ipfx.x_to_nwb package

Submodules

ipfx.x_to_nwb.ABFConverter module

Convert ABF files, created by PClamp/Clampex, to NWB v2 files.

class ipfx.x_to_nwb.ABFConverter.ABFConverter(inFileOrFolder, outFile, outputFeedbackChannel, compression=True)

Bases: object

adcNamesWithRealData = ['IN 0', 'IN 1', 'IN 2', 'IN 3']

static outputMetadata(inFile)

protocolStorageDir = None

ipfx.x_to_nwb.DatConverter module

class ipfx.x_to_nwb.DatConverter.DatConverter(inFile, outFile, multipleGroupsPerFile=False, compression=True)

Bases: object

static outputMetadata(inFile)

Create a file with metadata of the given DAT file.

System Message: SEVERE/4 (/home/docs/checkouts/readthedocs.org/user_builds/ipfx/checkouts/v1.0.0.1/ipfx/x_to_nwb/DatConverter.py:docstring of ipfx.x_to_nwb.DatConverter.DatConverter.outputMetadata, line 4)

Unexpected section title.

Parameters
----------

inFile: DAT file

System Message: SEVERE/4 (/home/docs/checkouts/readthedocs.org/user_builds/ipfx/checkouts/v1.0.0.1/ipfx/x_to_nwb/DatConverter.py:docstring of ipfx.x_to_nwb.DatConverter.DatConverter.outputMetadata, line 8)

Unexpected section title.

Returns
-------

None

ipfx.x_to_nwb.conversion_utils module

Miscellaneous helper routines for the ABF/DAT to NWB v2 (aka X to NWB) conversion functionality.

ipfx.x_to_nwb.conversion_utils.clampModeToString(clampMode)

Return the given clamp mode as human readable string. Useful for error messages.

ipfx.x_to_nwb.conversion_utils.convertDataset(array, compression)

Convert to FP32 and optionally request compression for the given array and return it wrapped.

ipfx.x_to_nwb.conversion_utils.createCycleID(numbers, total)

Create an integer from all numbers which is unique for that combination.

Param:numbers: Iterable holding non-negative integer numbers Param:total: Total number of TimeSeries written to the NWB file

ipfx.x_to_nwb.conversion_utils.createSeriesName(prefix, number, total)

Format a unique series group name of the form prefix_XXX where XXX is the formatted number long enough for total number of groups.

ipfx.x_to_nwb.conversion_utils.getAcquiredSeriesClass(clampMode)

Return the appropriate pynwb acquisition class for the given clamp mode.

ipfx.x_to_nwb.conversion_utils.getChannelRecordIndex(pgf, sweep, trace)

Given a pgf node, a SweepRecord and TraceRecord this returns the corresponding ChannelRecordStimulus node as index.

ipfx.x_to_nwb.conversion_utils.getPackageInfo()

Return a dictionary with version information for the allensdk package

ipfx.x_to_nwb.conversion_utils.getStimulusRecordIndex(sweep)

ipfx.x_to_nwb.conversion_utils.getStimulusSeriesClass(clampMode)

Return the appropriate pynwb stimulus class for the given clamp mode.

ipfx.x_to_nwb.conversion_utils.parseUnit(unitString)

Split a SI unit string with prefix into the base unit and the prefix (as number).

ipfx.x_to_nwb.hr_bundle module

class ipfx.x_to_nwb.hr_bundle.Bundle(file_name)

Bases: object

Represent a PATCHMASTER tree file in memory

amp

The Amplifier object from this bundle.

data

The Data object from this bundle.

item_classes = {'.amp': <class 'ipfx.x_to_nwb.hr_nodes.AmplifierFile'>, '.dat': <class 'ipfx.x_to_nwb.hr_nodes.RawData'>, '.mrk': <class 'ipfx.x_to_nwb.hr_nodes.Marker'>, '.mth': <class 'ipfx.x_to_nwb.hr_nodes.ProtocolMethod'>, '.onl': <class 'ipfx.x_to_nwb.hr_nodes.Analysis'>, '.pgf': <class 'ipfx.x_to_nwb.hr_nodes.StimulusTemplate'>, '.pul': <class 'ipfx.x_to_nwb.hr_nodes.Pulsed'>, '.sol': <class 'ipfx.x_to_nwb.hr_nodes.Solutions'>}

mrk

The Markers object from this bundle.

mth

The ProtocolMethod object from this bundle.

onl

The Online Analysis object from this bundle.

pgf

The Stimulus Template object from this bundle.

pul

The Pulsed object from this bundle.

sol

The Solutions object from this bundle.

ipfx.x_to_nwb.hr_nodes module

All supported nodes are listed here. The root node of each bundle calls the TreeNode constructor explicitly the other are plain children of the root nodes.

