/usr/lib/python2.7/dist-packages/fabio/HiPiCimage.py is in python-fabio 0.3.0+dfsg-1build1.
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1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 | #!/usr/bin/env python# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/kif/fabio
#
#
# Copyright (C) European Synchrotron Radiation Facility, Grenoble, France
#
# Principal author: Jérôme Kieffer (Jerome.Kieffer@ESRF.eu)
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
"""
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
"""
# Get ready for python3:
from __future__ import with_statement, print_function
import numpy, logging
logger = logging.getLogger("HipiciImage")
from .fabioimage import FabioImage
class HipicImage(FabioImage):
""" Read HiPic images e.g. collected with a Hamamatsu CCD camera"""
def _readheader(self, infile):
"""
Read in a header from an already open file
"""
Image_tag = infile.read(2)
Comment_len = numpy.fromstring(infile.read(2), numpy.uint16)
Dim_1 = numpy.fromstring(infile.read(2), numpy.uint16)[0]
Dim_2 = numpy.fromstring(infile.read(2), numpy.uint16)[0]
Dim_1_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0]
Dim_2_offset = numpy.fromstring(infile.read(2), numpy.uint16)[0]
HeaderType = numpy.fromstring(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
logging.warning("no opening. Corrupt header of HiPic file " + \
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:
self.dim1 = int(self.header['Dim_1'])
self.dim2 = int(self.header['Dim_2'])
except:
raise Exception("HiPic file", str(fname) + \
"is corrupt, cannot read it")
bytecode = numpy.uint16
self.bpp = len(numpy.array(0, bytecode).tostring())
# Read image data
block = infile.read(self.dim1 * self.dim2 * self.bpp)
infile.close()
# now read the data into the array
try:
self.data = numpy.reshape(
numpy.fromstring(block, bytecode),
[self.dim2, self.dim1])
except:
print(len(block), bytecode, self.bpp, self.dim2, self.dim1)
raise IOError(
'Size spec in HiPic-header does not match size of image data field')
self.bytecode = self.data.dtype.type
# 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)
# ensure the PIL image is reset
self.pilimage = None
return self
HiPiCimage = HipicImage
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