FabIO Package

`fabio` Package

FabIO module

fabio.benchmarks(): Run the benchmarks

fabio.open(filename, frame=None)

Open an image.

It returns a FabioImage-class instance which can be used as a context manager to close the file at the termination.

with fabio.open("image.edf") as i:
    print(i.nframes)
    print(i.data)

Parameters

filename (Union[str,FilenameObject]) – A filename or a filename iterator.
frame (Union[int,None]) – A specific frame inside this file.

Return type

FabioImage

fabio.open_series(filenames=None, first_filename=None, single_frame=None, fixed_frames=None, fixed_frame_number=None)

Create an object to iterate frames through a file series.

This function is a wrapper over FileSeries to facilitate simple uses of file series iterations.

Parameters

filenames (Union[Generator,Iterator,List]) – Ordered list of filenames to process as a file series. It also can be a generator, and iterator, or filename_series or file_series objects.
first_filename (str) – If provided iterate filenames from this filename and try to consecutivelly open next files. If this argument is specified the filenames have to unspecified. Internally it uses filename_series to iterate the filenames.
single_frame (Union[Bool,None]) – If True, all files are supposed to contain only one frame.
fixed_frames (Union[Bool,None]) – If True, all files are supposed to contain the same amount of frames (this fixed amount will be reached from the first file of the serie).
fixed_frame_number (Union[Integer,None]) – If set, all files are supposed to contain the same amount of frames (sepecified by this argument)

Return type

FileSeries

fabio.register(codec_class)

Register a codec class with the set of formats supported by fabio.

It is a transitional function to prepare the next comming version of fabio.

On the current fabio library, when a module is imported, all the formats
inheriting FabioImage are automatically registred. And this function is doing nothing.
On the next fabio library. Importing a module containing classes
inheriting FabioImage will not be registered. And this function will register the class.

The following source code will then provide the same behaviour on both fabio versions, and it is recommended to use it.

@fabio.register
class MyCodec(fabio.fabioimage.FabioImage):
    pass

fabio.tests()

Run the FabIO test suite.

If the test-images are not already installed (via the debian package for example), they need to be downloaded from sourceforge.net, which make take a while. Ensure your network connection is operational and your proxy settings are correct, for example:

export http_proxy=http://proxy.site.com:3128

`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.FabioFrame(data=None, header=None)

Bases: _FabioArray

Identify a frame

property container

Returns the container providing this frame.

This FabioImage is stored as a weakref. If a reference to the file is not stored by user of the lib, this link is lost.

Return type: FabioImage

property dtype

property file_container

Returns the file container providing this frame.

This FabioImage is stored as a weakref. If a reference to the file is not stored by user of the lib, this link is lost.

Return type: FabioImage

property file_index

Returns the index of this frame in in it’s file container.

Return type: int

property header

Default header exposed by fabio

Return type: dict

property index

Returns the index of this frame in in it’s container.

Return type: int

next()

Returns the next frame from it’s file container.

Return type: FabioFrame

property shape

class fabio.fabioimage.FabioImage(data=None, header=None)

Bases: _FabioArray

A common object for images in fable

Contains a numpy array (.data) and dict of meta data (.header)

RESERVED_HEADER_KEYS = []

add(other)

Accumulate another fabioimage into the first image.

Warning, does not clip to 16 bit images by default

Parameters: other (FabioImage) – Another image to accumulate.

static check_data(data=None)

Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

Parameters: data – array like
Returns: numpy array or None

static check_header(header=None)

Empty for fabioimage but may be populated by others classes

Parameters: header – dict like object
Returns: Ordered dict

property classname: Retrieves the name of the class :return: the name of the class

close()

classmethod codec_name(): Returns the internal name of the codec

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

property dtype

classmethod factory(name)

A kind of factory… for image_classes

Parameters: name (str) – name of the class to instantiate
Returns: an instance of the class
Return type: fabio.fabioimage.FabioImage

frames()

Iterate all available frames stored in this image container.

Return type: Iterator[FabioFrame]

get_frame(num)

Returns a frame from the this fabio image.

Parameters: num (int) – Number of frames (0 is the first frame)
Return type: FabioFrame
Raises: IndexError – If the frame number is out of the available range.

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

property incomplete_file

Returns true if the readed file is not complete.

Return type: bool

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

next()

Returns the next file in the series as a fabioimage

Raises: IOError – When there is no next file in the series.

property nframes

Returns the number of frames contained in this file

Return type: int

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

Parameters

x_rebin_fact (int) – x binning factor
y_rebin_fact (int) – y binning factor
keep_I (bool) – shall the signal increase ?

save(fname): wrapper for write

property shape

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.fabioimage: alias of FabioImage

`fabio.fabioutils` Module

General purpose utilities functions for fabio

fabio.fabioutils.AVAILABLE_COMPRESSED_EXTENSIONS = {'bz2', 'gz'}: Set of available compressed file extensions. Do not contains extensions for uninstalled optional dependancies.

class fabio.fabioutils.BZ2File(name, mode='r', compresslevel=9)

Bases: BZ2File

Wrapper with lock

getSize()

setSize(value)

property size

class fabio.fabioutils.BytesIO(data, fname=None, mode='r')

Bases: BytesIO

just an interface providing the name and mode property to a BytesIO

BugFix for MacOSX mainly

getSize()

setSize(size)

property size

fabio.fabioutils.COMPRESSED_EXTENSIONS = {'bz2', 'gz'}: Set of compressed file extensions provided by Fabio

class fabio.fabioutils.DebugSemaphore(*arg, **kwarg)

Bases: Semaphore

threading.Semaphore like class with helper for fighting dead-locks

acquire(*arg, **kwarg)

Acquire a semaphore, decrementing the internal counter by one.

When invoked without arguments: if the internal counter is larger than zero on entry, decrement it by one and return immediately. If it is zero on entry, block, waiting until some other thread has called release() to make it larger than zero. This is done with proper interlocking so that if multiple acquire() calls are blocked, release() will wake exactly one of them up. The implementation may pick one at random, so the order in which blocked threads are awakened should not be relied on. There is no return value in this case.

When invoked with blocking set to true, do the same thing as when called without arguments, and return true.

When invoked with blocking set to false, do not block. If a call without an argument would block, return false immediately; otherwise, do the same thing as when called without arguments, and return true.