Documentation:

• https://github.com/neurodroid/stimfit/blob/master/src/libstfio/heka/hekalib.cpp
• ftp://server.hekahome.de/pub/FileFormat/Patchmasterv9/
• For the field_info type parameters see https://docs.python.org/3/library/struct.html#format-characters
• The CARD types are unsigned, see e.g. https://www.common-lisp.net/project/cmucl/doc/clx/1_6_Data_Types.html

The nodes are tailored for patchmaster version 2x90.x.

class ipfx.x_to_nwb.hr_nodes.AmplifierFile(fh, endianess)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Version', 'i'), ('Mark', 'i'), ('VersionName', '32s', <function cstr>), ('AmplifierName', '32s', <function cstr>), ('Amplifier', 'c'), ('ADBoard', 'c'), ('Creator', 'c'), ('Filler1', 'b', None), ('CRC', 'I')]

rectypes = [None, <class 'ipfx.x_to_nwb.hr_nodes.AmplifierSeriesRecord'>, <class 'ipfx.x_to_nwb.hr_nodes.AmplifierStateRecord'>]

required_size = 80

class ipfx.x_to_nwb.hr_nodes.AmplifierSeriesRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('SeriesCount', 'i'), ('Filler1', 'i', None), ('CRC', 'I')]

required_size = 16

class ipfx.x_to_nwb.hr_nodes.AmplifierState(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

field_info = [('StateVersion', '8s', <function cstr>), ('RealCurrentGain', 'd'), ('RealF2Bandwidth', 'd'), ('F2Frequency', 'd'), ('RsValue', 'd'), ('RsFraction', 'd'), ('GLeak', 'd'), ('CFastAmp1', 'd'), ('CFastAmp2', 'd'), ('CFastTau', 'd'), ('CSlow', 'd'), ('GSeries', 'd'), ('StimDacScale', 'd'), ('CCStimScale', 'd'), ('VHold', 'd'), ('LastVHold', 'd'), ('VpOffset', 'd'), ('VLiquidJunction', 'd'), ('CCIHold', 'd'), ('CSlowStimVolts', 'd'), ('CCTrackVHold', 'd'), ('TimeoutLength', 'd'), ('SearchDelay', 'd'), ('MConductance', 'd'), ('MCapacitance', 'd'), ('SerialNumber', '8s', <function cstr>), ('E9Boards', 'h'), ('CSlowCycles', 'h'), ('IMonAdc', 'h'), ('VMonAdc', 'h'), ('MuxAdc', 'h'), ('TstDac', 'h'), ('StimDac', 'h'), ('StimDacOffset', 'h'), ('MaxDigitalBit', 'h'), ('HasCFastHigh', 'b'), ('CFastHigh', 'b'), ('HasBathSense', 'b'), ('BathSense', 'b'), ('HasF2Bypass', 'b'), ('F2Mode', 'b'), ('AmplKind', 'b', <function getAmplifierType>), ('IsEpc9N', 'b'), ('ADBoard', 'b', <function getADBoard>), ('BoardVersion', 'b'), ('ActiveE9Board', 'b'), ('Mode', 'b', <function getClampMode>), ('Range', 'b'), ('F2Response', 'b'), ('RsOn', 'b'), ('CSlowRange', 'b'), ('CCRange', 'b'), ('CCGain', 'b'), ('CSlowToTstDac', 'b'), ('StimPath', 'b'), ('CCTrackTau', 'b'), ('WasClipping', 'b'), ('RepetitiveCSlow', 'b'), ('LastCSlowRange', 'b'), ('Old2', 'b', None), ('CanCCFast', 'b'), ('CanLowCCRange', 'b'), ('CanHighCCRange', 'b'), ('CanCCTracking', 'b'), ('HasVmonPath', 'b'), ('HasNewCCMode', 'b'), ('Selector', 'c'), ('HoldInverted', 'b'), ('AutoCFast', '?'), ('AutoCSlow', '?'), ('HasVmonX100', 'b'), ('TestDacOn', 'b'), ('QMuxAdcOn', 'b'), ('Imon1Bandwidth', 'd'), ('StimScale', 'd'), ('Gain', 'b', <function getAmplifierGain>), ('Filter1', 'b'), ('StimFilterOn', 'b'), ('RsSlow', 'b'), ('Old1', 'b', None), ('CCCFastOn', '?'), ('CCFastSpeed', 'b'), ('F2Source', 'b'), ('TestRange', 'b'), ('TestDacPath', 'b'), ('MuxChannel', 'b'), ('MuxGain64', 'b'), ('VmonX100', 'b'), ('IsQuadro', 'b'), ('F1Mode', 'b'), ('Old3', 'b', None), ('StimFilterHz', 'd'), ('RsTau', 'd'), ('DacToAdcDelay', 'd'), ('InputFilterTau', 'd'), ('OutputFilterTau', 'd'), ('vMonFactor', 'd', None), ('CalibDate', '16s', <function cstr>), ('VmonOffset', 'd'), ('EEPROMKind', 'b'), ('VrefX2', 'b'), ('HasVrefX2AndF2Vmon', 'b'), ('Spare1', 'b', None), ('Spare2', 'b', None), ('Spare3', 'b', None), ('Spare4', 'b', None), ('Spare5', 'b', None), ('CCStimDacScale', 'd'), ('VmonFiltBandwidth', 'd'), ('VmonFiltFrequency', 'd')]

