ekpy.analysis.asylum package

Submodules

ekpy.analysis.asylum.main module

ekpy.analysis.asylum.main.load_image_from_binary(path, return_meta_data=True)

Loads data from binary file (from asylum research) into a dict of numpy arrays.

Parameters

• path (str) – Path to the data.

• return_meta_data (bool) – Return meta data, i.e. scan size etc.

Returns

Key labels image type, value is numpy array of img data.

Return type

(dict)

ekpy.analysis.asylum.main.load_pfmloop_from_binary(path, return_meta_data=False)

loads data from binary file (from asylum research) into a numpy array

path: str return_meta_data: bool - True returns (dict({‘label’:(numpy array) imgdata}, meta_data)

meta_data (dict) -> {ScanLines:(str)… etc}

The complete list of included keys in meta_data is given here:

[‘ScanSize’, ‘FastScanSize’, ‘SlowScanSize’, ‘ScanRate’, ‘XOffset’, ‘YOffset’, ‘PointsLines’, ‘ScanPoints’, ‘ScanLines’, ‘ScanAngle’, ‘ImagingMode’, ‘InvOLS’, ‘SpringConstant’, ‘AmpInvOLS’, ‘Amp2Invols’, ‘FastRatio’, ‘SlowRatio’, ‘TopLine’, ‘BottomLine’, ‘ScanMode’, ‘NapMode’, ‘FMapScanTime’, ‘FMapScanPoints’, ‘FMapScanLines’, ‘FMapXYVelocity’, ‘FMapBookWise’, ‘Channel1DataType’, ‘DataTypeSum’, ‘PhaseOffset’, ‘PhaseOffset1’, ‘NapPhaseOffset’, ‘VoltageParm’, ‘NapParms’, ‘PreScanSetting’, ‘OrcaOffset’, ‘OrcaOffset2’, ‘UserIn0Gain’, ‘UserIn0Offset’, ‘UserIn1Gain’, ‘UserIn1Offset’, ‘UserIn2Gain’, ‘UserIn2Offset’, ‘LateralGain’, ‘LateralOffset’, ‘OrcaGain’, ‘OrcaGain2’, ‘FastMapScanRate’, ‘FastMapZRate’, ‘Real Parms’, ‘Initial Parms’, ‘Initial ScanSize’, ‘Initial FastScanSize’, ‘Initial SlowScanSize’, ‘Initial ScanRate’, ‘ScanSpeed’, ‘Initial XOffset’, ‘Initial YOffset’, ‘Initial ScanPoints’, ‘Initial ScanLines’, ‘RoundFactor’, ‘IntegralGain’, ‘ProportionalGain’, ‘Initial ScanAngle’, ‘ScanAngleFactor’, ‘AmplitudeSetpointVolts’, ‘AmplitudeSetpointMeters’, ‘DriveAmplitude’, ‘DriveFrequency’, ‘SweepWidth’, ‘SlowScanEnabled’, ‘DeflectionSetpointVolts’, ‘DeflectionSetpointMeters’, ‘DeflectionSetpointNewtons’, ‘Initial ImagingMode’, ‘MaxScanSize’, ‘Initial InvOLS’, ‘Initial SpringConstant’, ‘DisplaySpringConstant’, ‘ScanStateChanged’, ‘ScanDown’, ‘XLVDTSens’, ‘YLVDTSens’, ‘ZLVDTSens’, ‘XLVDTOffset’, ‘YLVDTOffset’, ‘ZLVDTOffset’, ‘YIgain’, ‘YPgain’, ‘XIgain’, ‘XPgain’, ‘LastScan’, ‘XPiezoSens’, ‘YPiezoSens’, ‘ZPiezoSens’, ‘XDriveOffset’, ‘YDriveOffset’, ‘SweepPoints’, ‘SecretGain’, ‘YSgain’, ‘XSgain’, ‘DIsplayLVDTTraces’, ‘Initial