FabIO Package¶

`fabio` Package¶

`fabio.fabioimage` Module¶

Authors: Henning O. Sorensen & Erik Knudsen

Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk

and Jon Wright, Jerome Kieffer: ESRF

class fabio.fabioimage.fabioimage(data=None, header=None)¶

Bases: object

A common object for images in fable Contains a numpy array (.data) and dict of meta data (.header)

add(other)¶: Add another Image - warning, does not clip to 16 bit images by default

static checkData(data=None)¶: Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

static checkHeader(header=None)¶: Empty for fabioimage but may be populated by others classes

classname¶: Retrieves the name of the class :return: the name of the class

convert(dest)¶: Convert a fabioimage object into another fabioimage object (with possible conversions) :param dest: destination type “EDF”, “edfimage” or the class itself

getclassname()¶: Retrieves the name of the class :return: the name of the class

getframe(num)¶: returns the file numbered ‘num’ in the series as a fabioimage

getheader()¶: returns self.header

getmax()¶: Find max value in self.data, caching for the future

getmean()¶: return the mean

getmin()¶: Find min value in self.data, caching for the future

getstddev()¶: return the standard deviation

integrate_area(coords)¶: Sums up a region of interest if len(coords) == 4 -> convert coords to slices if len(coords) == 2 -> use as slices floor -> ? removed as unused in the function.

load(*arg, **kwarg)¶: Wrapper for read

make_slice(coords)¶: Convert a len(4) set of coords into a len(2) tuple (pair) of slice objects the latter are immutable, meaning the roi can be cached

next()¶: returns the next file in the series as a fabioimage

previous()¶: returns the previous file in the series as a fabioimage

read(filename, frame=None)¶: To be overridden - fill in self.header and self.data

readROI(filename, frame=None, coords=None)¶: Method reading Region of Interest. This implementation is the trivial one, just doing read and crop

readheader(filename)¶: Call the _readheader function...

rebin(x_rebin_fact, y_rebin_fact, keep_I=True)¶: Rebin the data and adjust dims :param x_rebin_fact: x binning factor :param y_rebin_fact: y binning factor :param keep_I: shall the signal increase ? :type x_rebin_fact: int :type y_rebin_fact: int :type keep_I: boolean

resetvals()¶: Reset cache - call on changing data

save(fname)¶: wrapper for write

toPIL16(filename=None)¶: Convert to Python Imaging Library 16 bit greyscale image

update_header(**kwds)¶: update the header entries by default pass in a dict of key, values.

write(fname)¶: To be overwritten - write the file

fabio.fabioimage.test()¶: check some basic fabioimage functionality

`fabio.file_series` Module¶

`fabio.openimage` Module¶

Authors: Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:henning.sorensen@risoe.dk

mods for fabio by JPW modification for HDF5 by Jérôme Kieffer

fabio.openimage.do_magic(byts)¶: Try to interpret the bytes starting the file as a magic number

fabio.openimage.openheader(filename)¶: return only the header

fabio.openimage.openimage(filename, frame=None)¶: Try to open an image

`fabio.adscimage` Module¶

Authors: Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk

mods for fabio by JPW

class fabio.adscimage.adscimage(*args, **kwargs)¶

Bases: fabio.fabioimage.fabioimage

Read an image in ADSC format (quite similar to edf?)

read(fname, frame=None)¶: read in the file

swap_needed()¶

write(fname)¶: Write adsc format

fabio.adscimage.test()¶: testcase

`fabio.binaryimage` Module¶

Authors: Gael Goret, Jerome Kieffer, ESRF, France

Emails: gael.goret@esrf.fr, jerome.kieffer@esrf.fr: Brian Richard Pauw <brian@stack.nl>

Binary files images are simple none-compressed 2D images only defined by their : data-type, dimensions, byte order and offset

This simple library has been made for manipulating exotic/unknown files format.

class fabio.binaryimage.binaryimage(*args, **kwargs)¶

Bases: fabio.fabioimage.fabioimage

This simple library has been made for manipulating exotic/unknown files format.