When invoked with a timeout other than None, it will block for at most timeout seconds. If acquire does not complete successfully in that interval, return false. Return true otherwise.

blocked = []

release(*arg, **kwarg)

Release a semaphore, incrementing the internal counter by one or more.

When the counter is zero on entry and another thread is waiting for it to become larger than zero again, wake up that thread.

write_lock = <threading.Semaphore object>

class fabio.fabioutils.File(name, mode='rb', temporary=False)

Bases: FileIO

wrapper for “file” with locking

close()

Close the file.

A closed file cannot be used for further I/O operations. close() may be called more than once without error.

getSize()

read(size=-1)

Read at most size bytes, returned as bytes.

Only makes one system call, so less data may be returned than requested. In non-blocking mode, returns None if no data is available. Return an empty bytes object at EOF.

setSize(size)

property size

write(readablebuffer)

Write buffer b to file, return number of bytes written.

Only makes one system call, so not all of the data may be written. The number of bytes actually written is returned. In non-blocking mode, returns None if the write would block.

class fabio.fabioutils.FilenameObject(stem=None, num=None, directory=None, format_=None, extension=None, postnum=None, digits=4, filename=None)

Bases: object

The ‘meaning’ of a filename …

deconstruct_filename(filename): Break up a filename to get image type and number

str(): Return a string representation

tostring(): convert yourself to a string

class fabio.fabioutils.GzipFile(filename=None, mode=None, compresslevel=9, fileobj=None)

Bases: GzipFile

Just a wrapper for gzip.GzipFile providing the correct seek capabilities for python 2.5

measure_size()

exception fabio.fabioutils.NotGoodReader

Bases: RuntimeError

The reader used is probably not the good one

class fabio.fabioutils.OrderedDict

Bases: OrderedDict

Ordered dictionary with pretty print

class fabio.fabioutils.UnknownCompressedFile(name, mode='rb', buffering=0)

Bases: File

wrapper for “File” with locking

fabio.fabioutils.construct_filename(filename, frame=None): Try to construct the filename for a given frame

fabio.fabioutils.deconstruct_filename(filename): Function for backward compatibility. Deprecated

fabio.fabioutils.exists(path)

Test whether a path exists.

Replaces os.path.exists and handles in addition “::” based URI as defined in http://odo.pydata.org/en/latest/uri.html#separating-parts-with

Parameters: path – string
Returns: boolean

fabio.fabioutils.extract_filenumber(name): extract file number

fabio.fabioutils.getnum(name): # try to figure out a file number # guess it starts at the back

fabio.fabioutils.isAscii(name, listExcluded=None)

Parameters

name – string to check
listExcluded – list of char or string excluded.

Returns

True of False whether name is pure ascii or not

fabio.fabioutils.jump_filename(name, num, padding=True): jump to number

fabio.fabioutils.next_filename(name, padding=True): increment number

fabio.fabioutils.nice_int(s)

Workaround that int(‘1.0’) raises an exception

Parameters: s – string to be converted to integer

fabio.fabioutils.numstem(name): cant see how to do without reversing strings Match 1 or more digits going backwards from the end of the string

fabio.fabioutils.pad(mystr, pattern=' ', size=80)

Performs the padding of the string to the right size with the right pattern

Parameters

mystr – input string
pattern – the filling pattern
size – the size of the block

Returns

the padded string to a multiple of size

fabio.fabioutils.previous_filename(name, padding=True): decrement number

fabio.fabioutils.toAscii(name, excluded=None)

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

fabio.fabioutils.to_str(s)

`fabio.file_series` 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.file_series.FileSeries(filenames, single_frame=None, fixed_frames=None, fixed_frame_number=None)

Bases: FabioImage

Provide a FabioImage abstracting a file series.

This abstraction provide the set of the filenames as the container of frames.

# Sequencial access through all the frames
with FileSeries(filenames) as serie:
    for frame in serie.frames():
        frame.data
        frame.header
        frame.index                    # index inside the file series
        frame.file_index               # index inside the file (edf, tif)
        frame.file_container.filename  # name of the source file

# Random access to frames
with FileSeries(filenames) as serie:
    frame = serie.get_frame(200)
    frame = serie.get_frame(201)
    frame = serie.get_frame(10)
    frame = serie.get_frame(2)

Files of the series can be set using a list of filenames, an iterator or a generator. It also supports a file series described using filename_series or file_series objects.

# Iterate known files
filenames = ["foo.edf", "bar.tif"]
serie = FileSeries(filenames=filenames)

# Iterate all images from foobar_0001.edf to 0003
filenames = numbered_file_series("foobar_", 1, 3, ".edf", digits=4)
serie = FileSeries(filenames=filenames)

# Iterate all images from foobar_0000.edf to the last consecutive number found
filenames = filename_series("foobar_0000.edf")
serie = FileSeries(filenames=filenames)

Options are provided to optimize a non-sequencial access by providing the amount of frames stored per files. This options (single_frame, fixed_frames and fixed_frame_number) can be used if we know an a priori on the way frames are stored in the files (the exact same amount of frames par file).

# Each files contains a single frame
serie = FileSeries(filenames=filenames, single_frame=True)

# Each files contains a fixed amout of frames.  This value is
# automatically found
serie = FileSeries(filenames=filenames, fixed_frames=True)

# Each files contains 100 frames (the last one could contain less)
serie = FileSeries(filenames=filenames, fixed_frame_number=100)

DEFAULT_EXTENSIONS = []

close(): Close any IO handler openned.

property data

property dtype

frames(): Returns an iterator throug all frames of all filenames of this file series.

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

property header

property nframes

Returns the number of available frames in the full file series.

