spectrochempy.read

read(*paths, **kwargs)[source][source]

Read data from various file formats.

This method is generally able to load experimental files based on extensions.

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.
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.
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.
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.

See also

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_omnic: Read Omnic spectra (.spa, .spg, .srs).
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 OPUS file (providing a windows type filename relative to the default datadir )

>>> scp.read('irdata\\OPUS\\test.0000')
NDDataset: [float64] a.u. (shape: (y:1, x:2567))

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

>>> scp.read('irdata/OPUS/test.0000')
NDDataset: [float64] a.u. (shape: (y:1, x:2567))

Single file specified with pathlib.Path object

>>> from pathlib import Path
>>> folder = Path('irdata/OPUS')
>>> p = folder / 'test.0000'
>>> scp.read(p)
NDDataset: [float64] a.u. (shape: (y:1, x:2567))

Multiple files not merged (return a list of datasets). Note that a directory is specified

>>> le = scp.read('test.0000', 'test.0001', 'test.0002', directory='irdata/OPUS')
>>> len(le)
3
>>> le[0]
NDDataset: [float64] a.u. (shape: (y:1, x:2567))

Multiple files merged as the merge keyword is set to true

>>> scp.read('test.0000', 'test.0001', 'test.0002', directory='irdata/OPUS', merge=True)
NDDataset: [float64] a.u. (shape: (y:3, x:2567))

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

>>> scp.read(['test.0000', 'test.0001', 'test.0002'], directory='irdata/OPUS')
NDDataset: [float64] a.u. (shape: (y:3, x:2567))

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

>>> le = scp.read(['test.0000', 'test.0001', 'test.0002'], directory='irdata/OPUS', merge=False)
>>> len(le)
3

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

>>> nd = scp.read()

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

>>> le = scp.read(directory='irdata/OPUS')
>>> len(le)
2

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

>>> scp.read(directory='irdata/OPUS', merge=True)
[NDDataset: [float64] a.u. (shape: (y:1, x:5549)), NDDataset: [float64] a.u. (shape: (y:4, x:2567))]