required_size = 400

class ipfx.x_to_nwb.hr_nodes.AmplifierStateRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('StateCount', 'i'), ('StateVersion', 'b'), ('Filler1', 'b', None), ('Filler2', 'b', None), ('Filler3', 'b', None), ('Filler4', 'i', None), ('LockInParams', <class 'ipfx.x_to_nwb.hr_nodes.LockInParams'>), ('AmplifierState', <class 'ipfx.x_to_nwb.hr_nodes.AmplifierState'>), ('IntSol', 'i'), ('ExtSol', 'i'), ('Filler5', '36s', None), ('CRC', 'I')]

required_size = 560

class ipfx.x_to_nwb.hr_nodes.Analysis(fh, endianess)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Version', 'i'), ('Mark', 'i'), ('VersionName', '32s', <function cstr>), ('Obsolete', 'b', None), ('MaxTraces', 'c'), ('WinDefined', '?'), ('rt1', 'b'), ('CRC', 'I'), ('WinNr', '12b'), ('rt2', 'i')]

rectypes = [None, <class 'ipfx.x_to_nwb.hr_nodes.AnalysisMethodRecord'>, <class 'ipfx.x_to_nwb.hr_nodes.AnalysisFunctionRecord'>]

required_size = 64

class ipfx.x_to_nwb.hr_nodes.AnalysisEntryRecord(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

field_info = [('XWave', 'h'), ('YWave', 'h'), ('MarkerSize', 'h'), ('MarkerColorRed', 'H'), ('MarkerColorGreen', 'H'), ('MarkerColorBlue', 'H'), ('MarkerKind', 'b'), ('EActive', '?'), ('Line', '?'), ('TraceColor', '?')]

required_size = 16

class ipfx.x_to_nwb.hr_nodes.AnalysisFunctionRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('Name', '32s', <function cstr>), ('Unit', '8s', <function cstr>), ('LeftOperand', 'h'), ('RightOperand', 'h'), ('LeftBound', 'd'), ('RightBound', 'd'), ('Constant', 'd'), ('XSegmentOffset', 'i'), ('YSegmentOffset', 'i'), ('TcEnumarator', 'h'), ('Function', 'b'), ('DoNotebook', '?'), ('NoFit', '?'), ('NewName', '?'), ('TargetValue', 'h'), ('CursorKind', 'b'), ('TcKind1', 'b'), ('TcKind2', 'b'), ('CursorSource', 'b'), ('CRC', 'I'), ('Equation', '64s', <function cstr>), ('BaselineMode', 'b'), ('SearchDirection', 'b'), ('SourceValue', 'h'), ('CursorAnker', 'h'), ('Spare1', 'h', None)]

required_size = 168

class ipfx.x_to_nwb.hr_nodes.AnalysisGraphRecord(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

