/usr/lib/python2.7/dist-packages/fabio/bruker100image.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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 | # 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
Jérôme Kieffer, ESRF, Grenoble, France
"""
# get ready for python3
from __future__ import absolute_import, print_function, with_statement, division
__authors__ = ["Henning O. Sorensen" , "Erik Knudsen", "Jon Wright", "Jérôme Kieffer"]
__date__ = "29/10/2015"
__status__ = "production"
__copyright__ = "2007-2009 Risoe National Laboratory; 2015 ESRF"
__licence__ = "GPLv3+"
import numpy
import math
import logging
logger = logging.getLogger("bruker100image")
try:
from PIL import Image
except ImportError:
logger.warning("PIL is not installed ... trying to do without")
Image = None
from .brukerimage import BrukerImage
from .readbytestream import readbytestream
class Bruker100Image(BrukerImage):
def __init__(self, data=None , header=None):
BrukerImage.__init__(self, data, header)
self.version = 100
def toPIL16(self, filename=None):
if not Image:
raise RuntimeError("PIL is not installed !!! ")
if filename:
self.read(filename)
PILimage = Image.frombuffer("F",
(self.dim1, self.dim2),
self.data,
"raw",
"F;16", 0, -1)
return PILimage
def read(self, fname, frame=None):
with self._open(fname, "rb") as infile:
try:
self._readheader(infile)
except:
raise
rows = self.dim1
cols = self.dim2
npixelb = int(self.header['NPIXELB'][0])
# you had to read the Bruker docs to know this!
# We are now at the start of the image - assuming bruker._readheader worked
# Get image block size from NPIXELB.
# The total size is nbytes * nrows * ncolumns.
self.data = readbytestream(infile, infile.tell(), rows, cols, npixelb,
datatype="int", signed='n', swap='n')
# now process the overflows
for k, nover in enumerate(self.header['NOVERFL'].split()):
if k == 0:
# read the set of "underflow pixels" - these will be completely disregarded for now
continue
nov = int(nover)
if nov <= 0:
continue
bpp = 1 << k # (2 ** k)
datatype = self.bpp_to_numpy[bpp]
# upgrade data type
self.data = self.data.astype(datatype)
# pad nov*bpp to a multiple of 16 bytes
nbytes = (nov * bpp + 15) & ~(15)
# Multiple of 16 just above
data_str = infile.read(nbytes)
ar = numpy.fromstring(data_str[:nov * bpp], datatype)
# insert the the overflow pixels in the image array:
lim = (1 << (8 * k)) - 1
# generate an array comprising of the indices into data.ravel()
# where its value equals lim.
flat = self.data.ravel()
mask = numpy.where(flat == lim)[0]
# now put values from ar into those indices
flat.put(mask, ar)
logger.debug("%s bytes read + %d bytes padding" % (nov * bpp, nbytes - nov * bpp))
# infile.close()
self.resetvals()
return self
def write(self, fname):
"""
"""
raise NotImplementedError
#TODO: make a writer !!!
bruker100image = Bruker100Image
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