wxStfDoc Class Reference

The document class, derived from both wxDocument and Recording. More...

#include <doc.h>

Inheritance diagram for wxStfDoc:

Collaboration diagram for wxStfDoc:

Public Member Functions
	wxStfDoc ()
	Constructor.
	~wxStfDoc ()
	Destructor.
void	OnSwapChannels (wxCommandEvent &event)
	Swaps active and inactive channel.
virtual bool	OnOpenDocument (const wxString &filename)
	Override default file opening.
virtual bool	OnOpenPyDocument (const wxString &filename)
	Open document without progress dialog.
virtual bool	SaveAs ()
	Override default file saving.
virtual bool	DoSaveDocument (const wxString &filename)
	Override default file saving.
virtual bool	OnCloseDocument ()
	Override default file closing.
virtual bool	OnNewDocument ()
	Override default file creation.
void	SetData (const Recording &c_Data, const wxStfDoc *Sender, const wxString &title)
	Sets the content of a newly created file.
bool	GetIsAverage () const
	Indicates whether an average has been created.
bool	GetStartFitAtPeak () const
	Indicates whether the left decay cursor should always be at the peak of the trace.
bool	GetPeakAtEnd () const
	Indicates whether the right peak cursor should always be at the end of a trace.
bool	IsInitialized () const
	Indicates whether the the document is fully initialised.
void	SetPeakAtEnd (bool value)
	Sets the right peak cursor to the end of a trace.
void	SetStartFitAtPeak (bool value)
	Sets the left decay cursor to the peak of the trace.
const Recording &	GetAverage () const
	Retrieves the average trace(s).
void	CheckBoundaries ()
	Checks whether any cursor is reversed or out of range and corrects it if required.
bool	SetSection (std::size_t section)
	Sets the current section to the specified value.
bool	OnNewfromselectedThis ()
	Creates a new window containing the selected sections of this file.
void	Selectall (wxCommandEvent &event)
	Selects all sections.
void	Deleteselected (wxCommandEvent &event)
	Unselects all sections.
void	UpdateSelectedButton ()
	Updates the status of the selection button.
void	CreateAverage (bool calcSD, bool align)
	Creates an average trace from the selected sections.
void	ToggleSelect ()
	Toggles the selection status of the current section.
void	Select ()
	Selects the current section if previously unselected.
void	Remove ()
	Unselects the current section if previously selected.
void	Extract (wxCommandEvent &event)
	Creates a new document from the checked events.
void	InteractiveEraseEvents (wxCommandEvent &event)
	Erases all events, independent of whether they are checked or not.
void	AddEvent (wxCommandEvent &event)
	Adds an event at the current eventPos.
void	OnAddAnnotation (wxCommandEvent &WXUNUSED(event))
	Adds an annotation at the current eventPos.
void	OnRemoveAnnotation (wxCommandEvent &WXUNUSED(event))
	Removes an annotation at the current eventPos or a very close one to it.
void	OnEraseAllAnnotations (wxCommandEvent &WXUNUSED(event))
	Erase all annotations at the current channel and sweep.
void	OnExportAnnotations (wxCommandEvent &WXUNUSED(event))
	Export all annotations of current doc.
void	OnImportAnnotations (wxCommandEvent &WXUNUSED(event))
	Import all annotations of current doc.
void	OnExpertDetectEvents (wxCommandEvent &WXUNUSED(event))
	detects events based on the expert scoring using simple filter
bool	SubtractBase ()
	Subtracts the baseline of all selected traces.
void	FitDecay (wxCommandEvent &event)
	Fit a function to the data.
void	SetFileMenu (wxMenu *menu)
	Sets a pointer to the file menu attached to this document.
void	Measure ()
	Measure everything using functions defined in measlib.h.
stfnum::Table	CurResultsTable ()
	Put the current measurement results into a text table.
std::size_t	GetMeasCursor () const
	Retrieves the position of the measurement cursor (crosshair).
stfnum::baseline_method	GetBaselineMethod () const
	Retrieves the computation mode for baseline.
std::size_t	GetBaseBeg () const
	Retrieves the position of the left baseline cursor.
std::size_t	GetBaseEnd () const
	Retrieves the position of the right baseline cursor.
std::size_t	GetPeakBeg () const
	Retrieves the position of the left peak cursor.
std::size_t	GetPeakEnd () const
	Retrieves the position of the right peak cursor.
std::size_t	GetFitBeg () const
	Retrieves the position of the left fitting cursor.
std::size_t	GetFitEnd () const
	Retrieves the position of the right fitting cursor.
int	GetPM () const
	Retrieves the number of points used for averaging during peak calculation.