Binary files images are simple none-compressed 2D images only defined by their:: data-type, dimensions, byte order and offset

if offset is set to a negative value, the image is read using the last data but n data in the file, skipping any header.

estimate_offset_value(fname, dim1, dim2, bytecode='int32')¶: Estimates the size of a file

read(fname, dim1, dim2, offset=0, bytecode='int32', endian='<')¶

Read a binary image

Parameters:

fname (string) – file name
dim1 – image dimensions (Fast index)
dim2 – image dimensions (Slow index)
offset – starting position of the data-block. If negative, starts at the end.
bytecode – can be “int8”,”int16”,”int32”,”int64”,”uint8”,”uint16”,”uint32”,”uint64”,”float32”,”float64”,...
endian – among short or long endian (“<” or “>”)

static swap_needed(endian)¶: Decide if we need to byteswap

write(fname)¶

`fabio.bruker100image` Module¶

Authors: Henning O. Sorensen & Erik Knudsen

Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk

Jérôme Kieffer, ESRF, Grenoble, France

class fabio.bruker100image.bruker100image(data=None, header=None)¶

Bases: fabio.brukerimage.brukerimage

read(fname, frame=None)¶

toPIL16(filename=None)¶

write(fname)¶

`fabio.brukerimage` Module¶

Authors: Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk
Based on: openbruker,readbruker, readbrukerheader functions in the opendata: module of ImageD11 written by Jon Wright, ESRF, Grenoble, France

Writer by Jérôme Kieffer, ESRF, Grenoble, France

class fabio.brukerimage.brukerimage(data=None, header=None)¶

Bases: fabio.fabioimage.fabioimage

Read and eventually write ID11 bruker (eg smart6500) images

TODO: int32 -> float32 conversion according to the “linear” keyword. This is done and works but we need to check with other program that we are appliing the right formula and not the reciprocal one.

HEADERS_KEYS = ['FORMAT', 'VERSION', 'HDRBLKS', 'TYPE', 'SITE', 'MODEL', 'USER', 'SAMPLE', 'SETNAME', 'RUN', 'SAMPNUM', 'TITLE', 'NCOUNTS', 'NOVERFL', 'MINIMUM', 'MAXIMUM', 'NONTIME', 'NLATE', 'FILENAM', 'CREATED', 'CUMULAT', 'ELAPSDR', 'ELAPSDA', 'OSCILLA', 'NSTEPS', 'RANGE', 'START', 'INCREME', 'NUMBER', 'NFRAMES', 'ANGLES', 'NOVER64', 'NPIXELB', 'NROWS', 'NCOLS', 'WORDORD', 'LONGORD', 'TARGET', 'SOURCEK', 'SOURCEM', 'FILTER', 'CELL', 'MATRIX', 'LOWTEMP', 'TEMP', 'HITEMP', 'ZOOM', 'CENTER', 'DISTANC', 'TRAILER', 'COMPRES', 'LINEAR', 'PHD', 'PREAMP', 'CORRECT', 'WARPFIL', 'WAVELEN', 'MAXXY', 'AXIS', 'ENDING', 'DETPAR', 'LUT', 'DISPLIM', 'PROGRAM', 'ROTATE', 'BITMASK', 'OCTMASK', 'ESDCELL', 'DETTYPE', 'NEXP', 'CCDPARM', 'BIS', 'CHEM', 'MORPH', 'CCOLOR', 'CSIZE', 'DNSMET', 'DARK', 'AUTORNG', 'ZEROADJ', 'XTRANS', 'HKL&XY', 'AXES2', 'ENDING2', 'FILTER2', 'LEPTOS', 'CFR']¶

SPACER = '\x1a\x04'¶

basic_translate(fname=None)¶: Does some basic population of the headers so that the writing is possible

bpp_to_numpy = {1: <type 'numpy.uint8'>, 2: <type 'numpy.uint16'>, 4: <type 'numpy.uint32'>}¶

calc_bpp(data=None, max_entry=4096)¶

Calculate the number of byte per pixel to get an optimal overflow table.

Returns:	byte per pixel

gen_header()¶: Generate headers (with some magic and guesses) :param format can be 86 or 100

gen_overflow()¶: Generate an overflow table

read(fname, frame=None)¶: Read in and unpack the pixels (including overflow table

write(fname)¶: Write a bruker image

fabio.brukerimage.test()¶: a testcase

`fabio.cbfimage` Module¶

Authors: Jérôme Kieffer, ESRF: email:jerome.kieffer@esrf.fr

Cif Binary Files images are 2D images written by the Pilatus detector and others. They use a modified (simplified) byte-offset algorithm.

