabel (std::size_t row) const
	Retrieves the label of a row.
const std::string &	stfnum::Table::GetColLabel (std::size_t col) const
	Retrieves the label of a column.
std::size_t	stfnum::Table::nRows () const
	Retrieves the number of rows.
std::size_t	stfnum::Table::nCols () const
	Retrieves the number of columns.
void	stfnum::Table::AppendRows (std::size_t nRows)
	Appends rows to the table.
Table	stfnum::defaultOutput (const Vector_double &pars, const std::vector< parInfo > &parsInfo, double chisqr)
	Default fit output function, constructing a stfnum::Table from the parameters, their description and chisqr.
	stfnum::storedFunc::storedFunc (const std::string &name_, const std::vector< parInfo > &pInfo_, const Func &func_, const Init &init_, const Jac &jac_, bool hasJac_=true, const Output &output_=defaultOutput)
	Constructor.
	stfnum::storedFunc::~storedFunc ()
	Destructor.
template<typename T>
T	stfnum::SQR (T a)
	Calculates the square of a number.
StfnumDll Vector_double	stfnum::filter (const Vector_double &toFilter, std::size_t filter_start, std::size_t filter_end, const Vector_double &a, int SR, stfnum::Func func, bool inverse=false)
	Convolves a data set with a filter function.
std::map< double, int >	stfnum::histogram (const Vector_double &data, int nbins=-1)
	Computes a histogram.
StfnumDll Vector_double	stfnum::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 >	stfnum::cubicSpline (const std::vector< T > &y, T oldF, T newF)
	Interpolates a dataset using cubic splines.
template<class T>
std::vector< T >	stfnum::diff (const std::vector< T > &input, T x_scale)
	Differentiate data.
StfnumDll double	stfnum::integrate_simpson (const Vector_double &input, std::size_t a, std::size_t b, double x_scale)
	Integration using Simpson's rule.
StfnumDll double	stfnum::integrate_trapezium (const Vector_double &input, std::size_t a, std::size_t b, double x_scale)
	Integration using the trapezium rule.
int	stfnum::linsolv (int m, int n, int nrhs, Vector_double &A, Vector_double &B)
	Solves a linear equation system using LAPACK.
StfnumDll Vector_double	stfnum::quad (const Vector_double &data, std::size_t begin, std::size_t end)
	Solve quadratic equations for 3 adjacent sampling points.
StfnumDll Vector_double	stfnum::detectionCriterion (const Vector_double &data, const Vector_double &templ, stfio::ProgressInfo &progDlg)
	Computes the event detection criterion according to Clements & Bekkers (1997).
StfnumDll std::vector< int >	stfnum::peakIndices (const Vector_double &data, double threshold, int minDistance)
	Searches for positive-going peaks.
StfnumDll Vector_double	stfnum::linCorr (const Vector_double &va1, const Vector_double &va2, stfio::ProgressInfo &progDlg)
	Computes the linear correlation between two arrays.
StfnumDll double	stfnum::fgaussColqu (double x, const Vector_double &p)
	Computes a Gaussian that can be used as a filter kernel.
double	stfnum::fboltz (double x, const Vector_double &p)
	Computes a Boltzmann function.
double	stfnum::fbessel (double x, int n)
	Computes a Bessel polynomial.
StfnumDll double	stfnum::fbessel4 (double x, const Vector_double &p)
	Computes a 4th-order Bessel polynomial that can be used as a filter kernel.
int	stfnum::fac (int arg)
	Computes the faculty of an integer.
int	stfnum::pow2 (int arg)
	Computes \( 2^{arg} \). Uses the bitwise-shift operator (<<).
	stf::wxProgressInfo::wxProgressInfo (const std::string &title, const std::string &message, int maximum, bool verbose=true)
bool	stf::wxProgressInfo::Update (int value, const std::string &newmsg="", bool *skip=NULL)
	Updates the progress info.
std::string	stf::wx2std (const wxString &wxs)
wxString	stf::std2wx (const std::string &sst)
wxString	stf::sectionToString (const Section &section)
	Converts a Section to a wxString.
wxString	stf::CreatePreview (const wxString &fName)
	Creates a preview of a text file.
wxString	stf::noPath (const wxString &fName)
	Strips the directory off a full path name, returns only the filename.
	stf::UserInput::UserInput (const std::vector< std::string > &labels_=std::vector< std::string >(0), const Vector_double &defaults_=Vector_double(0), std::string title_="\0")
	Constructor.
	stf::Plugin::Plugin (const wxString &menuEntry_, const PluginFunc &pluginFunc_, const UserInput &input_=UserInput())
	Constructor.
	stf::Plugin::~Plugin ()
	Destructor.
	stf::Extension::Extension (const std::string &menuEntry_, void *pyFunc_, const std::string &description_, bool requiresFile_)
	Constructor.
	stf::Extension::~Extension ()
	Destructor.
	stf::ifstreamMan::ifstreamMan (const wxString &filename)
	Constructor.
	stf::ifstreamMan::~ifstreamMan ()
	Destructor.
	stf::ofstreamMan::ofstreamMan (const wxString &filename)
	Constructor.
	stf::ofstreamMan::~ofstreamMan ()
	Destructor.
	stf::Event::Event (std::size_t start, std::size_t peak, std::size_t size, wxCheckBox *cb)
	Constructor.
	stf::Event::~Event ()
	Destructor.
std::size_t	stf::Event::GetEventStartIndex () const
	Retrieves the start index of an event.
std::size_t	stf::Event::GetEventPeakIndex () const
	Retrieves the index of an event's peak.
std::size_t	stf::Event::GetEventSize () const
	Retrieves the size of an event.
bool	stf::Event::GetDiscard () const
	Indicates whether an event should be discarded.
wxCheckBox *	stf::Event::GetCheckBox ()
	Get the check box associated with this event.
void	stf::Event::SetEventStartIndex (std::size_t value)
	Sets the start index of an event.
void	stf::Event::SetEventPeakIndex (std::size_t value)
	Sets the index of an event's peak.
void	stf::Event::SetEventSize (std::size_t value)
	Sets the size of an event.
	stf::PyMarker::PyMarker (double xv, double yv)
	Constructor.
	stf::SectionAttributes::SectionAttributes ()
	stf::SectionPointer::SectionPointer (Section *pSec=NULL, const SectionAttributes &sa=SectionAttributes())
int	stf::round (double toRound)
	Does what it says.

Variables
std::string	stfnum::parInfo::desc
bool	stfnum::parInfo::toFit
bool	stfnum::parInfo::constrained
double	stfnum::parInfo::constr_lb
double	stfnum::parInfo::constr_ub
Scale	stfnum::parInfo::scale
Scale	stfnum::parInfo::unscale
std::string	stfnum::storedFunc::name
std::vector< parInfo >	stfnum::storedFunc::pInfo
Func	stfnum::storedFunc::func
Init	stfnum::storedFunc::init
Jac	stfnum::storedFunc::jac
bool	stfnum::storedFunc::hasJac
Output	stfnum::storedFunc::output
std::vector< std::string >	stf::UserInput::labels
Vector_double	stf::UserInput::defaults
std::string	stf::UserInput::title
int	stf::Plugin::id
static int	stf::Plugin::n_plugins
wxString	stf::Plugin::menuEntry
PluginFunc	stf::Plugin::pluginFunc
UserInput	stf::Plugin::input
int	stf::Extension::id
static int	stf::Extension::n_extensions
std::string	stf::Extension::menuEntry
void *	stf::Extension::pyFunc
std::string	stf::Extension::description
bool	stf::Extension::requiresFile
wxFFile	stf::ifstreamMan::myStream
	The managed stream.
wxFFile	stf::ofstreamMan::myStream
	The managed stream.
double	stf::PyMarker::x
double	stf::PyMarker::y
std::vector< stf::Event >	stf::SectionAttributes::eventList
std::vector< stf::PyMarker >	stf::SectionAttributes::pyMarkers
bool	stf::SectionAttributes::isFitted
bool	stf::SectionAttributes::isIntegrated
stfnum::storedFunc *	stf::SectionAttributes::fitFunc
Vector_double	stf::SectionAttributes::bestFitP
Vector_double	stf::SectionAttributes::quad_p
std::size_t	stf::SectionAttributes::storeFitBeg
std::size_t	stf::SectionAttributes::storeFitEnd
std::size_t	stf::SectionAttributes::storeIntBeg
std::size_t	stf::SectionAttributes::storeIntEnd
stfnum::Table	stf::SectionAttributes::bestFit
Section *	stf::SectionPointer::pSection
SectionAttributes	stf::SectionPointer::sec_attr
const double	stf::PI =3.14159265358979323846
	Add decimals if you are not satisfied.

Detailed Description

Typedef Documentation

◆ Func

typedef boost::function<double(double, const Vector_double&)> stfnum::Func

A function taking a double and a vector and returning a double.

Type definition for a function (or, to be precise, any 'callable entity') that takes a double (the x-value) and a vector of parameters and returns the function's result (the y-value).

Definition at line 87 of file stfnum.h.

◆ Init

typedef boost::function<void(const Vector_double&, double, double, double, double, double, Vector_double&)> stfnum::Init

Initialising function for the parameters in stfnum::Func to start a fit.

Definition at line 250 of file stfnum.h.

◆ Jac

typedef boost::function<Vector_double(double, const Vector_double&)> stfnum::Jac

The jacobian of a stfnum::Func.

Definition at line 90 of file stfnum.h.

◆ Output

typedef boost::function<Table(const Vector_double&,const std::vector<stfnum::parInfo>,double)> stfnum::Output

Print the output of a fit into a stfnum::Table.

Definition at line 242 of file stfnum.h.

◆ PluginFunc

typedef boost::function<Recording(const Recording&,const Vector_double&,std::map<std::string, double>&)> stf::PluginFunc

Get a Recording, do something with it, return the new Recording.

Definition at line 140 of file stf.h.

◆ Scale

typedef boost::function<double(double, double, double, double, double)> stfnum::Scale

Scaling function for fit parameters.

Definition at line 93 of file stfnum.h.

Enumeration Type Documentation

◆ baseline_method

enum stfnum::baseline_method

Methods for Baseline computation.

Enumerator
mean_sd	Compute mean and s.d. for Baseline and Base SD.
median_iqr	Compute median and IQR for Baseline and Base SD.

Definition at line 538 of file stfnum.h.

◆ cursor_type

enum stf::cursor_type

Mouse cursor types.

