specio’s user API¶
Spectra reader functions¶
These functions represent specio’s main interface for the user. They provide a
common API to read spectra data for a large variety of formats. All read
functions accept keyword arguments, which are passed on to the format that does
the actual work. To see what keyword arguments are supported by a specific
format, use the help()
function.
Functions for reading:
specread()
- read a file with spectra from the specified uri
For a larger degree of control, specio provides a function
get_reader()
. It returns an Reader
object, which can be used
to read data and meta data in a more controlled manner. This also allows
specific scientific formats to be exposed in a way that best suits that
file-format.
Functions¶
specio.help ([name]) |
Print the help regarding a given format. |
specio.show_formats |
Show a nicely formatted list of available formats. |
specio.specread (uri[, format, tol_wavelength]) |
Read spectra in a given format. |
specio.get_reader (uri[, format]) |
Return a Reader instance. |
Classes¶
specio.core.format.Reader (format, request) |
Context manager to read the spectra. |
Core data structure¶
specio.specread()
will return either a list of instances or an instance
from the class specio.core.Spectrum
. This class is composed of three
attributes:
- a 1D ndarray of shape (n_wavelength,) or 2D ndarray of shape
(n_spectra, n_wavelength)
amplitudes
containing the counts/amplitude for the different wavelengths; - a 1D ndarray of shape (n_wavelength,)
wavelength
containing the wavelength for which the spectra have been acquired; - a dictionary
meta
containing the metadata.
For more information, you can check the full API documentation above.
specio.core.Spectrum (amplitudes, wavelength) |
Class containing the spectrum information. |
Command line interface¶
specio
provides a command line interface to make basic data manipulation.
Conversion to CSV¶
Any format can be exported using the specio
command line:
specio convert input_file.spc output_file.csv
convert
receive the input and output arguments. It is also possible to omit
the output argument and an automatic output file will be generated depending of
the input file name:
specio convert input_file.spc
As with specio.specread()
, an input can get a name with a wildcard:
specio convert "*.spc"
In addition, this is also possible to increase the tolerance to aggregate
several spectra in the same CSV as in specio.specread()
:
specio convert "*.spc" --tolerance 1e-2
Example datasets¶
The module specio.datasets includes some toy file which are supported by the plugins reader.
datasets.load_csv_path () |
Return the path to the CSV toy file. |
datasets.load_fsm_path () |
Return the path to the FSM toy file. |
datasets.load_mzml_path () |
Return the path to the mzML toy file. |
datasets.load_sp_path () |
Return the path to the SP toy file. |
datasets.load_spc_path () |
Return the path to the SPC toy file. |