double	GetLatencyBeg () const
	Retrieves the position of the left latency cursor.
double	GetLatencyEnd () const
	Retrieves the position of the right latency cursor.
double	GetLatency () const
	Retrieves the latency.
double	GetTLoReal () const
	Retrieves the time point at which Lo% of the maximal amplitude have been reached.
double	GetTHiReal () const
	Retrieves the time point at which Hi% of the maximal amplitude have been reached.
double	GetInnerLoRT () const
	Retrieves the time point at which Lo% of the maximal amplitude have been reached.
double	GetInnerHiRT () const
	Retrieves the time point at which Hi% of the maximal amplitude have been reached.
double	GetOuterLoRT () const
	Retrieves the time point at which Lo% of the maximal amplitude have been reached.
double	GetOuterHiRT () const
	Retrieves the time point at which Hi% of the maximal amplitude have been reached.
double	GetT0Real () const
	Retrieves the extrapolated onset time point of an event in the active channel.
double	GetT50LeftReal () const
	Retrieves the time point at which 50% of the maximal amplitude have been reached from the left of the peak.
double	GetT50RightReal () const
	Retrieves the time point at which 50% of the maximal amplitude have been reached from the right of the peak.
double	GetT50Y () const
	Retrieves the y value at 50% of the maximal amplitude.
double	GetMaxRise () const
	Retrieves the maximal slope of the rising phase.
double	GetMaxDecay () const
	Retrieves the maximal slope of the decaying phase.
double	GetAPMaxRiseT () const
	Retrieves the time point of the maximal slope of the rising phase in the second channel.
double	GetAPMaxT () const
	Retrieves the time point of the peak in the second channel.
double	GetAPT50LeftReal () const
	Retrieves the time point at which 50% of the max. amplitude have been reached from the left of the peak in the reference channel.
double	GetAPT0Real () const
	Retrieves the extrapolated onset time point of an event in the reference channel.
double	GetMaxRiseT () const
	Retrieves the time point of the maximal slope during the rising phase.
double	GetMaxRiseY () const
	Retrieves the y-value at the time point of the maximal slope during the rising phase.
double	GetMaxDecayT () const
	Retrieves the time point of the maximal slope during the decaying phase.
double	GetMaxDecayY () const
	Retrieves the y-value at the time point of the maximal slope during the decaying phase.
double	GetMeasValue ()
	Retrieves the y-value at the measurement cursor (crosshair). Will update measCursor if out of range.
double	GetPeak () const
	Retrieves the peak value.
double	GetPeakTime () const
	Retrieves the peak time value.
double	GetBase () const
	Retrieves the baseline.
double	GetAPBase () const
	Retrieves the baseline in the second channel.
double	GetBaseSD () const
	Retrieves the standard deviation of the baseline.
double	GetThreshold () const
	Retrieves the value at which the threshold slope is crossed.
double	GetMaxT () const
	Retrieves the time point at which the peak is found.
double	GetThrT () const
	Retrieves the time point at which the threshold slope is crossed.
double	GetRTLoHi () const
	Retrieves the Lo to Hi% rise time.
double	GetInnerRiseTime () const
	Retrieves the inner rise time.
double	GetOuterRiseTime () const
	Retrieves the outer rise time.
double	GetHalfDuration () const
	Retrieves the full width at half-maximal amplitude ("half duration").
double	GetSlopeRatio () const
	Retrieves ratio of the maximal slopes during the rising and decaying phase.
int	GetRTFactor () const
	Retrieves lower factor (e.g 20) for the rise time calculation.
stf::latency_mode	GetLatencyStartMode () const
	Retrieves the mode of the latency start cursor.
stf::latency_mode	GetLatencyEndMode () const
	Retrieves the mode of the latency end cursor.
stf::latency_window_mode	GetLatencyWindowMode () const
	Retrieves the mode of the latency window.
stfnum::direction	GetDirection () const
	Retrieves the direction of peak calculations.
bool	GetFromBase () const
	Indicates whether to use the baseline as a reference for AP kinetics.
bool	GetViewCrosshair () const
	Indicates whether the measurement cursor (crosshair) value should be shown in the results table.
bool	GetViewBaseline () const
	Indicates whether the baseline value should be shown in the results table.
bool	GetViewBaseSD () const
	Indicates whether the baseline's standard deviation should be shown in the results table.
bool	GetViewThreshold () const
	Indicates whether the threshold should be shown in the results table.
