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# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# Permission is hereby granted, free of charge, to any person obtaining a copy
# of this software and associated documentation files (the "Software"), to deal
# in the Software without restriction, including without limitation the rights
# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
# copies of the Software, and to permit persons to whom the Software is
# furnished to do so, subject to the following conditions:
#
# The above copyright notice and this permission notice shall be included in
# all copies or substantial portions of the Software.
#
# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
# THE SOFTWARE.
#
"""
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
"""
import logging
import sys
import os.path
import collections
logger = logging.getLogger(__name__)
import fabio
from .fabioutils import FilenameObject, next_filename
from .openimage import openimage
from .fabioimage import FabioImage
from .utils import deprecation
def new_file_series0(first_object, first=None, last=None, step=1):
"""
Created from a fabio image
first and last are file numbers
"""
im = first_object
nimages = 0
# for counting images
if None in (first, last):
step = 0
total = 1
else:
total = last - first
yield im
while nimages < total:
nimages += step
try:
newim = im.next()
im = newim
except Exception as error:
# Skip bad images
logger.warning("Got a problem here: %s", error)
logger.debug("Backtrace", exc_info=True)
try:
im.filename = next_filename(im.filename)
except Exception as error:
# KE: This will not work and will throw an exception
# fabio.next_filename doesn't understand %nnnn on the end
logger.warning("Got another problem here: %s", error)
im.filename = next_filename(im.sequencefilename)
yield None
yield im
def 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.
:param first_object: the starting fabioimage, which will be the first one yielded
in the sequence
:param 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)
:param 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
:param 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:
.. code-block:: python
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])
"""
im = first_object
nprocessed = 0
abort = False
if nimages > 0:
yield im
nprocessed += 1
while nprocessed < nimages:
try:
newim = im.next()
im = newim
retVal = im
except Exception as ex:
retVal = sys.exc_info()
# Skip bad images
logger.warning("Got a problem here: next() failed %s", ex)
if(traceback):
logger.error("Backtrace", exc_info=True)
else:
logger.debug("Backtrace", exc_info=True)
# Skip bad images
try:
im.filename = next_filename(im.filename)
except Exception as ex:
logger.warning("Got another problem here: next_filename(im.filename) %s", ex)
if nprocessed % step == 0:
yield retVal
# Avoid cyclic references with exc_info ?
retVal = None
if abort:
break
nprocessed += 1
class file_series(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
"""
def __init__(self, list_of_strings):
"""
Constructor:
:param list_of_strings: arg should be a list of strings which are filenames
"""
super(file_series, self).__init__(list_of_strings)
# track current position in list
self._current = 0
# methods which return a filename
def first(self):
"""
First image in series
"""
return self[0]
def last(self):
"""
Last in series
"""
return self[-1]
def previous(self):
"""
Prev in a sequence
"""
self._current -= 1
return self[self._current]
def current(self):
"""Current position in a sequence
"""
return self[self._current]
def next(self):
"""
Next in a sequence
"""
self._current += 1
return self[self._current]
def jump(self, num):
"""
Goto a position in sequence
"""
assert num < len(self) and num >= 0, "num out of range"
self._current = num
return self[self._current]
def len(self):
"""
Number of files
"""
return len(self)
# Methods which return a fabioimage
def first_image(self):
"""
First image in a sequence
:return: fabioimage
"""
return openimage(self.first())
def last_image(self):
"""
Last image in a sequence
:return: fabioimage
"""
return openimage(self.last())
def next_image(self):
"""
Return the next image
:return: fabioimage
"""
return openimage(self.next())
def previous_image(self):
"""
Return the previous image
:return: fabioimage
"""
return openimage(self.previous())
def jump_image(self, num):
"""
Jump to and read image
:return: fabioimage
"""
return openimage(self.jump(num))
def current_image(self):
"""
Current image in sequence
:return: fabioimage
"""
return openimage(self.current())
# methods which return a file_object
def first_object(self):
"""
First image in a sequence
:return: file_object
"""
return FilenameObject(self.first())
def last_object(self):
"""
Last image in a sequence
:return: file_object
"""
return FilenameObject(self.last())
def next_object(self):
"""
Return the next image
:return: file_object
"""
return FilenameObject(self.next())
def previous_object(self):
"""
Return the previous image
:return: file_object
"""
return FilenameObject(self.previous())
def jump_object(self, num):
"""
Jump to and read image
:return: file_object
"""
return FilenameObject(self.jump(num))
def current_object(self):
"""
Current image in sequence
:return: file_object
"""
return FilenameObject(self.current())
class numbered_file_series(file_series):
"""
mydata0001.edf = "mydata" + 0001 + ".edf"
mydata0002.edf = "mydata" + 0002 + ".edf"
mydata0003.edf = "mydata" + 0003 + ".edf"
"""
def __init__(self, stem, first, last, extension,
digits=4, padding='Y', step=1):
"""
Constructor
:param stem: first part of the name
:param step: in case of every nth file
:param padding: possibility for specifying that numbers are not padded with zeroes up to digits
"""
if padding == 'Y':
fmt = "%s%0" + str(digits) + "d%s"
else:
fmt = "%s%i%s"
strings = [fmt % (stem, i, extension) for i in range(first, last + 1, step)]
super(numbered_file_series, self).__init__(strings)
class filename_series(object):
"""Iterator through a list of files indexed by a number.