Enumerator
measure_cursor	Measurement cursor (crosshair).
peak_cursor	Peak calculation limits cursor.
base_cursor	Baseline calculation limits cursor.
decay_cursor	Fit limits cursor.
latency_cursor	Latency cursor.
zoom_cursor	Zoom rectangle cursor.
event_cursor	Event mode cursor.
annotation_cursor	Annotation mode cursor.
undefined_cursor	Undefined cursor.

Definition at line 364 of file stf.h.

◆ direction

enum stfnum::direction

The direction of peak calculations.

Enumerator
up	Find positive-going peaks.
down	Find negative-going peaks.
both	Find negative- or positive-going peaks, whichever is larger.
undefined_direction	Undefined direction.

Definition at line 530 of file stfnum.h.

◆ extraction_mode

enum stf::extraction_mode

Deconvolution.

Enumerator
criterion	Clements & Bekkers criterion.
correlation	Jonas et al. correlation coefficient.
deconvolution	Pernia-Andrade et al. deconvolution.

Definition at line 424 of file stf.h.

◆ latency_mode

enum stf::latency_mode

Latency cursor settings.

Enumerator
manualMode	Set the corresponding latency cursor manually (by clicking on the graph).
peakMode	Set the corresponding latency cursor to the peak.
riseMode	Set the corresponding latency cursor to the maximal slope of rise.
halfMode	Set the corresponding latency cursor to the half-maximal amplitude.
footMode	Set the corresponding latency cursor to the beginning of an event.
undefinedMode	undefined mode.

Definition at line 387 of file stf.h.

◆ latency_window_mode

enum stf::latency_window_mode

Latency window settings.

Enumerator
defaultMode	Use the current peak cursor window for the active channel.
windowMode	Use a window of 100 sampling points around the peak.

Definition at line 397 of file stf.h.

◆ zoom_channels

enum stf::zoom_channels

Determines which channels to scale.

Enumerator
zoomch1	Scaling applies to channel 1 only.
zoomch2	Scaling applies to channel 2 only.
zoomboth	Scaling applies to both channels.

Definition at line 380 of file stf.h.

Function Documentation

◆ AddAnnotation()

void Section::AddAnnotation ( Annotation annotation )

◆ AddRec()

void Recording::AddRec ( const Recording & toAdd )

Add a Recording at the end of this Recording.

Parameters

toAdd The Recording to be added.

References Recording().

◆ AppendRows()

void stfnum::Table::AppendRows ( std::size_t nRows )

Appends rows to the table.

Parameters

nRows The number of rows to be appended.

References nRows().

◆ at() [1/8]

Section & Channel::at ( std::size_t at_ )

Range-checked access to a section (read and write).

Will throw std::out_of_range if out of range.

Parameters

at_	The index of the section.

Returns: The section at index at_.

◆ at() [2/8]

const Section & Channel::at ( std::size_t at_ ) const

Range-checked access to a section (read-only).

Will throw std::out_of_range if out of range.

Parameters

at_	The index of the section.

Returns: The section at index at_.

◆ at() [3/8]

Channel & Recording::at ( std::size_t n_c )

Range-checked access to a channel (read and write).

Will throw std::out_of_range if out of range.

Parameters

n_c	The index of the channel.

Returns: The channel at index n_c.

◆ at() [4/8]

const Channel & Recording::at ( std::size_t n_c ) const

Range-checked access to a channel (read-only).

Will throw std::out_of_range if out of range.

Parameters

n_c	The index of the channel.

Returns: The channel at index n_c.

Referenced by operator[](), and operator[]().

◆ at() [5/8]

double & Section::at ( std::size_t at_ )

Range-checked access. Returns a non-const reference.

Throws std::out_of_range if out of range.

Parameters

at_	Data point index.

Returns: Reference to the data point at index at_

◆ at() [6/8]

double Section::at ( std::size_t at_ ) const

Range-checked access. Returns a copy.

Throws std::out_of_range if+#include "./annotation.h" out of range.

Parameters

at_	Data point index.

Returns: Copy of the data point at index at_

Referenced by operator[](), and operator[]().

◆ at() [7/8]

double & stfnum::Table::at	(	std::size_t	row,
		std::size_t	col )

Range-checked access. Returns a reference. Throws std::out_of_range if out of range.

Parameters

row	0-based row index.
col	0-based column index.

Returns: A reference to the double at row, col.

◆ at() [8/8]

double stfnum::Table::at	(	std::size_t	row,
		std::size_t	col ) const

Range-checked access. Returns a copy. Throws std::out_of_range if out of range.

Parameters

row	0-based row index.
col	0-based column index.

Returns: A copy of the double at row, col.

◆ base()

StfnumDll double stfnum::base	(	enum stfnum::baseline_method	method,
		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.

Parameters

method	0: mean and s.d.; 1: median
var	Will contain the variance on exit (only when method=0).
data	The data waveform to be analysed.
llb	Averaging will be started at this index.
ulb	Index of the last data point included in the average (legacy of the PASCAL version).
llp	Lower limit of the peak window (see stfnum::peak()).
ulp	Upper limit of the peak window (see stfnum::peak()).

Returns: The baseline value - either the mean or the median depending on method.

References StfnumDll.

Referenced by falpha_init(), fexp_init(), fexp_init2(), fexpbde_init(), fexpde_init(), fexptde_init(), fgauss_init(), fgnabiexp_init(), fHH_init(), flin_init(), peak(), risetime(), risetime2(), and t_half().

◆ Channel() [1/4]

Channel::Channel ( const Section & c_Section )

explicit

Constructor.

Parameters

c_Section A single section from which to construct the channel

◆ Channel() [2/4]

Channel::Channel ( const std::deque< Section > & SectionList )

explicit

Constructor.

Parameters

SectionList A vector of Sections from which to construct the channel

◆ Channel() [3/4]

Channel::Channel	(	std::size_t	c_n_sections,
		std::size_t	section_size = 0 )

explicit

Constructor.

Setting the number of sections at construction time will avoid unnecessary memory re-allocations.

Parameters

c_n_sections	The number of sections.
section_size	Initial section size. Will serve additional re-alocations if known at construction time.

◆ Channel() [4/4]

Channel::Channel ( void )

explicit

Default constructor.

◆ CopyAttributes()

void Recording::CopyAttributes ( const Recording & c_Recording )

Copy descriptive attributes from another Recording to this Recording.

This will copy the file and global section decription, the scaling, time, date, comment and global y units strings and the x-scale.

Parameters

c_Recording The Recording from which to copy the attributes.

References Recording().

◆ CreatePreview()

wxString stf::CreatePreview ( const wxString & fName )

Creates a preview of a text file.

Parameters

fName Full path name of the file.

Returns: A string showing at most the initial 100 lines of the text file.

◆ cubicSpline()

template<class T>

std::vector< T > stfnum::cubicSpline	(	const std::vector< T > &	y,
		T	oldF,
		T	newF )

Interpolates a dataset using cubic splines.

Parameters

y	The valarray to be interpolated.
oldF	The original sampling frequency.
newF	The new frequency of the interpolated array.

Returns: The interpolated data set.

Definition at line 564 of file stfnum.h.

References size, spline_cubic_set(), and spline_cubic_val().

◆ curch() [1/2]

Channel & Recording::curch ( )

inline

Retrieves active channel (read and write)

Returns: The active channel.

Definition at line 194 of file recording.h.

◆ curch() [2/2]

const Channel & Recording::curch ( ) const

inline

Retrieves the active channel (read-only)

Returns: The active channel.

Definition at line 189 of file recording.h.

◆ cursec() [1/2]

Section & Recording::cursec ( )

inline

Retrieves the currently accessed section in the active channel (read and write)

Returns: The currently accessed section in the active channel.

Definition at line 179 of file recording.h.

◆ cursec() [2/2]

const Section & Recording::cursec ( ) const

inline

Retrieves the currently accessed section in the active channel (read-only)

Returns: The currently accessed section in the active channel.

Definition at line 174 of file recording.h.

◆ deconvolve()

StfnumDll Vector_double stfnum::deconvolve	(	const Vector_double &	data,
		const Vector_double &	templ,
		int	SR,
		double	hipass,
		double	lopass,
		stfio::ProgressInfo &	progDlg )

Deconvolves a template from a signal.

Parameters

data	The input signal
templ	The template
SR	The sampling rate in kHz.
hipass	Highpass filter cutoff frequency in kHz
lopass	Lowpass filter cutoff frequency in kHz

Returns: The result of the deconvolution

References StfnumDll.

◆ defaultOutput()

Table stfnum::defaultOutput	(	const Vector_double &	pars,
		const std::vector< parInfo > &	parsInfo,
		double	chisqr )

Default fit output function, constructing a stfnum::Table from the parameters, their description and chisqr.

Referenced by stfnum::storedFunc::storedFunc().

◆ detectionCriterion()

StfnumDll Vector_double stfnum::detectionCriterion	(	const Vector_double &	data,
		const Vector_double &	templ,
		stfio::ProgressInfo &	progDlg )

Computes the event detection criterion according to Clements & Bekkers (1997).

Parameters

data	The valarray from which to extract events.
templ	A template waveform that is used for event detection.

Returns: The detection criterion for every value of data.

◆ diff()

template<class T>

std::vector< T > stfnum::diff	(	const std::vector< T > &	input,
		T	x_scale )

Differentiate data.

Definition at line 593 of file stfnum.h.

References n.

◆ EraseAllAnnotations()

void Section::EraseAllAnnotations ( )

◆ Event()

stf::Event::Event	(	std::size_t	start,
		std::size_t	peak,
		std::size_t	size,
		wxCheckBox *	cb )

explicit

Constructor.

References size.

◆ Extension()

stf::Extension::Extension	(	const std::string &	menuEntry_,
		void *	pyFunc_,
		const std::string &	description_,
		bool	requiresFile_ )

inline

Constructor.

Parameters

menuEntry_	Menu entry string for this extension.
pyFunc_	Python function to be called.
description_	Description for this function.
requiresFile_	Whether a file needs to be open for this function to work

Definition at line 212 of file stf.h.

References description, menuEntry, n_extensions, pyFunc, and requiresFile.

◆ fac()

int stfnum::fac ( int arg )

Computes the faculty of an integer.

Parameters

arg	Argument of the function.

Returns: The faculty of arg.

◆ falpha()

StfnumDll double stfnum::falpha	(	double	x,
		const Vector_double &	p )

Alpha function.

\[f(x)=p_0 \frac{x}{p_1} \mathrm{e}^{\left(1 - \frac{x}{p_1} \right)} + p_2\]

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the amplitude, p[1] is the rate and p[2] is the offset.

Returns: The evaluated function.

References StfnumDll.