bool	GetViewPeakZero () const
	Indicates whether the peak value (measured from zero) should be shown in the results table.
bool	GetViewPeakBase () const
	Indicates whether the peak value (measured from baseline) should be shown in the results table.
bool	GetViewPeakThreshold () const
	Indicates whether the peak value (measured from threshold) should be shown in the results table.
bool	GetViewRTLoHi () const
	Indicates whether the Lo to Hi% rise time should be shown in the results table.
bool	GetViewInnerRiseTime () const
	Indicates whether the inner rise time should be shown in the results table.
bool	GetViewOuterRiseTime () const
	Indicates whether the outer rise time should be shown in the results table.
bool	GetViewT50 () const
	Indicates whether the half duration should be shown in the results table.
bool	GetViewRD () const
	Indicates whether the ratio of the maximal slopes during rise and decay should be shown in the results table.
bool	GetViewSlopeRise () const
	Indicates whether the maximal slope during the rising phase should be shown in the results table.
bool	GetViewSlopeDecay () const
	Indicates whether the maximal slope during the decaying phase should be shown in the results table.
bool	GetViewLatency () const
	Indicates whether the latency should be shown in the results table.
bool	GetViewCursors () const
	Indicates whether two additional rows showing the positions of start and end cursors should be shown in the results table.
double	GetSlopeForThreshold () const
	Returns the slope for threshold detection.
const XZoom &	GetXZoom ()
	Returns the current zoom settings for this channel (read-only).
XZoom &	GetXZoomW ()
	Returns the current zoom settings for this channel (read & write).
const YZoom &	GetYZoom (int ch)
	Returns the current zoom settings for this channel (read-only).
YZoom &	GetYZoomW (int ch)
	Returns the current zoom settings for this channel (read & write).
void	SetMeasCursor (int value)
	Sets the position of the measurement cursor (crosshair).
void	SetMeasRuler (bool value)
	Sets whether the measurement cursor (crosshair) should be visible.
bool	GetMeasRuler () const
	Retrieves whether the measurement cursor (crosshair) is visible.
void	SetBaselineMethod (stfnum::baseline_method value)
	Sets the method to compute the baseline.
void	SetBaseBeg (int value)
	Sets the position of the left baseline cursor.
void	SetBaseEnd (int value)
	Sets the position of the right baseline cursor.
void	SetPeakBeg (int value)
	Sets the position of the left peak cursor.
void	SetPeakEnd (int value)
	Sets the position of the right peak cursor.
void	SetFitBeg (int value)
	Sets the position of the left fitting cursor.
void	SetFitEnd (int value)
	Sets the position of the right fitting cursor.
void	SetLatencyBeg (double value)
	Sets the position of the left latency cursor.
void	SetLatencyEnd (double value)
	Sets the position of the right latency cursor.
void	SetLatency (double value)
	Sets the latency.
void	SetPM (int value)
	Sets the number of points used for averaging during peak calculation.
void	SetRTFactor (int value)
	Sets the lower value (e.g 20) to calculate the rise time.
void	SetLatencyStartMode (stf::latency_mode value)
	Sets the mode of the latency start cursor.
void	SetLatencyEndMode (stf::latency_mode value)
	Sets the mode of the latency end cursor.
void	SetLatencyWindowMode (stf::latency_window_mode value)
	Sets the mode of the latency end cursor.
void	SetLatencyStartMode (int value)
	Sets the mode of the latency start cursor.
void	SetLatencyEndMode (int value)
	Sets the mode of the latency end cursor.
void	SetLatencyWindowMode (int value)
	Sets the mode of the latency end cursor.
void	SetDirection (stfnum::direction value)
	Sets the direction of peak calculations.
void	SetFromBase (bool frombase)
	Sets the reference for AP kinetics measurements.
void	SetViewCrosshair (bool value)
	Determines whether the measurement cursor (crosshair) value should be shown in the results table.
void	SetViewBaseline (bool value)
	Determines whether the baseline value should be shown in the results table.
void	SetViewBaseSD (bool value)
	Determines whether the baseline's standard deviation should be shown in the results table.
void	SetViewThreshold (bool value)
	Determines whether the threshold should be shown in the results table.
void	SetViewPeakZero (bool value)
	Determines whether the peak value (measured from zero) should be shown in the results table.
void	SetViewPeakBase (bool value)