field_info = [('GActive', '?'), ('Overlay', '?'), ('Wrap', 'b'), ('OvrlSwp', '?'), ('Normalize', 'b'), ('Spare1', 'b', None), ('Spare2', 'b', None), ('Spare3', 'b', None), ('XScaling', <class 'ipfx.x_to_nwb.hr_nodes.AnalysisScalingRecord'>), ('YScaling', <class 'ipfx.x_to_nwb.hr_nodes.AnalysisScalingRecord'>), ('Entry0', <class 'ipfx.x_to_nwb.hr_nodes.AnalysisEntryRecord'>), ('Entry1', <class 'ipfx.x_to_nwb.hr_nodes.AnalysisEntryRecord'>), ('Entry2', <class 'ipfx.x_to_nwb.hr_nodes.AnalysisEntryRecord'>), ('Entry3', <class 'ipfx.x_to_nwb.hr_nodes.AnalysisEntryRecord'>)]

required_size = 152

class ipfx.x_to_nwb.hr_nodes.AnalysisMethodRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('EntryName', '32s', <function cstr>), ('SharedXWin1', '?'), ('SharedXWin2', '?'), ('m1', '?'), ('m2', '?'), ('Graph0', <class 'ipfx.x_to_nwb.hr_struct.AnalysisGraphRecord[12]'>), ('m3', 'i'), ('CRC', 'I'), ('Headers', '384s', <function cstr>), ('LastXmin', '12d'), ('LastXmax', '12d'), ('LastYmin', '12d'), ('LastYmax', '12d')]

required_size = 2640

class ipfx.x_to_nwb.hr_nodes.AnalysisScalingRecord(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

field_info = [('MinValue', 'd'), ('MaxValue', 'd'), ('GridFactor', 'd'), ('TicLength', 'h'), ('TicNumber', 'h'), ('TicDirection', 'b'), ('AxisLevel', 'b'), ('AxisType', 'b'), ('ScaleMode', 'b'), ('NoUnit', '?'), ('Obsolete', '?', None), ('ZeroLine', '?'), ('Grid', '?'), ('Nice', '?'), ('Label', '?'), ('Centered', '?'), ('IncludeZero', '?')]

required_size = 40

class ipfx.x_to_nwb.hr_nodes.BundleHeader(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

field_info = [('Signature', '8s', <function cstr>), ('Version', '32s', <function cstr>), ('Time', 'd'), ('Items', 'i'), ('IsLittleEndian', '?'), ('Reserved', '11s', None), ('BundleItems', <class 'ipfx.x_to_nwb.hr_struct.BundleItem[12]'>)]

required_size = 256

class ipfx.x_to_nwb.hr_nodes.BundleItem(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

field_info = [('Start', 'i'), ('Length', 'i'), ('Extension', '8s', <function cstr>)]

required_size = 16

class ipfx.x_to_nwb.hr_nodes.ChannelRecordStimulus(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('LinkedChannel', 'i'), ('CompressionFactor', 'i'), ('YUnit', '8s', <function cstr>), ('AdcChannel', 'H'), ('AdcMode', 'b', <function getADCMode>), ('DoWrite', '?'), ('LeakStore', 'b'), ('AmplMode', 'b', <function getAmplMode>), ('OwnSegTime', '?'), ('SetLastSegVmemb', '?'), ('DacChannel', 'H'), ('DacMode', 'b'), ('HasLockInSquare', 'b'), ('RelevantXSegment', 'i'), ('RelevantYSegment', 'i'), ('DacUnit', '8s', <function cstr>), ('Holding', 'd'), ('LeakHolding', 'd'), ('LeakSize', 'd'), ('LeakHoldMode', 'b'), ('LeakAlternate', '?'), ('AltLeakAveraging', '?'), ('LeakPulseOn', '?'), ('StimToDacID', 'H', <function convertStimToDacID>), ('CompressionMode', 'H'), ('CompressionSkip', 'i'), ('DacBit', 'H'), ('HasLockInSine', '?'), ('BreakMode', 'b'), ('ZeroSeg', 'i'), ('StimSweep', 'i'), ('Sine_Cycle', 'd'), ('Sine_Amplitude', 'd'), ('LockIn_VReversal', 'd'), ('Chirp_StartFreq', 'd'), ('Chirp_EndFreq', 'd'), ('Chirp_MinPoints', 'd'), ('Square_NegAmpl', 'd'), ('Square_DurFactor', 'd'), ('LockIn_Skip', 'i'), ('Photo_MaxCycles', 'i'), ('Photo_SegmentNo', 'i'), ('LockIn_AvgCycles', 'i'), ('Imaging_RoiNo', 'i'), ('Chirp_Skip', 'i'), ('Chirp_Amplitude', 'd'), ('Photo_Adapt', 'b'), ('Sine_Kind', 'b'), ('Chirp_PreChirp', 'b'), ('Sine_Source', 'b'), ('Square_NegSource', 'b'), ('Square_PosSource', 'b'), ('Chirp_Kind', 'b', <function getChirpKind>), ('Chirp_Source', 'b'), ('DacOffset', 'd'), ('AdcOffset', 'd'), ('TraceMathFormat', 'b'), ('HasChirp', '?'), ('Square_Kind', 'b', <function getSquareKind>), ('Filler1', '5s', None), ('Square_BaseIncr', 'd'), ('Square_Cycle', 'd'), ('Square_PosAmpl', 'd'), ('CompressionOffset', 'i'), ('PhotoMode', 'i'), ('BreakLevel', 'd'), ('TraceMath', '128s', <function cstr>), ('Filler2', 'i', None), ('CRC', 'I'), ('UnknownFiller', '?', None)]