PhaseOffset’, ‘BaseSuffix’, ‘SaveImage’, ‘ParmChange’, ‘ADCgain’, ‘OldADCgain’, ‘OldScanSize’, ‘OldYOffset’, ‘OldXOffset’, ‘ZIgain’, ‘ZPgain’, ‘ZSgain’, ‘Initial AmpInvOLS’, ‘UpdateCounter’, ‘DoMunge’, ‘XMungeAlpha’, ‘YMungeAlpha’, ‘ZMungeAlpha’, ‘StartHeadTemp’, ‘StartScannerTemp’, ‘Has1xACDeflGain’, ‘DontChangeXPT’, ‘LowNoise’, ‘ScreenRatio’, ‘XDriftRate’, ‘YDriftRate’, ‘XDriftTotal’, ‘YDriftTotal’, ‘DriftBIts’, ‘DriftCount’, ‘Setpoint’, ‘Initial FastRatio’, ‘Initial SlowRatio’, ‘Initial TopLine’, ‘Initial BottomLine’, ‘ScanStatus’, ‘Is1DPlus’, ‘DelayUpdate’, ‘MarkerRatio’, ‘StartLineCount’, ‘OldAmplitudeSetpointVolts’, ‘OldDeflectionSetPointVolts’, ‘Initial ScanMode’, ‘Interpolate’, ‘TipVoltage’, ‘SurfaceVoltage’, ‘FreqIgain’, ‘FreqPgain’, ‘FreqSgain’, ‘Initial OrcaGain’, ‘FreqGainOn’, ‘Initial UserIn0Gain’, ‘Initial UserIn1Gain’, ‘Initial UserIn2Gain’, ‘Initial LateralGain’, ‘IsBipolar’, ‘FrequencyHack’, ‘MagneticField’, ‘DriveGainOn’, ‘DriveIGain’, ‘DrivePGain’, ‘DriveSGain’, ‘Initial UserIn0Offset’, ‘Initial UserIn1Offset’, ‘Initial UserIn2Offset’, ‘Initial LateralOffset’, ‘LastImage’, ‘ZoomSize’, ‘ZoomXOffset’, ‘ZoomYOffset’, ‘User0Voltage’, ‘User1Voltage’, ‘ExtendedZ’, ‘DriveAmplitude1’, ‘DriveFrequency1’, ‘SweepWidth1’, ‘Initial PhaseOffset1’, ‘Initial Amp2InvOLS’, ‘Initial VoltageParm’, ‘MicroscopeID’, ‘CapacitanceSens’, ‘CapacitanceOffset’, ‘CapPhaseOffset’, ‘TipBiasOffset’, ‘TipHeaterOffset’, ‘SurfaceBiasOffset’, ‘UseCantHolder’, ‘CurrentCantHolder’, ‘HasClickRing’, ‘XScanDirection’, ‘YScanDirection’, ‘SaveImageCount’, ‘SaveImageLines’, ‘Initial OrcaGain2’, ‘UpdateSlowWave’, ‘FBFilterBW’, ‘CurrentSetpointAmps’, ‘CurrentSetpointVolts’, ‘OldCurrentSetpointVolts’, ‘OldCurrentSetpointAmps’, ‘HasFM’, ‘LastScanWithdraw’, ‘HasLaserRelay’, ‘ToggleLaserRelay’, ‘Decimation’, ‘DARTIGain’, ‘DARTPGain’, ‘SampleHolder’, ‘ManualSampleHolder’, ‘CypherXPTLock’, ‘XPTLock’, ‘LogFeedback’, ‘ARSysScanBusy’, ‘SimpleControls’, ‘Initial PointsLines’, ‘FreeAirAmplitude’, ‘FreeAirPhase’, ‘FreeAirDeflection’, ‘FreeAirDriveAmplitude’, ‘ContinualRetune’, ‘ForceFilter’, ‘TemperatureSens’, ‘TemperatureOffset’, ‘OffsetBehavior’, ‘InputRange’, ‘XLVDTSensSlope’, ‘YLVDTSensSlope’, ‘XLVDTSensIntercept’, ‘YLVDTSensIntercept’, ‘HaveWeKilledTheProgressBar’, ‘Initial