nmrglue.sparky

Functions for reading and writing Sparky (.ucsf) files.

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

User Information

User Functions

read(filename) Read a Sparky file.
write(filename, dic, data[, overwrite]) Write a Sparky file.
read_lowmem(filename) Read a Sparky file using minimal memory.
write_lowmem(filename, dic, data[, overwrite]) Write a Sparky using minimum amounts of memory (tile by tile)
make_uc(dic, data[, dim]) Create a unit conversion object.
guess_udic(dic, data) Guess parameter of universal dictionary from dic,data pair.
create_dic(udic[, datetimeobj, user]) Create a Sparky parameter dictionary from universal dictionary.
datetime2dic(datetimeobj, dic) Add datetime object to dictionary
dic2datetime(dic) Create a datetime object from a Sparky dictionary

Developer Information

from __future__ import print_function

__developer_info__ = “”” Sparky file format information

Developer Functions

These functions are typically not used directly by users. Developers who want fine control over Sparky files may be interested in these functions.

create_data(data) Create a Sparky data array (recast into float32 array)
create_axisdic(adic, tlen, dlen) Make an Sparky axis dictionary from a universal axis dictionary.
calc_tshape(shape[, kbyte_max]) Calculate a tile shape from data shape.
read_2D(filename) Read a 2D sparky file.
write_2D(filename, dic, data[, overwrite]) Write a 2D Sparky file.
read_3D(filename) Read a 3D Sparky file.
write_3D(filename, dic, data[, overwrite]) Write a 3D Sparky file.
read_lowmem_2D(filename) Read a 2D Sparky file using minimal memory.
read_lowmem_3D(filename) Read a 3D sparky file using minimal memory.
get_tilen(f, n_tile, tw_tuple) Read a tile from a Sparky file object.
get_tile(f, num_points) Read the next tile from a Sparky file object.
put_tile(f, tile) Put a tile to a Sparky file object.
get_data(f) Read all data from sparky file object.
put_data(f, data) Put data to a Sparky file object.
find_tilen_2d(data, ntile, tile_size) Return a tile from a 2D NMR data set.
tile_data2d(data, tile_size) Tile 2D data into a 1D array.
untile_data2D(data, tile_size, data_size) Rearrange 2D Tiled/Sparky formatted data into standard format.
find_tilen_3d(data, ntile, tile_size) Return a single tile from a 3D NMR data set.
tile_data3d(data, tile_size) Tile 3D data into a 1D numpy array
untile_data3D(data, tile_size, data_size) Rearrange 3D tiled/Sparky formatted data into standard format.
get_fileheader(f) Get fileheader from file and return a list.
put_fileheader(f, fl) Write fileheader list to file (180-bytes).
fileheader2dic(header) Convert a fileheader list into a Sparky parameter dictionary.
dic2fileheader(dic) Convert a Sparky parameter dictionary into a fileheader list.
get_axisheader(f) Get an axisheader from file and return a list.
put_axisheader(f, al) Write an axisheader list to file (128-bytes written).
axisheader2dic(header) Convert an axisheader list into Sparky parameter axis dictionary.
dic2axisheader(dic) Convert a Sparky parameter axis diction into a axisherder list.

Developer Classes

sparky_2d(filename[, order]) Emulates a ndarray object without loading data into memory for low memory reading of 2D Sparky files.
sparky_3d(filename[, order]) Emulates a ndarray object without loading data into memory for low memory read of 3D Sparky files.