Return type: int

property shape

use_edf_shortcut: If true a custom file sequencial file reader is used for EDF formats

class fabio.file_series.file_series(list_of_strings)

Bases: list

Represents a series of files to iterate has an idea of a current position to do next and prev

You also get from the list python superclass:: append count extend insert pop remove reverse sort

current(): Current position in a sequence

current_image()

Current image in sequence

Returns: fabioimage

current_object()

Current image in sequence

Returns: file_object

first(): First image in series

first_image()

First image in a sequence

Returns: fabioimage

first_object()

First image in a sequence

Returns: file_object

jump(num): Goto a position in sequence

jump_image(num)

Jump to and read image

Returns: fabioimage

jump_object(num)

Jump to and read image

Returns: file_object

last(): Last in series

last_image()

Last image in a sequence

Returns: fabioimage

last_object()

Last image in a sequence

Returns: file_object

len(): Number of files

next(): Next in a sequence

next_image()

Return the next image

Returns: fabioimage

next_object()

Return the next image

Returns: file_object

previous(): Prev in a sequence

previous_image()

Return the previous image

Returns: fabioimage

previous_object()

Return the previous image

Returns: file_object

class fabio.file_series.filename_series(filename)

Bases: object

Iterator through a list of files indexed by a number.

Supports next, prevous and jump accessors.

Parameters: filename (Union[str,FilenameObject]) – The first filename of the iteration.

current(): return current filename string

current_image(): returns the current image as a fabioimage

current_object(): returns the current filename as a fabio.FilenameObject

jump(num): jump to a specific number

jump_image(num): returns the image number as a fabioimage

jump_object(num): returns the filename num as a fabio.FilenameObject

next(): increment number

next_image(): returns the next image as a fabioimage

next_object(): returns the next filename as a fabio.FilenameObject

prev_image(): returns the previos image as a fabioimage

previous(): decrement number

previous_object(): returns the previous filename as a fabio.FilenameObject

fabio.file_series.new_file_series(first_object, nimages=0, step=1, traceback=False)

A generator function that creates a file series starting from a fabioimage. Iterates through all images in a file (if more than 1), then proceeds to the next file as determined by fabio.next_filename.

Parameters

first_object – the starting fabioimage, which will be the first one yielded in the sequence
nimages – the maximum number of images to consider step: step size, will yield the first and every step’th image until nimages is reached. (e.g. nimages = 5, step = 2 will yield 3 images (0, 2, 4)
traceback – if True causes it to print a traceback in the event as a logging error. Otherwise the exception is logged as a debug message. the exception as it chooses
yields – the next fabioimage in the series. In the event there is an exception, it yields the sys.exec_info for the exception instead. sys.exec_info is a tuple: ( exceptionType, exceptionValue, exceptionTraceback ) from which all the exception information can be obtained.

Suggested usage:

for obj in new_file_series( ... ):
    if not isinstance(obj, fabio.fabioimage.FabioImage):
        # In case of problem (missing images, non readable files, etc)
        # obj contains the result of exc_info
        traceback.print_exception(obj[0], obj[1], obj[2])

fabio.file_series.new_file_series0(first_object, first=None, last=None, step=1): Created from a fabio image first and last are file numbers

class fabio.file_series.numbered_file_series(stem, first, last, extension, digits=4, padding='Y', step=1)

Bases: file_series

mydata0001.edf = “mydata” + 0001 + “.edf” mydata0002.edf = “mydata” + 0002 + “.edf” mydata0003.edf = “mydata” + 0003 + “.edf”

`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 mods for APS GE by JVB

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

fabio.openimage.open_series(filenames=None, first_filename=None, single_frame=None, fixed_frames=None, fixed_frame_number=None)

Create an object to iterate frames through a file series.

This function is a wrapper over FileSeries to facilitate simple uses of file series iterations.

Parameters

filenames (Union[Generator,Iterator,List]) – Ordered list of filenames to process as a file series. It also can be a generator, and iterator, or filename_series or file_series objects.
first_filename (str) – If provided iterate filenames from this filename and try to consecutivelly open next files. If this argument is specified the filenames have to unspecified. Internally it uses filename_series to iterate the filenames.
single_frame (Union[Bool,None]) – If True, all files are supposed to contain only one frame.
fixed_frames (Union[Bool,None]) – If True, all files are supposed to contain the same amount of frames (this fixed amount will be reached from the first file of the serie).
fixed_frame_number (Union[Integer,None]) – If set, all files are supposed to contain the same amount of frames (sepecified by this argument)

Return type

FileSeries

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

fabio.openimage.openimage(filename, frame=None)

Open an image.

It returns a FabioImage-class instance which can be used as a context manager to close the file at the termination.

with fabio.open("image.edf") as i:
    print(i.nframes)
    print(i.data)

Parameters

filename (Union[str,FilenameObject]) – A filename or a filename iterator.
frame (Union[int,None]) – A specific frame inside this file.

Return type

FabioImage

`fabio.adscimage` Module

Compatibility code with ADSC format.

This module is now renamed into fabio.dtrekimage.

`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: 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.

DEFAULT_EXTENSIONS = ['bin']

DESCRIPTION = 'Binary format (none-compressed 2D images)'

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 (str) – file name
dim1 (int) – image dimensions (Fast index)
dim2 (int) – image dimensions (Slow index)
offset (int) – 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): To be overwritten - write the file

fabio.binaryimage.binaryimage: alias of BinaryImage

`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 Sigmund Neher, GWDG, Göttingen, Germany

class fabio.bruker100image.Bruker100Image(data=None, header=None)

Bases: BrukerImage

DEFAULT_EXTENSIONS = ['sfrm']

DESCRIPTION = 'SFRM File format used by Bruker detectors (version 100)'

bpp_to_numpy = {1: <class 'numpy.uint8'>, 2: <class 'numpy.uint16'>, 4: <class 'numpy.int32'>}

gen_header(): Generate headers (with some magic and guesses) format is Bruker100

read(fname, frame=None)

Read the data.

Data is stored in three blocks:

data (uint8 mainly when bpp=1), possibly int32 if bpp=4
overflow1 (2 bytes/value in uint16)
overflow2 (4 bytes/value in int32)
underflow (int8, int16 or int32).

The blocks are zero padded to a multiple of 16 bytes.

version = 100

write(fname): Write a bruker100 format image

fabio.bruker100image.bruker100image: alias of Bruker100Image

fabio.bruker100image.mround(value, multiple=16): Round a value up to the multiple of multiple

`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: 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.

DEFAULT_EXTENSIONS = []

DESCRIPTION = 'File format used by Bruker detectors (version 86)'

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: <class 'numpy.uint8'>, 2: <class 'numpy.uint16'>, 4: <class '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)

gen_overflow(): Generate an overflow table

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

version = 86

write(fname): Write a bruker image

fabio.brukerimage.brukerimage: alias of BrukerImage

`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 = b'--CIF-BINARY-FORMAT-SECTION--'

BLANK = [b' ', b'\t', b'\r', b'\n', b'\r\n', b'\n\r']

DATA = b'data_'

DOT = b'.'

