hyperspy.io_plugins.ripple module

hyperspy.io_plugins.ripple.file_reader(filename, rpl_info=None, encoding='latin-1', mmap_mode='c', *args, **kwds)

Parses a Lispix (http://www.nist.gov/lispix/) ripple (.rpl) file and reads the data from the corresponding raw (.raw) file; or, read a raw file if the dictionary rpl_info is provided.

This format is often uses in EDS/EDX experiments.

Images and spectral images or data cubes that are written in the (Lispix) raw file format are just a continuous string of numbers.

Data cubes can be stored image by image, or spectrum by spectrum. Single images are stored row by row, vector cubes are stored row by row (each row spectrum by spectrum), image cubes are stored image by image.

All of the numbers are in the same format, such as 16 bit signed integer, IEEE 8-byte real, 8-bit unsigned byte, etc.

The “raw” file should be accompanied by text file with the same name and “.rpl” extension. This file lists the characteristics of the raw file so that it can be loaded without human intervention.

Alternatively, dictionary ‘rpl_info’ containing the information can be given.

Some keys are specific to HyperSpy and will be ignored by other software.

RPL stands for “Raw Parameter List”, an ASCII text, tab delimited file in which HyperSpy reads the image parameters for a raw file.

Key

Type

Description

width

int

pixels per row

height

int

number of rows

depth

int

number of images or spectral pts

offset

int

bytes to skip

data-type

str

‘signed’, ‘unsigned’, or ‘float’

data-length

str

bytes per pixel ‘1’, ‘2’, ‘4’, or ‘8’

byte-order

str

‘big-endian’, ‘little-endian’, or ‘dont-care’

record-by

str

‘image’, ‘vector’, or ‘dont-care’

# X-ray keys:

ev-per-chan

int

optional, eV per channel

detector-peak-width-ev

int

optional, FWHM for the Mn K-alpha line

# HyperSpy-specific keys

depth-origin

int

energy offset in pixels

depth-scale

float

energy scaling (units per pixel)

depth-units

str

energy units, usually eV

depth-name

str

Name of the magnitude stored as depth

width-origin

int

column offset in pixels

width-scale

float

column scaling (units per pixel)

width-units

str

column units, usually nm

width-name

str

Name of the magnitude stored as width

height-origin

int

row offset in pixels

height-scale

float

row scaling (units per pixel)

height-units

str

row units, usually nm

height-name

str

Name of the magnitude stored as height

signal

str

Type of the signal stored, e.g. EDS_SEM

convergence-angle

float

TEM convergence angle in mrad

collection-angle

float

EELS spectrometer collection semi-angle in mrad

beam-energy

float

TEM beam energy in keV

elevation-angle

float

Elevation angle of the EDS detector

azimuth-angle

float

Elevation angle of the EDS detector

live-time

float

Live time per spectrum

energy-resolution

float

Resolution of the EDS (FHWM of MnKa)

tilt-stage

float

The tilt of the stage

date

str

date in ISO 8601

time

str

time in ISO 8601

title

str

title of the signal to be stored

Note

When ‘data-length’ is 1, the ‘byte order’ is not relevant as there is only one byte per datum, and ‘byte-order’ should be ‘dont-care’.

When ‘depth’ is 1, the file has one image, ‘record-by’ is not relevant and should be ‘dont-care’. For spectral images, ‘record-by’ is ‘vector’. For stacks of images, ‘record-by’ is ‘image’.

Floating point numbers can be IEEE 4-byte, or IEEE 8-byte. Therefore if data-type is float, data-length MUST be 4 or 8.

The rpl file is read in a case-insensitive manner. However, when providing a dictionary as input, the keys MUST be lowercase.

Comment lines, beginning with a semi-colon ‘;’ are allowed anywhere.

The first non-comment in the rpl file line MUST have two column names: ‘name_1’<TAB>’name_2’; any name would do e.g. ‘key’<TAB>’value’.

Parameters can be in ANY order.

In the rpl file, the parameter name is followed by ONE tab (spaces are ignored) e.g.: ‘data-length’<TAB>’2’

In the rpl file, other data and more tabs can follow the two items on each row, and are ignored.

Other keys and values can be included and are ignored.

Any number of spaces can go along with each tab.

hyperspy.io_plugins.ripple.parse_ripple(fp)

Parse information from ripple (.rpl) file. Accepts file object ‘fp. Returns dictionary rpl_info.

hyperspy.io_plugins.ripple.read_raw(rpl_info, fp, mmap_mode='c')

Read the raw file object ‘fp’ based on the information given in the ‘rpl_info’ dictionary.

Parameters
  • rpl_info (dict) – A dictionary containing the keywords as parsed by read_rpl

  • fp

  • mmap_mode ({None, 'r+', 'r', 'w+', 'c'}, optional) –

  • not None, then memory-map the file, using the given mode (If) –

  • numpy.memmap) The mode has no effect for pickled or ((see) –

  • files. (zipped) –

  • memory-mapped array is stored on disk, and not directly loaded (A) –

  • memory. However, it can be accessed and sliced like any (into) –

  • Memory mapping is especially useful for accessing (ndarray.) –

  • fragments of large files without reading the entire file (small) –

  • memory. (into) –

hyperspy.io_plugins.ripple.write_raw(filename, signal, record_by)

Writes the raw file object

Parameters
  • filename (str) – the filename, either with the extension or without it

  • record_by (str) – ‘vector’ or ‘image’