fabio.file_series — FabIO 0.1.3 documentation

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# Source code for fabio.file_series

    #!/usr/bin/env python

    """

    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, sys
    logger = logging.getLogger("fileseries")
    import traceback as pytraceback

    from fabioutils import FilenameObject, next_filename

    from openimage import openimage

    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, error:
                pytraceback.print_exc()

                # Skip bad images
                logger.warning("Got a problem here: %s", error)
                try:
                    im.filename = next_filename(im.filename)
                except Exception, 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 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 of an
            exception (missing image, etc.).  Otherwise the calling routine can handle
            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:

        ::

            for obj in new_file_series( ... ):
              if not isinstance(obj, fabio.fabioimage.fabioimage ):
                # deal with errors like missing images, non readable files, etc
                # e.g.
                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, ex:
                retVal = sys.exc_info()
                if(traceback):
                    pytraceback.print_exc()
                    # Skip bad images
                    logger.warning("Got a problem here: next() failed %s", ex)
                # Skip bad images
                try:
                    im.filename = next_filename(im.filename)
                except Exception, 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"

            super(numbered_file_series, self).__init__(
                [ fmt % (stem, i, extension) for i in range(first,
                                                              last + 1,
                                                              step) ])

    class filename_series:
        """ Much like the others, but created from a string filename """
        def __init__(self, filename):
            """ create from a filename (String)"""
            self.obj = FilenameObject(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

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