DOUBLE_QUOTE = b'"'

EOL = [b'\r', b'\n', b'\r\n', b'\n\r']

GLOBAL = b'global_'

HASH = b'#'

LOOP = b'loop_'

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

QUESTIONMARK = b'?'

SAVE = b'save_'

SEMICOLUMN = b';'

SINGLE_QUOTE = b"'"

START_COMMENT = (b"'", b'"')

STOP = b'stop_'

UNDERSCORE = 95

exists(sKey)

Check if the key exists in the CIF and is non empty.

Parameters

sKey (str) – CIF key
cif – CIF dictionary

Returns

True if the key exists in the CIF dictionary and is non empty

Return type

boolean

existsInLoop(sKey)

Check if the key exists in the CIF dictionary.

Parameters

sKey (str) – CIF key
cif – CIF dictionary

Returns

True if the key exists in the CIF dictionary and is non empty

Return type

boolean

static isAscii(text)

Check if all characters in a string are ascii,

Parameters: text (str) – 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 (str) – 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

Parameters: _strFilename (str) – the name of the file to open
Returns: None

pop(k[, d]) → v, remove specified key and return the corresponding value.: If key is not found, default is returned if given, otherwise KeyError is raised

popitem(key, default=None)

Remove and return a (key, value) pair as a 2-tuple.

Pairs are returned in LIFO (last-in, first-out) order. Raises KeyError if the dict is empty.

readCIF(_strFilename, _bKeepComment=False)

Load the CIF file and populates the CIF dictionary into the object

Parameters: _strFilename (str) – the name of the file to open
Returns: 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.

Parameters

_strFilename (str) – the name of the filename to be appended in the header of the CIF file.
linesep – default line separation (can be ‘n’ or ‘rn’).

Returns

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

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

Bases: FabioImage

Read the Cif Binary File data format

BINARAY_SECTION = b'--CIF-BINARY-FORMAT-SECTION--'

CIF_BINARY_BLOCK_KEY = '_array_data.data'

DEFAULT_EXTENSIONS = ['cbf']

DESCRIPTION = 'Cif Binary Files format (used by the Pilatus detectors and others)'

PADDING = 512

STARTER = b'\x0c\x1a\x04\xd5'

static checkData(data=None)

read(fname, frame=None, check_MD5=True, only_raw=False)

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

Parameters: fname (str) – name of the file
Returns: fabioimage instance

read_raw_data(infile)

Read and return the raw data chunk

Parameters: infile – opened file at correct position
Returns: raw compressed stream

write(fname): write the file in CBF format :param str fname: name of the file

class fabio.cbfimage.PilatusHeader(content, convention='PILATUS_1.2')

Bases: object

KEYWORDS = {'Alpha': PilatusKey(keyword='Alpha', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Alpha {} deg.'), 'Angle_increment': PilatusKey(keyword='Angle_increment', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Angle_increment {} deg.'), 'Beam_xy': PilatusKey(keyword='Beam_xy', key_index=0, value_indices=[1, 2], types=[<class 'float'>, <class 'float'>], repr='Beam_xy ({}, {}) pixels'), 'Chi': PilatusKey(keyword='Chi', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Chi {} deg.'), 'Chi_increment': PilatusKey(keyword='Chi_increment', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Chi_increment {} deg.'), 'Count_cutoff': PilatusKey(keyword='Count_cutoff', key_index=0, value_indices=[1], types=[<class 'int'>], repr='Count_cutoff {} counts'), 'Detector': PilatusKey(keyword='Detector', key_index=0, value_indices=slice(1, None, None), types=<class 'str'>, repr='Detector: {}'), 'Detector_2theta': PilatusKey(keyword='Detector_2theta', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Detector_2theta {} deg.'), 'Detector_Voffset': PilatusKey(keyword='Detector_Voffset', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Detector_Voffset {} m'), 'Detector_distance': PilatusKey(keyword='Detector_distance', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Detector_distance {} m'), 'Energy_range': PilatusKey(keyword='Energy_range', key_index=0, value_indices=[1, 2], types=[<class 'float'>, <class 'float'>], repr='Energy_range {} {} eV'), 'Excluded_pixels': PilatusKey(keyword='Excluded_pixels', key_index=0, value_indices=[1], types=[<class 'str'>], repr='Excluded_pixels: {}'), 'Exposure_period': PilatusKey(keyword='Exposure_period', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Exposure_period {} s'), 'Exposure_time': PilatusKey(keyword='Exposure_time', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Exposure_time {} s'), 'Filter_transmission': PilatusKey(keyword='Filter_transmission', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Filter_transmission {}'), 'Flat_field': PilatusKey(keyword='Flat_field', key_index=0, value_indices=[1], types=[<class 'str'>], repr='Flat_field: {}'), 'Flux': PilatusKey(keyword='Flux', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Flux {}'), 'Gain_setting': PilatusKey(keyword='Gain_setting', key_index=0, value_indices=[1, 2], types=[<class 'str'>, <class 'str'>], repr='Gain_setting: {} {} (vrf = -0.200)'), 'Image_path': PilatusKey(keyword='Image_path', key_index=0, value_indices=[1], types=[<class 'str'>], repr='Image_path: {}'), 'Kappa': PilatusKey(keyword='Kappa', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Kappa {} deg.'), 'N_excluded_pixels': PilatusKey(keyword='N_excluded_pixels', key_index=0, value_indices=[1], types=[<class 'int'>], repr='N_excluded_pixels = {}'), 'N_oscillations': PilatusKey(keyword=" ('N_oscillations", key_index=0, value_indices=[1], types=[<class 'int'>], repr='N_oscillations {}'), 'Omega': PilatusKey(keyword='Omega', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Omega {} deg.'), 'Omega_increment': PilatusKey(keyword='Omega_increment', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Omega_increment {} deg.'), 'Oscillation_axis': PilatusKey(keyword='Oscillation_axis', key_index=0, value_indices=[1], types=[<class 'str'>], repr='Oscillation_axis {}'), 'Phi': PilatusKey(keyword='Phi', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Phi {} deg.'), 'Phi_increment': PilatusKey(keyword='Phi_increment', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Phi_increment {} deg.'), 'Pixel_size': PilatusKey(keyword='Pixel_size', key_index=0, value_indices=[1, 4], types=[<class 'float'>, <class 'float'>], repr='Pixel_size {} m x {} m'), 'Polarization': PilatusKey(keyword='Polarization', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Polarization {}'), 'Position_increment': PilatusKey(keyword='Position_increment', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Position_increment'), 'Shutter_time': PilatusKey(keyword='Shutter_time', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Shutter_time {} s'), 'Start_angle': PilatusKey(keyword='Start_angle', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Start_angle {} deg.'), 'Start_position': PilatusKey(keyword='Start_position', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Start_position {}'), 'Tau': PilatusKey(keyword='Tau', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Tau = {} s'), 'Threshold_setting': PilatusKey(keyword='Threshold_setting', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Threshold_setting: {} eV'), 'Trim_file': PilatusKey(keyword='Trim_file', key_index=0, value_indices=[1], types=[<class 'str'>], repr='Trim_file: {}'), 'Wavelength': PilatusKey(keyword='Wavelength', key_index=0, value_indices=[1], types=[<class 'float'>], repr='Wavelength {} A'), 'sensor': PilatusKey(keyword='sensor', key_index=1, value_indices=[0, 3], types=[<class 'str'>, <class 'float'>], repr='{} sensor, thickness {} m')}

