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 ato_
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_csdm()[source]
Return a csdm object containing data.
- Returns
- datacsdm object
CSDM object containing parameters and data
- to_pipe(datetimeobj=datetime.datetime(2021, 12, 5, 22, 53, 6, 943145))[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(2021, 12, 5, 22, 53, 6, 943149), 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.
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.