CIF is a library for manipulating Crystallographic information files and tries to conform to the specification of the IUCR

class fabio.cbfimage.CIF(_strFilename=None)¶

Bases: dict

This is the CIF class, it represents the CIF dictionary; and as a a python dictionary thus inherits from the dict built in class.

keys are always unicode (str in python3) values are bytes

BINARY_MARKER = '--CIF-BINARY-FORMAT-SECTION--'¶

BLANK = [' ', '\t', '\r', '\n', '\r\n', '\n\r']¶

DATA = 'data_'¶

DOUBLE_QUOTE = '"'¶

EOL = ['\r', '\n', '\r\n', '\n\r']¶

GLOBAL = 'global_'¶

HASH = '#'¶

LOOP = 'loop_'¶

static LoopHasKey(loop, key)¶: Returns True if the key (string) exist in the array called loop

QUESTIONMARK = '?'¶

SAVE = 'save_'¶

SEMICOLUMN = ';'¶

SINGLE_QUOTE = "'"¶

START_COMMENT = ("'", '"')¶

STOP = 'stop_'¶

UNDERSCORE = '_'¶

exists(sKey)¶: Check if the key exists in the CIF and is non empty. :param sKey: CIF key :type sKey: string :param cif: CIF dictionary :return: True if the key exists in the CIF dictionary and is non empty :rtype: boolean

existsInLoop(sKey)¶: Check if the key exists in the CIF dictionary. :param sKey: CIF key :type sKey: string :param cif: CIF dictionary :return: True if the key exists in the CIF dictionary and is non empty :rtype: boolean

i = '\t'¶

static isAscii(text)¶

Check if all characters in a string are ascii,

Parameters:	_strIn (python string) – input string
Returns:	boolean
Return type:	boolean

loadCHIPLOT(_strFilename)¶

Load the powder diffraction CHIPLOT file and returns the pd_CIF dictionary in the object

Parameters:	_strFilename (string) – the name of the file to open
Returns:	the CIF object corresponding to the powder diffraction
Return type:	dictionary

loadCIF(_strFilename, _bKeepComment=False)¶: Load the CIF file and populates the CIF dictionary into the object :param _strFilename: the name of the file to open :type _strFilename: string :param _strFilename: the name of the file to open :type _strFilename: string :return: None

pop(key, default=None)¶

popitem(key, default=None)¶

readCIF(_strFilename, _bKeepComment=False)¶: Load the CIF file and populates the CIF dictionary into the object :param _strFilename: the name of the file to open :type _strFilename: string :param _strFilename: the name of the file to open :type _strFilename: string :return: None

saveCIF(_strFilename='test.cif', linesep='\n', binary=False)¶: Transforms the CIF object in string then write it into the given file :param _strFilename: the of the file to be written :param linesep: line separation used (to force compatibility with windows/unix) :param binary: Shall we write the data as binary (True only for imageCIF/CBF) :return: None

tostring(_strFilename=None, linesep='\n')¶

Converts a cif dictionnary to a string according to the CIF syntax

param _strFilename:

the name of the filename to be appended in the header of the CIF file

type _strFilename:

string

param linesep: default line separation: can be “

” or ” “

return: a string that corresponds to the content of the CIF-file.

class fabio.cbfimage.cbfimage(data=None, header=None, fname=None)¶

Bases: fabio.fabioimage.fabioimage

Read the Cif Binary File data format

static checkData(data=None)¶

read(fname, frame=None)¶

Read in header into self.header and: the data into self.data

write(fname)¶: write the file in CBF format :param fname: name of the file :type: string

`fabio.dm3image` Module¶

Authors: Henning O. Sorensen & Erik Knudsen

Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk

Jon Wright, ESRF

class fabio.dm3image.dm3image(*args, **kwargs)¶

Bases: fabio.fabioimage.fabioimage

Read and try to write the dm3 data format

read(fname, frame=None)¶

read_data()¶

read_tag_entry()¶

read_tag_group()¶

read_tag_type()¶

readbytes(bytes_to_read, format, swap=True)¶

`fabio.edfimage` Module¶

License: GPLv2+

Authors:¶

Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
Jon Wright & Jérôme Kieffer: European Synchrotron Radiation Facility; Grenoble (France)

class fabio.edfimage.Frame(data=None, header=None, header_keys=None, number=None)¶

Bases: object

A class representing a single frame in an EDF file

bytecode¶

data¶

Unpack a binary blob according to the specification given in the header

Returns:	dataset as numpy.ndarray

getByteCode()¶

getData()¶

Unpack a binary blob according to the specification given in the header

Returns:	dataset as numpy.ndarray

getEdfBlock(force_type=None, fit2dMode=False)¶

Parameters:	force_type (string or numpy.dtype) – type of the dataset to be enforced like “float64” or “uint16” fit2dMode (boolean) – enforce compatibility with fit2d and starts counting number of images at 1
Returns:	ascii header block + binary data block
Return type:	python bytes with the concatenation of the ascii header and the binary data block

parseheader(block)¶

Parse the header in some EDF format from an already open file

Parameters:	block (string, should be full ascii) – string representing the header block.
Returns:	size of the binary blob

setByteCode(_iVal)¶

setData(npa=None)¶: Setter for data in edf frame

swap_needed()¶: Decide if we need to byteswap

class fabio.edfimage.edfimage(data=None, header=None, header_keys=None, frames=None)¶