SPACE_LIKE = '()#:=,'

classmethod clean_string(input_string)

class fabio.cbfimage.PilatusKey(keyword, key_index, value_indices, types, repr)

Bases: NamedTuple

key_index: int: Alias for field number 1

keyword: str: Alias for field number 0

repr: str: Alias for field number 4

types: list: Alias for field number 3

value_indices: list: Alias for field number 2

fabio.cbfimage.cbfimage: alias of CbfImage

`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: FabioImage

Read and try to write the dm3 data format

DEFAULT_EXTENSIONS = ['dm3']

DESCRIPTION = 'Digital Micrograph DM3 file format'

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

read_data()

read_tag_entry()

read_tag_group()

read_tag_type()

readbytes(bytes_to_read, format, swap=True)

fabio.dm3image.dm3image: alias of Dm3Image

`fabio.dtrekimage` 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.dtrekimage.DtrekImage(*args, **kwargs)

Bases: FabioImage

Read an image using the d*TREK format.

This format is used to process X-ray diffraction data from area detectors. It supports processing of data from multiple detector types (imaging plates, CCDs and pixel arrays) and from multiple vendors (Rigaku, Mar, Dectris, Bruker and ADSC).

Rigaku providing a specification.

DEFAULT_EXTENSIONS = ['img']

DESCRIPTION = 'D*trek format (Rigaku specification 1.1)'

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

swap_needed(check=True)

Returns True if the header does not use the same endianness than the system.

Return type: bool

write(fname): Write d*TREK format

`fabio.edfimage` Module

License: MIT

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.EdfFrame(data=None, header=None, number=None)

Bases: FabioFrame

A class representing a single frame in an EDF file

bfname: If set, the data must be read from this file and not from the blob The external file must be located in the same folder as the edf data file. It must be different from the edf data file.

bfstart: Start position of the raw data in the external file.

blobsize: Size of the raw data blob in the file (including padding)

property data

Returns the data after unpacking it if needed.

Returns: dataset as numpy.ndarray

file: Opened file object with locking capabilities

getData()

Returns the data after unpacking it if needed.

Returns: dataset as numpy.ndarray

getEdfBlock(force_type=None, fit2dMode=False)

static get_data_counts(shape=None)

Counts items specified by shape (returns 1 for shape==None)

Param: tuple shape
Returns: int counts

static get_data_rank(header=None, capsHeader=None)

Get the rank of the data array by searching the header for the key DIM_i with the highest index i. The smallest index of DIM_i is 1 (1-based). The highest index is equal to the rank.

Param: dict header
Param: dict capsHeader (optional)
Returns: int rank

static get_data_shape(rank=0, header=None, capsHeader=None)

Returns a tuple with the number of dimensions up to the given rank. The dimensions DIM_i are read from the header dictionary. The values of missing DIM_i keys are set to 1, except DIM_1 which has the default 0.

The DIM_i header indices are 1-based and are equal to the number of elements in each dimension of a data array, starting with DIM_1 as the number of elements of a linear array, DIM_2 is the number of stacked linear arrays with DIM_1 elements, etc. (FORTRAN-type indexing).

The shape tuple is filled from the end to the beginning with the values of DIM_i, i.e. shape[0] is equal to value of DIM_rank, shape[rank-i] is equal to the value of DIM_i (e.g. for rank==2, shape[0]==value(DIM_2), shape[1]==value(DIM_1)). The returned shape tuple can be used with numpy arrays.

Param: int rank
Param: dict header
Param: dict capsHeader (optional)
Returns: tuple shape

get_edf_block(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

property iFrame: Returns the frame index of this frame

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

size: Size of the retrieved data (after unpacking and decompressing)

start: Start position of the raw data blob in the file

swap_needed(): Decide if we need to byteswap

class fabio.edfimage.EdfImage(data=None, header=None, frames=None, generalframe=None)

Bases: FabioImage

Read and try to write the ESRF edf data format

DEFAULT_EXTENSIONS = ['edf', 'cor']

DESCRIPTION = 'European Synchrotron Radiation Facility data format'

RESERVED_HEADER_KEYS = ['HEADERID', 'IMAGE', 'BYTEORDER', 'DATATYPE', 'DIM_1', 'DIM_2', 'DIM_3', 'SIZE']

appendFrame(frame=None, data=None, header=None)

append_frame(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

property bpp: Getter for bpp: data superseeds _bpp

property bytecode: Getter for bpp: data superseeds _bytecode

static check_header(header=None): Empty for FabioImage but may be populated by other classes

property data

delData(): deleter for edf Data

delHeader(): Deleter for edf header

deleteFrame(frameNb=None)

delete_frame(frameNb=None): Method used to remove a frame from an EDF image. by default the last one is removed. :param int frameNb: frame number to remove, by default the last.

property dim1

property dim2

property dims

property dtype

fastReadData(filename)

fastReadROI(filename, coords=None)

fast_read_data(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

fast_read_roi(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()

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,

getNbFrames(): Getter for number of frames

getframe(num): returns the file numbered ‘num’ in the series as a FabioImage

property header

property incomplete_data

property incomplete_file

Returns true if the file is not complete.