◆ falpha_init()

void stfnum::falpha_init	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHI,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Initialises parameters for fitting stfnum::falpha() to data.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 3. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ falpha_jac()

Vector_double stfnum::falpha_jac	(	double	x,
		const Vector_double &	p )

Computes the Jacobian of stfnum::falpha().

\begin{eqnarray*} j_0(x) &=& \frac{\partial f(x)}{\partial p_0} = \frac{x \mathrm{e}^{\left(1 - \frac{x}{p_1} \right)}}{p_1} \\ j_1(x) &=& \frac{\partial f(x)}{\partial p_1} = \frac{x \mathrm{e}^{\left(1 - \frac{x}{p_1} \right)}}{p_1} \left(\frac{p_0 x}{p_1^2} - \frac{p_0}{p_1} \right) \\ j_2(x) &=& \frac{\partial f(x)}{\partial p_2} = 1 \end{eqnarray*}

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the amplitude, p[1] is the rate and p[2] is the offset.

Returns: A valarray j with the evaluated Jacobian, where
j[0] contains the derivative with respect to p[0],
j[1] contains the derivative with respect to p[1] and
j[2] contains the derivative with respect to p[2].

◆ fbessel()

double stfnum::fbessel	(	double	x,
		int	n )

Computes a Bessel polynomial.

\[ f(x, n) = \sum_{k=0}^n \frac{ \left( 2n - k \right) ! }{ \left( n - k \right) ! k! } \frac{x^k}{ 2^{n-k} } \]

Parameters

x	Argument of the function.
n	Order of the polynomial.

Returns: The evaluated function.

References n, and StfnumDll.

◆ fbessel4()

StfnumDll double stfnum::fbessel4	(	double	x,
		const Vector_double &	p )

Computes a 4th-order Bessel polynomial that can be used as a filter kernel.

\[ f(x) = \frac{b(0,4)}{b(\frac{0.355589x}{p_0},4)} \]

where \( b(a,n) \) is the bessel polynomial stfnum::fbessel().

Parameters

x	Argument of the function.
p	Function parameters, where p[0] is the corner frequency (-3 dB attenuation)

Returns: The evaluated function.

◆ fboltz()

double stfnum::fboltz	(	double	x,
		const Vector_double &	p )

Computes a Boltzmann function.

\[f(x)=\frac{1}{1+\mathrm{e}^{\frac{p_0-x}{p_1}}}\]

Parameters

x	Argument of the function.
p	Function parameters, where p[0] is the midpoint and p[1] is the slope of the function.

Returns: The evaluated function.

◆ fexp()

StfnumDll double stfnum::fexp	(	double	x,
		const Vector_double &	p )

Sum of n exponential functions.

\[f(x)=p_{2n} + \sum_{i=0}^{n - 1}p_{2i}\mathrm{e}^{\left( \frac{x}{p_{2i + 1}}\right)}\]

Parameters

x	Function argument.
p	A valarray of parameters of size 2n+1, where n is the number of exponential terms, p[2i] is the amplitude term, p[2i+1] is the time constant, p[2n], the last element, contains the offset and i denotes the i -th exponential term (running from 0 to n-1).

Returns: The evaluated function.

References StfnumDll.

◆ fexp_init()

void stfnum::fexp_init	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHi,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Initialises parameters for fitting stfnum::fexp() to data.

This needs to be made more robust.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 2n+1, where n is the number of exponential functions. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ fexp_init2()

void stfnum::fexp_init2	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHi,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Yet another initialiser for fitting stfnum::fexp() to data.

In this case, one of the amplitude terms will have another sign than the others, making it more suitable for fitting PSCs or PSPs. However, this often fails to work in practice.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 2n+1, where n is the number of exponential functions. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ fexp_jac()

Vector_double stfnum::fexp_jac	(	double	x,
		const Vector_double &	p )

Computes the Jacobian of stfnum::fexp().

\begin{eqnarray*} j_{2i}(x) &=& \frac{\partial f(x)}{\partial p_{2i}} = \mathrm{e}^{\left(\frac{-x}{p_{2i+1}}\right)} \\ j_{2i+1}(x) &=& \frac{\partial f(x)}{\partial p_{2i+1}} = \frac{p_{2i}}{p_{2i+1}^2} x \mathrm{e}^{\left( \frac{-x}{p_{2i+1}}\right)} \\ j_n(x) &=& \frac{\partial f(x)}{\partial p_{n}} = 1 \end{eqnarray*}

Parameters

x	Function argument.
p	A valarray of parameters of size 2n+1, where n is the number of exponential terms, p[2i] is the amplitude term, p[2i+1] is the time constant, p[2n], the last element, contains the offset and i denotes the i -th exponential term (running from 0 to n-1).

Returns: A valarray j of size 2n+1 with the evaluated Jacobian, where
j[2i] contains the derivative with respect to p[2i],
j[2i+1] contains the derivative with respect to p[2i+1] and
j[2n], the last element, contains the derivative with respect to p[2n].

◆ fexpbde()

StfnumDll double stfnum::fexpbde	(	double	x,
		const Vector_double &	p )

Biexponential function with delay.

\begin{eqnarray*} f(x)= \begin{cases} p_0 & \mbox{if }x < p_1 \\ p_3 \left( \mathrm{e}^{\frac{p_1 - x}{p_2}} - \mathrm{e}^{\frac{p_1 - x}{p_4}} \right) + p_0 & \mbox{if }x \geq p_1 \end{cases} \end{eqnarray*}

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the baseline, p[1] is the delay, p[2] is the later (slower) time constant, p[3] is the amplitude and p[4] is the earlier (faster) time constant,

Returns: The evaluated function.

References StfnumDll.

◆ fexpbde_init()

void stfnum::fexpbde_init	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHi,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Initialises parameters for fitting stfnum::fexpde() to data.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 4. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ fexpde()

StfnumDll double stfnum::fexpde	(	double	x,
		const Vector_double &	p )

Monoexponential function with delay.

\begin{eqnarray*} f(x)= \begin{cases} p_0, & \mbox{if }x < p_3 \\ \left( p_0 - p_2 \right) \mathrm{e}^{\left (\frac{p_3 - x}{p_1}\right )} + p_2, & \mbox{if }x \geq p_3 \end{cases} \end{eqnarray*}

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the baseline, p[1] is the time constant, p[2] is the amplitude and p[3] is the delay.

Returns: The evaluated function.

References StfnumDll.

◆ fexpde_init()

void stfnum::fexpde_init	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHi,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Initialises parameters for fitting stfnum::fexpde() to data.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 4. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ fexptde()

double stfnum::fexptde	(	double	x,
		const Vector_double &	p )

Triexponential function with delay.

\begin{eqnarray*} f(x)= \begin{cases} p_0 & \mbox{if }x < p_1 \\ p_3 \left( p_6\mathrm{e}^{\frac{p_1 - x}{p_2}} + (1-p_6)\mathrm{e}^{\frac{p_1 - x}{p_5}} - \mathrm{e}^{\frac{p_1 - x}{p_4}} \right) + p_0 & \mbox{if }x \geq p_1 \end{cases} \end{eqnarray*}

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the baseline, p[1] is the delay, p[2] is the first later (slower) time constant, p[3] is the amplitude and p[4] is the earlier (faster) time constant, p[5] is the second later (slower) time constant, p[6] is the relative weight of p[2],

Returns: The evaluated function.

◆ fexptde_init()

void stfnum::fexptde_init	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHi,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Initialises parameters for fitting stfnum::fexpde() to data.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 4. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ fgauss()

StfnumDll double stfnum::fgauss	(	double	x,
		const Vector_double &	p )

Computes the sum of an arbitrary number of Gaussians.

\[ f(x) = \sum_{i=0}^{n-1}p_{3i}\mathrm{e}^{- \left( \frac{x-p_{3i+1}}{p_{3i+2}} \right) ^2} \]

Parameters

x	Argument of the function.
p	A valarray of function parameters of size 3n, where p[3i] is the amplitude of the Gaussian p[3i+1] is the position of the center of the peak, p[3i+2] is the width of the Gaussian, n is the number of Gaussian functions and i is the 0-based index of the i-th Gaussian.

Returns: The evaluated function.

◆ fgauss_init()

void stfnum::fgauss_init	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHI,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Initialises parameters for fitting stfnum::fgauss() to data.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 3. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ fgauss_jac()

Vector_double stfnum::fgauss_jac	(	double	x,
		const Vector_double &	p )

Computes the Jacobian of a sum of Gaussians.

◆ fgaussColqu()

StfnumDll double stfnum::fgaussColqu	(	double	x,
		const Vector_double &	p )

Computes a Gaussian that can be used as a filter kernel.

\[ f(x) = \mathrm{e}^{-0.3466 \left( \frac{x}{p_{0}} \right) ^2} \]

Parameters

x	Argument of the function.
p	Function parameters, where p[0] is the corner frequency (-3 dB according to Colquhoun)

Returns: The evaluated function.

◆ fgnabiexp()

StfnumDll double stfnum::fgnabiexp	(	double	x,
		const Vector_double &	p )

power of 1 sodium conductance function.

\[f(x)=p_0\left(1-\mathrm{e}^{\frac{-x}{p_1}}\right)\mathrm{e}^{\frac{-x}{p_2}} + p_3\]

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the amplitude \(g'_{Na}\), p[1] is \(\tau_m\), p[2] is \(\tau_h\) and p[3] is the offset.

Returns: The evaluated function.

References StfnumDll.

◆ fgnabiexp_init()

void stfnum::fgnabiexp_init	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHi,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Initialises parameters for fitting stfnum::falpha() to data.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 4. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ fgnabiexp_jac()

Vector_double stfnum::fgnabiexp_jac	(	double	x,
		const Vector_double &	p )

Computes the Jacobian of stfnum::fgnabiexp().

\begin{eqnarray*} j_0(x) &=& \frac{\partial f(x)}{\partial p_0} = \left(1 -\mathrm{e}^{\frac{-x}{p_1}}\right) \mathrm{e}^{\frac{-x}{p_2}} \\ j_1(x) &=& \frac{\partial f(x)}{\partial p_1} = p_0 \frac{ -x \mathrm{e}^{\left(-\frac{x}{p_1} - \frac{x}{p_2} \right)}}{p_1^2} \\ j_2(x) &=& \frac{\partial f(x)}{\partial p_2} = p_0 \frac{ x \left(1 -\mathrm{e}^{\frac{-x}{p_1}}\right) \mathrm{e}^{\frac{-x}{p_2}}} {p_2^2}\\ j_3(x) &=& \frac{\partial f(x)}{\partial p_3} = 1 \end{eqnarray*}

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the amplitude \(g'_{Na}\), p[1] is \(\tau_m\), p[2] is \(\tau_h\) and p[3] is the offset.