Bases: fabio.fabioimage.fabioimage

Read and try to write the ESRF edf data format

appendFrame(frame=None, data=None, header=None)¶: Method used add a frame to an EDF file :param frame: frame to append to edf image :type frame: instance of Frame :return: None

bpp¶

bytecode¶

capsHeader¶: property: capsHeader of EDF file, i.e. the keys of the header in UPPER case.

static checkHeader(header=None)¶: Empty for fabioimage but may be populated by others classes

data¶: property: data of EDF file

delCapsHeader()¶: deleter for edf capsHeader

delData()¶: deleter for edf Data

delHeader()¶: Deleter for edf header

delHeaderKeys()¶: Deleter for edf header_keys

deleteFrame(frameNb=None)¶: Method used to remove a frame from an EDF image. by default the last one is removed. :param frameNb: frame number to remove, by default the last. :type frameNb: integer :return: None

dim1¶

dim2¶

dims¶

fastReadData(filename=None)¶

This is a special method that will read and return the data from another file ... The aim is performances, ... but only supports uncompressed files.

Returns:	data from another file using positions from current edfimage

fastReadROI(filename, coords=None)¶

Method reading Region of Interest of another file based on metadata available in current edfimage. The aim is performances, ... but only supports uncompressed files.

Returns:	ROI-data from another file using positions from current edfimage
Return type:	numpy 2darray

getBpp()¶

getByteCode()¶

getCapsHeader()¶: getter for edf headers keys in upper case :return: data for current frame :rtype: dict

getData()¶: getter for edf Data :return: data for current frame :rtype: numpy.ndarray

getDim1()¶

getDim2()¶

getDims()¶

getHeader()¶: Getter for the headers. used by the property header,

getHeaderKeys()¶: Getter for edf header_keys

getNbFrames()¶: Getter for number of frames

getframe(num)¶: returns the file numbered ‘num’ in the series as a fabioimage

header¶: property: header of EDF file

header_keys¶: property: header_keys of EDF file

next()¶: returns the next file in the series as a fabioimage

nframes¶: Getter for number of frames

previous()¶: returns the previous file in the series as a fabioimage

read(fname, frame=None)¶

Read in header into self.header and: the data into self.data

setBpp(_iVal)¶

setByteCode(_iVal)¶

setCapsHeader(_data)¶: Enforces the propagation of the header_keys to the list of frames :param _data: numpy array representing data

setData(_data)¶: Enforces the propagation of the data to the list of frames :param _data: numpy array representing data

setDim1(_iVal)¶

setDim2(_iVal)¶

setHeader(_dictHeader)¶: Enforces the propagation of the header to the list of frames

setHeaderKeys(_listtHeader)¶: Enforces the propagation of the header_keys to the list of frames :param _listtHeader: list of the (ordered) keys in the header :type _listtHeader: python list

setNbFrames(val)¶: Setter for number of frames ... should do nothing. Here just to avoid bugs

swap_needed()¶

Decide if we need to byteswap

:return True if needed, False else and None if not understood

unpack()¶

Unpack a binary blob according to the specification given in the header and return the dataset

Returns:	dataset as numpy.ndarray

write(fname, force_type=None, fit2dMode=False)¶

Try to write a file check we can write zipped also mimics that fabian was writing uint16 (we sometimes want floats)

Parameters:	force_type – can be numpy.uint16 or simply “float”
Returns:	None

`fabio.fit2dmaskimage` Module¶

Author: Andy Hammersley, ESRF Translation into python/fabio: Jon Wright, ESRF. Writer: Jérôme Kieffer

class fabio.fit2dmaskimage.fit2dmaskimage(data=None, header=None)¶

Bases: fabio.fabioimage.fabioimage

Read and try to write Andy Hammersley’s mask format

static checkData(data=None)¶

read(fname, frame=None)¶

Read in header into self.header and: the data into self.data

write(fname)¶: Try to write a file

`fabio.fit2dspreadsheetimage` Module¶

Read the fit2d ascii image output

Jon Wright, ESRF

class fabio.fit2dspreadsheetimage.fit2dspreadsheetimage(data=None, header=None)¶

Bases: fabio.fabioimage.fabioimage

Read a fit2d ascii format

read(fname, frame=None)¶

Read in header into self.header and: the data into self.data

`fabio.GEimage` Module¶

class fabio.GEimage.GEimage(data=None, header=None)¶

Bases: fabio.fabioimage.fabioimage

getframe(num)¶: Returns a frame as a new fabioimage object

next()¶: Get the next image in a series as a fabio image

previous()¶: Get the previous image in a series as a fabio image

read(fname, frame=None)¶: Read in header into self.header and the data into self.data

