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) –
None (If not) –
file (small fragments of large files without reading the entire) –
mode (using the given) –
or ((see numpy.memmap). The mode has no effect for pickled) –
files. (zipped) –
disk (A memory-mapped array is stored on) –
loaded (and not directly) –
However (into memory.) –
any (it can be accessed and sliced like) –
accessing (ndarray. Memory mapping is especially useful for) –
file –
memory. (into) –