Koch Lab:Publications/Drafts/Versatile Feedback/Paper/Header description

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Description of the Header File Contents

 

In this appendix, we describe all the fields present in the header files. For each field, we will describe or define the contents and give an example. Variables are shown in italics.

 

The following fields are present in the program’s own header file:

 

<tbody> </tbody>

[section]: keyname

Description and Example

[General]: UsersDirectoryPath

Path string showing where to find each user’s initialization file.

Example: UsersDirectoryPath=/C/Users

[General]: NameList

ASCII-encoded tab-separated string containing a list of the manipulation module names available in the program. The order of this list does not matter, because the data header files record the name of each module used.

Example: NameList="Create Offset Array\09Create Wiggle Array\09Load Wiggle Arrays\09Hold and Take Data\09Piezo Hold and Take Data\09Find Tether Center Piezo\09Find Short Tether Center Piezo\09Force Clamp Piezo\09Velocity Clamp Piezo\09Reset AODs\09Await Footswitch\09Piezo Velocity, Velocity, Hold 010410\09Piezo Velocity, Force, Hold 010410\09Power Spectrum (interactive)\09Find Tether Center\09Position Ramp\09Position Ramp Piezo\09Force Clamp\09Velocity Clamp\09Velocity Clamp New\09Force Clamp New\09Velocity Clamp RTWS\09Sum Fix Tester\09Step Frequency Hack\09Loading Rate Clamp Piezo"

[General]: Captions (default)

The individual modules may require parameters to be set in different ways; this field is an ASCII-encoded tab-separated string with a list of the captions for the form fields shown in Figure 2. The order of this list does matter.

Example: Captions (default)="Initial Frequency ("MHz")\09Initial Voltage ("V")\09Feedback Set Point\09Reverse Acting\09SP & PV range (4096)\09Kp\09Ti\09Td\09Freq Ramp Rate (MHz/sec)\09Averaging/decimation factor (100)\09Control bitfield\09Control string\0D\0A"

[General]: VSSRevisionInfo

String placeholder for our source code control system.

Example: VSSRevisionInfo="$Header: /DAQ08/Versatile Feedback DAQ/Feedback0b.ini 14    7/16/01 2:34a Koch $"

[General]: LastModifiedBy

String providing traceability before we started using the source code control system.

LastModifiedBy="see VSS database history"

[module name]: FilePath

The instructions for the particular configuration and use of each module are stored in a special field in the module source code file itself. In order to allow the main program to retrieve these data at run time (to present as guidance in the dialog shown in Figure 2) the program needs to know where to find the module source code file.

Example: FilePath="/C/Cprog/Daq08/Versatile Feedback DAQ/Modules/Feedback0B-Module-Velocity Clamp.vi"

[module name]: Captions

If present, this module-specific field can override the default captions specified in the [General]: Captions field. The format is the same.

 

 

The following fields are present in the header files accompanying each data file:

 

<tbody> </tbody>

[section]: keyname

Description and Example

[General]: DataFilePath

 

Example: DataFilePath="/D/Aatte/koch/data/Project 3 -- Overstretch and Y Templates/010405/0075.dat"

[General]:

 

[General]: TimestampInMacSeconds

Example: TimestampInMacSeconds=3069290473.730000

[General]: BinaryType

Integer flag describing the data file format. A zero value means that the data file is tab-separated ASCII text; unity means that the data file is in the LabVIEW big-endian data format.

Example: BinaryType=1

[General]: NumberOfColumns

Integer count of the number of fields stored for each time point in the data file. (This number is constant over an entire single file, and is used only if the file is binary.)

Example: NumberOfColumns=8

[General]: List

Tab-separated text list of the data types stored in the binary-format data file. The strings correspond to the LabVIEW basic numerical types. This is needed to interpret the data correctly, but ignored if the file is in ASCII text format.

Example: List=int32\09int32\09int32\09int32\09int32\09int32\09int32\09int32\0D\0A

[Versatile Feedback DAQ]: Channels

 

Example: Channels=0,1\092\093\0D\0A

[Versatile Feedback DAQ]: GainMenuRingArray

Example: GainMenuRingArray=2\090\090\0D\0A

[Versatile Feedback DAQ]: BufferSize

Integer count of the maximum number of data points that can be acquired by a single module. We predimension the LabVIEW arrays in an effort to improve performance.

Example: BufferSize=500000

AOD2HardLimits

Example: AOD2HardLimits=35.000000\0910.000000\095.870000\091.000000\0D\0A

AODIntFreqConversionBitsHz

AODIntFreqConversionBitsHz=28.633115

AODPosConversionumMHz

AODPosConversionumMHz=1.410000

BitsAssumedADCPrecision

BitsAssumedADCPrecision=16

SpikeValueSegment

SpikeValueSegment=2147483647

SpikeValueFindTetherCenter

SpikeValueFindTetherCenter=2147483646

SpikeValueStep

SpikeValueStep=2147483645

BitsActualMIOPrecision

BitsActualMIOPrecision=16

DesiredSampleInterval

DesiredSampleInterval=6.000000

NumberOfFeedbackSteps

Example: NumberOfFeedbackSteps=1

 

 

 

The following fields are appended to the header file during data analysis and processing:

 

<tbody> </tbody>

[section]: keyname

Description and Example

[General]: VSSRevisionInfo

String placeholder for our source code control system.