Return type: bool

isIncompleteData()

classmethod lazy_iterator(filename)

Iterates over the frames of an EDF multi-frame file.

This function optimizes sequential access to multi-frame EDF files by avoiding to read the whole file at first in order to get the number of frames and build an index of frames for faster random access.

Usage:

>>> from fabio.edfimage import EdfImage

>>> for frame in EdfImage.lazy_iterator("multiframe.edf"):
...     print('Header:', frame.header)
...     print('Data:', frame.data)

Parameters: filename (str) – File name of the EDF file to read
Yield: frames one after the other

next()

Returns the next file in the series as a fabioimage

Raises: IOError – When there is no next file or image in the series.

property nframes

Returns the number of frames contained in this file

Return type: int

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=None, _iVal=None)

setByteCode(iVal=None, _iVal=None)

setData(_data=None): Enforces the propagation of the data to the list of frames :param data: numpy array representing data

setDim1(_iVal=None)

setDim2(_iVal=None)

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

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

property shape

swap_needed()

Decide if we need to byteswap

Returns: 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”

fabio.edfimage.Frame: Compatibility code with fabio <= 0.8

class fabio.edfimage.HeaderBlockType(header, header_size, binary_size, data_format_version)

Bases: tuple

binary_size: Alias for field number 2

data_format_version: Alias for field number 3

header: Alias for field number 0

header_size: Alias for field number 1

exception fabio.edfimage.MalformedHeaderError

Bases: OSError

Raised when a header is malformed

fabio.edfimage.edfimage: alias of EdfImage

`fabio.eigerimage` Module

Eiger data/master file reader for FabIO

Eiger data files are HDF5 files with one group called “entry” and a dataset called “data” in it (now in a data group).

Those dataset are usually compressed using LZ4 and/or bitshuffle compression:

H5py (>2.5) and libhdf5 (>1.8.10) with the corresponding compression plugin are needed to actually read the data. Under windows, those plugins can easily be installed via this repository: https://github.com/silx-kit/hdf5plugin

class fabio.eigerimage.EigerImage(data=None, header=None)

Bases: FabioImage

FabIO image class for Images from Eiger data files (HDF5)

DEFAULT_EXTENSIONS = ['h5', 'hdf5']

DESCRIPTION = 'Eiger data files based on HDF5'

close()

property data

get_data()

getframe(num): returns the frame numbered ‘num’ in the stack if applicable

next()

Returns the next file in the series as a fabioimage

Raises: IOError – When there is no next file or image in the series.

property nframes

Returns the number of frames contained in this file

Return type: int

previous(): returns the previous file in the series as a FabioImage

read(fname, frame=None)

Try to read image

Parameters

fname – name of the file
frame – number of the frame

set_data(data, index=None)

Set the data for frame index

Parameters

data – numpy array
index (int) – index of the frame (by default: current one)

Raises

IndexError – If the frame number is out of the available range.

write(fname): try to write image :param fname: name of the file

fabio.eigerimage.eigerimage: alias of EigerImage

`fabio.fit2dimage` Module

FabIO reader for Fit2D binary images

TODO: handle big-endian files

class fabio.fit2dimage.Fit2dImage(*arg, **kwargs)

Bases: FabioImage

FabIO image class for Images for XXX detector

BUFFER_SIZE = 512

DEFAULT_EXTENSIONS = ['f2d']

DESCRIPTION = 'Fit2d file format'

ENC = 'ascii'

PIXELS_PER_CHUNK = 128

read(fname, frame=None)

try to read image

Parameters: fname – name of the file

fabio.fit2dimage.fit2dimage: alias of Fit2dImage

fabio.fit2dimage.hex_to(stg, type_='int')

convert a 8-byte-long string (bytes) into an int or a float

Parameters

stg – bytes string
type (str) – “int” or “float”

`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: FabioImage

Read and try to write Andy Hammersley’s mask format

DEFAULT_EXTENSIONS = ['msk']

DESCRIPTION = 'Fit2d mask file format'

static check_data(data=None)

Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

Parameters: data – array like
Returns: numpy array or 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.fit2dmaskimage.fit2dmaskimage: alias of Fit2dMaskImage

`fabio.fit2dspreadsheetimage` Module

Read the fit2d ascii image output

Jon Wright, ESRF

class fabio.fit2dspreadsheetimage.Fit2dSpreadsheetImage(data=None, header=None)

Bases: FabioImage

Read a fit2d ascii format

DEFAULT_EXTENSIONS = ['spr']

DESCRIPTION = 'Fit2d spreadsheet ascii file format'

read(fname, frame=None)

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

fabio.fit2dspreadsheetimage.fit2dspreadsheetimage: alias of Fit2dSpreadsheetImage

`fabio.GEimage` Module

Reads the header from a GE a-Si Angio Detector using version 8001 of the header from file:

c:adeptcoreDefaultImageInfoConfig.csv

fabio.GEimage.GEimage: alias of GeImage

class fabio.GEimage.GeImage(data=None, header=None)

Bases: FabioImage

GE a-Si Angio detector file format.

BITDEPTH_TO_DATATYPES = {8: <class 'numpy.uint8'>, 16: <class 'numpy.uint16'>, 32: <class 'numpy.uint32'>}

BLANKED_HEADER_METADATA = {'ImageDepthInBits': 16, 'NumberOfColsInFrame': 2048, 'NumberOfRowsInFrame': 2048, 'StandardHeaderSizeInBytes': 8192, 'UserHeaderSizeInBytes': 0}

BLANK_IMAGE_FORMAT = b'\x00\x00\x00\x00\x00\x00\x00\x00\x00\x00': At APS they blanked the header with 8192 bytes of zeros when updating the GE firmware. This happened in ~2018 to the best of my knowledge, and a lot of data has been measured with the GE detectors that are missing the magic bytes and header.