	Determines whether the peak value (measured from baseline) should be shown in the results table.
void	SetViewPeakThreshold (bool value)
	Determines whether the peak value (measured from threshold) should be shown in the results table.
void	SetViewRTLoHi (bool value)
	Determines whether the Lo to Hi% rise time should be shown in the results table.
void	SetViewInnerRiseTime (bool value)
	Determines whether the inner rise time should be shown in the results table.
void	SetViewOuterRiseTime (bool value)
	Determines whether the outer rise time should be shown in the results table.
void	SetViewT50 (bool value)
	Determines whether the half duration should be shown in the results table.
void	SetViewRD (bool value)
	Determines whether the ratio of the maximal slopes during rise and decay should be shown in the results table.
void	SetViewSlopeRise (bool value)
	Determines whether the maximal slope during the rising phase should be shown in the results table.
void	SetViewSlopeDecay (bool value)
	Determines whether the maximal slope during the decaying phase should be shown in the results table.
void	SetViewLatency (bool value)
	Determines whether the latency should be shown in the results table.
void	SetViewCursors (bool value)
	Determines whether two additional rows showing the positions of start and end cursors should be shown in the results table.
void	SetSlopeForThreshold (double value)
	Sets the slope where the baseline should be set.
stfnum::Table	CurAsTable () const
	Put the current trace into a text table.
void	CopyCursors (const wxStfDoc &c_Recording)
	Copies the cursor positions from another Recording to this Recording.
virtual void	resize (std::size_t c_n_channels)
	Resize the Recording to a new number of channels.
virtual void	InsertChannel (Channel &c_Channel, std::size_t pos)
	Insert a Channel at a given position.
const stf::SectionAttributes &	GetSectionAttributes (std::size_t nchannel, std::size_t nsection) const
const stf::SectionAttributes &	GetCurrentSectionAttributes () const
stf::SectionAttributes &	GetCurrentSectionAttributesW ()
void	DeleteFit (std::size_t nchannel, std::size_t nsection)
	Deletes the current fit, sets isFitted to false;.
void	SetIsFitted (std::size_t nchannel, std::size_t nsection, const Vector_double &bestFitP_, stfnum::storedFunc *fitFunc_, double chisqr, std::size_t fitBeg_, std::size_t fitEnd_)
	Sets the best-fit parameters when a fit has been performed on this section.
void	SetIsIntegrated (std::size_t nchannel, std::size_t nsection, bool value, std::size_t begin, std::size_t end, const Vector_double &quad_p_)
	Determines whether an integral has been calculated in this section.
void	ClearEvents (std::size_t nchannel, std::size_t nsection)
	Erases all events.
void	correctRangeR (int &value)
void	correctRangeR (std::size_t &value)
bool	LoadTDMS (const std::string &filename, Recording &ReturnData)
std::vector< double >	CalcRawDetectionTrace (std::size_t filterOrder, std::size_t startPoint, std::size_t endPoint)
std::vector< int >	CalcScoringTrace (std::vector< Annotation > expertAnnotations, std::size_t startPoint, std::size_t endPoint)
double	CalcAreaUnderCurve (std::vector< double > d, std::vector< int > c)
std::pair< std::size_t, double >	CalcMaxKappa (std::vector< double > &sortedRawDetectionTrace, std::vector< int > &sortedScoringTrace)
std::vector< double >	SortScoringTraceByRawDetection (std::vector< double > &rawDetectionTrace, std::vector< int > &scoringTrace)
std::vector< stf::Event >	DetectEvents (double threshold_, std::vector< double > &rawDetectionTrace)
void	OnCalculatedThresholdExpertDetectEvents (double threshold, std::size_t filterOrder)
Public Member Functions inherited from Recording
	Recording ()
	Default constuctor.
	Recording (const Channel &c_Channel)
	Constructor.
	Recording (const std::deque< Channel > &ChannelList)
	Constructor.
	Recording (std::size_t c_n_channels, std::size_t c_n_sections=0, std::size_t c_n_points=0)
	Constructor.
virtual	~Recording ()
	Destructor.
std::size_t	GetChannelSize (std::size_t n_channel) const
	Retrieves the number of sections in a channel.
const std::deque< Channel > &	get () const
	Retrieves the channels (read-only).
std::deque< Channel > &	get ()
	Retrieves the channels (read and write).
const std::string &	GetFileDescription () const
	Retrieves the file description.
const std::string &	GetGlobalSectionDescription () const
	Retrieves the common section description.
const std::string &	GetScaling () const
	Retrieves the scaling as a string.