Example: VSSRevisionInfo="$Header: /Reference/Calibration/Geometry10.ini 27    11/09/01 3:18p Rcy3 $"

[File Formats]: formatname

Tab-separated list of data-column names.

Example: Eight-Column (Piezo) Format=X\09Y\09Sum\09Piezo\09Freq\09Voltage\09deltaT\09PiezoFreq\0D\0A

[calibration set]: Description

Text description of calibration data set.

Example: Description="These calibration data are based on Alla's May 2001 calibration of tweezers setup #1, with the following modification history: 010703 bead diameter to 0.48 microns (MDW), 010713 consistent Z conversion factor to 4000 (AS SJK RCY), 010902 kx/kz to 4.5 (See \\\\Asgard\\Data\\Aatte\\koch\\data\\Calibration\\Calibration August\0A2001\\Z\0AStiffness\\010902_ButterworthFilter\\Analyzed\\010902_Analysis.OPJ) (SJK). We have not compensated for the piezo voltage impedance problem (See U:\\rcy3\\2001\\6-June\\010624 piezo impedance issue.txt) (SJK RCY); it remains outstanding.\0AAlso includes Y sensitivity and stiffness by RCY 010618 (010621a), but the default conversion method doesn't use this information.\0AOlder calibration data sets (such as that used to convert Brent's 2001 nucleosome paper data) can be found in U:\\Common\\Reference\\Calibration\\Old\\."

[calibration set]: TimestampInMacSeconds

When multiple calibration sets existed, the conversion program would suggest the most appropriate one based on experimental parameters recorded at run time, including: setup number, bead size, date and time that the data were acquired. This stores a floating-point time stamp giving the date of calibration.

Example: TimestampInMacSeconds=3072398941.00

[calibration set]: BeadDiameterMicrons

Floating-point number giving the diameter of the optical bead in microns.

Example: BeadDiameterMicrons=0.480000

[calibration set]: Setup

Integer describing which experimental setup was used to acquire the calibration data and to which these data apply.

Example: Setup=1

[calibration set]: BeadType

Text description of the optical microspheres used to obtain the calibration data and to which these data apply.

Example: BeadType="Bangs streptavidin 0.53-um CP01N/4241 L991215A"

[calibration set]: DataFilePath

Path string citing the file whose analysis led to these data.

Example: DataFilePath=/V/Aatte/alla/calibration2/010510/0041.ini

[calibration set]: WiggleDataFilePath

Path string naming the data file used to compensate acousto-optic deflector-steered trapping data for systematic variations in intensity and position.

Example: WiggleDataFilePath=/

[calibration set]: TransformationExpressions

 

Example: TransformationExpressions=""

[calibration set]: Method

String naming the data processing module needed to process the calibration data.

Example: Method="Polynomial 010215"

[calibration set]: XSensitivity_nm_per_mV

[calibration set]: YSensitivity_nm_per_mV

Example: XSensitivity_nm_per_mV=

7.50E+1;5.81E-3;1.40E-1;4.17E-7;5.41E-9;1.36E-15;1.59E-14\09

1.38E+2;2.10E-3;1.33E-1;-9.06E-7;3.40E-9;4.99E-15;1.36E-14\09

2.00E+2;1.01E-2;1.27E-1;-7.07E-7;3.62E-9;5.07E-15;1.07E-14\09

2.63E+2;-1.36E-2;1.22E-1;-5.38E-7;6.42E-9;-2.04E-15;7.58E-15\09

3.25E+2;1.96E-2;1.19E-1;-5.15E-7;4.31E-9;-4.04E-16;7.83E-15\09

3.88E+2;-4.65E-3;1.18E-1;7.78E-7;3.24E-9;-6.83E-17;7.62E-15\09

4.50E+2;-9.00E-4;1.16E-1;-5.51E-7;4.28E-9;2.22E-15;6.98E-15\09

5.13E+2;4.81E-3;1.17E-1;-1.90E-7;3.16E-9;7.11E-15;7.90E-15\09

5.75E+2;3.45E-2;1.19E-1;-8.08E-7;3.68E-9;-5.89E-15;8.41E-15\0D\0A

[calibration set]: Stiffness_pN_per_nm_per_mV

 

[calibration set]: Stiffness_Kx_per_Kz

 

[calibration set]: XAODFrequency_nm_per_MHz

 

[calibration set]: XPiezo_nm_per_mV

 

[calibration set]: Journal_to_nm_ConversionFormula

 

[calibration set]: XStiffness_pN_per_nm_per_mV

[calibration set]: YStiffness_pN_per_nm_per_mV

 

 

 

 

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