# FabIO Package

## `fabio` Package

FabIO module

`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.``benchmarks`()

  Run the benchmarks

`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: `fabio.fabioimage._FabioArray`

  Identify a frame

  `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

  `dtype`
  `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

  `file_index`

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

    Return type: | int

  `header`

    Default header exposed by fabio

    Return type: | dict

  `index`

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

    Return type: | int

  `shape`

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

  Bases: `fabio.fabioimage._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

  `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

  `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

  `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.

  `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

  `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 `fabio.fabioimage.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', buffering=0, compresslevel=9)

  Bases: `bz2.BZ2File`

  Wrapper with lock

  `getSize`()
  `setSize`(value)
  `size`

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

  Bases: `_io.BytesIO`

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

  BugFix for MacOSX mainly

  `getSize`()
  `setSize`(size)
  `size`

`fabio.fabioutils.``COMPRESSED_EXTENSIONS` = {'bz2', 'gz'}

  Set of compressed file extensions provided by Fabio

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

  Bases: `threading.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.

    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', buffering=0, temporary=False)

  Bases: `_io.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`()
  `setSize`(size)
  `size`

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: `gzip.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: `collections.OrderedDict`

  Ordered dictionary with pretty print

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

  Bases: `fabio.fabioutils.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: `fabio.fabioimage.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.

  `data`
  `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

  `header`
  `nframes`

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

    Return type: | int

  `shape`
  `use_edf_shortcut` = None

    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: `fabio.file_series.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

`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: `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.

  `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 `fabio.binaryimage.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: `fabio.brukerimage.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

  `gen_overflow`()

    Generate an overflow table, including the underflow, marked as 65535 .

  `gen_underflow100`()

    Generate an underflow table

  `overflows_one_byte`()

    Generate one-byte overflow table

  `overflows_two_byte`()

    Generate two byte overflow table

  `read`(fname, frame=None)

    Read the data.

    Data is stored in three blocks:

    - data (uint8)
    - overflow (uint32)
    - underflow (int32).

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

  `underflows`()

    Generate underflow table

  `version` = 100
  `write`(fname)

    Write a bruker image

`fabio.bruker100image.``bruker100image`

  alias of `fabio.bruker100image.Bruker100Image`

## `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.

  `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 `fabio.brukerimage.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_'
  `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` = 63
  `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, d 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: `fabio.fabioimage.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 are correct position
    Returns: | raw compressed stream

  `write`(fname)

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

`fabio.cbfimage.``cbfimage`

  alias of `fabio.cbfimage.CbfImage`

## `fabio.dm3image` Module

class `fabio.dm3image.``Dm3Image`(*args, **kwargs)

  Bases: `fabio.fabioimage.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 `fabio.dm3image.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: `fabio.fabioimage.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

class `fabio.edfimage.``EdfFrame`(data=None, header=None, number=None)

  Bases: `fabio.fabioimage.FabioFrame`

  A class representing a single frame in an EDF file

  `data`

    Returns the data after unpacking it if needed.

    Returns: | dataset as numpy.ndarray

  `file` = None

    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)
  `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

  `iFrame`

    Returns the frame index of this frame

  `parseheader`(block)

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

    Parameters: | block (str) – string representing the header block.
    Returns: | size of the binary blob

  `setData`(npa=None)

    Setter for data in edf frame

  `size` = None

    Size of raw data block in file (including padding)

  `start` = None

    Position of start of raw data in file

  `swap_needed`()

    Decide if we need to byteswap

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

  Bases: `fabio.fabioimage.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

  `bpp`

    Getter for bpp: data superseeds _bpp

  `bytecode`

    Getter for bpp: data superseeds _bytecode

  static `check_header`(header=None)

    Empty for FabioImage but may be populated by others classes

  `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.

  `dim1`
  `dim2`
  `dims`
  `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

  `header`
  `incomplete_data`
  `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.