Returns: A valarray j with the evaluated Jacobian, where
j[0] contains the derivative with respect to p[0],
j[1] contains the derivative with respect to p[1],
j[2] contains the derivative with respect to p[2] and
j[3] contains the derivative with respect to p[3].

◆ fHH()

StfnumDll double stfnum::fHH	(	double	x,
		const Vector_double &	p )

Hodgkin-Huxley sodium conductance function.

\[f(x)=p_0\left(1-\mathrm{e}^{\frac{-x}{p_1}}\right)^3\mathrm{e}^{\frac{-x}{p_2}} + p_3\]

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the amplitude \(g'_{Na}\), p[1] is \(\tau_m\), p[2] is \(\tau_h\) and p[3] is the offset.

Returns: The evaluated function.

References StfnumDll.

◆ fHH_init()

void stfnum::fHH_init	(	const Vector_double &	data,
		double	base,
		double	peak,
		double	RTLoHi,
		double	HalfWidth,
		double	dt,
		Vector_double &	pInit )

Initialises parameters for fitting stfnum::falpha() to data.

Parameters

data	The waveform of the data for the fit.
base	Baseline of data.
peak	Peak value of data.
dt	The sampling interval.
pInit	On entry, pass a valarray of size 4. On exit, will contain initial parameter estimates.

References base(), and peak().

◆ filter()

StfnumDll Vector_double stfnum::filter	(	const Vector_double &	toFilter,
		std::size_t	filter_start,
		std::size_t	filter_end,
		const Vector_double &	a,
		int	SR,
		stfnum::Func	func,
		bool	inverse = false )

Convolves a data set with a filter function.

Parameters

toFilter	The valarray to be filtered.
filter_start	The index from which to start filtering.
filter_end	The index at which to stop filtering.
a	A valarray of parameters for the filter function.
SR	The sampling rate.
func	The filter function in the frequency domain.
inverse	true if (1- func) should be used as the filter function, false otherwise

Returns: The convolved data set.

◆ flin()

double stfnum::flin	(	double	x,
		const Vector_double &	p )

Linear function.

\[f(x)=p_0 x + p_1\]

Parameters

x	Function argument.
p	A valarray of parameters, where p[0] is the slope and p[1] is the y intersection.

Returns: The evaluated function.

◆ flin_init()

void stfnum::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 stfnum::storedFunc for linear functions.

References base(), peak(), and StfnumDll.

◆ get() [1/5]

std::deque< Section > & Channel::get ( )

inline

Low-level access to the section array (read and write).

Returns: The vector containing the sections.

Definition at line 119 of file channel.h.

◆ get() [2/5]

const std::deque< Section > & Channel::get ( ) const

inline

Low-level access to the section array (read-only).

Returns: The vector containing the sections.

Definition at line 113 of file channel.h.

◆ get() [3/5]

std::deque< Channel > & Recording::get ( )

inline

Retrieves the channels (read and write).

Returns: A vector containing the channels.

Definition at line 89 of file recording.h.

◆ get() [4/5]

const std::deque< Channel > & Recording::get ( ) const

inline

Retrieves the channels (read-only).

Returns: A vector containing the channels.

Definition at line 84 of file recording.h.

◆ get() [5/5]

const Vector_double & Section::get ( ) const

inline

Low-level access to the valarray (read-only).

An explicit function is used instead of implicit type conversion to access the valarray.

Returns: The valarray containing the data points.

Definition at line 97 of file section.h.

◆ get_scale()

Vector_double stfnum::get_scale	(	Vector_double &	data,
		double	oldx )

Compute and perform normalisation.

Parameters

data	Data vector; will be scaled upon return
oldx	original x interval

Returns: A vector with
[0] x scale [1] x offset [2] y scale [3] y offset

◆ get_w()

Vector_double & Section::get_w ( )

inline

Low-level access to the valarray (read and write).

An explicit function is used instead of implicit type conversion to access the valarray.

Returns: The valarray containing the data points.

Definition at line 104 of file section.h.

◆ GetAnnotationList()

std::vector< Annotation > Section::GetAnnotationList ( )

◆ GetChannelName()

const std::string & Channel::GetChannelName ( ) const

inline

Retrieves the channel name.

Returns: The channel name.

Definition at line 84 of file channel.h.

◆ GetChannelSize()

std::size_t Recording::GetChannelSize ( std::size_t n_channel ) const

Retrieves the number of sections in a channel.

Parameters

n_channel The index of the channel (range-checked).

Returns: The number of sections in n_channel.

◆ GetCheckBox()

wxCheckBox * stf::Event::GetCheckBox ( )

inline

Get the check box associated with this event.

Returns: The wxCheckBox associated with this event

Definition at line 291 of file stf.h.

◆ GetColLabel()

const std::string & stfnum::Table::GetColLabel ( std::size_t col ) const

Retrieves the label of a column.

Parameters

col	0-based column index.

Returns: Column label string.

◆ GetComment()

const std::string & Recording::GetComment ( ) const

inline

Retrieves a comment string.

Returns: A string containing a comment.

Definition at line 114 of file recording.h.

◆ GetCurChIndex()

std::size_t Recording::GetCurChIndex ( ) const

inline

Retrieves the index of the current channel.

Returns: The index of the current channel.

Definition at line 139 of file recording.h.

◆ GetCurSecIndex()

std::size_t Recording::GetCurSecIndex ( ) const

inline

Retrieves the index of the current section.

Returns: The index of the current section.

Definition at line 149 of file recording.h.

◆ GetDateTime()

struct tm Recording::GetDateTime ( ) const

inline

Retrieves the date of recording as a string.

Returns: A string containing the date of recording.

Definition at line 109 of file recording.h.

References GetDateTime().

Referenced by GetDateTime().

◆ GetDiscard()

bool stf::Event::GetDiscard ( ) const

inline

Indicates whether an event should be discarded.

Returns: true if it should be discarded, false otherwise.

Definition at line 287 of file stf.h.

◆ GetEventDescription()

std::string Recording::GetEventDescription ( int type )

Get Description of Event Type.

◆ GetEventPeakIndex()

std::size_t stf::Event::GetEventPeakIndex ( ) const

inline

Retrieves the index of an event's peak.

Returns: The index of an event's peak within a section.

Definition at line 279 of file stf.h.

◆ GetEventSize()

std::size_t stf::Event::GetEventSize ( ) const

inline

Retrieves the size of an event.

Returns: The size of an event in units of data points.

Definition at line 283 of file stf.h.

◆ GetEventStartIndex()

std::size_t stf::Event::GetEventStartIndex ( ) const

inline

Retrieves the start index of an event.

Returns: The start index of an event within a section.

Definition at line 275 of file stf.h.

◆ GetFileDescription()

const std::string & Recording::GetFileDescription ( ) const

inline

Retrieves the file description.

Returns: The file description.

Definition at line 94 of file recording.h.

◆ GetFirstAnnotationPosition()

std::size_t Section::GetFirstAnnotationPosition ( )

◆ GetFuncLib()

StfnumDll std::vector< stfnum::storedFunc > stfnum::GetFuncLib ( )

Returns the library of functions for non-linear regression.

Returns: A vector of non-linear regression functions.

◆ GetGlobalSectionDescription()

const std::string & Recording::GetGlobalSectionDescription ( ) const

inline

Retrieves the common section description.

Returns: The common section description.

Definition at line 99 of file recording.h.

◆ GetLastAnnotationPosition()

std::size_t Section::GetLastAnnotationPosition ( )

◆ getParInfoExp()

std::vector< stfnum::parInfo > stfnum::getParInfoExp ( int n_exp )

Creates stfnum::parInfo structs for n-exponential functions.

Parameters

n_exp Number of exponential terms.

Returns: A vector of parameter information structs.

◆ GetRowLabel()

const std::string & stfnum::Table::GetRowLabel ( std::size_t row ) const

Retrieves the label of a row.

Parameters

row	0-based row index.

Returns: Row label string.

◆ GetScaling()

const std::string & Recording::GetScaling ( ) const

inline

Retrieves the scaling as a string.

Returns: A string containing the description.

Definition at line 104 of file recording.h.

◆ GetSecChIndex()

std::size_t Recording::GetSecChIndex ( ) const

inline

Retrieves the index of the second channel.

Returns: The index of the second channel.

Definition at line 144 of file recording.h.

◆ GetSectionDescription()

const std::string & Section::GetSectionDescription ( ) const

inline

Retrieves a section description.

Returns: A string describing this section.

Definition at line 131 of file section.h.

◆ GetSectionSize()

std::size_t Section::GetSectionSize ( )

Range-checked access. Returns a non-const reference.

Throws std::out_of_range if out of range.

Parameters

at_	Data point index.

Returns: Reference to the data point at index at_ Retrieves a section's data size.; A size_t describing this section's data size.

◆ GetSectionType()

int Recording::GetSectionType ( size_t section_number )

Get Type of Section.

◆ GetSelectBase()

const Vector_double & Recording::GetSelectBase ( ) const

inline

Retrieves the stored baseline values of the selected sections (read-only).

Returns: A vector containing the stored baseline values of the selected sections.

Definition at line 164 of file recording.h.

◆ GetSelectBaseW()

Vector_double & Recording::GetSelectBaseW ( )

inline

Retrieves the stored baseline values of the selected sections (read and write).

Returns: A vector containing the stored baseline values of the selected sections.

Definition at line 169 of file recording.h.

◆ GetSelectedSections()

const std::vector< std::size_t > & Recording::GetSelectedSections ( ) const

inline

Retrieves the indices of the selected sections (read-only).

Returns: A vector containing the indices of the selected sections.

Definition at line 154 of file recording.h.

◆ GetSelectedSectionsW()

std::vector< std::size_t > & Recording::GetSelectedSectionsW ( )

inline

Retrieves the indices of the selected sections (read and write).

Returns: A vector containing the indices of the selected sections.

Definition at line 159 of file recording.h.

◆ GetSR()

double Recording::GetSR ( ) const

inline

Retrieves the sampling rate ( 1 / x-scale )

Returns: The sampling rate.

Definition at line 134 of file recording.h.

◆ GetXScale() [1/2]

double Recording::GetXScale ( ) const

inline

Retrieves the x scaling (sampling interval).

Returns: The x scaling.

Definition at line 129 of file recording.h.

◆ GetXScale() [2/2]

double Section::GetXScale ( ) const

inline

Retrieves the x scaling.

