File MIES_PulseAveraging.ipf¶

PA Routines for dealing with pulse averaging.

Averaging is done for all pulses in a set
Zeroing is done for all pulses
Deconvolution is done for the average wave only
See also PA_AutomaticTimeAlignment

Drawing layers:

ProgAxes: X=0 line for images
ProgFront: Scale bars
ProgBack: Failed pulses triangles

Unnamed Group

static const string PA_DRAWLAYER_XZEROLINE = "ProgAxes"¶

static const string PA_DRAWLAYER_SCALEBAR = "ProgFront"¶

static const string PA_DRAWLAYER_FAILED_PULSES = "ProgBack"¶

Pulse sort order

Popupmenu indizes for the PA plot controls

static const double PA_PULSE_SORTING_ORDER_SWEEP = 0x0¶

static const double PA_PULSE_SORTING_ORDER_PULSE = 0x1¶

Defines

PA_HIDE_AXIS¶

PA_HIDE_EXECUTION_TIME¶

Functions

static string PA_GetGraphs(string win, variable displayMode)¶: Return a list of all graphs.

static string PA_GetGraphName(string win, PulseAverageSettings *pa, variable displayMode, variable channelNumber, variable activeRegionCount)¶

static string PA_GetGraphPrefix(string win, variable displayMode)¶

string PA_GetColorScalePanel(string win)¶

Return the subwindow path to the panel which holds the graphs with the color scales.

Only present for PA_DISPLAYMODE_IMAGES graphs.

string PA_GetColorScaleGraph(string win)¶

Return the subwindow path to the graph which holds the color scales.

Only present for PA_DISPLAYMODE_IMAGES graphs.

static string PA_GetGraph(string mainWin, PulseAverageSettings *pa, variable displayMode, variable channelNumber, variable region, variable activeRegionCount, variable activeChanCount, variable numRegions)¶

Return the name of the pulse average graph.

This function takes care of creating a graph if it does not exist, and laying it out correctly

Layout scheme for multiple graphs turned on:

Positions the graphs right to mainWin in matrix form
Columns: Regions (aka headstages with pulse starting time information respecting region selection in GUI)
Rows: Active unique channels

static wave PA_GetAxes(PulseAverageSettings *pa, variable channel, variable region)¶: Return the names of the vertical and horizontal axes.

static wave PA_CalculatePulseInfos(wave DA, string fullPath, variable channelNumber, variable totalOnsetDelay)¶

Derive the pulse infos from a DA wave.

Uses plain FindLevels after the onset delay using 10% of the full range above the minimum as threshold

Returns:: pulse info wave or if nothing could be found, an invalid wave reference

static wave PA_GetUniqueHeadstages(WaveText traceData)¶: Return a wave with headstage numbers, duplicates replaced with NaN so that the indizes still correspond the ones in traceData.

wave PA_GetPulseInfos(WaveText traceData, variable idx, variable region, string channelTypeStr)¶

Return pulse infos.

Parameters:

traceData – 2D wave with trace information, from GetTraceInfos()
idx – Index into traceData, used for determining sweep numbers, labnotebooks, etc.
region – Region (headstage) to get pulse starting times for
channelTypeStr – Type of the channel, one of XOP_CHANNEL_NAMES

Returns:

invalid wave reference if no pulses could be found or 2D wave see GetPulseInfoWave()

static variable PA_DiffPulseInfos(wave numericalValues, variable sweepNo, WaveOrNull pulseInfosEpochs, WaveOrNull pulseInfosCalc)¶: Compare epoch and calculated pulse infos.

static wave PA_RetrievePulseInfosFromEpochs(string epochInfo)¶

Extracts the pulse info from the lab notebook and returns them as wave.