write(fname, force_type=<type 'numpy.uint16'>)¶: Not yet implemented

fabio.GEimage.demo()¶

`fabio.hdf5mage` Module¶

HDF5 image for FabIO

Authors: Jerome Kieffer email: Jerome.Kieffer@terre-adelie.org

Specifications: input should being the form:

hdf5:///filename?path#slice=[:,:,1]

class fabio.hdf5image.hdf5image(*arg, **kwargs)¶

Bases: fabio.fabioimage.fabioimage

FabIO image class for Images from an HDF file

get_slice()¶

getframe(num)¶: Returns a frame as a new fabioimage object :param num: frame number

next()¶: Get the next image in a series as a fabio image

previous()¶: Get the previous image in a series as a fabio image

read(fname, frame=None)¶: try to read image :param fname: name of the file as hdf5:///filename?path#slice=[:,:,1]

set_url(url)¶: set the url of the data

write(fname, force_type=<type 'numpy.uint16'>)¶

`fabio.HiPiCimage` Module¶

Authors: Henning O. Sorensen & Erik Knudsen

Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:erik.knudsen@risoe.dk

Jon Wright, ESRF

Information about the file format from Masakatzu Kobayashi is highly appreciated

class fabio.HiPiCimage.HiPiCimage(data=None, header=None)¶

Bases: fabio.fabioimage.fabioimage

Read HiPic images e.g. collected with a Hamamatsu CCD camera

read(fname, frame=None)¶

Read in header into self.header and: the data into self.data

`fabio.kcdimage` Module¶

Authors: Jerome Kieffer, ESRF: email:jerome.kieffer@esrf.fr

kcd images are 2D images written by the old KappaCCD diffractometer built by Nonius in the 1990’s Based on the edfimage.py parser.

class fabio.kcdimage.kcdimage(data=None, header=None)¶

Bases: fabio.fabioimage.fabioimage

Read the Nonius kcd data format

static checkData(data=None)¶

read(fname, frame=None)¶

Read in header into self.header and: the data into self.data

`fabio.mar345image` Module¶

Authors:¶

Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
Jon Wright, Jérôme Kieffer & Gaël Goret: European Synchrotron Radiation Facility; Grenoble (France)

Supports Mar345 imaging plate and Mar555 flat panel

Documentation on the format is available from: http://rayonix.com/site_media/downloads/mar345_formats.pdf

class fabio.mar345image.mar345image(*args, **kwargs)¶

Bases: fabio.fabioimage.fabioimage

ascii_header(linesep='\n', size=4096)¶

Generate the ASCII header for writing

Parameters:	linesep – end of line separator size – size of the header (without the binary header)
Returns:	string (unicode) containing the mar345 header

binary_header()¶

Returns:	Binary header of mar345 file

static checkData(data=None)¶

nb_overflow_pixels()¶

read(fname, frame=None)¶: Read a mar345 image

write(fname)¶: Try to write mar345 file. This is still in beta version. It uses CCP4 (LGPL) PCK1 algo from JPA

`fabio.mrcimage` Module¶

`fabio.marccdimage` Module¶

Authors:¶

Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
Jon Wright: European Synchrotron Radiation Facility; Grenoble (France)

marccdimage can read MarCCD and MarMosaic images including header info.

JPW : Use a parser in case of typos (sorry?)

fabio.marccdimage.interpret_header(header, fmt, names)¶: given a format and header interpret it

fabio.marccdimage.make_format(c_def_string)¶: Reads the header definition in c and makes the format string to pass to struct.unpack

class fabio.marccdimage.marccdimage(*args, **kwds)¶

Bases: fabio.tifimage.tifimage

Read in data in mar ccd format, also MarMosaic images, including header info

`fabio.OXDimage` Module¶

Reads Oxford Diffraction Sapphire 3 images

Authors:¶

Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
Jon Wright, Jérôme Kieffer & Gaël Goret: European Synchrotron Radiation Facility; Grenoble (France)

class fabio.OXDimage.OXDimage(data=None, header=None)¶

Bases: fabio.fabioimage.fabioimage

Oxford Diffraction Sapphire 3 images reader/writer class

Note: We assume the binary format is alway little-endian, is this True ?

static checkData(data=None)¶

getCompressionRatio()¶: calculate the compression factor obtained vs raw data

read(fname, frame=None)¶

Read in header into self.header and: the data into self.data

write(fname)¶: Write Oxford diffraction images: this is still beta Only TY1 compressed images is currently possible :param fname: output filename

class fabio.OXDimage.Section(size, dictHeader)¶

Bases: object

Small helper class for writing binary headers

getSize(dtype)¶

setData(key, offset, dtype, default=None)¶

Parameters:	offset – int, starting position in the section key – name of the header key dtype – type of the data to insert (defines the size!)