Returns: The x scaling.

Definition at line 126 of file section.h.

◆ GetXUnits()

const std::string & Recording::GetXUnits ( ) const

inline

Retrieves the x units.

Returns: The x units. Currently hard-coded to be "ms".

Definition at line 119 of file recording.h.

◆ GetYUnits()

const std::string & Channel::GetYUnits ( ) const

inline

Retrieves the y units string.

Returns: The y units string.

Definition at line 89 of file channel.h.

◆ histogram()

std::map< double, int > stfnum::histogram	(	const Vector_double &	data,
		int	nbins = -1 )

Computes a histogram.

Parameters

data	The signal
nbins	Number of bins in the histogram.

Returns: A map with lower bin limits as keys, number of observations as values.

References StfnumDll.

◆ ifstreamMan()

stf::ifstreamMan::ifstreamMan ( const wxString & filename )

inline

Constructor.

See fstream documentation for details

Definition at line 237 of file stf.h.

References myStream.

◆ initLinFunc()

StfnumDll stfnum::storedFunc stfnum::initLinFunc ( )

initializes a linear function

Returns: An stfnum::storedFunc that can be used to store a linear function after a fit

◆ InitSectionMarkerList()

void Recording::InitSectionMarkerList ( size_t n )

Initialize List of Section Markers.

References n.

◆ InsertChannel()

virtual void Recording::InsertChannel	(	Channel &	c_Channel,
		std::size_t	pos )

virtual

Insert a Channel at a given position.

Will throw std::out_of_range if range check fails.

Parameters

c_Channel	The Channel to be inserted.
pos	The position at which to insert the channel (0-based).

Reimplemented in wxStfDoc.

◆ InsertSection()

void Channel::InsertSection	(	const Section &	c_Section,
		std::size_t	pos )

Inserts a section at the given position, overwriting anything that's currently stored at that position.

Meant to be used after constructing with Channel(const unsigned int& c_n_sections}. The section array size has to be larger than pos because it won't be resized. Will throw std::out_of_range if out of range.

Parameters

c_Section	The section to be inserted.
pos	The position at which to insert the section.

◆ integrate_simpson()

StfnumDll double stfnum::integrate_simpson	(	const Vector_double &	input,
		std::size_t	a,
		std::size_t	b,
		double	x_scale )

Integration using Simpson's rule.

Parameters

input	The valarray to be integrated.
a	Start of the integration interval.
b	End of the integration interval.
x_scale	Sampling interval.

Returns: The integral of input between a and b.

References StfnumDll.

◆ integrate_trapezium()

StfnumDll double stfnum::integrate_trapezium	(	const Vector_double &	input,
		std::size_t	a,
		std::size_t	b,
		double	x_scale )

Integration using the trapezium rule.

Parameters

input	The valarray to be integrated.
a	Start of the integration interval.
b	End of the integration interval.
x_scale	Sampling interval.

Returns: The integral of input between a and b.

◆ IsEmpty()

bool stfnum::Table::IsEmpty	(	std::size_t	row,
		std::size_t	col ) const

Check whether a cell is empty.

Parameters

row	0-based row index.
col	0-based column index.

Returns: true if empty, false otherwise.

◆ linCorr()

StfnumDll Vector_double stfnum::linCorr	(	const Vector_double &	va1,
		const Vector_double &	va2,
		stfio::ProgressInfo &	progDlg )

Computes the linear correlation between two arrays.

Parameters

va1	First array.
va2	Second array.

Returns: The linear correlation between the two arrays for each data point of va1.

References StfnumDll.

◆ linFit()

template<typename T>

T stfnum::linFit	(	const std::vector< T > &	x,
		const std::vector< T > &	y,
		T &	m,
		T &	c )

Performs a linear fit.

Parameters

x	The x- values of the data that are to be fitted.
y	The y- values of the data that are to be fitted.
m	On exit, the slope of the regression line.
c	On exit, the y-intercept of the regression line.

Returns: A valarray containing the waveform of the fitted function.

Definition at line 107 of file fit.h.

References n.

◆ linsolv()

int stfnum::linsolv	(	int	m,
		int	n,
		int	nrhs,
		Vector_double &	A,
		Vector_double &	B )

Solves a linear equation system using LAPACK.

Uses column-major order for matrices. For an example, see Section::SetIsIntegrated()

Parameters

m	Number of rows of the matrix A.
n	Number of columns of the matrix A.
nrhs	Number of columns of the matrix B.
A	On entry, the left-hand-side matrix. On exit, the factors L and U from the factorization A = PLU; the unit diagonal elements of L are not stored.
B	On entry, the right-hand-side matrix. On exit, the solution to the linear equation system.

Returns: At present, always returns 0.

References n, and StfnumDll.

◆ LM_default_opts()

StfnumDll Vector_double stfnum::LM_default_opts ( )

Return default LM options.

Returns: Default LM options

References StfnumDll.

◆ lmFit()

double StfnumDll stfnum::lmFit	(	const Vector_double &	data,
		double	dt,
		const stfnum::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.

Parameters

data	A valarray containing the data.
dt	The sampling interval of data.
fitFunc	An stfnum::storedFunc to be fitted to data.
opts	Options controlling Lourakis' implementation of the algorithm.
use_scaling	Whether to scale x and y-amplitudes to 1.0
p	func's parameters. Should be set to an initial guess on entry. Will contain the best-fit values on exit.
info	Information about why the fit stopped iterating
warning	A warning code on return.

Returns: The sum of squred errors between data and the best-fit function.

References StfnumDll.

◆ MakeAverage()

void Recording::MakeAverage	(	Section &	AverageReturn,
		Section &	SigReturn,
		std::size_t	channel,
		const std::vector< std::size_t > &	section_index,
		bool	isSig,
		const std::vector< int > &	shift ) const

Calculates an average of several traces.

Parameters

AverageReturn	The average will be returned in this variable by passing a reference. AverageReturn has to have the correct size upon entering this function already, it won't be resized.
SigReturn	The standard deviation will be returned in this variable by passing a reference if isSig == true. SigReturn has to have the correct size upon entering this function already, it won't be resized.
channel	The index of the channel to be used.
section_index	A vector containing the indices of the sections to be used for the average.
isSig	Set to true if the standard deviation should be calculated as well.
shift	A vector indicating by how many data points each section should be shifted before averaging.

References channel.

◆ maxDecay()

StfnumDll double stfnum::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.

Parameters

data	The data waveform to be analysed.
left	Delimits the search to the left.
right	Delimits the search to the right.
maxDecayT	The interpolated time point of the maximal slope of decay in units of sampling points.
maxDecayY	The interpolated value of data at maxDecayT.
windowLength	is the distance (in number of samples) used to compute the slope, the default value is 1.

Returns: The maximal slope during the decaying phase.

◆ maxRise()

StfnumDll double stfnum::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.

Parameters

data	The data waveform to be analysed.
left	Delimits the search to the left.
right	Delimits the search to the right.
maxRiseT	The interpolated time point of the maximal slope of rise in units of sampling points.
maxRiseY	The interpolated value of data at maxRiseT.
windowLength	is the distance (in number of samples) used to compute the slope, the default value is 1.

Returns: The maximal slope during the rising phase.

References StfnumDll.

◆ MoveAnnotation()

void Section::MoveAnnotation	(	size_t	index,
		int	new_position )

◆ nCols()

std::size_t stfnum::Table::nCols ( ) const

inline

Retrieves the number of columns.

Returns: The number of columns.

Definition at line 225 of file stfnum.h.

Referenced by Table().

◆ nojac()

Vector_double stfnum::nojac	(	double	x,
		const Vector_double &	p )

Dummy function, serves as a placeholder to initialize functions without a Jacobian.

◆ noPath()

wxString stf::noPath ( const wxString & fName )

Strips the directory off a full path name, returns only the filename.

Parameters

fName The full path of a file.

Returns: The file name without the directory.

◆ noscale()

double stfnum::noscale	(	double	param,
		double	xscale,
		double	xoff,
		double	yscale,
		double	yoff )

Dummy function, serves as a placeholder to initialize parameters without a scaling function.

References xscale(), and yscale().

Referenced by stfnum::parInfo::parInfo(), and stfnum::parInfo::parInfo().

◆ nRows()

std::size_t stfnum::Table::nRows ( ) const

inline

Retrieves the number of rows.

Returns: The number of rows.

Definition at line 220 of file stfnum.h.

Referenced by AppendRows(), and Table().

◆ ofstreamMan()

stf::ofstreamMan::ofstreamMan ( const wxString & filename )

inline

Constructor.

See fstream documentation for details

Definition at line 253 of file stf.h.

References myStream.

◆ operator[]() [1/6]

Section & Channel::operator[] ( std::size_t at_ )

inline

Unchecked access to a section (read and write)

Use at() for range-checked access.

Parameters

at_	The section index.

Returns: The section at index at_.

Definition at line 70 of file channel.h.

◆ operator[]() [2/6]

const Section & Channel::operator[] ( std::size_t at_ ) const

inline

Unchecked access to a section (read-only)

Use at() for range-checked access.

Parameters

at_	The section index.

Returns: The section at index at_.

Definition at line 77 of file channel.h.

◆ operator[]() [3/6]

Channel & Recording::operator[] ( std::size_t at )

inline

Unchecked channel access (read and write)

Use at() for range-checked access.

Parameters

at	The channel index.

Definition at line 355 of file recording.h.

References at().

◆ operator[]() [4/6]

const Channel & Recording::operator[] ( std::size_t at ) const

inline

Unchecked channel access (read-only)

Use at() for range-checked access.

Parameters

at	The channel index.

Definition at line 361 of file recording.h.

References at().

◆ operator[]() [5/6]

double & Section::operator[] ( std::size_t at )

inline

Unchecked access. Returns a non-const reference.

Parameters

at	Data point index.

Returns: Copy of the data point with index at.

Definition at line 68 of file section.h.

References at().

◆ operator[]() [6/6]

double Section::operator[] ( std::size_t at ) const

inline

Unchecked access. Returns a copy.

Parameters

at	Data point index.

Returns: Reference to the data point with index at.

Definition at line 74 of file section.h.

References at().

◆ outputWTau()

stfnum::Table stfnum::outputWTau	(	const Vector_double &	p,
		const std::vector< stfnum::parInfo > &	parsInfo,
		double	chisqr )

Calculates a weighted time constant.

Parameters

p	Parameters of an exponential function (see stfnum::fexp()).
parsInfo	Information about the parameters p.
chisqr	The sum of squared errors, as returned from a least-squares fit.

