nmrglue.pipe

Functions for reading and writing NMRPipe files and table (.tab) files

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

User Information

User Functions

read(filename) Read a NMRPipe file.
write(filename, dic, data[, overwrite]) Write a NMRPipe file to disk.
read_lowmem(filename) Read a NMRPipe file with minimal memory usage.
write_lowmem(filename, dic, data[, overwrite]) Write a NMRPipe file to disk using minimal memory (trace by trace).
read_table(filename) Read a NMRPipe database table (.tab) file.
write_table(filename, pcomments, pformats, rec) Write a NMRPipe database table (.tab) file.
make_uc(dic, data[, dim]) Create a unit conversion object
guess_udic(dic, data) Guess parameters of universal dictionary from dic, data pair.
create_dic(udic[, datetimeobj]) Crate a NMRPipe parameter dictionary from universal dictionary
datetime2dic(dt, dic) Add datatime object to a NMRPipe dictionary
dic2datetime(dic) Create a datetime object from a NMRPipe dictionary

User Classes

iter3D(filemask[, in_lead, out_lead]) Object which allows for graceful iteration over 3D NMRPipe files.

Developer Information

from __future__ import print_function, division

Developer Functions

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

create_data(data) Create a NMRPipe data array (recast into float32 or complex64)
add_axis_to_dic(dic, adic, n) Add an axis dictionary (adic) to a NMRPipe dictionary (dic) as axis n.
create_empty_dic() Creates a NMRPipe dictionary with default values
read_1D(filename) Read a 1D NMRPipe file.
read_2D(filename) Read a 2D NMRPipe file or NMRPipe data stream.
read_lowmem_2D(filename) Read a 2D NMRPipe file or NMRPipe data stream using minimal memory.
read_stream(filename) Read a NMRPipe data stream (one file 3D or 4D files).
read_lowmem_stream(filename) Read a NMRPipe data stream using minimal memory.
read_3D(filemask) Read a 3D NMRPipe file.
read_lowmem_3D(filemask) Read a 3D NMRPipe file using minimal memory.
read_4D(filemask) Read a 3D NMRPipe file.
read_lowmem_4D(filemask) Read a NMRPipe file using minimal memory.
write_single(filename, dic, data[, overwrite]) Write data to a single NMRPipe file from memory.
write_3D(filemask, dic, data[, overwrite]) Write a standard multi-file 3D NMRPipe file
write_4D(filemask, dic, data[, overwrite]) Write a one or two index 4D NMRPipe file.
write_lowmem_2D(filename, dic, data[, overwrite]) Write a 2D NMRPipe file using minimal memory (trace by trace)
write_lowmem_3D(filename, dic, data[, overwrite]) Write a standard multi-file 3D NMRPipe file using minimal memory.
write_lowmem_3Ds(filename, dic, data[, ...]) Write 3D NMRPipe data stream file using minimal memory (trace by trace)
write_lowmem_4D(filename, dic, data[, overwrite]) Write a multi-file (single or double index) 4D NMRPipe file using minimal memory.
write_lowmem_4Ds(filename, dic, data[, ...]) Write 4D NMRPipe data stream file using minimal memory (trace by trace)
put_fdata(fh, fdata) Put NMR data, fdata, to a NMRPipe file described by file object fh.
put_trace(fh, trace) Put a trace (real or complex) to NMRPipe file described by file object fh.
put_data(filename, fdata, data[, overwrite]) Put fdata and data to 2D NMRPipe.
write_slice_3D(filemask, dic, data, shape, ...) Write a slice of a 3D data array to file.
pack_complex(data) Pack inteleaved real,imag array into complex array.
transpose_3D(dic, data[, axes]) Transpose pipe_3d object and dictionary
find_shape(dic) Find the shape (tuple) of data in a NMRPipe file from parameters.
reshape_data(data, shape) Reshape data or return 1D data after warning.
unshape_data(data) Return 1D version of data.
unappend_data(data) Return complex data with last axis (-1) unappended.
append_data(data) Return data with last axis (-1) appeneded.
fdata2dic(fdata) Convert a fdata array to fdata dictionary.
dic2fdata(dic) Converts a NMRPipe dictionary into an array.
get_fdata(filename) Get an array of length 512-bytes holding NMRPipe header.
get_data(filename) Get array of data
get_fdata_data(filename) Get fdata and data array, return (fdata, data)
get_trace(fhandle, ntrace, pts, bswap, cplex) Get a single trace from a NMRPipe file

Developer Classes

pipe_2d(filename[, order]) Emulate a ndarray objects without loading data into memory for low memory reading of 2D NMRPipe files.
pipe_3d(filemask[, order, fcheck]) Emulate a ndarray objects without loading data into memory for low memory reading of 3D NMRPipe files (multiple file data sets).
pipestream_3d(filename[, order]) Emulate a ndarray objects without loading data into memory for low memory reading of 3D NMRPipe data stream files (one file data sets).
pipe_4d(filemask[, order, fcheck]) Emulate a ndarray objects without loading data into memory for low memory reading of single/two index 4D NMRPipe data files.
pipestream_4d(filename[, order]) Emulate a ndarray objects without loading data into memory for low memory reading of 4D NMRPipe data steams (one file 4D data sets).