`fabio.pilatusimage` Module¶

Authors:¶

Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
Jon Wright: European Synchrotron Radiation Facility; Grenoble (France)

class fabio.pilatusimage.pilatusimage(*args, **kwds)¶

Bases: fabio.tifimage.tifimage

Read in Pilatus format, also pilatus images, including header info

`fabio.pixiimage` Module¶

Author: Jon Wright, ESRF.

fabio.pixiimage.demo(fname)¶

class fabio.pixiimage.pixiimage(data=None, header=None)¶

Bases: fabio.fabioimage.fabioimage

getframe(num)¶: Returns a frame as a new fabioimage object

next()¶: Get the next image in a series as a fabio image

previous()¶: Get the previous image in a series as a fabio image

read(fname, frame=None)¶

write(fname, force_type=<type 'numpy.uint16'>)¶

`fabio.pnmimage` Module¶

Authors: Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions Risoe National Laboratory Frederiksborgvej 399 DK-4000 Roskilde email:henning.sorensen@risoe.dk

Jérôme Kieffer: European Synchrotron Radiation Facility; Grenoble (France)

License: GPLv3+

class fabio.pnmimage.pnmimage(*arg, **kwargs)¶

Bases: fabio.fabioimage.fabioimage

P1dec(buf, bytecode)¶

P2dec(buf, bytecode)¶

P3dec(buf, bytecode)¶

P4dec(buf, bytecode)¶

P5dec(buf, bytecode)¶

P6dec(buf, bytecode)¶

P7dec(buf, bytecode)¶

static checkData(data=None)¶

read(fname, frame=None)¶: try to read PNM images :param fname: name of the file :param frame: not relevant here! PNM is always single framed

write(filename)¶

`fabio.raxisimage` Module¶

Authors: Brian R. Pauw email: brian@stack.nl

Written using information gleaned from the ReadRAXISImage program written by T. L. Hendrixson, made available by Rigaku Americas. Available at: http://www.rigaku.com/downloads/software/readimage.html

class fabio.raxisimage.raxisimage(*arg, **kwargs)¶

Bases: fabio.fabioimage.fabioimage

FabIO image class to read Rigaku RAXIS image files. Write functions are not planned as there are plenty of more suitable file formats available for storing detector data. In particular, the MSB used in Rigaku files is used in an uncommon way: it is used as a multiply-by flag rather than a normal image value bit. While it is said to multiply by the value specified in the header, there is at least one case where this is found not to hold, so YMMV and be careful.

read(fname, frame=None)¶: try to read image :param fname: name of the file :param frame:

rigakuKeys()¶

swap_needed()¶: not sure if this function is needed

`fabio.tifimage` Module¶

FabIO class for dealing with TIFF images. In facts wraps TiffIO from V. Armando Solé (available in PyMca) or falls back to PIL

Authors:¶

Henning O. Sorensen & Erik Knudsen: Center for Fundamental Research: Metal Structures in Four Dimensions; Risoe National Laboratory; Frederiksborgvej 399; DK-4000 Roskilde; email:erik.knudsen@risoe.dk
Jérôme Kieffer: European Synchrotron Radiation Facility; Grenoble (France)

License: GPLv3+

class fabio.tifimage.Image_File_Directory(instring=None, offset=-1)¶

Bases: object

unpack(instring, offset=-1)¶

class fabio.tifimage.Image_File_Directory_entry(tag=0, tag_type=0, count=0, offset=0)¶

Bases: object

extract_data(full_string)¶

unpack(strInput)¶

class fabio.tifimage.Tiff_header(string)¶: Bases: object

class fabio.tifimage.tifimage(*args, **kwds)¶

Bases: fabio.fabioimage.fabioimage

Images in TIF format Wraps TiffIO

read(fname, frame=None)¶: Wrapper for TiffIO.

write(fname)¶: Overrides the fabioimage.write method and provides a simple TIFF image writer. :param fname: name of the file to save the image to @tag_type fname: string or unicode (file?)...

