Import/Export of JCAMP-DX files

JCAMP-DX is an open format initially developed for IR data and extended to other spectroscopies. At present, the JCAMP-DX reader implemented in SpectroChemPy is limited to IR data and AFFN encoding (see [McDonald and Paul A. Wilks, 1988].

The JCAMP-DX reader of SpectroChemPy has been essentially written to read JCAMP-DX files exported by the SpectroChemPy write_jdx() writer.

[1]:

import spectrochempy as scp

X = scp.read_omnic("irdata//CO@Mo_Al2O3.SPG")
S0 = X[0]
S0

[1]:
NDDataset [CO@Mo_Al2O3] — float64, shape: (y:1, x:3112), a.u.
name
:
CO@Mo_Al2O3
author
:
runner@runnervmzvulz
created
:
2026-08-16 03:11:15+00:00
description
:
Omnic title: Group sust Mo_Al2O3_base line.SPG
Omnic filename: /home/runner/.spectrochempy/testdata/irdata/CO@Mo_Al2O3.SPG
history
:
2026-08-16 03:11:15+00:00> Imported from spg file /home/runner/.spectrochempy/testdata/irdata/CO@Mo_Al2O3.SPG.
2026-08-16 03:11:15+00:00> Sorted by date
2026-08-16 03:11:15+00:00> Slice extracted: (0)
Data
title
:
absorbance
values
:
[[0.0008032 3.788e-05 ... 0.0003027 0.0003745]] a.u.
shape
:
(y:1, x:3112)
Dimension `x`
size
:
3112
title
:
wavenumbers
coordinates
:
[ 4000 3999 ... 1001 999.9] cm⁻¹
Dimension `y`
size
:
1
title
:
acquisition timestamp (GMT)
coordinates
:
[1.477e+09] s
labels
:
[[ 2016-10-18 13:49:35+00:00]
[ *Résultat de Soustraction:04_Mo_Al2O3_calc_0.003torr_LT_after sulf_Oct 18 15:46:42 2016 (GMT+02:00)]]
[2]:

S0.write_jcamp("CO@Mo_Al2O3_0.jdx", confirm=False)

[2]:

PosixPath('/home/runner/work/spectrochempy/tempdirs/scp_yf458zyp/docs/sources/userguide/importexport/CO@Mo_Al2O3_0.jdx')

The namespace API is also available for writing:

[3]:

scp.jcamp.write(S0, "CO@Mo_Al2O3_0.jdx", confirm=False, overwrite=True)

[3]:

PosixPath('/home/runner/work/spectrochempy/tempdirs/scp_yf458zyp/docs/sources/userguide/importexport/CO@Mo_Al2O3_0.jdx')

Then used (and maybe changed) by a 3rd party software, and re-imported in spectrochempy:

[4]:

newS0 = scp.read_jcamp("CO@Mo_Al2O3_0.jdx")
newS0

[4]:
NDDataset [CO@Mo_Al2O3] — float64, shape: (y:1, x:3112), a.u.
name
:
CO@Mo_Al2O3
author
:
runner@runnervmzvulz
created
:
2026-08-16 03:11:16+00:00
description
:
Dataset from jdx file: 'CO@Mo_Al2O3'
history
:
2026-08-16 03:11:16+00:00> Imported from jdx file
Data
title
:
absorbance
values
:
[[0.0008032 3.787e-05 ... 0.0003027 0.0003745]] a.u.
shape
:
(y:1, x:3112)
Dimension `x`
size
:
3112
title
:
wavenumbers
coordinates
:
[ 4000 3999 ... 1001 999.9] cm⁻¹
Dimension `y`
title
:
coordinates
:
Undefined

The namespace API works identically:

[5]:

newS0 = scp.jcamp.read("CO@Mo_Al2O3_0.jdx")
newS0

[5]:
NDDataset [CO@Mo_Al2O3] — float64, shape: (y:1, x:3112), a.u.
name
:
CO@Mo_Al2O3
author
:
runner@runnervmzvulz
created
:
2026-08-16 03:11:16+00:00
description
:
Dataset from jdx file: 'CO@Mo_Al2O3'
history
:
2026-08-16 03:11:16+00:00> Imported from jdx file
Data
title
:
absorbance
values
:
[[0.0008032 3.787e-05 ... 0.0003027 0.0003745]] a.u.
shape
:
(y:1, x:3112)
Dimension `x`
size
:
3112
title
:
wavenumbers
coordinates
:
[ 4000 3999 ... 1001 999.9] cm⁻¹
Dimension `y`
title
:
coordinates
:
Undefined

It is important to note here that the conversion to JCAMP-DX changes the last digits of absorbance and wavenumbers:

The writer preserves the numeric values it writes. It does not silently convert wavelength to wavenumber or transmittance to absorbance. Current export support is therefore limited to exact-scale JCAMP mappings:

  • x: cm^-1, um, nm, or no unit (ARBITRARY UNITS);

  • y: absorbance, transmittance, or no unit (ARBITRARY UNITS).

Other merely convertible or named arbitrary units are rejected until you convert them explicitly before export.

[6]:

from spectrochempy.utils.compare import difference

[7]:

max_error, max_rel_error = difference(S0, newS0)
print(f"Max absolute difference in absorbance: {max_error:.3g}")
print(f"Max relative difference in absorbance: {max_rel_error:.3g}")

Max absolute difference in absorbance: 1.12e-08
Max relative difference in absorbance: 0.863

[8]:

max_error, max_rel_error = difference(S0.x, newS0.x)
print(f"Max absolute difference in wavenumber: {max_error:.3g}")
print(f"Max relative difference in wavenumber: {max_rel_error:.3g}")

Max absolute difference in wavenumber: 0
Max relative difference in wavenumber: 0

But this is much beyond the experimental accuracy of the data.