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#!/usr/bin/env python
# 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
Information about the file format from Masakatzu Kobayashi is highly appreciated
"""
import numpy
import logging
logger = logging.getLogger(__name__)
from .fabioimage import FabioImage
class HipicImage(FabioImage):
""" Read HiPic images e.g. collected with a Hamamatsu CCD camera"""
DESCRIPTION = "HiPic file format from Hamamatsu CCD cameras"
DEFAULT_EXTENSIONS = ["img"]
def _readheader(self, infile):
"""
Read in a header from an already open file
"""
Image_tag = infile.read(2)
Comment_len = numpy.frombuffer(infile.read(2), numpy.uint16)
Dim_1 = numpy.frombuffer(infile.read(2), numpy.uint16)[0]
Dim_2 = numpy.frombuffer(infile.read(2), numpy.uint16)[0]
Dim_1_offset = numpy.frombuffer(infile.read(2), numpy.uint16)[0]
Dim_2_offset = numpy.frombuffer(infile.read(2), numpy.uint16)[0]
_HeaderType = numpy.frombuffer(infile.read(2), numpy.uint16)[0]
_Dump = infile.read(50)
Comment = infile.read(Comment_len)
self.header['Image_tag'] = Image_tag
self.header['Dim_1'] = Dim_1
self.header['Dim_2'] = Dim_2
self.header['Dim_1_offset'] = Dim_1_offset
self.header['Dim_2_offset'] = Dim_2_offset
# self.header['Comment'] = Comment
if Image_tag != 'IM':
# This does not look like an HiPic file
logger.warning("No opening. Corrupt header of HiPic file %s",
str(infile.name))
Comment_split = Comment[:Comment.find('\x00')].split('\r\n')
for topcomment in Comment_split:
topsplit = topcomment.split(',')
for line in topsplit:
if '=' in line:
key, val = line.split('=', 1)
# Users cannot type in significant whitespace
key = key.rstrip().lstrip()
self.header_keys.append(key)
self.header[key] = val.lstrip().rstrip()
self.header[key] = val.lstrip('"').rstrip('"')
def read(self, fname, frame=None):
"""
Read in header into self.header and
the data into self.data
"""
self.header = self.check_header()
self.resetvals()
infile = self._open(fname, "rb")
self._readheader(infile)
# Compute image size
try:
dim1 = int(self.header['Dim_1'])
dim2 = int(self.header['Dim_2'])
self._shape = dim2, dim1
except (ValueError, KeyError):
raise IOError("HiPic file %s is corrupted, cannot read it" % str(fname))
dtype = numpy.dtype(numpy.uint16)
self._dtype = dtype
# Read image data
block = infile.read(dim1 * dim2 * dtype.itemsize)
infile.close()
# now read the data into the array
try:
self.data = numpy.frombuffer(block, dtype).copy().reshape((dim2, dim1))
except Exception:
logger.debug("%s %s %s %s %s", len(block), dtype, self.bpp, dim2, dim1)
logger.debug("Backtrace", exc_info=True)
raise IOError('Size spec in HiPic-header does not match size of image data field')
self._dtype = None
self._shape = None
# Sometimes these files are not saved as 12 bit,
# But as 16 bit after bg subtraction - which results
# negative values saved as 16bit. Therefore values higher
# 4095 is really negative values
if self.data.max() > 4095:
gt12bit = self.data > 4095
self.data = self.data - gt12bit * (2 ** 16 - 1)
return self
HiPiCimage = HipicImage
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