Supports `next`, `prevous` and jump accessors.
:param Union[str,FilenameObject] filename: The first filename of the
iteration.
"""
""" Much like the others, but created from a string filename """
def __init__(self, filename):
""" create from a filename (String)"""
if isinstance(filename, FilenameObject):
self.obj = filename
else:
self.obj = FilenameObject(filename=filename)
def next(self):
""" increment number """
self.obj.num += 1
return self.obj.tostring()
def previous(self):
""" decrement number """
self.obj.num -= 1
return self.obj.tostring()
def current(self):
""" return current filename string"""
return self.obj.tostring()
def jump(self, num):
""" jump to a specific number """
self.obj.num = num
return self.obj.tostring()
# image methods
def next_image(self):
""" returns the next image as a fabioimage """
return openimage(self.next())
def prev_image(self):
""" returns the previos image as a fabioimage """
return openimage(self.previous())
def current_image(self):
""" returns the current image as a fabioimage"""
return openimage(self.current())
def jump_image(self, num):
""" returns the image number as a fabioimage"""
return openimage(self.jump(num))
# object methods
def next_object(self):
""" returns the next filename as a fabio.FilenameObject"""
self.obj.num += 1
return self.obj
def previous_object(self):
""" returns the previous filename as a fabio.FilenameObject"""
self.obj.num -= 1
return self.obj
def current_object(self):
""" returns the current filename as a fabio.FilenameObject"""
return self.obj
def jump_object(self, num):
""" returns the filename num as a fabio.FilenameObject"""
self.obj.num = num
return self.obj
_FileDescription = collections.namedtuple('_FileDescription',
['filename', 'file_number', 'first_frame_number', 'nframes'])
"""Object storing description of a file from a file serie"""
def _filename_series_adapter(series):
"""Adapter to list all available files from a `filename_series` class.
Without the adaptater `filename_series` will not list the first element,
and will loop to the infinite.
"""
assert(isinstance(series, filename_series))
filename = series.current()
if not os.path.exists(filename):
return
yield filename
if series.obj.num is None:
# It's a single filename
return
while True:
filename = series.next()
if not os.path.exists(filename):
return
yield filename
class FileSeries(FabioImage):
"""Provide a `FabioImage` abstracting a file series.
This abstraction provide the set of the filenames as the container of
frames.
.. code-block:: python
# 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
:class:`filename_series` or :class:`file_series` objects.
.. code-block:: python
# 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).
.. code-block:: python
# 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 = []
def __init__(self, filenames, single_frame=None, fixed_frames=None, fixed_frame_number=None):
"""
Constructor
:param Union[Generator,Iterator,List] filenames: 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.
:param Union[Bool,None] single_frame: If True, all files are supposed to
contain only one frame.
:param Union[Bool,None] fixed_frames: 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).