Returns: A formatted table of results.

◆ parInfo() [1/2]

stfnum::parInfo::parInfo ( )

inline

Default constructor.

Definition at line 120 of file stfnum.h.

References constr_lb, constr_ub, constrained, desc, stfnum::noscale(), scale, toFit, and unscale.

◆ parInfo() [2/2]

stfnum::parInfo::parInfo	(	const std::string &	desc_,
		bool	toFit_,
		bool	constrained_ = false,
		double	constr_lb_ = 0,
		double	constr_ub_ = 0,
		Scale	scale_ = noscale,
		Scale	unscale_ = noscale )

inline

Constructor.

Parameters

desc_	Parameter description string
toFit_	true if this parameter should be fitted, false if it should be kept fixed.
constrained_	true if this is a constrained fit
constr_lb_	lower bound for constrained fit
constr_ub_	upper bound for constrained fit
scale_	scaling function
unscale_	unscaling function

Definition at line 133 of file stfnum.h.

References constr_lb, constr_ub, constrained, desc, stfnum::noscale(), scale, toFit, and unscale.

◆ peak()

StfnumDll double stfnum::peak	(	const std::vector< double > &	data,
		double	base,
		std::size_t	llp,
		std::size_t	ulp,
		int	pM,
		stfnum::direction	,
		double &	maxT )

Find the peak value of data between llp and ulp.

Note that peaks will be detected by measuring from base, but the return value is given from 0. Data points at both llp and ulp will be included in the search (legacy of Stimfit for PASCAL).

Parameters

data	The data waveform to be analysed.
base	The baseline value.
llp	Lower limit of the peak window.
ulp	Upper limit of the peak window.
pM	If pM > 1, a sliding (boxcar) average of width pM will be used to measure the peak.
dir	Can be stfnum::up for positive-going peaks, stfnum::down for negative-going peaks or stfnum::both for negative- or positive-going peaks, whichever is larger.
maxT	On exit, the index of the peak value. May be interpolated if pM > 1.

Returns: The peak value, measured from 0.

References base(), pM, and StfnumDll.

Referenced by falpha_init(), fexp_init(), fexp_init2(), fexpbde_init(), fexpde_init(), fexptde_init(), fgauss_init(), fgnabiexp_init(), fHH_init(), and flin_init().

◆ peakIndices()

StfnumDll std::vector< int > stfnum::peakIndices	(	const Vector_double &	data,
		double	threshold,
		int	minDistance )

Searches for positive-going peaks.

Parameters

data	The valarray to be searched for peaks.
threshold	Minimal amplitude of a peak.
minDistance	Minimal distance between subsequent peaks.

Returns: A vector of indices where peaks have occurred in data.

References StfnumDll, and threshold().

◆ Plugin()

stf::Plugin::Plugin	(	const wxString &	menuEntry_,
		const PluginFunc &	pluginFunc_,
		const UserInput &	input_ = UserInput() )

inline

Constructor.

Parameters

menuEntry_	Menu entry string for this plugin.
pluginFunc_	Function to be executed by this plugin.
input_	Dialog entries required by this plugin.

Definition at line 180 of file stf.h.

References input, menuEntry, n_plugins, and pluginFunc.

◆ pow2()

int stfnum::pow2 ( int arg )

inline

Computes \( 2^{arg} \). Uses the bitwise-shift operator (<<).

Parameters

arg	Argument of the function.

Returns: \( 2^{arg} \).

Definition at line 549 of file stfnum.h.

◆ PyMarker()

stf::PyMarker::PyMarker	(	double	xv,
		double	yv )

inline

Constructor.

Parameters

xv	x-coordinate.
yv	y-coordinate.

Definition at line 328 of file stf.h.

References x, and y.

◆ quad()

StfnumDll Vector_double stfnum::quad	(	const Vector_double &	data,
		std::size_t	begin,
		std::size_t	end )

Solve quadratic equations for 3 adjacent sampling points.

Parameters

data	The data vector
begin	Start of interval to be used
end	End of interval to be used

Returns: Parameters of quadratic equation

References StfnumDll.

◆ Recording() [1/4]

Recording::Recording ( )

explicit

Default constuctor.

Referenced by AddRec(), CopyAttributes(), wxStfDoc::GetAverage(), wxStfDoc::LoadTDMS(), and wxStfDoc::SetData().

◆ Recording() [2/4]

Recording::Recording ( const Channel & c_Channel )

explicit

Constructor.

Parameters

c_Channel The Channel from which to construct a new Recording.

◆ Recording() [3/4]

Recording::Recording ( const std::deque< Channel > & ChannelList )

explicit

Constructor.

Parameters

ChannelList A vector of channels from which to construct a new Recording.

◆ Recording() [4/4]

Recording::Recording	(	std::size_t	c_n_channels,
		std::size_t	c_n_sections = 0,
		std::size_t	c_n_points = 0 )

explicit

Constructor.

Setting the number of channels and sections at construction time will avoid unnecessary memory re-allocations.

Parameters

c_n_channels	The number of channels.
c_n_sections	The number of sections.
c_n_points	The number of sampling points per section.

◆ RemoveAnnotation()

void Section::RemoveAnnotation ( size_t index )

◆ reserve()

void Channel::reserve ( std::size_t resSize )

Reserve memory for a number of sections.

This will avoid unnecessary memory re-allocations.

Parameters

resSize The number of sections to reserve memory for.

◆ resize() [1/3]

void Channel::resize ( std::size_t newSize )

Resize the section array.

Parameters

newSize The new number of sections.

◆ resize() [2/3]

virtual void Recording::resize ( std::size_t c_n_channels )

virtual

Resize the Recording to a new number of channels.

Resizes both the channel and the global y units arrays.

Parameters

c_n_channels The new number of channels.

Reimplemented in wxStfDoc.

◆ resize() [3/3]

void Section::resize ( std::size_t new_size )

inline

Resize the Section to a new number of data points; deletes all previously stored data when gcc is used.

Note that in the gcc implementation of std::vector, resizing will delete all the original data. This is different from std::vector::resize().

Parameters

new_size The new number of data points.

Definition at line 111 of file section.h.

◆ risetime()

StfnumDll double stfnum::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.

Although t80real is not explicitly returned, it can be calculated from t20Real+risetime.

Parameters

data	The data waveform to be analysed.
base	The baseline value.
ampl	The amplitude of the event (typically, peak-base).
left	Delimits the search to the left.
right	Delimits the search to the right.
t20Id	On exit, the index wich is closest to the 20%-point.
t80Id	On exit, the index wich is closest to the 80%-point.
t20Real	the linearly interpolated 20%-timepoint in units of sampling points.

Returns: The rise time.

References base(), and StfnumDll.

◆ risetime2()

StfnumDll double stfnum::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.

Although t80real is not explicitly returned, it can be calculated from t20Real+risetime.

Parameters

data	The data waveform to be analysed.
base	The baseline value.
ampl	The amplitude of the event (typically, peak-base).
left	Delimits the search to the left.
right	Delimits the search to the right.
innerTLoReal	interpolated starting point of the inner risetime
innerTHiReal	interpolated end point of the inner risetime
outerTLoReal	interpolated starting point of the outer risetime
outerTHiReal	interpolated end point of the outer risetime the inner rise time is (innerTHiReal-innerTLoReal), the outer rise time is (outerTHiReal-outerTLoReal), in case of noise free data, inner and outer rise time are the same.

Returns: The inner rise time.

References base(), and StfnumDll.

◆ round()

int stf::round ( double toRound )

inline

Does what it says.

Parameters

toRound The double to be rounded.

Returns: The rounded integer.

Definition at line 434 of file stf.h.

◆ secch()

const Channel & Recording::secch ( ) const

inline

Retrieves the second (reference) channel (read-only)

Returns: The second (reference) channel.

Definition at line 199 of file recording.h.

◆ secsec()

const Section & Recording::secsec ( ) const

inline

Retrieves the currently accessed section in the second (reference) channel (read-only)

Returns: The currently accessed section in the second (reference) channel.

Definition at line 184 of file recording.h.

◆ Section() [1/3]

Section::Section ( )

explicit

Default constructor.

◆ Section() [2/3]

Section::Section	(	const Vector_double &	valA,
		const std::string &	label = "\0" )

explicit

Constructor.

Parameters

valA	A vector of values that will make up the section.
label	An optional section label string.

◆ Section() [3/3]

Section::Section	(	std::size_t	size,
		const std::string &	label = "\0" )

explicit

Yet another constructor.

Parameters

size	Number of data points.
label	An optional section label string.

References size().

◆ SectionAttributes()

stf::SectionAttributes::SectionAttributes ( )

◆ SectionPointer()

stf::SectionPointer::SectionPointer	(	Section *	pSec = NULL,
		const SectionAttributes &	sa = SectionAttributes() )

◆ sectionToString()

wxString stf::sectionToString ( const Section & section )

Converts a Section to a wxString.

Parameters

section The Section to be written to a string.

Returns: A string containing the x- and y-values of the section in two columns.

◆ SelectTrace()

void Recording::SelectTrace	(	std::size_t	sectionToSelect,
		std::ptrdiff_t	base_start,
		std::ptrdiff_t	base_end )

Selects a section.

Parameters

sectionToSelect	The index of the section to be selected.
base_start	Start index for baseline
base_end	End index for baseline

◆ SetChannelName()

void Channel::SetChannelName ( const std::string & value )

inline

Sets the channel name.

Parameters

value The channel name.

Definition at line 126 of file channel.h.

◆ SetColLabel()

void stfnum::Table::SetColLabel	(	std::size_t	col,
		const std::string &	label )

Sets the label of a column.

Parameters

col	0-based column index.
label	Column label string.

◆ SetComment()

void Recording::SetComment ( const std::string & value )

inline

Sets a comment string.

Parameters

value A string containing a comment.

Definition at line 257 of file recording.h.

◆ SetCurChIndex()

void Recording::SetCurChIndex ( std::size_t value )

Sets the index of the current channel.

Parameters

value The index of the current channel.

◆ SetCurSecIndex()

void Recording::SetCurSecIndex ( std::size_t value )

Sets the index of the current section.

Parameters

value The index of the current section.

◆ SetDate() [1/2]

int Recording::SetDate ( const std::string & value )

Sets the date of recording as a string.

Parameters

value A string containing the date of recording.

Returns: 0 in case of success, non-zero in case of failure

◆ SetDate() [2/2]

int Recording::SetDate	(	int	year,
		int	month,
		int	mday )

◆ SetDateTime() [1/2]

void Recording::SetDateTime ( const struct tm & value )

inline

Sets the date and time of recording as struct tm.