PreScanSetting’, ‘ImageFrameTime’, ‘FBFilterSelectivity’, ‘HasDriveChoke’, ‘DriveChokeOn’, ‘CFCWFOS’, ‘SkewAngle’, ‘ContinualRetuneTime’, ‘DRTimeStamp’, ‘CRTimeStamp’, ‘Cypher15VPower’, ‘HasBlueDrive’, ‘BlueDriveOn’, ‘blueDriveOffset’, ‘blueDriveMaxAmplitude’, ‘bDDriveAmplitude’, ‘bDDriveAmplitude1’, ‘bDDiffEfficiencyV’, ‘BackPackIn0Gain’, ‘BackPackIn0Offset’, ‘BackPackIn1Gain’, ‘BackPackIn1Offset’, ‘BackPackIn2Gain’, ‘BackPackIn2Offset’, ‘BackPackIn3Gain’, ‘BackPackIn3Offset’, ‘BackPackIn4Gain’, ‘BackPackIn4Offset’, ‘bdReCalibrateTime’, ‘bdMotorError’, ‘ScanModeGUI’, ‘FastMapSetpointVolts’, ‘FastMapSetpointNewtons’, ‘OldFastMapSetpointVolts’, ‘OldFastMapSetpointNewtons’, ‘Initial FastMapZRate’, ‘FastMapAmplitude’, ‘FastMapFBMethod’, ‘FastMapFBPhase’, ‘FastMapFBWindow’, ‘FastMapAmpSetpointVolts’, ‘FastMapAmpSetpointMeters’, ‘FastMapIndex’, ‘QueueProgress’, ‘QueueEstimate’, ‘QueueExpand’, ‘FastMapIGain’, ‘Initial FastMapScanRate’, ‘FastMapBaseLine’, ‘blueThermOn’, ‘FastMapScanPoints’, ‘FastMapScanLines’, ‘FastMapOptScanPoints’, ‘FastMapOptScanLines’, ‘FreqDGain’, ‘DriveDGain’, ‘ImageSaveExpand’, ‘Saturated’, ‘FrameCount’, ‘SinusoidalOn’, ‘StartHeaterTemp’, ‘StartHeaterHumidity’, ‘MicroscopeModel’, ‘BlueDriveDissipationInWatts’, ‘NapIntegralGain’, ‘NapProportionalGain’, ‘NapDeflectionSetpointVolts’, ‘NapAmplitudeSetpointVolts’, ‘NapDissipationSetpointVolts’, ‘NapFrequencySetPointHz’, ‘NapCurrentSetpointAmps’, ‘NapDriveAmplitude’, ‘NapDriveFrequency’, ‘NapDriveAmplitude1’, ‘NapDriveFrequency1’, ‘NapTipVoltage’, ‘NapSurfaceVoltage’, ‘NapUser0Voltage’, ‘NapUser1Voltage’, ‘NapHeight’, ‘NapStartHeight’, ‘NapTime’, ‘PotentialIGain’, ‘PotentialPGain’, ‘PotentialGainOn’, ‘ElectricTune’, ‘NapCurrentSetpointVolts’, ‘PotentialLoopLimit’, ‘ClosedNap’, ‘NapZIGain’, ‘NapZPGain’, ‘AutoNapZGain’, ‘bDNapDriveAmplitude’, ‘bDNapDriveAmplitude1’, ‘Channel2DataType’, ‘Channel3DataType’, ‘Channel4DataType’, ‘Channel5DataType’, ‘Channel6DataType’, ‘Channel7DataType’, ‘Channel8DataType’, ‘UserCalcFunc’, ‘UserCalcBFunc’, ‘FastMap1DataType’, ‘FastMap2DataType’, ‘FastMap3DataType’, ‘FastMap4DataType’, ‘FastMapCapture’, ‘InA’, ‘InB’, ‘InFast’, ‘InAOffset’, ‘InBOffset’, ‘InFastOffset’, ‘OutXMod’, ‘OutYMod’, ‘OutZMod’, ‘FilterIn’, ‘BNCOut0’, ‘BNCOut1’, ‘BNCOut2’, ‘PogoOut’, ‘Chip’, ‘Shake’, ‘Input.Z.Filter.Freq’, ‘Input.X.Filter.Freq’, ‘Input.Y.Filter.Freq’, ‘Input.A.Filter.Freq’, ‘Input.B.Filter.Freq’, ‘Input.Fast.Filter.Freq’, ‘Lockin.0.Filter.Freq’, ‘Lockin.1.Filter.Freq’, ‘Sample