:param Union[Integer,None] fixed_frame_number: If set, all files are
supposed to contain the same amount of frames (sepecified by this
argument)
"""
if isinstance(filenames, filename_series):
filenames = _filename_series_adapter(filenames)
if isinstance(filenames, list):
self.__filenames = filenames
self.__filename_generator = None
else:
self.__filenames = []
self.__filename_generator = filenames
self.__current_fabio_file_index = -1
self.__current_fabio_file = None
self.__file_descriptions = None
self.__current_file_description = None
if single_frame is not None:
self.__fixed_frames = True
self.__fixed_frame_number = 1
elif fixed_frame_number is not None:
self.__fixed_frames = True
self.__fixed_frame_number = int(fixed_frame_number)
elif fixed_frames is not None and fixed_frames:
self.__fixed_frames = bool(fixed_frames)
# We do not yet know the amount of frames per files
self.__fixed_frame_number = None
else:
self.__fixed_frames = False
self.__fixed_frame_number = None
self.__file_descriptions = []
self.__nframes = None
self.use_edf_shortcut = True
"""If true a custom file sequencial file reader is used for EDF formats"""
def close(self):
"""Close any IO handler openned."""
if self.__current_fabio_file is not None:
self.__current_fabio_file.close()
self.__current_fabio_file_index = -1
self.__current_fabio_file = None
def __iter_filenames(self):
"""Returns an iterator throug all filenames of the file series."""
for filename in self.__filenames:
yield filename
if self.__filename_generator is not None:
for filename in self.__filename_generator:
# Store it in case there is backward requests
self.__filenames.append(filename)
yield filename
self.__filename_generator = None
def frames(self):
"""Returns an iterator throug all frames of all filenames of this
file series."""
import fabio.edfimage
nframe = 0
for filename in self.__iter_filenames():
if self.use_edf_shortcut:
info = FilenameObject(filename=filename)
# It is the supported formats
if fabio.edfimage.EdfImage in info.codec_classes:
# Custom iterator implementation
frames = fabio.edfimage.EdfImage.lazy_iterator(filename)
for frame in frames:
frame._set_container(self, nframe)
yield frame
nframe += 1
continue
# Default implementation
with fabio.open(filename) as image:
if image.nframes == 0:
# The container is empty
pass
elif image.nframes == 1:
yield image
else:
for frame_num in range(image.nframes):
frame = image.get_frame(frame_num)
frame._set_container(self, nframe)
yield frame
nframe += 1
self.__nframes = nframe
def __load_all_filenames(self):
"""Load all filenames using the generator.
It is needed to know the number of frames.
.. note:: If the generator do not have endding, it will result an
infinite loop.
"""
if self.__filename_generator is not None:
for next_filename in self.__filename_generator:
self.__filenames.append(next_filename)
self.__filename_generator = None
def __get_filename(self, file_number):
"""Returns the filename from it's file position.
:param int file_number: Position of the file in the file series
:rtype: str
:raise IndexError: It the requested position is out of the available
number of files
"""
if file_number < len(self.__filenames):
filename = self.__filenames[file_number]
elif self.__filename_generator is not None:
# feed the filenames using the generator
amount = file_number - len(self.__filenames) + 1
try:
for _ in range(amount):
next_filename = next(self.__filename_generator)
self.__filenames.append(next_filename)
except StopIteration:
# No more filenames
self.__filename_generator = None
if file_number < len(self.__filenames):
filename = self.__filenames[file_number]
else:
raise IndexError("File number '%s' is not reachable" % file_number)
else:
raise IndexError("File number %s is not reachable" % file_number)
return filename
def __get_file(self, file_number):
"""Returns the opennned FabioImage from it's file position.
:param int file_number: Position of the file in the file series
:rtype: FabioImage
:raise IndexError: It the requested position is out of the available
number of files
"""
if self.__current_fabio_file_index == file_number:
return self.__current_fabio_file
filename = self.__get_filename(file_number)
if self.__current_fabio_file is not None:
self.__current_fabio_file.close()
self.__current_fabio_file_index = file_number
self.__current_fabio_file = fabio.open(filename)
return self.__current_fabio_file
def __iter_file_descriptions(self):
"""Iter all file descriptions.
Use a cached structure which grows according to the requestes.
"""
assert(self.__file_descriptions is not None)
for description in self.__file_descriptions:
yield description
# Construct the following descriptions
if len(self.__file_descriptions) > 0:
description = self.__file_descriptions[-1]
last_frame_number = description.first_frame_number + description.nframes
else:
last_frame_number = 0
while True:
# Get the next file
file_number = len(self.__file_descriptions)
try:
filename = self.__get_filename(file_number)
except IndexError:
# No more filenames
break
fabiofile = self.__get_file(file_number)
first_frame = last_frame_number
nframes = fabiofile.nframes
description = _FileDescription(filename, file_number, first_frame, nframes)
self.__file_descriptions.append(description)
yield description
last_frame_number = first_frame + nframes
def __find_file_description(self, frame_number):
"""Returns a file description from a cached list of stored descriptions.