Parameters

value has type struct tm

Definition at line 251 of file recording.h.

◆ SetDateTime() [2/2]

void Recording::SetDateTime	(	int	year,
		int	month,
		int	mday,
		int	hour,
		int	minute,
		int	sec )

◆ SetEmpty()

void stfnum::Table::SetEmpty	(	std::size_t	row,
		std::size_t	col,
		bool	value = true )

Empties or un-empties a cell.

Parameters

row	0-based row index.
col	0-based column index.
value	true if the cell should be empty, false otherwise.

◆ SetEventDescription()

void Recording::SetEventDescription	(	int	type,
		const char *	Description )

Set Description of Event Type.

◆ SetEventPeakIndex()

void stf::Event::SetEventPeakIndex ( std::size_t value )

inline

Sets the index of an event's peak.

Parameters

value The index of an event's peak within a section.

Definition at line 299 of file stf.h.

◆ SetEventSize()

void stf::Event::SetEventSize ( std::size_t value )

inline

Sets the size of an event.

Parameters

value The size of an event in units of data points.

Definition at line 303 of file stf.h.

◆ SetEventStartIndex()

void stf::Event::SetEventStartIndex ( std::size_t value )

inline

Sets the start index of an event.

Parameters

value The start index of an event within a section.

Definition at line 295 of file stf.h.

◆ SetFileDescription()

void Recording::SetFileDescription ( const std::string & value )

inline

Sets the file description.

Parameters

value The file description.

Definition at line 220 of file recording.h.

◆ SetGlobalSectionDescription()

void Recording::SetGlobalSectionDescription ( const std::string & value )

inline

Sets the common section description.

Parameters

value The common section description.

Definition at line 225 of file recording.h.

◆ SetGlobalYUnits()

void Recording::SetGlobalYUnits	(	std::size_t	n_channel,
		const std::string &	value )

Sets the y units for a channel.

Parameters

n_channel	The channel index for which to set the units.
value	A string containing the y units.

◆ SetRowLabel()

void stfnum::Table::SetRowLabel	(	std::size_t	row,
		const std::string &	label )

Sets the label of a row.

Parameters

row	0-based row index.
label	Row label string.

◆ SetScaling()

void Recording::SetScaling ( const std::string & value )

inline

Sets the scaling as a string.

Parameters

value A string containing the description.

Definition at line 232 of file recording.h.

◆ SetSecChIndex()

void Recording::SetSecChIndex ( std::size_t value )

Sets the index of the second channel.

Parameters

value The index of the second channel.

◆ SetSectionDescription()

void Section::SetSectionDescription ( const std::string & value )

inline

Sets a section description.

Parameters

value A string describing this section.

Definition at line 136 of file section.h.

◆ SetSectionType()

void Recording::SetSectionType	(	size_t	section_number,
		int	type )

Set Type of Section.

◆ SetTime() [1/2]

int Recording::SetTime ( const std::string & value )

Sets the time of recording as a string.

Parameters

value A string containing the time of recording.

Returns: 0 in case of success, non-zero in case of failure

◆ SetTime() [2/2]

int Recording::SetTime	(	int	hour,
		int	minute,
		int	sec )

◆ SetXScale() [1/2]

void Recording::SetXScale ( double value )

Sets the x scaling.

Note that setting the global x-scale will set it for all sections

Parameters

value The x scaling.

◆ SetXScale() [2/2]

void Section::SetXScale ( double value )

Sets the x scaling.

Parameters

value The x scaling.

◆ SetXUnits()

void Recording::SetXUnits ( const std::string & value )

inline

Sets the x units.

Parameters

value A string containing the x units.

Definition at line 268 of file recording.h.

◆ SetYUnits()

void Channel::SetYUnits ( const std::string & value )

inline

Sets the y units string.

Parameters

value The new y units string.

Definition at line 131 of file channel.h.

◆ size() [1/3]

size_t Channel::size ( ) const

inline

Retrieves the size of the section array.

Returns: The size of the section array.

Definition at line 94 of file channel.h.

◆ size() [2/3]

std::size_t Recording::size ( ) const

inline

Retrieves the size of the channel array.

Returns: The size of the channel array.

Definition at line 124 of file recording.h.

◆ size() [3/3]

size_t Section::size ( ) const

inline

Retrieve the number of data points.

Returns: The number of data points.

Definition at line 116 of file section.h.

Referenced by Section().

◆ SQR()

template<typename T>

T stfnum::SQR ( T a )

inline

Calculates the square of a number.

Parameters

a	Argument of the function.

Returns: a ^2

Definition at line 602 of file stfnum.h.

◆ std2wx()

wxString stf::std2wx ( const std::string & sst )

◆ storedFunc()

stfnum::storedFunc::storedFunc	(	const std::string &	name_,
		const std::vector< parInfo > &	pInfo_,
		const Func &	func_,
		const Init &	init_,
		const Jac &	jac_,
		bool	hasJac_ = true,
		const Output &	output_ = defaultOutput )

inline

Constructor.

Parameters

name_	Plain function name.
pInfo_	A vector containing information about the function parameters.
func_	The function that will be fitted to the data.
jac_	Jacobian of func_.
hasJac_	true if a Jacobian is available.
init_	A function for initialising the parameters.
output_	Output of the fit.

Definition at line 281 of file stfnum.h.

References stfnum::defaultOutput(), func, hasJac, init, jac, name, output, and pInfo.

◆ t_half()

StfnumDll double stfnum::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.

Although t50RightReal is not explicitly returned, it can be calculated from t50LeftReal+t_half.

Parameters

data	The data waveform to be analysed.
base	The baseline value.
ampl	The amplitude of the event (typically, peak-base).
left	Delimits the search to the left.
right	Delimits the search to the right.
center	The estimated center of an event from which to start searching to the left and to the right (typically, the index of the peak).
t50LeftId	On exit, the index wich is closest to the left 50%-point.
t50RightId	On exit, the index wich is closest to the right 50%-point.
t50LeftReal	the linearly interpolated left 50%-timepoint in units of sampling points.

Returns: The full width at half-maximal amplitude.

References base(), and StfnumDll.

◆ Table() [1/2]

stfnum::Table::Table ( const std::map< std::string, double > & map )

Constructor.

Parameters

map	A map used to initialise the table.

◆ Table() [2/2]

stfnum::Table::Table	(	std::size_t	nRows,
		std::size_t	nCols )

Constructor.

Parameters

nRows	Initial number of rows.
nCols	Initial number of columns.

References nCols(), and nRows().

◆ threshold()

StfnumDll double stfnum::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.

Parameters

data	The data waveform to be analysed.
llp	Lower limit of the peak window.
ulp	Upper limit of the peak window.
thrT	On exit, The interpolated time point of the threshold crossing in units of sampling points, or a negative value if the threshold wasn't found.
windowLength	is the distance (in number of samples) used to compute the difference, the default value is 1.

Returns: The interpolated threshold value.

References StfnumDll.

Referenced by peakIndices().

◆ UnselectTrace()

bool Recording::UnselectTrace ( std::size_t sectionToUnselect )

Unselects a section if it was selected before.

Parameters

sectionToUnselect The index of the section to be unselected.

Returns: true if the section was previously selected, false otherwise.

◆ Update()

bool stf::wxProgressInfo::Update	(	int	value,
		const std::string &	newmsg = "",
		bool *	skip = NULL )

virtual

Updates the progress info.

Parameters

value	New value of the progress meter
newmsg	New message for the info text
skip	This is set to true if the user has chosen to skip the operation

Returns: True unless the operation was cancelled.

Implements stfio::ProgressInfo.

◆ UserInput()

stf::UserInput::UserInput	(	const std::vector< std::string > &	labels_ = std::vector<std::string>(0),
		const Vector_double &	defaults_ = Vector_double(0),
		std::string	title_ = "\0" )

inline

Constructor.

Parameters

labels_	A vector of dialog entry label strings.
defaults_	A vector of default dialog entries.
title_	Dialog title.

Definition at line 156 of file stf.h.

References defaults, labels, and title.

◆ whereis()

std::size_t stfnum::whereis	(	const Vector_double &	data,
		double	value )

Finds the index of data where value is encountered for the first time.

Parameters

data	The waveform to be searched.
value	The value to be found.

Returns: The index of data right after value has been crossed.

References StfnumDll.

◆ wx2std()

std::string stf::wx2std ( const wxString & wxs )

◆ wxProgressInfo()

stf::wxProgressInfo::wxProgressInfo	(	const std::string &	title,
		const std::string &	message,
		int	maximum,
		bool	verbose = true )

◆ xscale()

double stfnum::xscale	(	double	param,
		double	xscale,
		double	xoff,
		double	yscale,
		double	yoff )

Scales a parameter that linearly depends on x.

Parameters

The	parameter to scale
xscale	x scaling factor
xoff	x offset
yscale	y scaling factor
yoff	y offset

Returns: Scaled parameter

References xscale(), and yscale().

Referenced by noscale(), xscale(), xunscale(), yscale(), yscaleoffset(), yunscale(), and yunscaleoffset().

◆ xunscale()

double stfnum::xunscale	(	double	param,
		double	xscale,
		double	xoff,
		double	yscale,
		double	yoff )

Unscales a parameter that linearly depends on x.

Parameters

The	parameter to scale
xscale	x scaling factor
xoff	x offset
yscale	y scaling factor
yoff	y offset

Returns: Unscaled parameter

References xscale(), and yscale().

◆ yscale()

double stfnum::yscale	(	double	param,
		double	xscale,
		double	xoff,
		double	yscale,
		double	yoff )

Scales a parameter that linearly depends on y.

Parameters

The	parameter to scale
xscale	x scaling factor
xoff	x offset
yscale	y scaling factor
yoff	y offset

References xscale(), and yscale().

Referenced by noscale(), xscale(), xunscale(), yscale(), yscaleoffset(), yunscale(), and yunscaleoffset().

◆ yscaleoffset()

double stfnum::yscaleoffset	(	double	param,
		double	xscale,
		double	xoff,
		double	yscale,
		double	yoff )

Scales a parameter that linearly depends on y and adds an offset.

Parameters

The	parameter to scale
xscale	x scaling factor
xoff	x offset
yscale	y scaling factor
yoff	y offset

References xscale(), and yscale().

◆ yunscale()

double stfnum::yunscale	(	double	param,
		double	xscale,
		double	xoff,
		double	yscale,
		double	yoff )

Unscales a parameter that linearly depends on y.