required_size = 401

class ipfx.x_to_nwb.hr_nodes.GroupRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('Label', '32s', <function cstr>), ('Text', '80s', <function cstr>), ('ExperimentNumber', 'i'), ('GroupCount', 'i'), ('CRC', 'I'), ('MatrixWidth', 'd'), ('MatrixHeight', 'd')]

required_size = 144

class ipfx.x_to_nwb.hr_nodes.LockInParams(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

field_info = [('ExtCalPhase', 'd'), ('ExtCalAtten', 'd'), ('PLPhase', 'd'), ('PLPhaseY1', 'd'), ('PLPhaseY2', 'd'), ('UsedPhaseShift', 'd'), ('UsedAttenuation', 'd'), ('Spares2', 'd', None), ('ExtCalValid', '?'), ('PLPhaseValid', '?'), ('LockInMode', 'b'), ('CalMode', 'b'), ('Spares', '28s', None)]

required_size = 96

class ipfx.x_to_nwb.hr_nodes.Marker(fh, endianess)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Version', 'i'), ('CRC', 'I')]

rectypes = [None]

required_size = 8

class ipfx.x_to_nwb.hr_nodes.ProtocolMethod(fh, endianess)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Version', 'i'), ('Mark', 'i'), ('VersionName', '32s', <function cstr>), ('MaxSamples', 'i'), ('Filler1', 'i', None), ('Params', '10s', <function cstr>), ('ParamText', '320s', <function cstr>), ('Reserved', '128s', None), ('Filler2', 'i', None), ('CRC', 'I')]

rectypes = [None]

required_size = 514

class ipfx.x_to_nwb.hr_nodes.Pulsed(fh, endianess)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Version', 'i'), ('Mark', 'i'), ('VersionName', '32s', <function cstr>), ('AuxFileName', '80s', <function cstr>), ('RootText', '400s', <function cstr>), ('StartTime', 'd'), ('MaxSamples', 'i'), ('CRC', 'I'), ('Features', 'h'), ('Filler1', 'h', None), ('Filler2', 'i', None), ('RoTcEnumerator', '32h'), ('RoTcKind', '32s', <function cstr>)]

rectypes = [None, <class 'ipfx.x_to_nwb.hr_nodes.GroupRecord'>, <class 'ipfx.x_to_nwb.hr_nodes.SeriesRecord'>, <class 'ipfx.x_to_nwb.hr_nodes.SweepRecord'>, <class 'ipfx.x_to_nwb.hr_nodes.TraceRecord'>]

required_size = 640

class ipfx.x_to_nwb.hr_nodes.RawData(bundle)

Bases: object

class ipfx.x_to_nwb.hr_nodes.SeriesRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('Label', '32s', <function cstr>), ('Comment', '80s', <function cstr>), ('SeriesCount', 'i'), ('NumberSweeps', 'i'), ('AmplStateOffset', 'i'), ('AmplStateSeries', 'i'), ('MethodTag', 'i'), ('Time', 'd'), ('PageWidth', 'd'), ('SwUserParamDescr', <class 'ipfx.x_to_nwb.hr_struct.UserParamDescrType[4]'>), ('MethodName', '32s', None), ('UserParams', '4d'), ('LockInParams', <class 'ipfx.x_to_nwb.hr_nodes.LockInParams'>), ('AmplifierState', <class 'ipfx.x_to_nwb.hr_nodes.AmplifierState'>), ('Username', '80s', <function cstr>), ('SeUserParamDescr1', <class 'ipfx.x_to_nwb.hr_struct.UserParamDescrType[4]'>), ('Filler1', 'i', None), ('CRC', 'I'), ('SeUserParams2', '4d'), ('SeUserParamDescr2', <class 'ipfx.x_to_nwb.hr_struct.UserParamDescrType[4]'>), ('ScanParams', '96s', <function cstr>)]