Rate’, ‘ThermalDC’, ‘ThermalQ’, ‘ThermalFrequency’, ‘ThermalWhiteNoise’, ‘ScaleLog’, ‘FitWidth’, ‘ThermalSamples’, ‘ThermalCounter’, ‘SectionSamples’, ‘SectionCounter’, ‘DoThermal’, ‘ThermalResolution’, ‘ThermalZoom’, ‘DoCantTune’, ‘ZoomCounter’, ‘AutoTuneLow’, ‘AutoTuneHigh’, ‘TargetVoltage’, ‘TargetPercent’, ‘CheckTuneTraces’, ‘ButtonTime’, ‘ShowThermalFit’, ‘AppendThermalBit’, ‘TuneQ’, ‘TuneGain’, ‘TunePeakResult’, ‘TuneFreqResult’, ‘TuneQResult’, ‘ThermalSamplesLimit’, ‘TuneFeedback’, ‘TuneDDSOutput’, ‘TipVoltCenter’, ‘TipVoltWidth’, ‘ThermalFrequencyRange’, ‘AutoTuneLimit’, ‘AutoTuneLow1’, ‘AutoTuneHigh1’, ‘TargetVoltage1’, ‘TargetPercent1’, ‘DualACMode’, ‘WhichACMode’, ‘BackwardsTune’, ‘TuneCaptureRate’, ‘TuneTime’, ‘TuneFilter’, ‘iDriveOn’, ‘FrequencyRatio’, ‘DFRTFrequencyCenter’, ‘DFRTFrequencyWidth’, ‘DFRTOn’, ‘ThermalCenter’, ‘ThermalWidth’, ‘DFWMAMT’, ‘LastXPos’, ‘LastYPos’, ‘PFMFrequencyLimit’, ‘TuneLockin’, ‘TipHeaterDrive’, ‘AdjustSpringConstant’, ‘DrawThermalFit’, ‘LateralTune’, ‘ThermalTemperature’, ‘UseCypherThermal’, ‘UseCypherMultiThread’, ‘Illumination’, ‘ARCZ’, ‘TuneAngle’, ‘IsDefaultFrequency’, ‘TargetAmplitude’, ‘TargetPhase’, ‘LossTanAmp1’, ‘LossTanPhase1’, ‘LossTanAmp2’, ‘LossTanPhase2’, ‘LossTanFreq1’, ‘LossTanFreq2’, ‘LossTanQ1’, ‘LossTanQ2’, ‘SecondFrequency’, ‘TryFitAgain’, ‘HighFrequencyMode’, ‘ThermalLever’, ‘DoSader’, ‘CustomLeverLength’, ‘CustomLeverWidth’, ‘CustomLeverFrequency’, ‘ResFreq1’, ‘ResFreq2’, ‘GetStartedRoughness’, ‘GetStartedOn’, ‘GSGainGain’, ‘GSSetpointPercent’, ‘GSHardness’, ‘GSLeverRange’, ‘GetStartedMorePanel’, ‘GSUseManualThermal’, ‘GSMotorHeight’, ‘GSStickySample’, ‘GSDateTime’, ‘YourVariablesStartHere’, ‘DARTAnalysisImage’, ‘DARTAmplitude1Label’, ‘DARTAmplitude2Label’, ‘DARTPhase1Label’, ‘DARTPhase2Label’, ‘DARTFrequency1Label’, ‘Log