nmrglue.sparky

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

Information on the sparky file format can be found online at: http://www.cgl.ucsf.edu/home/sparky/manual/files.html and in the source file ucsffile.cc .

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

High-Level Functions

These are the functions most users will use from the sparky module.

nmrglue.fileio.sparky.read(filename)

Read a sparky file returning a dic,data pair

nmrglue.fileio.sparky.read_lowmem(filename)

Read a sparky file with minimal memory returning a dic,data pair.

nmrglue.fileio.sparky.write(filename, dic, data, overwrite=False)

Write a sparky file

Parameters:

• filename Name of file to write to.
• data Data array.
• dic Sparky parameter dictionary.
• overwrite Set to True to overwrite existing file.

No return

nmrglue.fileio.sparky.write_lowmem(filename, dic, data, overwrite=False)

Write a sparky file tile by tile (low memory)

Parameters:

• filename Name of file to write to.
• data Data array.
• dic Sparky parameter dictionary.
• overwrite Set to True to overwrite existing file.

No return

nmrglue.fileio.sparky.make_uc(dic, data, dim=-1)

Make a unit conversion object

Parameters:

• dic Sparky dictionary
• data data array
• dim dimention to make converter for (0,1,2,3 or -1, last)

nmrglue.fileio.sparky.guess_udic(dic, data)

Guess parameter of universal dictionary from dic,data pair

nmrglue.fileio.sparky.create_dic(udic, datetimeobj=datetime.datetime(2011, 4, 6, 16, 39, 24, 715379), user='user')

Create a sparky dictionary from universal dictionary

nmrglue.fileio.sparky.datetime2dic(datetimeobj, dic)

Add time datetime object to dictionary

nmrglue.fileio.sparky.dic2datetime(dic)

Create a datetime object from sparky dictionary

Low-Level Functions

These functions are typically not used directly by users. They are called by high level functions. Developers and user who want fine control over sparky files will be interested in these functions.

nmrglue.fileio.sparky.create_data(data)

Create a sparky data array (recast into float32 array)

nmrglue.fileio.sparky.create_axisdic(adic, tlen, dlen)

Make an sparky axis dictionary from a universal axis dictionary

Parameters:

• adic axis dictionary from universal dictionary
• tlen tile length
• dlen data length

nmrglue.fileio.sparky.calc_tshape(shape, kbyte_max=128)

Calculate tile shape from data shape

shape is a tuple representing the data shape (data.shape) kbyte_max determined the largest tile size in Kbytes

Algorithm divides each dimention by 2 until under kbyte_max tile size.

nmrglue.fileio.sparky.read_2D(filename)

Read a 2D sparky file returning a dic,data pair.

nmrglue.fileio.sparky.write_2D(filename, dic, data, overwrite=False)

Write a sparky file from 2D data

nmrglue.fileio.sparky.read_3D(filename)

Read a 3D sparky file returning a dic,data pair

nmrglue.fileio.sparky.write_3D(filename, dic, data, overwrite=False)

Write a sparky file from 3D data

nmrglue.fileio.sparky.read_lowmem_2D(filename)

Read a 2D sparky file with minimal memory usage.

nmrglue.fileio.sparky.read_lowmem_3D(filename)

Read a 3D sparky file with minimal memory usage

nmrglue.fileio.sparky.get_tilen(f, n_tile, tw_tuple)

Read in tile n from file object with tile sizes given by tw_tuple

Current file position is loss (store before calling if desired)

nmrglue.fileio.sparky.get_tile(f, num_points)

Read tile data from file object

nmrglue.fileio.sparky.put_tile(f, tile)

Put tile data to file

nmrglue.fileio.sparky.get_data(f)

Read all data from sparky file object

nmrglue.fileio.sparky.put_data(f, data)

Put data to file

Does not untile data, assumes this has been done

nmrglue.fileio.sparky.find_tilen_2d(data, ntile, (lentY, lentX))

Return a single tile from untiled data

Parameters:

• data untiled data
• ntile Tile number to return
• (lentY,lentX) Tuple representing tile size

Returns 1D numpy array of floats, zero filling as needed.

nmrglue.fileio.sparky.tile_data2d(data, (lentY, lentX))

Tile sparky data into 1D numpy array

Parameters:

• data Two-dimensional data array
• lentY Y (w1) dimention tile size
• lentX X (w2) dimention tile size

Returns 1D numpy array of floats

nmrglue.fileio.sparky.untile_data2D(data, (lentY, lentX), (lenY, lenX))

Reorganize tiled sparky data into 2D data

Parameters:

• data 1D numpy array of tile data
• lentY size of tile in Y (w1) dim
• lentX size of tile in X (w2) dim
• lenY size of data in Y dim
• lenX size of data in X dim

Returns 2D np.array of floats with size (lenY,lenX)

nmrglue.fileio.sparky.find_tilen_3d(data, ntile, (lentZ, lentY, lentX))

Return a single tile from untiled data

Parameters:

• data untiled data
• ntile Tile number to return
• lentZ Tile Z (w1) size
• lentY Tile Y (w2) size
• lentX Tile X (w3) size

Returns 1D numpy array of floats, zero filling as needed.

nmrglue.fileio.sparky.tile_data3d(data, (lentZ, lentY, lentX))

Tile sparky data into 1D numpy array

Parameters:

• data Three-dimensional data array
• lentZ Z (w1) dimention tile size
• lentY Y (w2) dimention tile size
• lentX X (w3) dimention tile size

Returns 1D numpy array of floats

nmrglue.fileio.sparky.untile_data3D(data, (lentZ, lentY, lentX), (lenZ, lenY, lenX))

Reorganize tiled sparky data into 3D data

Parameters:

• data 1D numpy array of tile data
• lentZ size of tile in Z (w1) dim
• lentY size of tile in Y (w2) dim
• lentX size of tile in X (w3) dim
• lenZ size of data in Z dim
• lenY size of data in Y dim
• lenX size of data in X dim

Returns 3D np.array of floats with size (lenZ,lenY,lenX)

nmrglue.fileio.sparky.get_fileheader(f)

Get fileheader from file and return a list

Reads the 180 byte file header of a sparky file

nmrglue.fileio.sparky.put_fileheader(f, fl)

Write fileheader list to file (180-bytes)

nmrglue.fileio.sparky.fileheader2dic(header)

Convert fileheader list into dictionary

nmrglue.fileio.sparky.dic2fileheader(dic)

Convert fileheader dictionary to list

nmrglue.fileio.sparky.get_axisheader(f)

Get axisheader from file and return a list

Only the first 44 bytes are examined, the NMR_PROCESSED and other header parameters are ignored since the current version of sparky does not use them.

nmrglue.fileio.sparky.put_axisheader(f, al)

Write axisheader list to file (128-bytes)

nmrglue.fileio.sparky.axisheader2dic(header)

Convert axisheader list into dictionary

nmrglue.fileio.sparky.dic2axisheader(dic)

Convert axisheader dictionary to list

Low-Level Classes

class nmrglue.fileio.sparky.sparky_2d(filename, order=None)

Emulates a numpy.ndarray object without loading data into memory for low memory reading of 2D Sparky files.

• 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.

class nmrglue.fileio.sparky.sparky_3d(filename, order=None)

Emulates a numpy.ndarray object without loading data into memory for low memory reading of 3D Sparky files.

• 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.