  `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

  `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

  alias of `fabio.edfimage.EdfFrame`

exception `fabio.edfimage.``MalformedHeaderError`

  Bases: `OSError`

  Raised when a header is malformed

`fabio.edfimage.``edfimage`

  alias of `fabio.edfimage.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:

- https://github.com/nexusformat/HDF5-External-Filter-Plugins/tree/master/LZ4
- https://github.com/kiyo-masui/bitshuffle

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: `fabio.fabioimage.FabioImage`

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

  `DEFAULT_EXTENSIONS` = ['h5']
  `DESCRIPTION` = 'Eiger data files based on HDF5'
  `close`()
  `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 :param fname: name of the file

  `write`(fname)

    try to write image :param fname: name of the file

`fabio.eigerimage.``eigerimage`

  alias of `fabio.eigerimage.EigerImage`

## `fabio.fit2dimage` Module

FabIO reader for Fit2D binary images

TODO: handle big-endian files

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

  Bases: `fabio.fabioimage.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 `fabio.fit2dimage.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: `fabio.fabioimage.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 `fabio.fit2dmaskimage.Fit2dMaskImage`

## `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

  `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 `fabio.fit2dspreadsheetimage.Fit2dSpreadsheetImage`

## `fabio.GEimage` Module

`fabio.GEimage.``GEimage`

  alias of `fabio.GEimage.GeImage`

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

  Bases: `fabio.fabioimage.FabioImage`

  `DEFAULT_EXTENSIONS` = []
  `DESCRIPTION` = 'GE a-Si Angio detector 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)

    Read in 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: `fabio.fabioimage.FabioFrame`

  Identify a slice of dataset from an HDF5 file

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

  Bases: `fabio.fabioimage.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 `fabio.hdf5image.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 `fabio.HiPiCimage.HipicImage`

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

  Bases: `fabio.fabioimage.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: `fabio.fabioimage.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 `fabio.kcdimage.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: `fabio.fabioimage.FabioImage`

  `DEFAULT_EXTENSIONS` = ['mar2300']
  `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 `fabio.mar345image.Mar345Image`

## `fabio.mrcimage` Module

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

  Bases: `fabio.fabioimage.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 `fabio.mrcimage.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: `fabio.tifimage.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 `fabio.marccdimage.MarccdImage`

## `fabio.numpyimage` Module

Generic numpy file reader for FabIO

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

  Bases: `fabio.fabioimage.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 `fabio.numpyimage.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 `fabio.OXDimage.OxdImage`

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 ?

  `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: `fabio.tifimage.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: `fabio.tifimage.TiffFrame`

  Frame container for TIFF format generated by a Pilatus detector

`fabio.pilatusimage.``pilatusimage`

  alias of `fabio.pilatusimage.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: `fabio.fabioimage.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 `fabio.pixiimage.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: `fabio.fabioimage.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 `fabio.pnmimage.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: `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.

  `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 `fabio.raxisimage.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: `fabio.fabioimage.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: `fabio.fabioimage.FabioFrame`

  Frame container for TIFF format

`fabio.tifimage.``tifimage`

  alias of `fabio.tifimage.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: `fabio.fabioimage.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 `fabio.xsdimage.XsdImage`

## `fabio.compression` Module

Compression and decompression algorithm for various formats

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

class `fabio.compression.``ExternalCompressors`

  Bases: `object`

  Class to handle lazy discovery of external compression programs

  `COMMANDS` = (('.bz2', ['bzip2-dcf']), ('.gz', ['gzip', '-dcf']))

`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_cython`(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, dtype='int64')
  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, dtype='int64')
  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, dtype='int64')
  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 system or from Python

  Parameters: | stream – compressed data
  Returns: | uncompressed stream

`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)

  Returns: | 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.``is_incomplete_gz_block_exception`(exception)

  True if the exception looks to be generated when a GZ block is incomplete.

  Return type: | bool

`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…

  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: `fabio.datIO.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