required_size = 1408

class ipfx.x_to_nwb.hr_nodes.Solutions(fh, endianess)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('RoVersion', 'H'), ('RoDataBaseName', '80s', <function cstr>), ('RoSpare1', 'H', None), ('RoCRC', 'I')]

rectypes = [None]

required_size = 88

class ipfx.x_to_nwb.hr_nodes.StimSegmentRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('Class', 'b', <function getSegmentClass>), ('StoreKind', 'b', <function getStoreType>), ('VoltageIncMode', 'b', <function getIncrementMode>), ('DurationIncMode', 'b', <function getIncrementMode>), ('Voltage', 'd'), ('VoltageSource', 'i', <function getSourceType>), ('DeltaVFactor', 'd'), ('DeltaVIncrement', 'd'), ('Duration', 'd'), ('DurationSource', 'i', <function getSourceType>), ('DeltaTFactor', 'd'), ('DeltaTIncrement', 'd'), ('Filler1', 'i', None), ('CRC', 'I'), ('ScanRate', 'd')]

required_size = 80

class ipfx.x_to_nwb.hr_nodes.StimulationRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('EntryName', '32s', <function cstr>), ('FileName', '32s', <function cstr>), ('AnalName', '32s', <function cstr>), ('DataStartSegment', 'i'), ('DataStartTime', 'd'), ('SampleInterval', 'd'), ('SweepInterval', 'd'), ('LeakDelay', 'd'), ('FilterFactor', 'd'), ('NumberSweeps', 'i'), ('NumberLeaks', 'i'), ('NumberAverages', 'i'), ('ActualAdcChannels', 'i'), ('ActualDacChannels', 'i'), ('ExtTrigger', 'b'), ('NoStartWait', '?'), ('UseScanRates', '?'), ('NoContAq', '?'), ('HasLockIn', '?'), ('OldStartMacKind', '?'), ('OldEndMacKind', '?'), ('AutoRange', 'b'), ('BreakNext', '?'), ('IsExpanded', '?'), ('LeakCompMode', '?'), ('HasChirp', '?'), ('OldStartMacro', '32s', <function cstr>), ('OldEndMacro', '32s', <function cstr>), ('IsGapFree', '?'), ('HandledExternally', '?'), ('Filler1', '?', None), ('Filler2', '?', None), ('CRC', 'I')]

required_size = 248

class ipfx.x_to_nwb.hr_nodes.StimulusTemplate(fh, endianess)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Version', 'i'), ('Mark', 'i'), ('VersionName', '32s', <function cstr>), ('MaxSamples', 'i'), ('Filler1', 'i', None), ('StimParams', '10d'), ('StimParamChars', '320s', <function cstr>), ('Reserved', '128s', None), ('Filler2', 'i', None), ('CRC', 'I')]

rectypes = [None, <class 'ipfx.x_to_nwb.hr_nodes.StimulationRecord'>, <class 'ipfx.x_to_nwb.hr_nodes.ChannelRecordStimulus'>, <class 'ipfx.x_to_nwb.hr_nodes.StimSegmentRecord'>]

required_size = 584

class ipfx.x_to_nwb.hr_nodes.SweepRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('Label', '32s', <function cstr>), ('AuxDataFileOffset', 'i'), ('StimCount', 'i'), ('SweepCount', 'i'), ('Time', 'd'), ('Timer', 'd'), ('SwUserParams', '4d'), ('Temperature', 'd'), ('OldIntSol', 'i'), ('OldExtSol', 'i'), ('DigitalIn', 'h'), ('SweepKind', 'h'), ('DigitalOut', 'h'), ('Filler1', 'h', None), ('Markers', '4d'), ('Filler2', 'i', None), ('CRC', 'I'), ('SwHolding', '16d')]

required_size = 288

class ipfx.x_to_nwb.hr_nodes.TraceRecord(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_treenode.TreeNode