DEFAULT_EXTENSIONS = []

DESCRIPTION = 'GE a-Si Angio detector file format'

getframe(num): Return 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 header into self.header and the data into self.data.

`fabio.hdf5image` Module

HDF5 image for FabIO

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

Specifications: input should being the form:

filename::path

Only supports ndim=2 or 3 (exposed as a stack of images

class fabio.hdf5image.Hdf5Frame(hdf5image, frame_num)

Bases: FabioFrame

Identify a slice of dataset from an HDF5 file

class fabio.hdf5image.Hdf5Image(*arg, **kwargs)

Bases: FabioImage

FabIO image class for Images from an HDF file

filename::dataset

DEFAULT_EXTENSIONS = ['h5']

DESCRIPTION = 'Hierarchical Data Format HDF5 flat reader'

close()

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: filename::datasetpath

fabio.hdf5image.hdf5image: alias of Hdf5Image

`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

fabio.HiPiCimage.HiPiCimage: alias of HipicImage

class fabio.HiPiCimage.HipicImage(data=None, header=None)

Bases: FabioImage

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

DEFAULT_EXTENSIONS = ['img']

DESCRIPTION = 'HiPic file format from Hamamatsu CCD cameras'

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: FabioImage

Read the Nonius kcd data format

DEFAULT_EXTENSIONS = ['kcd']

DESCRIPTION = "KCD file format from Nonius's KappaCCD diffractometer"

static checkData(data=None)

read(fname, frame=None)

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

fabio.kcdimage.kcdimage: alias of KcdImage

`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: FabioImage

DEFAULT_EXTENSIONS = ['mar2300', 'mar1200', 'mar1600', 'mar2000', 'mar3450', 'mar3000', 'mar2400', 'mar1800']

DESCRIPTION = 'File format from Mar345 imaging plate and Mar555 flat panel'

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. It uses a MIT implementation of the CCP4 (LGPL) PCK1 algo from JPA

fabio.mar345image.mar345image: alias of Mar345Image

`fabio.mrcimage` Module

MRC image for FabIO

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

Specifications from: http://ami.scripps.edu/software/mrctools/mrc_specification.php New version on: https://www.ccpem.ac.uk/mrc_format/mrc_format.php https://www.fei-software-center.com/tem-apps/MRC-2014-Specifications/

class fabio.mrcimage.MrcImage(data=None, header=None)

Bases: FabioImage

FabIO image class for Images from a mrc image stack

DEFAULT_EXTENSIONS = ['mrc', 'map', 'fei']

DESCRIPTION = 'Medical Research Council file format for 3D electron density and 2D images'

KEYS = ('NX', 'NY', 'NZ', 'MODE', 'NXSTART', 'NYSTART', 'NZSTART', 'MX', 'MY', 'MZ', 'CELL_A', 'CELL_B', 'CELL_C', 'CELL_ALPHA', 'CELL_BETA', 'CELL_GAMMA', 'MAPC', 'MAPR', 'MAPS', 'DMIN', 'DMAX', 'DMEAN', 'ISPG', 'NSYMBT', 'EXTRA', 'ORIGIN', 'MAP', 'MACHST', 'RMS', 'NLABL')

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 :param frame:

fabio.mrcimage.mrcimage: alias of MrcImage

`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?)

class fabio.marccdimage.MarccdImage(*args, **kwds)

Bases: TifImage

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

DEFAULT_EXTENSIONS = ['mccd']

DESCRIPTION = 'File format from MarCCD and MarMosaic images'

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

fabio.marccdimage.marccdimage: alias of MarccdImage

`fabio.numpyimage` Module

Generic numpy file reader for FabIO

class fabio.numpyimage.NumpyImage(data=None, header=None)

Bases: FabioImage

FabIO image class for Images for numpy array dumps

Source: http://docs.scipy.org/doc/numpy/neps/npy-format.html

Format Specification: Version 1.0:

The first 6 bytes are a magic string: exactly “x93NUMPY”.

The next 1 byte is an unsigned byte: the major version number of the file
format, e.g. x01.

The next 1 byte is an unsigned byte: the minor version number of the file
format, e.g. x00.
Note: the version of the file format is not tied to the version of the numpy
package.

The next 2 bytes form a little-endian unsigned short int: the length of the
header data HEADER_LEN.

The next HEADER_LEN bytes form the header data describing the array’s
format. It is an ASCII string which contains a Python literal expression of
a dictionary. It is terminated by a newline (‘n’) and padded with
spaces (‘x20’) to make the total length of the magic string + 4 + HEADER_LEN
be evenly divisible by 16 for alignment purposes.

The dictionary contains three keys:

    “descr” : dtype.descr
        An object that can be passed as an argument to the numpy.dtype()
        constructor to create the array’s dtype.
    “fortran_order” : bool
        Whether the array data is Fortran-contiguous or not.
        Since Fortran-contiguous arrays are a common form of
        non-C-contiguity, we allow them to be written directly
        to disk for efficiency.
    “shape” : tuple of int
        The shape of the array.

For repeatability and readability, this dictionary is formatted using
pprint.pformat() so the keys are in alphabetic order.

Following the header comes the array data. If the dtype contains Python
objects (i.e. dtype.hasobject is True), then the data is a Python pickle of
the array. Otherwise the data is the contiguous (either C- or Fortran-,
depending on fortran_order) bytes of the array. Consumers can figure out the
number of bytes by multiplying the number of elements given by the shape
(noting that shape=() means there is 1 element) by dtype.itemsize.

Format Specification: Version 2.0:

The version 1.0 format only allowed the array header to have a total size of
65535 bytes. This can be exceeded by structured arrays with a large number
of columns. The version 2.0 format extends the header size to 4 GiB.
numpy.save will automatically save in 2.0 format if the data requires it,
else it will always use the more compatible 1.0 format.

The description of the fourth element of the header therefore has become:

The next 4 bytes form a little-endian unsigned int: the length of the
header data HEADER_LEN.