`fabio.xsdimage` Module¶

Authors: Jérôme Kieffer, ESRF: email:jerome.kieffer@esrf.fr

XSDimge are XML files containing numpy arrays

class fabio.xsdimage.xsdimage(data=None, header=None, fname=None)¶

Bases: fabio.fabioimage.fabioimage

Read the XSDataImage XML File data format

read(fname, frame=None)¶

`fabio.compression` Module¶

Authors: Jérôme Kieffer, ESRF: email:jerome.kieffer@esrf.fr

FabIO library containing compression and decompression algorithm for various

fabio.compression.compByteOffset(data)¶

Compress a dataset into a string using the byte_offet algorithm

Parameters:	data – ndarray
Returns:	string/bytes with compressed data

test = numpy.array([0,1,2,127,0,1,2,128,0,1,2,32767,0,1,2,32768,0,1,2,2147483647,0,1,2,2147483648,0,1,2,128,129,130,32767,32768,128,129,130,32768,2147483647,2147483648])

fabio.compression.compByteOffset_numpy(data)¶

Compress a dataset into a string using the byte_offet algorithm

Parameters:	data – ndarray
Returns:	string/bytes with compressed data

test = numpy.array([0,1,2,127,0,1,2,128,0,1,2,32767,0,1,2,32768,0,1,2,2147483647,0,1,2,2147483648,0,1,2,128,129,130,32767,32768,128,129,130,32768,2147483647,2147483648])

fabio.compression.compPCK(data)¶

Modified CCP4 pck compressor used in MAR345 images

Parameters:	data – numpy.ndarray (square array)
Returns:	compressed stream

fabio.compression.compTY1(data)¶

Modified byte offset compressor used in Oxford Diffraction images

Parameters:	data – numpy.ndarray with the input data (integers!)
Returns:	3-tuple of strings: raw_8,raw_16,raw_32 containing raw data with integer of the given size

fabio.compression.decByteOffset(stream, size=None)¶

Analyze a stream of char with any length of exception:: 2, 4, or 8 bytes integers

Parameters:	stream – string representing the compressed data size – the size of the output array (of longInts)
Returns:	1D-ndarray

fabio.compression.decByteOffset_cython(stream, size=None)¶

Analyze a stream of char with any length of exception:: 2, 4, or 8 bytes integers

Parameters:	stream – string representing the compressed data size – the size of the output array (of longInts)
Returns:	1D-ndarray

fabio.compression.decByteOffset_numpy(stream, size=None)¶

Analyze a stream of char with any length of exception:: 2, 4, or 8 bytes integers

Parameters:	stream – string representing the compressed data size – the size of the output array (of longInts)
Returns:	1D-ndarray

fabio.compression.decBzip2(stream)¶: Decompress a chunk of data using the bzip2 algorithm from Python

fabio.compression.decGzip(stream)¶: Decompress a chunk of data using the gzip algorithm from Python or alternatives if possible

fabio.compression.decKM4CCD(raw_8, raw_16=None, raw_32=None)¶

Modified byte offset decompressor used in Oxford Diffraction images

Note: Always expect little endian data on the disk

Parameters:	raw_8 – strings containing raw data with integer 8 bits raw_16 – strings containing raw data with integer 16 bits raw_32 – strings containing raw data with integer 32 bits
Returns:	numpy.ndarray

fabio.compression.decPCK(stream, dim1=None, dim2=None, overflowPix=None, version=None, normal_start=None, swap_needed=None)¶

Modified CCP4 pck decompressor used in MAR345 images

Parameters:	raw – input string (bytes in python3) dim1,dim2 – optional parameters size overflowPix – optional parameters: number of overflowed pixels version – PCK version 1 or 2 normal_start – position of the normal value section (can be auto-guessed) swap_needed – set to True when reading data from a foreign endianness (little on big or big on little)

:return : ndarray of 2D with the right size

fabio.compression.decTY1(raw_8, raw_16=None, raw_32=None)¶

Modified byte offset decompressor used in Oxford Diffraction images

Note: Always expect little endian data on the disk

Parameters:	raw_8 – strings containing raw data with integer 8 bits raw_16 – strings containing raw data with integer 16 bits raw_32 – strings containing raw data with integer 32 bits
Returns:	numpy.ndarray

fabio.compression.decZlib(stream)¶: Decompress a chunk of data using the zlib algorithm from Python

fabio.compression.endianness()¶: Return the native endianness of the system

fabio.compression.md5sum(blob)¶: returns the md5sum of an object...