field_info = [('Mark', 'i'), ('Label', '32s', <function cstr>), ('TraceCount', 'i'), ('Data', 'i'), ('DataPoints', 'i'), ('InternalSolution', 'i'), ('AverageCount', 'i'), ('LeakCount', 'i'), ('LeakTraces', 'i'), ('DataKind', 'h', <function convertDataKind>), ('UseXStart', '?'), ('Kind', 'b'), ('RecordingMode', 'b', <function getRecordingMode>), ('AmplIndex', 'b'), ('DataFormat', 'b', <function getDataFormat>), ('DataAbscissa', 'b'), ('DataScaler', 'd'), ('TimeOffset', 'd'), ('ZeroData', 'd'), ('YUnit', '8s', <function cstr>), ('XInterval', 'd'), ('XStart', 'd'), ('XUnit', '8s', <function cstr>), ('YRange', 'd'), ('YOffset', 'd'), ('Bandwidth', 'd'), ('PipetteResistance', 'd'), ('CellPotential', 'd'), ('SealResistance', 'd'), ('CSlow', 'd'), ('GSeries', 'd'), ('RsValue', 'd'), ('GLeak', 'd'), ('MConductance', 'd'), ('LinkDAChannel', 'i'), ('ValidYrange', '?'), ('AdcMode', 'b', <function getADCMode>), ('AdcChannel', 'h'), ('Ymin', 'd'), ('Ymax', 'd'), ('SourceChannel', 'i'), ('ExternalSolution', 'i'), ('CM', 'd'), ('GM', 'd'), ('Phase', 'd'), ('DataCRC', 'I'), ('CRC', 'I'), ('GS', 'd'), ('SelfChannel', 'i'), ('InterleaveSize', 'i'), ('InterleaveSkip', 'i'), ('ImageIndex', 'i'), ('Markers', '10d'), ('SECM_X', 'd'), ('SECM_Y', 'd'), ('SECM_Z', 'd'), ('Holding', 'd'), ('Enumerator', 'i'), ('XTrace', 'i'), ('IntSolValue', 'd'), ('ExtSolValue', 'd'), ('IntSolName', '32s', <function cstr>), ('ExtSolName', '32s', <function cstr>), ('DataPedestal', 'd')]

required_size = 512

class ipfx.x_to_nwb.hr_nodes.UserParamDescrType(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

field_info = [('Name', '32s', <function cstr>), ('Unit', '8s', <function cstr>)]

required_size = 40

ipfx.x_to_nwb.hr_nodes.convertDataFormatToNP(dataFormat)

ipfx.x_to_nwb.hr_nodes.convertDataKind(byte)

ipfx.x_to_nwb.hr_nodes.convertStimToDacID(byte)

ipfx.x_to_nwb.hr_nodes.cstr(byte)

Convert C string bytes to python string.

ipfx.x_to_nwb.hr_nodes.getADBoard(byte)

ipfx.x_to_nwb.hr_nodes.getADCMode(byte)

ipfx.x_to_nwb.hr_nodes.getAmplMode(byte)

ipfx.x_to_nwb.hr_nodes.getAmplifierGain(byte)

Units: V/A

ipfx.x_to_nwb.hr_nodes.getAmplifierType(byte)

ipfx.x_to_nwb.hr_nodes.getChirpKind(byte)

ipfx.x_to_nwb.hr_nodes.getClampMode(byte)

ipfx.x_to_nwb.hr_nodes.getDataFormat(byte)

ipfx.x_to_nwb.hr_nodes.getFromList(lst, index)

ipfx.x_to_nwb.hr_nodes.getIncrementMode(byte)

ipfx.x_to_nwb.hr_nodes.getRecordingMode(byte)

ipfx.x_to_nwb.hr_nodes.getSegmentClass(byte)

ipfx.x_to_nwb.hr_nodes.getSourceType(byte)

ipfx.x_to_nwb.hr_nodes.getSquareKind(byte)

ipfx.x_to_nwb.hr_nodes.getStoreType(byte)

ipfx.x_to_nwb.hr_segments module

Create a numpy array with the stimulus set data from the stored parameters.

class ipfx.x_to_nwb.hr_segments.ChirpSegment(stimRec, channelRec, segmentRec)

Bases: ipfx.x_to_nwb.hr_segments.Segment

createArray(sweep)

Return a numpy array with the stimset data.

Units are [mV] for voltage clamp and [pA] for current clamp.

getAmplitude(channelRec, segmentRec)

Extract the value of the amplitude from the ChannelRecordStimulus and the StimSegmentRecord.

class ipfx.x_to_nwb.hr_segments.ConstantSegment(stimRec, channelRec, segmentRec)

Bases: ipfx.x_to_nwb.hr_segments.Segment

createArray(sweep)

Return a numpy array with the stimset data.