File’, ‘Date’, ‘Time’, ‘Seconds’, ‘UserCalcUnit’, ‘UserIn0Unit’, ‘UserIn1Unit’, ‘UserIn2Unit’, ‘LateralUnit’, ‘ARUserPanelName’, ‘UserIn0Name’, ‘UserIn1Name’, ‘UserIn2Name’, ‘UserCalcName’, ‘UserIn0Ab’, ‘UserIn1Ab’, ‘UserIn2Ab’, ‘UserCalcAb’, ‘UserIn0Force’, ‘UserIn1Force’, ‘UserIn2Force’, ‘UserCalcForce’, ‘SaveForce’, ‘LastSaveImage’, ‘LastSaveForce’, ‘NavLoadPath’, ‘LastNavLoadPath’, ‘UserCalcBUnit’, ‘UserCalcBName’, ‘UserCalcBForce’, ‘UserCalcBAb’, ‘BackPackIn0Unit’, ‘BackPackIn0Name’, ‘BackPackIn0Ab’, ‘BackPackIn0Force’, ‘BackPackIn1Unit’, ‘BackPackIn1Name’, ‘BackPackIn1Ab’, ‘BackPackIn1Force’, ‘BackPackIn2Unit’, ‘BackPackIn2Name’, ‘BackPackIn2Ab’, ‘BackPackIn2Force’, ‘BackPackIn3Unit’, ‘BackPackIn3Name’, ‘BackPackIn3Ab’, ‘BackPackIn3Force’, ‘BackPackIn4Unit’, ‘BackPackIn4Name’, ‘BackPackIn4Ab’, ‘BackPackIn4Force’, ‘DetectorSum’, ‘XSensor’, ‘YSensor’, ‘ZSensor’, ‘DDSAmplitude0’, ‘DDSDCOffset0’, ‘DDSFrequency0’, ‘DDSFrequencyOffset0’, ‘DDSPhaseOffset0’, ‘DDSAmplitude1’, ‘DDSFrequency1’, ‘DDSPhaseOffset1’, ‘Amplitude’, ‘Phase’, ‘Inputi’, ‘Inputq’, ‘Inputi1’, ‘Inputq1’, ‘Count’, ‘Count2’, ‘Potential’, ‘Amplitude1’, ‘Phase1’, ‘DDSQGain0’, ‘DDSQAngle0’, ‘DDSFrequencyOffset1’, ‘Deflection’, ‘Lateral’, ‘Frequency’, ‘LockIn’, ‘Height’, ‘DeflectionValue’, ‘TipBias’, ‘DartAmp’, ‘VerDate’, ‘Version’, ‘XopVersion’, ‘OSVersion’, ‘IgorFileVersion’, ‘BaseName’, ‘SkewAngleRead’, ‘ImageNote’, ‘TipSerialNumber’, ‘Planefit 0’, ‘PlanefitOrder 0’, ‘FlattenOrder 0’, ‘Planefit Offset 0’, ‘Planefit X Slope 0’, ‘Planefit Y Slope 0’, ‘Flatten Offsets 0’, ‘Flatten Slopes 0’, ‘Display Offset 0’, ‘Display Range 0’, ‘ColorMap 0’, ‘Planefit 1’, ‘PlanefitOrder 1’, ‘FlattenOrder 1’, ‘Planefit Offset 1’, ‘Planefit X Slope 1’, ‘Planefit Y Slope 1’, ‘Display Offset 1’, ‘Display Range 1’, ‘ColorMap 1’, ‘Planefit 2’, ‘PlanefitOrder 2’, ‘FlattenOrder 2’, ‘Planefit Offset 2’, ‘Planefit X Slope 2’, ‘Planefit Y Slope 2’, ‘Display Offset 2’, ‘Display Range 2’, ‘ColorMap 2’, ‘Planefit 3’, ‘PlanefitOrder 3’, ‘FlattenOrder 3’, ‘Planefit Offset 3’, ‘Planefit X Slope 3’, ‘Planefit Y Slope 3’, ‘Display Offset 3’, ‘Display Range 3’, ‘ColorMap 3’, ‘Planefit 4’, ‘PlanefitOrder 4’, ‘FlattenOrder 4’, ‘Planefit Offset 4’, ‘Planefit X Slope 4’, ‘Planefit Y Slope 4’, ‘Display Offset 4’, ‘Display Range 4’, ‘ColorMap 4’, ‘Planefit 5’, ‘PlanefitOrder 5’, ‘FlattenOrder 5’, ‘Planefit Offset 5’, ‘Planefit X Slope 5’, ‘Planefit Y Slope 5’, ‘Display Offset 5’, ‘Display Range 5’, ‘ColorMap 5’, ‘EndHeadTemp’, ‘EndScannerTemp’, ‘EndHeaterTemp’, ‘EndHeaterHumidity’]

ekpy.analysis.asylum.main.plot_pfm(imgdata_dict, meta_data, cmap='viridis', figsize=(20, 10))

Module contents