`fabio.converters` Module¶

Converter module. This is for the moment empty (populated only with almost pass through anonymous functions) but aims to be populated with more sofisticated translators ...

fabio.converters.convert_data(inp, outp, data)¶: Return data converted to the output format ... over-simplistic implementation for the moment ... :param inp,outp: input/output format like “cbfimage” :param data(ndarray): the actual dataset to be transformed

fabio.converters.convert_data_integer(data)¶: convert data to integer

fabio.converters.convert_header(inp, outp, header)¶: return header converted to the output format :param inp,outp: input/output format like “cbfimage” :param header(dict):the actual set of headers to be transformed

`fabio.datIO` Module¶

`fabio.third_party.TiffIO` Module¶

`fabio.readbytestream` Module¶

Reads a bytestream

Authors: Jon Wright Henning O. Sorensen & Erik Knudsen: ESRF Risoe National Laboratory

fabio.readbytestream.readbytestream(fil, offset, x, y, nbytespp, datatype='int', signed='n', swap='n', typeout=<type 'numpy.uint16'>)¶

Reads in a bytestream from a file (which may be a string indicating a filename, or an already opened file (should be “rb”)) offset is the position (in bytes) where the pixel data start nbytespp = number of bytes per pixel type can be int or float (4 bytes pp) or double (8 bytes pp) signed: normally signed data ‘y’, but ‘n’ to try to get back the right numbers when unsigned data are converted to signed (python once had no unsigned numeric types.) swap, normally do not bother, but ‘y’ to swap bytes typeout is the numpy type to output, normally uint16, but more if overflows occurred x and y are the pixel dimensions

TODO : Read in regions of interest

PLEASE LEAVE THE STRANGE INTERFACE ALONE - IT IS USEFUL FOR THE BRUKER FORMAT

Parameters:	name – string to check listExcluded – list of char or string excluded.
Returns:	True of False whether name is pure ascii or not

Parameters:	name – string to check excluded – tuple of char or string excluded (not list: they are mutable).
Returns:	the name with all non valid char removed

param _strFilename:
	the name of the filename to be appended in the header of the CIF file
type _strFilename:
	string
param linesep:	default line separation: can be “

FabIO Package¶

fabio Package¶

fabio.fabioimage Module¶

fabio.fabioutils Module¶

fabio.file_series Module¶

fabio.openimage Module¶

fabio.adscimage Module¶

fabio.binaryimage Module¶

fabio.bruker100image Module¶

fabio.brukerimage Module¶

fabio.cbfimage Module¶

fabio.dm3image Module¶

fabio.edfimage Module¶

Authors:¶

fabio.fit2dmaskimage Module¶

fabio.fit2dspreadsheetimage Module¶

fabio.GEimage Module¶

fabio.hdf5mage Module¶

fabio.HiPiCimage Module¶

fabio.kcdimage Module¶

fabio.mar345image Module¶

Authors:¶

fabio.mrcimage Module¶

fabio.marccdimage Module¶

Authors:¶

fabio.OXDimage Module¶

Authors:¶

fabio.pilatusimage Module¶

Authors:¶

fabio.pixiimage Module¶

fabio.pnmimage Module¶

fabio.raxisimage Module¶

fabio.tifimage Module¶

Authors:¶

fabio.xsdimage Module¶

fabio.compression Module¶

fabio.converters Module¶

fabio.datIO Module¶

fabio.third_party.TiffIO Module¶

fabio.readbytestream Module¶

`fabio` Package¶

`fabio.fabioimage` Module¶

`fabio.fabioutils` Module¶

`fabio.file_series` Module¶

`fabio.openimage` Module¶

`fabio.adscimage` Module¶

`fabio.binaryimage` Module¶

`fabio.bruker100image` Module¶

`fabio.brukerimage` Module¶

`fabio.cbfimage` Module¶

`fabio.dm3image` Module¶

`fabio.edfimage` Module¶

`fabio.fit2dmaskimage` Module¶

`fabio.fit2dspreadsheetimage` Module¶

`fabio.GEimage` Module¶

`fabio.hdf5mage` Module¶

`fabio.HiPiCimage` Module¶

`fabio.kcdimage` Module¶

`fabio.mar345image` Module¶

`fabio.mrcimage` Module¶

`fabio.marccdimage` Module¶

`fabio.OXDimage` Module¶

`fabio.pilatusimage` Module¶

`fabio.pixiimage` Module¶

`fabio.pnmimage` Module¶

`fabio.raxisimage` Module¶

`fabio.tifimage` Module¶

`fabio.xsdimage` Module¶

`fabio.compression` Module¶

`fabio.converters` Module¶

`fabio.datIO` Module¶

`fabio.third_party.TiffIO` Module¶

`fabio.readbytestream` Module¶