Units are [mV] for voltage clamp and [pA] for current clamp.

class ipfx.x_to_nwb.hr_segments.RampSegment(stimRec, channelRec, segmentRec)

Bases: ipfx.x_to_nwb.hr_segments.Segment

createArray(sweep)

Return a numpy array with the stimset data.

Units are [mV] for voltage clamp and [pA] for current clamp.

class ipfx.x_to_nwb.hr_segments.Segment(stimRec, channelRec, segmentRec)

Bases: abc.ABC

Base class for all segment types. Derived class must implement createArray only.

The following segment types are supported: - Constant - Ramp - Square - Chirp

Support for the following types is missing: - Continous - Sine

Note: Only currently used segment options/modes/specialities are implemented.

applyAmplitudeScale(amplitude)

Scale the amplitude so that we get the correct units. See also Segment.createArray.

calculateNumberOfPoints(duration)

Return the number of points of this segment.

createArray(sweep)

Return a numpy array with the stimset data.

Units are [mV] for voltage clamp and [pA] for current clamp.

doStepping(sweepNo)

Apply the delta modes the given number of times (once per sweep)

getAmplitude(channelRec, segmentRec)

Extract the value of the amplitude from the ChannelRecordStimulus and the StimSegmentRecord.

hasXDelta()

Return true if delta mode is active for the x dimension.

hasYDelta()

Return true if delta mode is active for the y dimension.

class ipfx.x_to_nwb.hr_segments.SquareSegment(stimRec, channelRec, segmentRec)

Bases: ipfx.x_to_nwb.hr_segments.Segment

createArray(sweep)

Return a numpy array with the stimset data.

Units are [mV] for voltage clamp and [pA] for current clamp.

getAmplitude(channelRec, segmentRec)

Extract the value of the amplitude from the ChannelRecordStimulus and the StimSegmentRecord.

ipfx.x_to_nwb.hr_segments.getSegmentClass(stimRec, channelRec, segmentRec)

Return the correct derived class instance of Segment for the given records.

ipfx.x_to_nwb.hr_stimsetgenerator module

class ipfx.x_to_nwb.hr_stimsetgenerator.StimSetGenerator(bundle)

Bases: object

High level class for creating stimsets

fetch(sweep, trace)

Fetch a stimulus set from the cache, generate it if it is not present.

Parameters:

• sweep – SweepRecord node
• trace – TraceRecord node

Return: python list of numpy arrays, one array per sweep

ipfx.x_to_nwb.hr_struct module

class ipfx.x_to_nwb.hr_struct.Struct(data, endian='<')

Bases: object

High-level wrapper around struct.Struct that makes it a bit easier to unpack large, nested structures.

• Unpacks to dictionary allowing fields to be retrieved by name
• Optionally massages field data on read
• Handles arrays and nested structures

fields must be a list of tuples like (name, format) or (name, format, function) where format must be a simple struct format string like ‘i’, ‘d’, ’32s’, or ‘4d’; or another Struct instance.

function may be either a function that filters the data for that field or None to exclude the field altogether.

If size is given, then an exception will be raised if the final struct size does not match the given size.

Example:

class MyStruct(Struct):
    field_info = [
        ('char_field', 'c'),            # single char
        ('char_array', '8c'),           # list of 8 chars
        ('str_field',  '8s', cstr),     # C string of len 8
        ('sub_struct', MyOtherStruct),  # dict generated by s2.unpack
        ('filler', '32s', None),        # ignored field
    ]
    required_size = 300

fh = open(fname, 'rb')
data = MyStruct(fh)

classmethod array(x)

Return a new StructArray class of length x and using this struct as the array item type.

field_info = None

get_fields()

Recursively convert struct fields+values to nested dictionaries.

required_size = None

classmethod size()

class ipfx.x_to_nwb.hr_struct.StructArray(data, endian='<')

Bases: ipfx.x_to_nwb.hr_struct.Struct

array_size = None

item_struct = None

classmethod size()

ipfx.x_to_nwb.hr_treenode module

Wrapper class around the native struct

class ipfx.x_to_nwb.hr_treenode.TreeNode(fh, endianess, record_types, level_sizes, level=0)

Bases: ipfx.x_to_nwb.hr_struct.Struct

Struct that also represents a node in the tree.

Module contents

This package allows to create NeuroDataWithoutBorders v2 files from ABF and DAT files.

See Readme.md for more information.