zmzhang / spc

Module for reading, exploring and converting *.spc spectroscopic binary data in Python.

spc

A module for working with .SPC files in Python. SPC is a binary data format to store a variety of spectral data, developed by Galactic Industries Corporation in the '90s. Popularly used Thermo Fisher/Scientific software GRAMS/AI. Also used by others including Ocean Optics, Jobin Yvon Horiba. Can store a variety of spectrum including FT-IR, UV-VIS, X-ray Diffraction, Mass Spectroscopy, NMR, Raman and Fluorescence spectra.

The SPC file format can store either single or multiple y-values, and the x-values can either be given explicitly or even spaced x-values can be generated based on initial and final points as well as number of points. In addition the format can store various log data and parameters, as well as various information such as axis labels and scan type.

Based mainly on the Thermo Scientific SPC File SDK [1]

May not work with all spc file formats

Graphical converter not functional

Basic Usage

As a standalone converter. Call the following from a terminal/command prompt

$ python convert %file_name1% %file_name2%

Or convert an entire directory

$ python convert %dir_name%

In a python script

# import file to python object
import spc
ftir_1 = spc.File('/path/to/ftir.spc')

# extract info from header metadata
ftir_1.debug_info()

# output file data as columns (tab seperated)
ftir_1.output_txt()

# plot using matplotlib
ftir_1.plot()

Features

1. Extracts header information into object members
2. For each subfile, extract subfile data into subFile class objects sub[0] (, sub[1], sub[2], ...)
3. Extract x and y values into numpy ndarray
4. Attempts to interpret x,y, and z labels, as well as scan type
5. Member functions to output data in text, or plot using matplotlib

###To Be implemented

1. z-values
2. Old data format

###Dependencies

• numpy
• matplotlib (for plotting)

###Module Organization

• class File (spc.py)
  • output_txt()
  • debug_info()
  • plot()
  • x
  • log_data
• class subFile (sub.py)
  • (optional) x
  • y

###Notes

• Used format specificiton [1]
• Loads entire file into memory
• Data uses variable naming as in SPC.H
• Class variables not in SPC.H prefixed with pr_

An SPC trace file normally has these components in the following order:

SPCHDR		Main header (512 bytes in new format, 224 or 256 in old)
  [X Values]	Optional FNPTS 32-bit floating X values if TXVALS flag
SUBHDR		Subfile Header for 1st subfile (32 bytes)
Y Values	FNPTS 32 or 16 bit fixed Y fractions scaled by exponent
  [SUBHDR	]	Optional Subfile Header for 2nd subfile if TMULTI flag
  [Y Values]	Optional FNPTS Y values for 2nd subfile if TMULTI flag
...		Additional subfiles if TMULTI flag (up to FNSUB total)
  [Log Info]	Optional LOGSTC and log data if flogoff is non-zero

However, files with the TXYXYS ftflgs flag set have these components:

SPCHDR		Main header (512 bytes in new format)
SUBHDR		Subfile Header for 1st subfile (32 bytes)
X Values	FNPTS 32-bit floating X values
Y Values	FNPTS 32 or 16 bit fixed Y fractions scaled by exponent
  [SUBHDR	]	Subfile Header for 2nd subfile
  [X Values]	FNPTS 32-bit floating X values for 2nd subfile
  [Y Values]	FNPTS Y values for 2nd subfile
...		Additional subfiles (up to FNSUB total)
  [Directory]	Optional FNSUB SSFSTC entries pointed to by FNPTS
  [Log Info]	Optional LOGSTC and log data if flogoff is non-zero

##References [1] "Thermo Scientific SPC File Format." Thermo Fisher Scientific, Web. 20 July 2014. http://ftirsearch.com/features/converters/SPCFileFormat.htm.