nmrglue.convert¶

Functions to convert between NMR file formats

This modules is imported as nmrglue.convert and can be called as such.

User Information¶

User Classes¶

This class is targetted for users of nmrglue.

class nmrglue.fileio.convert.converter[source]¶

Object which allows conversion between NMR file formats, including low memory data objects.

Conversion between NMR file formats with this class involves three steps. First a new converter object must be created. Then the converter must be loaded with data using a from_ method. Finally, the dictionary and data representation of a NMR data in the desired format is extracted using a to_ method. This can then be written to disk.

Example conversion:

vdic, vdata = ng.varian.read("varian_dir")
C = ng.convert.converter()
C.from_varian(vdic, vdata)
pdic, pdata = C.to_pipe()
ng.pipe.write("test.fid", pdic, pdata)

Spectral parameters can be provided directly by passing a Universal dictionary to any of the from_ methods. If not provided the spectral parameters are guessed from the file format’s dictionary of parameters.

from_bruker(dic, data, udic=None, remove_digital_filter=False)[source]¶

Load converter with Bruker data.

Parameters

dicdict: Dictionary of Bruker parameters.
dataarray_like: NMR data.
udicdict, optional: Universal dictionary, if not provided will be guesses from dic.
remove_digital_filterbool, optional: True to remove the Bruker digital filter. Do not use this option with low memory data or when the udic parameter is specified. False leave the digital filter in place.

from_pipe(dic, data, udic=None)[source]¶

Load converter with NMRPipe data.

Parameters

dicdict: Dictionary of NMRPipe parameters.
dataarray_like: NMR data.
udicdict, optional: Universal dictionary, if not provided will be guesses from dic.

from_rnmrtk(dic, data, udic=None, agilent_compatible=False)[source]¶

Load converter with RNMRTK data.

Parameters

dicdict: Dictionary of RNMRTK parameters.
dataarray_like: NMR data.
udicdict, optional: Universal dictionary, if not provided will be guesses from dic.
agilent_compatiblebool, optional: True when RNMRTK data is being compared to Agilent/Varian data.

from_sparky(dic, data, udic=None)[source]¶

Load converter with Sparky data.

Parameters

dicdict: Dictionary of Sparky parameters.
dataarray_like: NMR data.
udicdict, optional: Universal dictionary, if not provided will be guesses from dic.

from_universal(dic, data)[source]¶

Load converter with Universal data.

Parameters

dicdict: Dictionary of universal parameters.
dataarray_like: NMR data.

from_varian(dic, data, udic=None)[source]¶

Load converter with Agilent/Varian data.

Parameters

dicdict: Dictionary of Agilent/Varian parameters.
dataarray_like: NMR data.
udicdict, optional: Universal dictionary, if not provided will be guesses from dic.

to_bruker()[source]¶

Return Bruker format data.

Returns

dicdict: Dictionary of Bruker parameters.
dataarray_like: NMR data in Bruker format.

to_pipe(datetimeobj=datetime.datetime(2020, 10, 29, 17, 6, 52, 238754))[source]¶

Return NMRPipe format data.

Parameters

datetimedatetime object, optional: Datetime object to include in the NMRPipe parameters. The current date and time is used by default.

Returns

dicdict: Dictionary of NMRPipe parameters.
dataarray_like: NMR data in NMRPipe format.

to_rnmrtk(agilent_compatible=False, dim_order=None)[source]¶

Return RNMRTK format data.

Parameters

agilent_compatiblebool, optional: True when RNMRTK data is being compared to Agilent/Varian data.
dim_orderlist, optional: List mapping axis numbers in the universal dictionary to the to the order in which they will appear in the RNMRTK dictionary. If None, the default, [0, 1, 2, …] will be used.

Returns

dicdict: Dictionary of RNMRTK parameters.
dataarray_like: NMR data in RNMRTK format.

to_sparky(datetimeobj=datetime.datetime(2020, 10, 29, 17, 6, 52, 238763), user='user')[source]¶

Return Sparky format data.

Parameters

datetimedatetime object, optional: Datetime object to include in the Sparky parameters. The current date and time is used by default.
userstr, optional: Username to include in the Sparky parameters. ‘user’ is the default.

Returns

dicdict: Dictionary of Sparky parameters.
dataarray_like: NMR data in Sparky format.

to_universal()[source]¶

Return Universal format data.

Returns

dicdict: Dictionary of Universal parameters.
dataarray_like: NMR data in format as provided.

to_varian()[source]¶

Return Agilent/Varian format data.

Returns

dicdict: Dictionary of Agilent/Varian parameters.
dataarray_like: NMR data in Agilent/Varian format.

Developer Information¶

Developer Classes¶

These classes are typically not used directly by users. Developers who want fine control over file conversion will be interested in these classes

class nmrglue.fileio.convert.udata_nd(edata, iproc, oproc, odtype, order=None)[source]¶

Wrap other fileiobase.data_nd derived objects with input/output conversion when slices are requested.

slicing operations return ndarray objects.
can iterate over with expected results.
transpose and swapaxes methods create a new objects with correct axes ordering.
has ndim, shape, and dtype attributes.

Parameters

edatafileiobase.data_nd derived object: Data object to wrap.
iprocdict: Dictionary of processing required by input format.
oproc :: Dictionary of processing required by output format.
odtypedtype: Output dtype.
ordertuple: Axis ordering relative to input data.

Notes

The iproc and oproc dictionary can contains the following keys and values.

key	value	Description
alt_id_sign	True/False	True alternates signs along indirect dims.
realfactor	float	Real channel scaling factor.
imagfactor	float	Imaginary channel scaling factor.