:param int frame_number: A frame number
:rtype: _FileDescription
"""
assert(self.__file_descriptions is not None)
# Check it on the last cached description
if self.__current_file_description is not None:
description = self.__current_file_description
last_frame_number = description.first_frame_number + description.nframes
if description.first_frame_number <= frame_number < last_frame_number:
return description
# Check it on the cached list
for description in self.__iter_file_descriptions():
last_frame_number = description.first_frame_number + description.nframes
if description.first_frame_number <= frame_number < last_frame_number:
self.__current_file_description = description
return description
raise IndexError("Frame %s is out of range" % frame_number)
def __get_file_description(self, frame_number):
"""Returns file description at the frame number.
:rtype: _FileDescription
"""
if not self.__fixed_frames:
description = self.__find_file_description(frame_number)
return description
if self.__fixed_frame_number is None:
# The number of frames per files have to be reached
fabiofile = self.__get_file(0)
self.__fixed_frame_number = fabiofile.nframes
file_number = frame_number // self.__fixed_frame_number
try:
filename = self.__get_filename(file_number)
except IndexError:
raise IndexError("Frame %s is out of range" % frame_number)
first_frame = frame_number - (frame_number % self.__fixed_frame_number)
nframes = self.__fixed_frame_number
return _FileDescription(filename, file_number, first_frame, nframes)
def _get_frame(self, num):
"""Returns the frame numbered `num` in the series as a fabioimage.
:param int num: The number of the requested frame
:rtype: FabioFrame
"""
if num < 0:
raise IndexError("Frame %s is out of range" % num)
description = self.__get_file_description(num)
fileimage = self.__get_file(description.file_number)
local_frame = num - description.first_frame_number
if not (0 <= local_frame < description.nframes):
msg = "Index '%d' (local index '%d' from '%s') is out of range"
raise IndexError(msg % (num, local_frame, description.filename))
try:
frame = fileimage._get_frame(local_frame)
except IndexError:
logger.debug("Backtrace", exc_info=True)
msg = "Index '%d' (local index '%d' from '%s') is out of range"
raise IndexError(msg % (num, local_frame, description.filename))
frame._set_container(self, num)
return frame
@deprecation.deprecated(reason="Replaced by get_frame.", deprecated_since="0.10.0beta")
def getframe(self, num):
return self.get_frame(num)
@property
def nframes(self):
"""Returns the number of available frames in the full file series.
:rtype: int
"""
if self.__nframes is not None:
return self.__nframes
if not self.__fixed_frames:
# General case. All the information is needed
# Load all available descriptions
for _ in self.__iter_file_descriptions():
pass
if len(self.__file_descriptions) == 0:
self.__nframes = 0
return self.__nframes
description = self.__file_descriptions[-1]
self.__nframes = description.first_frame_number + description.nframes
return self.__nframes
if self.__fixed_frame_number is None:
# The number of frames per files have to be reached
try:
fabiofile = self.__get_file(0)
except IndexError:
self.__nframes = 0
return self.__nframes
self.__fixed_frame_number = fabiofile.nframes
# The last file can contains less frames
self.__load_all_filenames()
if len(self.__filenames) == 0:
self.__nframes = 0
return self.__nframes
file_number = len(self.__filenames) - 1
fabiofile = self.__get_file(file_number)
nframes = self.__fixed_frame_number * (len(self.__filenames) - 1) + fabiofile.nframes
self.__nframes = nframes
return nframes
@property
def data(self):
# This could provide access to the first or the current frame
raise NotImplementedError("Not implemented. Use serie.frames() or serie.get_frame(int)")
@property
def header(self):
# This could provide access to the first or the current frame
raise NotImplementedError("Not implemented. Use serie.frames() or serie.get_frame(int)")
@property
def shape(self):
# This could provide access to the first or the current frame
raise NotImplementedError("Not implemented. Use serie.frames() or serie.get_frame(int)")
@property
def dtype(self):
# This could provide access to the first or the current frame
raise NotImplementedError("Not implemented. Use serie.frames() or serie.get_frame(int)")
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