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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
"""
Author: Jon Wright, ESRF.
"""
# Get ready for python3:
from __future__ import with_statement, print_function
__authors__ = ["Jon Wright", "Jérôme Kieffer"]
__contact__ = "wright@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "25/06/2018"
import numpy
import os
import logging
logger = logging.getLogger(__name__)
from .fabioimage import FabioImage
from .fabioutils import previous_filename, next_filename
class PixiImage(FabioImage):
DESCRIPTION = "Pixi file format"
DEFAULT_EXTENSIONS = []
_need_a_seek_to_read = True
def _readheader(self, infile):
infile.seek(0)
self.header = self.check_header()
byt = infile.read(4)
framesize = numpy.frombuffer(byt, numpy.int32)
if framesize == 243722:
# life is good
width = 476
height = 512
offset = 24
self.header['framesize'] = framesize
self.header['width'] = width
self.header['height'] = height
self.header['offset'] = offset
else:
logger.warning("Pixiimage, bad framesize: %s", framesize)
raise
def read(self, fname, frame=None):
if frame is None:
frame = 0
self.header = self.check_header()
self.resetvals()
with self._open(fname, "rb") as infile:
self.sequencefilename = fname
self._readheader(infile)
self.nframes = os.path.getsize(fname) / 487448
self._readframe(infile, frame)
# infile.close()
return self
def _makeframename(self):
self.filename = "%s$%04d" % (self.sequencefilename,
self.currentframe)
def _readframe(self, filepointer, img_num):
if (img_num > self.nframes or img_num < 0):
raise Exception("Bad image number")
imgstart = self.header['offset'] + img_num * (512 * 476 * 2 + 24)
filepointer.seek(imgstart, 0)
self.data = numpy.frombuffer(filepointer.read(512 * 476 * 2),
numpy.uint16).copy()
self.data.shape = self.header['height'], self.header['width']
self.dim2, self.dim1 = self.data.shape
self.currentframe = int(img_num)
self._makeframename()
def getframe(self, num):
"""
Returns a frame as a new FabioImage object
"""
if num < 0 or num > self.nframes:
raise Exception("Requested frame number is out of range")
# Do a deep copy of the header to make a new one
newheader = {}
for k in self.header.keys():
newheader[k] = self.header[k]
frame = pixiimage(header=newheader)
frame.nframes = self.nframes
frame.sequencefilename = self.sequencefilename
infile = frame._open(self.sequencefilename, "rb")
frame._readframe(infile, num)
infile.close()
return frame
def next(self):
"""
Get the next image in a series as a fabio image
"""
if self.currentframe < (self.nframes - 1) and self.nframes > 1:
return self.getframe(self.currentframe + 1)
else:
newobj = pixiimage()
newobj.read(next_filename(
self.sequencefilename))
return newobj
def previous(self):
"""
Get the previous image in a series as a fabio image
"""
if self.currentframe > 0:
return self.getframe(self.currentframe - 1)
else:
newobj = pixiimage()
newobj.read(previous_filename(
self.sequencefilename))
return newobj
pixiimage = PixiImage
def demo(fname):
i = PixiImage()
i.read(fname)
import pylab
pylab.imshow(numpy.log(i.data))
print("%s\t%s\t%s\t%s" % (i.filename, i.data.max(), i.data.min(), i.data.mean()))
pylab.title(i.filename)
pylab.show()
while 1:
i = i.next()
pylab.imshow(numpy.log(i.data))
pylab.title(i.filename)
pylab.show()
raw_input()
if __name__ == "__main__":
import sys
demo(sys.argv[1])
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