HSDC Format

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Bede Pittenger replied on Wed, Jun 2 2010 9:29 PM

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HSDC files are usually so large that they are unmanageable when exported to ASCII.  It is usually much more efficient to directly read the native NanoScope files instead.  This is especially true if you plan on analyzing a large number of files.

Nanoscope files are composed of an ASCII header that contains information about the microscope configuration and scaling factors, followed by a binary section where the data is stored.  If you open a Nanoscope file with a text editor like notepad, you will see the header and you can get an idea of what is there.  There is a description of the header structure in the NanoScope software manual appendices.

Most modern analysis packages like MatLab, Python, Igor, LabView, etc. have simple functions to read binary data from a file.  

In Python it looks something like this:

with open(filename,"rb") as cc:
    cc.seek(DataOffset)
    dataA = DataScale * numpy.fromstring(cc.read(DataLength),numpy.int16).astype(float)/65536.0

In MatLab, something like:

cc=fopen('hsdc.000,'rb');

fseek(cc, DataOffset, -1);

dataA = DataScale * fread(cc, DataLength/2, 'int16');

fclose(cc);

In Igor, something like:

GBLoadWave /Q /B /A=dataA /T={16,4} /S=DataOffset /W=1 /U=DataLength "filename"

dataA=dataA*DataScale/65536.0

In all cases, the DataOffset, DataLength and DataScale for each channel comes from the ASCII header.  In notepad, that section of the header looks something like this:

\*Ciao HSDC list

\Data offset: 40960

\Data length: 5000000

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Jan replied on Thu, Jun 3 2010 6:00 AM

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Suggested by Jan

Hi Cosmin,

SPIP can read HSDC files and provides batch facility to convert the individual recordings to binary or ASCII files.

SPIP can be downloaded from www.imagemet.com/download

If you need any assistance just let me know.

Best regards,

Jan

Jan F. Jorgensen
Image Metrology
jfj@imagemet.com