afmformats.formats.fmt_jpk.jpk_data

Functions

afmformats.formats.fmt_jpk.jpk_data.find_column_dat(loc_list, column)[source]

Find a column in a list of strings

Parameters

  • loc_list (list of str) –

    The segment’s data location list (within the archive), e.g.

    [‘segments/0/channels/height.dat’,

    ’segments/0/channels/vDeflection.dat’, ‘segments/0/channels/strainGaugeHeight.dat’]

  • column (str) – afmformats column name afmformats.afm_data.known_columns

Returns

  • name (str) – Matched column name from JPK_COLUMNS, e.g. “strainGaugeHeight”

  • slot (str) – Default slot location from JPK_SLOTS

  • loc (str) – Matched data location in zip file, e.g. “segments/0/channels/strainGaugeHeight.dat”

afmformats.formats.fmt_jpk.jpk_data.load_dat_raw(fd, name, properties)[source]

Load data from binary JPK .dat files

Parameters

  • fd (file) – Open .dat file

  • name (str) – Name of the data to read (required for scale conversions) (valid options are values in JPK_COLUMNS)

  • properties (dict) – Property dictionary metadata (see also JPKReader._get_index_segment_properties())

Returns

data – A numpy array with the raw data.

Return type

1d ndarray

Notes

This method tries to correctly determine the data type of the binary data and scales it with the data.encoder.scaling values given in the header files.

See also

load_dat_unit

Includes conversion to useful units

afmformats.formats.fmt_jpk.jpk_data.load_dat_unit(fd, name, properties, slot='default')[source]

Load data from a JPK .dat file with a specific calibration slot

Parameters

  • fd (file) – Open .dat file

  • name (str) – Name of the data to read (required for scale conversions) (valid options are values in JPK_COLUMNS)

  • properties (dict) – Property dictionary metadata (see also JPKReader._get_index_segment_properties())

  • slot (str) –

    The .dat files in the JPK measurement zip files come with different calibration slots. Valid values are

    • For the height of the piezo crystal during measurement (the piezo height is not as accurate as the measured height from the height sensor; the piezo movement is not linear): “height.dat”: “volts”, “nominal”, “calibrated”

    • For the measured height of the cantilever: “strainGaugeHeight.dat”: “volts”, “nominal”, “absolute” “measuredHeight.dat”: “volts”, “nominal”, “absolute” “capacitiveSensorHeight”: “volts”, “nominal”, “absolute” (they are all the same)

    • For the recorded cantilever deflection: “vDeflection.dat”: “volts”, “distance”, “force”

Returns

  • data (1d ndarray) – A numpy array containing the scaled data.

  • unit (str) – A string representing the metric unit of the data.

  • name (str) – The name of the data column.

Notes

The raw data (see load_dat_raw) is usually stored in “volts” and needs to be converted to e.g. “force” for “vDeflection” or “nominal” for “strainGaugeHeight”. The conversion parameters (offset, multiplier) are stored in the header files and they are not stored separately for each slot, but the conversion parameters are stored relative to the slots. For instance, to compute the “force” slot from the raw “volts” data, one first needs to compute the “distance” slot. This conversion is taken care of by this method.

This is an example header:

channel.vDeflection.data.file.name=channels/vDeflection.dat channel.vDeflection.data.file.format=raw channel.vDeflection.data.type=short channel.vDeflection.data.encoder.type=signedshort channel.vDeflection.data.encoder.scaling.type=linear channel.vDeflection.data.encoder.scaling.style=offsetmultiplier channel.vDeflection.data.encoder.scaling.offset=-0.00728873489143207 channel.vDeflection.data.encoder.scaling.multiplier=3.0921021713588157E-4 channel.vDeflection.data.encoder.scaling.unit.type=metric-unit channel.vDeflection.data.encoder.scaling.unit.unit=V channel.vDeflection.channel.name=vDeflection channel.vDeflection.conversion-set.conversions.list=distance force channel.vDeflection.conversion-set.conversions.default=force channel.vDeflection.conversion-set.conversions.base=volts channel.vDeflection.conversion-set.conversion.volts.name=Volts channel.vDeflection.conversion-set.conversion.volts.defined=false channel.vDeflection.conversion-set.conversion.distance.name=Distance channel.vDeflection.conversion-set.conversion.distance.defined=true channel.vDeflection.conversion-set.conversion.distance.type=simple channel.vDeflection.conversion-set.conversion.distance.comment=Distance channel.vDeflection.conversion-set.conversion.distance.base-calibration-slot=volts channel.vDeflection.conversion-set.conversion.distance.calibration-slot=distance channel.vDeflection.conversion-set.conversion.distance.scaling.type=linear channel.vDeflection.conversion-set.conversion.distance.scaling.style=offsetmultiplier channel.vDeflection.conversion-set.conversion.distance.scaling.offset=0.0 channel.vDeflection.conversion-set.conversion.distance.scaling.multiplier=7.000143623002982E-8 channel.vDeflection.conversion-set.conversion.distance.scaling.unit.type=metric-unit channel.vDeflection.conversion-set.conversion.distance.scaling.unit.unit=m channel.vDeflection.conversion-set.conversion.force.name=Force channel.vDeflection.conversion-set.conversion.force.defined=true channel.vDeflection.conversion-set.conversion.force.type=simple channel.vDeflection.conversion-set.conversion.force.comment=Force channel.vDeflection.conversion-set.conversion.force.base-calibration-slot=distance channel.vDeflection.conversion-set.conversion.force.calibration-slot=force channel.vDeflection.conversion-set.conversion.force.scaling.type=linear channel.vDeflection.conversion-set.conversion.force.scaling.style=offsetmultiplier channel.vDeflection.conversion-set.conversion.force.scaling.offset=0.0 channel.vDeflection.conversion-set.conversion.force.scaling.multiplier=0.043493666407368466 channel.vDeflection.conversion-set.conversion.force.scaling.unit.type=metric-unit channel.vDeflection.conversion-set.conversion.force.scaling.unit.unit=N

To convert from the raw “volts” data to force data, these steps are performed:

  • Convert from “volts” to “distance” first, because the “base-calibration-slot” for force is “distance”.

    distance = volts*7.000143623002982E-8 + 0.0

  • Convert from “distance” to “force”:

    force = distance*0.043493666407368466 + 0.0

The multipliers shown above are the values for sensitivity and spring constant: sensitivity = 7.000143623002982E-8 m/V spring_constant = 0.043493666407368466 N/m

Classes

class afmformats.formats.fmt_jpk.jpk_data.ReadJPKError[source]

Inheritance

Inheritance diagram of ReadJPKError

Variables

afmformats.formats.fmt_jpk.jpk_data.JPK_COLUMNS

Maps afmformats column names to JPK column names

{'force': ['vDeflection'],
 'height (measured)': ['strainGaugeHeight',
                       'capacitiveSensorHeight',
                       'measuredHeight'],
 'height (piezo)': ['height', 'head-height']}
afmformats.formats.fmt_jpk.jpk_data.JPK_SLOTS

Maps afmformats column names to default JPK normalization slots

{'force': 'force',
 'height (measured)': 'nominal',
 'height (piezo)': 'calibrated'}
afmformats.formats.fmt_jpk.jpk_data.JPK_UNITS

Maps afmformats column names to default JPK units

{'force': 'N', 'height (measured)': 'm', 'height (piezo)': 'm'}