spectrochempy.read_omnic

read_omnic(*paths, **kwargs)[source]

Open a Thermo Nicolet OMNIC file.

This is the explicit OMNIC reader in the public import API. Use spectrochempy.read for generic format autodetection and scp.omnic.read(...) or spectrochempy.read_omnic when the OMNIC format is already known.

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 when an SPG file contains spectra with inconsistent x-axis definitions, unless allow_inconsistent_x=True is specified. In that case, a list containing one NDDataset per spectrum is returned.

Non-merged multi-file reads may also return a list-like ScpObjectList exposing helper methods for dataset selection. See spectrochempy.read for the complete description of the generic import convention and multi-object return behavior.

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

Returns:

object (NDDataset or ScpObjectList of NDDataset) – The returned dataset(s). When several datasets are returned, the result is a list-like ScpObjectList with helper attributes such as .names, .select_largest(), .select_by_name(), .filter_by_ndim(), and .filter_by_shape().

Other Parameters:

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.
csv_delimiter (str, optional, default: csv_delimiter) – Set the column delimiter in CSV file.
description (str, optional) – A custom description.
directory (Path object objects or valid urls, optional) – From where to read the files.
download_only (bool, optional, default: False) – Used only when url are specified. If True, only downloading and saving of the files is performed, with no attempt to read their content.
merge (bool, optional, default: False) – If True and several filenames or a directory have been provided as arguments, then a single NDDataset with merged dataset (stacked along the first dimension) is returned. In the case not all datasets have compatible dimensions or types/origins, then several NDDatasets can be returned for different groups of compatible datasets.
origin (str, optional) – If provided it may be used to define the type of experiment: e.g., ‘ir’, ‘raman’,.. or the origin of the data, e.g., ‘omnic’, ‘opus’, … It is often provided by the reader automatically, but can be set manually.

It is used, for instance, when reading a directory with different types of files and merging compatible datasets into separate groups by origin.

It is also 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.
pattern (str, optional) – A pattern to filter the files to read.

Added in version 0.7.2.
protocol (str, optional) – Protocol used for reading, for example 'scp', 'omnic', 'opus', 'matlab', 'jcamp', 'csv', or 'excel'. If not provided, the correct protocol is inferred whenever possible from the filename extension.
read_only (bool, optional, default: True) – Used only when url are specified. If True, saving of the files is performed in the current directory, or in the directory specified by the directory parameter.
recursive (bool, optional, default: False) – Read also in subfolders.
replace_existing (bool, optional, default: False) – Used only when url are specified. By default, existing files are not replaced so not downloaded.
sortbydate (bool, optional, default: True) – Sort multiple filename by acquisition date.
allow_inconsistent_x (bool, optional, default: False) – Allow SPG files whose spectra have different x-axis definitions. When enabled, return one NDDataset per spectrum instead of merging the spectra. This option has no effect on SPA or SRS files.

See also

read: Generic reader inferring protocol from the filename extension.
spectrochempy.read_zip: Read Zip archives (containing spectrochempy readable files)
spectrochempy.read_dir: Read an entire directory.
spectrochempy.read_opus: Read OPUS spectra.
spectrochempy.read_labspec: Read Raman LABSPEC spectra (.txt).
spectrochempy.read_omnic: Read Omnic spectra (.spa, .spg, .srs).
spectrochempy.read_soc: Read Surface Optics Corp. files (.ddr, .hdr, or .sdr).
spectrochempy.read_spc: Read Galactic files (.spc).
spectrochempy.read_quadera: Read a Pfeiffer Vacuum’s QUADERA mass spectrometer software file.
spectrochempy.read_csv: Read CSV files (.csv).
spectrochempy.read_matlab: Read Matlab files (.mat, .dso).
spectrochempy.read_wire: Read Renishaw Wire files (.wdf).
spectrochempy.read_spg: Alias of read_omnic.
spectrochempy.read_spa: Alias of read_omnic.
spectrochempy.read_srs: Alias of read_omnic.

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))

Using the explicit namespace API

>>> scp.omnic.read('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))

Multiple files not merged (return a list-like multi-dataset result). Note that a directory is specified

>>> 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 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
>>> names = l2.names
>>> len(names)
2
>>> largest = l2.select_largest()
>>> largest.ndim
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 OMNIC files are present in the directory (else we must use the generic read function instead)

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

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

>>> scp.read_omnic(directory='irdata/OMNIC/1-20', merge=True)
[NDDataset: [float64] a.u. (shape: (y:1, x:5549)), NDDataset: [float64] a.u. (shape: (y:4, x:5549))]