Parameters:: epochInfo – [in] epoch data to extract pulse starting times
Returns:: pulse info, see GetPulseInfoWave() or an invalid wave reference on error

static variable PA_GetPulseLength(wave pulseInfos, variable pulseIndex, variable overridePulseLength, variable fixedPulseLength)¶

static std::tuple<WAVE, WAVE> PA_CreateAndFillPulseWaveIfReq(WaveOrNull wv, dfref singleSweepFolder, variable channelType, variable channelNumber, variable clampMode, variable region, variable pulseIndex, variable first, variable length, wave pulseInfos)¶

Single pulse wave creator.

The wave note for the pulse waves is stored in a separate empty wave. This speeds up the caching logic for the pulse waves a lot.

The wave note is used for documenting the applied operations:

$NOTE_KEY_FAILED_PULSE_LEVEL: Level used for failed pulse search
$NOTE_KEY_NUMBER_OF_SPIKES: Number of spikes used for failed pulse search
$NOTE_KEY_PULSE_LENGTH: Length in points of the pulse wave (before any operations)
$NOTE_KEY_SEARCH_FAILED_PULSE: Checkbox state of “Search failed pulses”
$NOTE_KEY_TIMEALIGN: Time alignment was active and applied
$NOTE_KEY_TIMEALIGN_TOTAL_OFFSET: Calculated offset from time alignment
$NOTE_KEY_ZEROED: Zeroing was active and applied
$NOTE_KEY_WAVE_MINIMUM: Minimum value of the data
$NOTE_KEY_WAVE_MAXIMUM: Maximum value of the data
$NOTE_KEY_TIMEALIGN_FEATURE_POS: Position where the feature for time alignment was found
$NOTE_KEY_PULSE_IS_DIAGONAL: Stores if pulse is shown in the diagonal of the output layout
$PA_SOURCE_WAVE_TIMESTAMP: Last modification time of the pulse wave before creation.
$NOTE_KEY_PULSE_START: ms coordinates where the pulse starts
$NOTE_KEY_PULSE_END: ms coordinates where the pulse ends
$NOTE_KEY_PULSE_CLAMPMODE: Clamp mode of the pulse data, one of AmplifierClampModes

Diagonal pulses only with failed pulse search enabled:

$NOTE_KEY_PULSE_HAS_FAILED: Pulse has failed
$NOTE_KEY_PULSE_SPIKE_POSITIONS: Comma separated list of spike positions in ms. 0 is the start of the pulse.

static variable PA_UpdateMinAndMax(wave wv, wave noteWave)¶

static string PA_GenerateFailedPulseKey(variable sweep, variable region, variable pulse)¶

Generate a key for a pulse.

All pulses with that key are either failing or passing.

static std::tuple<WaveDouble, WaveText> PA_GetSweepsAndExperimentsFromIndices(string win, WaveOrNull additionalData)¶

static std::tuple<PulseAverageSetIndices> PA_GenerateAllPulseWaves(string win, PulseAverageSettings *pa, variable mode, WaveOrNull additionalData)¶

Create all single pulse waves.

This function needs to be called when ever traces in the databrowser/sweepbrowser are removed or added.

Idea:

Gather all AD sweep traces in the databrowser/sweepbrowser (skipping duplicates from oodDAQ)
Iterate over all regions (there are as many regions as unique headstages)
Now gather the pulse starting time from the region and create single pulse waves for all of them

The result is feed into GetPulseAverageProperties() and GetPulseAveragepropertiesWaves() for further consumption.

Fast path for incremental update:

The previous list of regions/channels is saved
We get the indizes of the new sweep (from additionalData)
Only these indizes are added to the properties wave, as well as the setIndice waves at the end
information is stored where the new data begins
The region/channels of the new Sweep(s) are merged with the old ones.
In case the layout changed compared to the old regions/channels it is calculated again.

static variable PA_SetDiagonalityNote(wave indices, variable startIndex, variable numEntries, WaveRefWave propertiesWaves, variable isDiagonal)¶

static std::tuple<PulseAverageSetIndices> PA_InitPASIInParts(PulseAverageSettings *pa, variable part, variable disableIncremental)¶

This function fills a structure with information we need in most further processing functions, e.g. PA DFs, references to properties, setIndice waves, regions, channels, axes, a.s.o. Since not every information might be available at the time this structure is filled there are two steps defined, that are enabled by setting ‘part’ with PA_PASIINIT_BASE and/or PA_PASIINIT_INDICEMETA.