Parameters

The	parameter to scale
xscale	x scaling factor
xoff	x offset
yscale	y scaling factor
yoff	y offset

Returns: Unscaled parameter

References xscale(), and yscale().

◆ yunscaleoffset()

double stfnum::yunscaleoffset	(	double	param,
		double	xscale,
		double	xoff,
		double	yscale,
		double	yoff )

Unscales a parameter that linearly depends on y and removes the offset.

Parameters

The	parameter to scale
xscale	x scaling factor
xoff	x offset
yscale	y scaling factor
yoff	y offset

Returns: Unscaled parameter

References xscale(), and yscale().

◆ ~Channel()

Channel::~Channel ( )

Destructor.

◆ ~Event()

stf::Event::~Event ( )

Destructor.

◆ ~Extension()

stf::Extension::~Extension ( )

inline

Destructor.

Definition at line 222 of file stf.h.

◆ ~ifstreamMan()

stf::ifstreamMan::~ifstreamMan ( )

inline

Destructor.

Definition at line 242 of file stf.h.

References myStream.

◆ ~ofstreamMan()

stf::ofstreamMan::~ofstreamMan ( )

inline

Destructor.

Definition at line 258 of file stf.h.

References myStream.

◆ ~Plugin()

stf::Plugin::~Plugin ( )

inline

Destructor.

Definition at line 191 of file stf.h.

◆ ~Recording()

virtual Recording::~Recording ( )

virtual

Destructor.

◆ ~Section()

Section::~Section ( )

Destructor.

◆ ~storedFunc()

stfnum::storedFunc::~storedFunc ( )

inline

Destructor.

Definition at line 297 of file stfnum.h.

Variable Documentation

◆ bestFit

stfnum::Table stf::SectionAttributes::bestFit

Definition at line 345 of file stf.h.

◆ bestFitP

Vector_double stf::SectionAttributes::bestFitP

Definition at line 339 of file stf.h.

◆ constr_lb

double stfnum::parInfo::constr_lb

Lower boundary for box-constrained fits

Definition at line 143 of file stfnum.h.

Referenced by parInfo(), and parInfo().

◆ constr_ub

double stfnum::parInfo::constr_ub

Upper boundary for box-constrained fits

Definition at line 144 of file stfnum.h.

Referenced by parInfo(), and parInfo().

◆ constrained

bool stfnum::parInfo::constrained

true if this parameter should be constrained

Definition at line 142 of file stfnum.h.

Referenced by parInfo(), and parInfo().

◆ defaults

Vector_double stf::UserInput::defaults

Default dialog entries.

Definition at line 148 of file stf.h.

Referenced by UserInput().

◆ desc

std::string stfnum::parInfo::desc

Parameter description string

Definition at line 140 of file stfnum.h.

Referenced by parInfo(), and parInfo().

◆ description

std::string stf::Extension::description

Description for this function.

Definition at line 228 of file stf.h.

Referenced by Extension().

◆ eventList

std::vector<stf::Event> stf::SectionAttributes::eventList

Definition at line 335 of file stf.h.

◆ fitFunc

stfnum::storedFunc* stf::SectionAttributes::fitFunc

Definition at line 338 of file stf.h.

◆ func

Func stfnum::storedFunc::func

The function that will be fitted to the data.

Definition at line 303 of file stfnum.h.

Referenced by storedFunc().

◆ hasJac

bool stfnum::storedFunc::hasJac

True if the function has an analytic Jacobian.

Definition at line 306 of file stfnum.h.

Referenced by storedFunc().

◆ id [1/2]

int stf::Extension::id

The extension id; set automatically upon construction, so don't touch.

Definition at line 224 of file stf.h.

◆ id [2/2]

int stf::Plugin::id

The plugin id; set automatically upon construction, so don't touch.

Definition at line 193 of file stf.h.

◆ init

Init stfnum::storedFunc::init

A function for initialising the parameters.

Definition at line 304 of file stfnum.h.

Referenced by storedFunc().

◆ input

UserInput stf::Plugin::input

Dialog entries

Definition at line 197 of file stf.h.

Referenced by Plugin().

◆ isFitted

bool stf::SectionAttributes::isFitted

Definition at line 337 of file stf.h.

◆ isIntegrated

bool stf::SectionAttributes::isIntegrated

Definition at line 337 of file stf.h.

◆ jac

Jac stfnum::storedFunc::jac

Jacobian of func.

Definition at line 305 of file stfnum.h.

Referenced by storedFunc().

◆ labels

std::vector<std::string> stf::UserInput::labels

Dialog entry labels.

Definition at line 147 of file stf.h.

Referenced by UserInput().

◆ menuEntry [1/2]

std::string stf::Extension::menuEntry

Menu entry string for this extension.

Definition at line 226 of file stf.h.

Referenced by Extension().

◆ menuEntry [2/2]

wxString stf::Plugin::menuEntry

Menu entry string for this plugin.

Definition at line 195 of file stf.h.

Referenced by Plugin().

◆ myStream [1/2]

wxFFile stf::ifstreamMan::myStream

The managed stream.

Definition at line 245 of file stf.h.

Referenced by ifstreamMan(), and ~ifstreamMan().

◆ myStream [2/2]

wxFFile stf::ofstreamMan::myStream

The managed stream.

Definition at line 261 of file stf.h.

Referenced by ofstreamMan(), and ~ofstreamMan().

◆ n_extensions

int stf::Extension::n_extensions

static

Static extension counter. Initialised in extensions/extensions.cpp.

Definition at line 225 of file stf.h.

Referenced by Extension().

◆ n_plugins

int stf::Plugin::n_plugins

static

Static plugin counter. Initialised in plugins/plugins.cpp.

Definition at line 194 of file stf.h.

Referenced by Plugin().

◆ name

std::string stfnum::storedFunc::name

Function name.

Definition at line 301 of file stfnum.h.

Referenced by storedFunc().

◆ output

Output stfnum::storedFunc::output

Output of the fit.

Definition at line 307 of file stfnum.h.

Referenced by storedFunc().

◆ PI

const double stf::PI =3.14159265358979323846

Add decimals if you are not satisfied.

Definition at line 355 of file stf.h.

◆ pInfo

std::vector<parInfo> stfnum::storedFunc::pInfo

A vector containing information about the function parameters.

Definition at line 302 of file stfnum.h.

Referenced by storedFunc().

◆ pluginFunc

PluginFunc stf::Plugin::pluginFunc

The function to be executed by this plugin.

Definition at line 196 of file stf.h.

Referenced by Plugin().

◆ pSection

Section* stf::SectionPointer::pSection

Definition at line 350 of file stf.h.

◆ pyFunc

void* stf::Extension::pyFunc

Python function to be called.

Definition at line 227 of file stf.h.

Referenced by Extension().

◆ pyMarkers

std::vector<stf::PyMarker> stf::SectionAttributes::pyMarkers

Definition at line 336 of file stf.h.

◆ quad_p

Vector_double stf::SectionAttributes::quad_p

Definition at line 340 of file stf.h.

◆ requiresFile

bool stf::Extension::requiresFile

Whether a file needs to be open for this function to work

Definition at line 229 of file stf.h.

Referenced by Extension().

◆ scale

Scale stfnum::parInfo::scale

Scaling function for this parameter

Definition at line 145 of file stfnum.h.

Referenced by parInfo(), and parInfo().

◆ sec_attr

SectionAttributes stf::SectionPointer::sec_attr

Definition at line 351 of file stf.h.

◆ storeFitBeg

std::size_t stf::SectionAttributes::storeFitBeg

Definition at line 341 of file stf.h.

◆ storeFitEnd

std::size_t stf::SectionAttributes::storeFitEnd

Definition at line 342 of file stf.h.

◆ storeIntBeg

std::size_t stf::SectionAttributes::storeIntBeg

Definition at line 343 of file stf.h.

◆ storeIntEnd

std::size_t stf::SectionAttributes::storeIntEnd

Definition at line 344 of file stf.h.

◆ title

std::string stf::UserInput::title

Dialog title.

Definition at line 149 of file stf.h.

Referenced by UserInput().

◆ toFit

bool stfnum::parInfo::toFit

true if this parameter should be fitted, false if it should be kept fixed.

Definition at line 141 of file stfnum.h.

Referenced by parInfo(), and parInfo().

◆ unscale

Scale stfnum::parInfo::unscale

Unscaling function for this parameter

Definition at line 146 of file stfnum.h.

Referenced by parInfo(), and parInfo().

◆ x

double stf::PyMarker::x

x-coordinate in units of sampling points

Definition at line 329 of file stf.h.

Referenced by PyMarker().

◆ y

double stf::PyMarker::y

y-coordinate in trace units (e.g. mV)

Definition at line 330 of file stf.h.

Referenced by PyMarker().

Classes

Typedefs

Enumerations

Functions

Variables

Detailed Description

Typedef Documentation

◆ Func

◆ Init

◆ Jac

◆ Output

◆ PluginFunc

◆ Scale

Enumeration Type Documentation

◆ baseline_method

◆ cursor_type

◆ direction

◆ extraction_mode

◆ latency_mode

◆ latency_window_mode

◆ zoom_channels

Function Documentation

◆ AddAnnotation()

◆ AddRec()

◆ AppendRows()

◆ at() [1/8]

◆ at() [2/8]

◆ at() [3/8]

◆ at() [4/8]

◆ at() [5/8]

◆ at() [6/8]

◆ at() [7/8]

◆ at() [8/8]

◆ base()

◆ Channel() [1/4]

◆ Channel() [2/4]

◆ Channel() [3/4]

◆ Channel() [4/4]

◆ CopyAttributes()

◆ CreatePreview()

◆ cubicSpline()

◆ curch() [1/2]

◆ curch() [2/2]

◆ cursec() [1/2]

◆ cursec() [2/2]

◆ deconvolve()

◆ defaultOutput()

◆ detectionCriterion()

◆ diff()

◆ EraseAllAnnotations()

◆ Event()

◆ Extension()

◆ fac()

◆ falpha()

◆ falpha_init()

◆ falpha_jac()

◆ fbessel()

◆ fbessel4()

◆ fboltz()

◆ fexp()

◆ fexp_init()

◆ fexp_init2()

◆ fexp_jac()

◆ fexpbde()

◆ fexpbde_init()

◆ fexpde()

◆ fexpde_init()

◆ fexptde()

◆ fexptde_init()

◆ fgauss()

◆ fgauss_init()

◆ fgauss_jac()

◆ fgaussColqu()

◆ fgnabiexp()

◆ fgnabiexp_init()

◆ fgnabiexp_jac()

◆ fHH()

◆ fHH_init()

◆ filter()

◆ flin()