spectrochempy.read_omnic

read_omnic(*paths, **kwargs)[source][source]

Open a Thermo Nicolet OMNIC file.

Open Omnic file or a list of .spg, .spa or .srs files and set data/metadata in the current dataset.

The collected metadata are: - names of spectra - acquisition dates (UTC) - units of spectra (absorbance, transmittance, reflectance, Log(1/R), Kubelka-Munk, Raman intensity, photoacoustics, volts) - units of xaxis (wavenumbers in \(cm^{-1}\), wavelengths in nm or micrometer, Raman shift in \(cm^{-1}\)) - spectra history (but only incorporated in the NDDataset if a single spa is read)

An error is generated if attempt is made to inconsistent datasets: units of spectra and xaxis, limits and number of points of the xaxis.

Parameters:

  • *paths (str, Path object objects or valid urls, optional) – The data source(s) can be specified by the name or a list of name for the file(s) to be loaded:

    • e.g., ( filename1, filename2, …, kwargs )

    If the list of filenames are enclosed into brackets:

    • e.g., ( [filename1, filename2, …], kwargs )

    The returned datasets are merged to form a single dataset, except if merge is set to False.

    If a source is not provided (i.e., no paths , nor content), a dialog box will be opened to select files.

  • **kwargs (keyword parameters, optional) – See Other Parameters.

Returns:

object (NDDataset or list of NDDataset) – The returned dataset(s).

Other Parameters:

  • protocol (str, optional) – Protocol used for reading. It can be one of {'scp', 'omnic', 'opus', 'topspin', 'matlab', 'jcamp', 'csv', 'excel'}. If not provided, the correct protocol is inferred (whenever it is possible) from the filename extension.

  • directory (Path object objects or valid urls, optional) – From where to read the files.

  • merge (bool, optional, default: False) – If True and several filenames or a directory have been provided as arguments, then a single NDDataset with merged (stacked along the first dimension) is returned.

  • sortbydate (bool, optional, default: True) – Sort multiple filename by acquisition date.

  • description (str, optional) – A Custom description.

  • origin (one of {'omnic', 'tga'}, optional) – Used when reading with the CSV protocol. In order to properly interpret CSV file it can be necessary to set the origin of the spectra. Up to now only 'omnic' and 'tga' have been implemented.

  • csv_delimiter (str, optional, default: csv_delimiter) – Set the column delimiter in CSV file.

  • content (bytes object, optional) – Instead of passing a filename for further reading, a bytes content can be directly provided as bytes objects. The most convenient way is to use a dictionary. This feature is particularly useful for a GUI Dash application to handle drag and drop of files into a Browser.

  • iterdir (bool, optional, default: True) – If True and no filename was provided, all files present in the provided directory are returned (and merged if merge is True. It is assumed that all the files correspond to current reading protocol.

    Changed in version 0.6.2: iterdir replace the deprecated listdir argument.

See also

read_spg

Read grouped Omnic spectra.

read_spa

Read single Omnic spectra.

read_srs

Read series Omnic spectra.

read

Generic reader inferring protocol from the filename extension.

read_zip

Read Zip archives (containing spectrochempy readable files)

read_dir

Read an entire directory.

read_opus

Read OPUS spectra.

read_labspec

Read Raman LABSPEC spectra (.txt).

read_soc

Read Surface Optics Corps. files (.ddr , .hdr or .sdr).

read_galactic

Read Galactic files (.spc).

read_quadera

Read a Pfeiffer Vacuum’s QUADERA mass spectrometer software file.

read_topspin

Read TopSpin Bruker NMR spectra.

read_csv

Read CSV files (.csv).

read_jcamp

Read Infrared JCAMP-DX files (.jdx, .dx).

read_matlab

Read Matlab files (.mat, .dso).

read_carroucell

Read files in a directory after a carroucell experiment.

read_wire

Read REnishaw Wire files (.wdf).

Examples

Reading a single OMNIC file (providing a windows type filename relative to the default datadir )

>>> scp.read_omnic('irdata\\nh4y-activation.spg')
NDDataset: [float64] a.u. (shape: (y:55, x:5549))

Reading a single OMNIC file (providing a unix/python type filename relative to the default datadir ) Note that here read_omnic is called as a classmethod of the NDDataset class

>>> scp.read_omnic('irdata/nh4y-activation.spg')
NDDataset: [float64] a.u. (shape: (y:55, x:5549))

Single file specified with pathlib.Path object

>>> from pathlib import Path
>>> folder = Path('irdata')
>>> p = folder / 'nh4y-activation.spg'
>>> scp.read_omnic(p)
NDDataset: [float64] a.u. (shape: (y:55, x:5549))

The directory can also be specified independently, either as a string or a pathlib object

>>> scp.read_omnic('nh4y-activation.spg', directory=folder)
NDDataset: [float64] a.u. (shape: (y:55, x:5549))

Multiple files not merged (return a list of datasets)

>>> le = scp.read_omnic('irdata/nh4y-activation.spg', 'wodger.spg')
>>> len(le)
2
>>> le[1]
NDDataset: [float64] a.u. (shape: (y:55, x:5549))

Multiple files merged as the merge keyword is set to true

>>> scp.read_omnic('irdata/nh4y-activation.spg', 'wodger.spg', merge=True)
NDDataset: [float64] a.u. (shape: (y:57, x:5549))

Multiple files to merge : they are passed as a list (note the brakets) instead of using the keyword merge

>>> scp.read_omnic(['irdata/nh4y-activation.spg', 'wodger.spg'])
NDDataset: [float64] a.u. (shape: (y:57, x:5549))

Multiple files not merged : they are passed as a list but merge is set to false

>>> l2 = scp.read_omnic(['irdata/nh4y-activation.spg', 'wodger.spg'], merge=False)
>>> len(l2)
2

Read without a filename. This has the effect of opening a dialog for file(s) selection

>>> nd = scp.read_omnic()

Read in a directory (assume that only OPUS files are present in the directory (else we must use the generic read function instead)

>>> l3 = scp.read_omnic(directory='irdata/subdir/1-20')
>>> len(l3)
3

Again we can use merge to stack all 4 spectra if thet have compatible dimensions.

>>> scp.read_omnic(directory='irdata/subdir', merge=True)
NDDataset: [float64] a.u. (shape: (y:4, x:5549))

An example, where bytes contents are passed directly to the read_omnic method.

>>> datadir = scp.preferences.datadir
>>> filename1 = datadir / 'irdata' / 'subdir' / '7_CZ0-100 Pd_101.SPA'
>>> content1 = filename1.read_bytes()
>>> filename2 = datadir / 'wodger.spg'
>>> content2 = filename2.read_bytes()
>>> listnd = scp.read_omnic({filename1.name: content1, filename2.name: content2})
>>> len(listnd)
2
>>> scp.read_omnic({filename1.name: content1, filename2.name: content2}, merge=True)
NDDataset: [float64] a.u. (shape: (y:3, x:5549))

Examples using spectrochempy.read_omnic

EFA example

EFA example

NMF analysis example

NMF analysis example

PCA analysis example

PCA analysis example

Loading an IR (omnic SPG) experimental file

Loading an IR (omnic SPG) experimental file