DEFAULT_EXTENSIONS = ['npy']

DESCRIPTION = 'Numpy array file format'

getframe(num): returns the frame numbered ‘num’ in the stack if applicable

next(): returns the next frame in the series as a fabioimage

previous(): returns the previous frame in the series as a fabioimage

read(fname, frame=None)

Try to read image

Parameters: fname – name of the file

slice_dataset(frame=None)

write(fname)

Try to write image

Parameters: fname – name of the file

fabio.numpyimage.numpyimage: alias of NumpyImage

`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)

fabio.OXDimage.OXDimage: alias of OxdImage

class fabio.OXDimage.OxdImage(data=None, header=None)

Bases: FabioImage

Oxford Diffraction Sapphire 3 images reader/writer class

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

DEFAULT_EXTENSIONS = ['img']

DESCRIPTION = 'Oxford Diffraction Sapphire 3 file format'

static checkData(data=None)

dec_TY5(stream)

Attempt to decode TY5 compression scheme

Parameters: stream – input stream
Returns: 1D array with data

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

class fabio.pilatusimage.PilatusImage(*args, **kwds)

Bases: TifImage

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

DEFAULT_EXTENSIONS = ['tif', 'tiff']

DESCRIPTION = 'Pilatus file format based on Tiff'

class fabio.pilatusimage.PilatusTiffFrame(data, tiff_header, pilatus_header)

Bases: TiffFrame

Frame container for TIFF format generated by a Pilatus detector

fabio.pilatusimage.pilatusimage: alias of PilatusImage

`fabio.pixiimage` Module

File format to read images from PiXIrad PCDs manufactured by Pixirad Imaging Counters SRL (http://www.pixirad.com/)

Author: Jon Wright, ESRF.

class fabio.pixiimage.PixiImage(data=None, header=None)

Bases: FabioImage

DEFAULT_EXTENSIONS = []

DESCRIPTION = 'Pixi file format'

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): To be overridden - fill in self.header and self.data

fabio.pixiimage.pixiimage: alias of PixiImage

`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: MIT

class fabio.pnmimage.PnmImage(*arg, **kwargs)

Bases: FabioImage

DEFAULT_EXTENSIONS = ['pnm', 'pgm', 'pbm']

DESCRIPTION = 'PNM file format'

P1dec(buf, bytecode)

P2dec(buf, bytecode)

P3dec(buf, bytecode)

P4dec(buf, bytecode)

P5dec(buf, bytecode)

P6dec(buf, bytecode)

P7dec(buf, bytecode)

static check_data(data=None)

Empty for fabioimage but may be populated by others classes, especially for format accepting only integers

Parameters: data – array like
Returns: numpy array or 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(fname): try to write image. For now, limited to :param fname: name of the file

fabio.pnmimage.pnmimage: alias of PnmImage

`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: 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.

DEFAULT_EXTENSIONS = ['img']

DESCRIPTION = 'Rigaku RAXIS file format'

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.raxisimage.raxisimage: alias of RaxisImage

`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)

class fabio.tifimage.TifImage(*args, **kwds)

Bases: FabioImage

Images in TIF format Wraps TiffIO

DEFAULT_EXTENSIONS = ['tif', 'tiff']

DESCRIPTION = 'Tagged image file format'

close()

getframe(num)

Returns the frame num.

This frame is not cached on the image structure.

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

write(fname)

Overrides the FabioImage.write method and provides a simple TIFF image writer.

Parameters: fname (str) – name of the file to save the image to

class fabio.tifimage.TiffFrame(data, tiff_header)

Bases: FabioFrame

Frame container for TIFF format

fabio.tifimage.tifimage: alias of TifImage

`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: FabioImage

Read the XSDataImage XML File data format

DEFAULT_EXTENSIONS = ['xml', 'xsd']

DESCRIPTION = 'XSDataImage XML file format'

read(fname, frame=None)

fabio.xsdimage.xsdimage: alias of XsdImage

`fabio.compression` Module

`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…

Parameters

inp (str) – input format (like “cbfimage”)
outp (str) – output format (like “cbfimage”)
data (numpy.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

Parameters

inp (str) – input format (like “cbfimage”)
outp (str) – output format (like “cbfimage”)
header (dict) – the actual set of headers to be transformed

`fabio.datIO` 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, ESRF

class fabio.datIO.columnfile(data=None, clabels=None, rlabels=None, fname=None)

Bases: fabiodata

Concrete fabiodata class

read(fname, frame=None): To be overridden by format specific subclasses

class fabio.datIO.fabiodata(data=None, clabels=None, rlabels=None, fname=None)

Bases: object

A common class for dataIO in fable Contains a 2d numpy array for keeping data, and two lists (clabels and rlabels) containing labels for columns and rows respectively

read(fname=None, frame=None): To be overridden by format specific subclasses

`fabio.TiffIO` Module

class fabio.TiffIO.TiffIO(filename, mode=None, cache_length=20, mono_output=False)

Bases: object

close()

getData(nImage, **kw)

getImage(nImage)

getImageFileDirectories(fd=None)

getInfo(nImage, **kw)

getNumberOfImages()

writeImage(image0, info=None, software=None, date=None)

`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=<class '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

FabIO Package

fabio Package

fabio.fabioimage Module

fabio.fabioutils Module

fabio.file_series Module

Authors:

fabio.openimage Module

fabio.adscimage Module

fabio.binaryimage Module

fabio.bruker100image Module

fabio.brukerimage Module

fabio.cbfimage Module

fabio.dm3image Module

fabio.dtrekimage Module

fabio.edfimage Module

Authors:

fabio.eigerimage Module

fabio.fit2dimage Module

fabio.fit2dmaskimage Module

fabio.fit2dspreadsheetimage Module

fabio.GEimage Module

fabio.hdf5image Module

fabio.HiPiCimage Module

fabio.kcdimage Module

fabio.mar345image Module

Authors:

fabio.mrcimage Module

fabio.marccdimage Module

Authors:

fabio.numpyimage Module

fabio.OXDimage Module

Authors:

fabio.pilatusimage Module

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.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.dtrekimage` Module

`fabio.edfimage` Module

`fabio.eigerimage` Module

`fabio.fit2dimage` Module

`fabio.fit2dmaskimage` Module

`fabio.fit2dspreadsheetimage` Module

`fabio.GEimage` Module

`fabio.hdf5image` Module

`fabio.HiPiCimage` Module

`fabio.kcdimage` Module

`fabio.mar345image` Module

`fabio.mrcimage` Module

`fabio.marccdimage` Module

`fabio.numpyimage` 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.TiffIO` Module

`fabio.readbytestream` Module