struct tm	GetDateTime () const
	Retrieves the date of recording as a string.
const std::string &	GetComment () const
	Retrieves a comment string.
const std::string &	GetXUnits () const
	Retrieves the x units.
std::size_t	size () const
	Retrieves the size of the channel array.
double	GetXScale () const
	Retrieves the x scaling (sampling interval).
double	GetSR () const
	Retrieves the sampling rate ( 1 / x-scale )
std::size_t	GetCurChIndex () const
	Retrieves the index of the current channel.
std::size_t	GetSecChIndex () const
	Retrieves the index of the second channel.
std::size_t	GetCurSecIndex () const
	Retrieves the index of the current section.
const std::vector< std::size_t > &	GetSelectedSections () const
	Retrieves the indices of the selected sections (read-only).
std::vector< std::size_t > &	GetSelectedSectionsW ()
	Retrieves the indices of the selected sections (read and write).
const Vector_double &	GetSelectBase () const
	Retrieves the stored baseline values of the selected sections (read-only).
Vector_double &	GetSelectBaseW ()
	Retrieves the stored baseline values of the selected sections (read and write).
const Section &	cursec () const
	Retrieves the currently accessed section in the active channel (read-only)
Section &	cursec ()
	Retrieves the currently accessed section in the active channel (read and write)
const Section &	secsec () const
	Retrieves the currently accessed section in the second (reference) channel (read-only)
const Channel &	curch () const
	Retrieves the active channel (read-only)
Channel &	curch ()
	Retrieves active channel (read and write)
const Channel &	secch () const
	Retrieves the second (reference) channel (read-only)
const Channel &	at (std::size_t n_c) const
	Range-checked access to a channel (read-only).
Channel &	at (std::size_t n_c)
	Range-checked access to a channel (read and write).
void	SetFileDescription (const std::string &value)
	Sets the file description.
void	SetGlobalSectionDescription (const std::string &value)
	Sets the common section description.
void	SetScaling (const std::string &value)
	Sets the scaling as a string.
int	SetTime (const std::string &value)
	Sets the time of recording as a string.
int	SetTime (int hour, int minute, int sec)
int	SetDate (const std::string &value)
	Sets the date of recording as a string.
int	SetDate (int year, int month, int mday)
void	SetDateTime (const struct tm &value)
	Sets the date and time of recording as struct tm.
void	SetDateTime (int year, int month, int mday, int hour, int minute, int sec)
void	SetComment (const std::string &value)
	Sets a comment string.
void	SetGlobalYUnits (std::size_t n_channel, const std::string &value)
	Sets the y units for a channel.
void	SetXUnits (const std::string &value)
	Sets the x units.
void	SetXScale (double value)
	Sets the x scaling.
void	SetCurChIndex (std::size_t value)
	Sets the index of the current channel.
void	SetSecChIndex (std::size_t value)
	Sets the index of the second channel.
void	SetCurSecIndex (std::size_t value)
	Sets the index of the current section.
void	CopyAttributes (const Recording &c_Recording)
	Copy descriptive attributes from another Recording to this Recording.
void	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	AddRec (const Recording &toAdd)
	Add a Recording at the end of this Recording.
void	SelectTrace (std::size_t sectionToSelect, std::ptrdiff_t base_start, std::ptrdiff_t base_end)
	Selects a section.
bool	UnselectTrace (std::size_t sectionToUnselect)
	Unselects a section if it was selected before.
Channel &	operator[] (std::size_t at)
	Unchecked channel access (read and write)
const Channel &	operator[] (std::size_t at) const
	Unchecked channel access (read-only)
std::string	GetEventDescription (int type)
	Get Description of Event Type.
void	SetEventDescription (int type, const char *Description)
	Set Description of Event Type.
void	InitSectionMarkerList (size_t n)
	Initialize List of Section Markers.
int	GetSectionType (size_t section_number)
	Get Type of Section.
void	SetSectionType (size_t section_number, int type)
	Set Type of Section.

Detailed Description

The document class, derived from both wxDocument and Recording.

The document class can be used to model an application’s file-based data. It is part of the document/view framework supported by wxWidgets.

Definition at line 34 of file doc.h.

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The documentation for this class was generated from the following file:

• src/stimfit/gui/doc.h