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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
"""
File format to read images from PiXIrad PCDs manufactured by Pixirad Imaging
Counters SRL (http://www.pixirad.com/)
Author: Jon Wright, ESRF.
"""
__authors__ = ["Jon Wright", "Jérôme Kieffer"]
__contact__ = "wright@esrf.fr"
__license__ = "MIT"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "03/04/2020"
import numpy
import os
import logging
logger = logging.getLogger(__name__)
from . import fabioimage
from .fabioutils import previous_filename, next_filename
class PixiImage(fabioimage.FabioImage):
DESCRIPTION = "Pixi file format"
DEFAULT_EXTENSIONS = []
_need_a_seek_to_read = True
_IMAGE_WIDTH = 476
_IMAGE_HEIGHT = 512
_MAGIC_SIZE = 4
_HEADER_SIZE = 24
_PIXEL_DEPTH = 2
"""Each pixel is stored as UINT16"""
_PIXEL_COUNT = _IMAGE_WIDTH * _IMAGE_HEIGHT
_IMAGE_SIZE = _PIXEL_COUNT * _PIXEL_DEPTH
_FRAME_SIZE = _HEADER_SIZE + _IMAGE_SIZE
def _readheader(self, infile):
infile.seek(0)
self.header = self.check_header()
byt = infile.read(4)
framesize = numpy.frombuffer(byt, numpy.int32)
if framesize * 2 == self._FRAME_SIZE - self._MAGIC_SIZE:
self.header['framesize'] = framesize
self.header['width'] = self._IMAGE_WIDTH
self.header['height'] = self._IMAGE_HEIGHT
self.header['offset'] = self._HEADER_SIZE
else:
logger.warning("Bad framesize: %s", framesize)
raise Exception("Bad framesize")
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.rsplit("$", 1)[0]
self._readheader(infile)
self._nframes = os.path.getsize(fname) // self._FRAME_SIZE
self._readframe(infile, frame)
# infile.close()
return self
def _get_frame(self, num):
"""Inherited function returning a FabioFrame"""
if num < 0:
raise IndexError("Requested frame id:%d out of bound" % num)
if num >= self.nframes:
raise IndexError("Requested frame id:%d out of bound" % num)
newheader = {}
for k in self.header.keys():
newheader[k] = self.header[k]
with self._open(self.filename, "rb") as infile:
data = self._readdata(infile, num)
frame = fabioimage.FabioFrame(data=data, header=newheader)
frame._set_container(self, num)
frame._set_file_container(self, num)
return frame
def _make_filename(self, img_num):
self.currentframe = int(img_num)
if self.nframes == 1:
self.filename = "%s$%04d" % (self.sequencefilename,
self.currentframe)
def _readdata(self, filepointer, img_num):
if (img_num >= self.nframes or img_num < 0):
raise Exception("Bad image number")
imgstart = self.header['offset'] + img_num * self._FRAME_SIZE
filepointer.seek(imgstart, 0)
data = numpy.frombuffer(filepointer.read(self._IMAGE_SIZE),
numpy.uint16).copy()
data.shape = self.header['height'], self.header['width']
return data
def _readframe(self, filepointer, img_num):
data = self._readdata(filepointer, img_num)
self.data = data
self._shape = None
def getframe(self, num):
"""
Returns a frame as a new FabioImage object
"""
if num < 0:
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.filename = self.filename
frame.sequencefilename = self.sequencefilename
frame._make_filename(num)
with frame._open(frame.filename, "rb") as infile:
if frame.nframes == 1:
num = 0
frame._readframe(infile, num)
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
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