Parameters:

pa – PulseAverageSettings structure
part – filling step for the returned structure, set depending on available data
disableIncremental – When set then the meta information for incremental updates is just initialized with zero.

static variable PA_CopySetIndiceSizeDispRestart(WaveRefWave setIndices)¶: For incremental display update copy current size of of setIndices to new display start.

static std::tuple<WaveRefWave, WAVE, WAVE, WAVE> PA_GetSetIndicesHelper(dfref pulseAverageHelperDFR, variable prevIndices)¶

Retrieve setIndices, channels and regions of the current or the previous layout, as is saved in the properties wave wave note.

Parameters:

pulseAverageHelperDFR – [in] Reference to pulse average helper DF
prevIndices – [in] When set then the indices, channels and regions of the previous layout are returned, otherwise the current layout is returned. Note that only the layout is considered, the returned indices always contain the current indices for each channel/region at the time of calling this function.

static variable PA_UpdateIndiceNotes(wave currentDisplayMapping, wave prevDisplayMapping, PulseAverageSetIndices *pasi, variable layoutChanged)¶

Updates the setIndices notes with information about the layout and layout changes. Therefore the function compares the previous display mapping and the current display mapping for each region/channel in the layout and determines if the setIndices at this region/channel are added as new/moved/stayed at the same position or were removed. In the setIndices wave note the following keys are set: ‘$PA_SETINDICES_KEY_DISPCHANGE’: change in the layout for this set ‘$PA_SETINDICES_KEY_ACTIVEREGIONCOUNT’: grid location on the vertical where this set is displayed ‘$PA_SETINDICES_KEY_ACTIVECHANCOUNT’: grid location on the horizontal where this set is displayed (this data is currently not used, but created for further PA plot extension)

Parameters:

currentDisplayMapping – [in] 3D wave, rows and columns map the region/channels, in the two layers the associated activeRegion and activeChannel are stored. The layer information is the position in the grid of the layout.
prevDisplayMapping – [in] Technically the same wave as currentDisplayMapping, but it stores the information about the previous layout.
pasi – [in] Pulse Average structure storing PA information
layoutChanged – [in] when set then the layout has changed compared to the previous one displayed. This is directly related to a region/channel change.

static variable PA_UpdateIndiceNotesImpl(wave indices, wave currentMap, wave oldMap, variable channel, variable region, variable layoutChanged, variable indiceType)¶: Evaluate the previous and current mapping and set the display change in the wave note of the indice sets as well as activeChanCount, activeRegionCount. IMPORTANT: To have a consistent state for the case the layout changed the function must be called with the current and the previous indices. Otherwise removed sets wont be flagged properly.

static variable PA_ApplyPulseSortingOrder(wave setIndices, variable channelNumber, variable region, wave properties, PulseAverageSettings *pa)¶

static variable PA_GatherSettings(string win, PulseAverageSettings *s)¶: Populates pps.pulseAverSett with the user selection from the panel.

static variable PA_DeconvGatherSettings(string win, PulseAverageDeconvSettings *deconvolution)¶: gather deconvolution settings from PA section in BSP

variable PA_Update(string win, variable mode, WaveOrNull additionalData = defaultValue)¶: Update the PA plot to accomodate changed settings.

static wave PA_GetSetWaves(dfref dfr, variable channelNumber, variable region, variable removeFailedPulses = defaultValue)¶: Returns the two column setWave with pulse/pulsenote.

static wave PA_GetSetWaves_TS(wave properties, WaveRefWave propertiesWaves, wave setIndizes, variable getMode, variable removeFailedPulses)¶

Returns a 1D wave ref wave containing the refs to the setwave2 refs of {all, new, old} sets, depending on the mode constant given in getModes. For mode constants.

File MIES_PulseAveraging.ipf¶

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