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# coding: utf-8
#
# Project: X-ray image reader
# https://github.com/silx-kit/fabio
#
# Copyright (C) 2015 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.
"""
Cif Binary Files images are 2D images written by the Pilatus detector and others.
They use a modified (simplified) byte-offset algorithm. This file contains the
decompression function from a string to an int64 numpy array.
"""
__author__ = "Jerome Kieffer"
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "MIT"
__copyright__ = "2010-2016, European Synchrotron Radiation Facility, Grenoble, France"
__date__ = "14/12/2020"
import numpy
import cython
from libc.stdint cimport int8_t, uint8_t, \
uint16_t, int16_t,\
int32_t, uint32_t,\
int64_t, uint64_t
@cython.boundscheck(False)
@cython.wraparound(False)
def comp_cbf32(data not None):
"""Compress a dataset using the byte-offset described for Pilatus
:param data: array of integers
:return: numpy array of chars
"""
cdef:
int32_t[::1] ary = numpy.ascontiguousarray(data.ravel(), dtype=numpy.int32)
int size = ary.size, i = 0, j = 0
int8_t[::1] output = numpy.zeros(size * 7, dtype=numpy.int8)
int32_t last, current, delta, absdelta
last = 0
for i in range(size):
current = ary[i]
delta = current - last
absdelta = delta if delta > 0 else -delta
if absdelta >= 1 << 15:
output[j] = -128
output[j + 1] = 0
output[j + 2] = -128
output[j + 3] = (delta & 255)
output[j + 4] = (delta >> 8) & 255
output[j + 5] = (delta >> 16) & 255
output[j + 6] = (delta >> 24)
j += 7
elif absdelta >= 1 << 7:
output[j] = -128
output[j + 1] = delta & 255
output[j + 2] = (delta >> 8) & 255
j += 3
else:
output[j] = delta
j += 1
last = current
return numpy.asarray(output)[:j]
@cython.boundscheck(False)
@cython.wraparound(False)
def comp_cbf(data not None):
"""Compress a dataset using the byte-offset described for any int64
:param data: array of integers
:return: numpy array of chars
"""
cdef:
int64_t[::1] ary = numpy.ascontiguousarray(data.ravel(), dtype=numpy.int64)
int size = ary.size, i = 0, j = 0
int8_t[::1] output = numpy.zeros(size * 15, dtype=numpy.int8)
int64_t last, current, delta, absdelta
last = 0
for i in range(size):
current = ary[i]
delta = current - last
absdelta = delta if delta > 0 else -delta
if absdelta >= 1 << 31:
output[j] = -128
output[j + 1] = 0
output[j + 2] = -128
output[j + 3] = 0
output[j + 4] = 0
output[j + 5] = 0
output[j + 6] = -128
output[j + 7] = (delta & 255)
output[j + 8] = (delta >> 8) & 255
output[j + 9] = (delta >> 16) & 255
output[j + 10] = (delta >> 24) & 255
output[j + 11] = (delta >> 32) & 255
output[j + 12] = (delta >> 40) & 255
output[j + 13] = (delta >> 48) & 255
output[j + 14] = (delta >> 56) & 255
j += 15
elif absdelta >= 1 << 15:
output[j] = -128
output[j + 1] = 0
output[j + 2] = -128
output[j + 3] = (delta & 255)
output[j + 4] = (delta >> 8) & 255
output[j + 5] = (delta >> 16) & 255
output[j + 6] = (delta >> 24)
j += 7
elif absdelta >= 1 << 7:
output[j] = -128
output[j + 1] = delta & 255
output[j + 2] = (delta >> 8) & 255
j += 3
else:
output[j] = delta
j += 1
last = current
return numpy.asarray(output)[:j]
@cython.boundscheck(False)
@cython.wraparound(False)
def dec_cbf(bytes stream not None, size=None):
"""
Analyze a stream of char with any length of exception (2,4, or 8 bytes integers)
:param stream: bytes (string) representing the compressed data
:param size: the size of the output array (of longInts)
:return: int64 ndArrays
"""
cdef:
int i = 0
int j = 0
uint8_t tmp8 = 0
int64_t last = 0
int64_t current = 0
int64_t tmp64 = 0
int64_t tmp64a = 0
int64_t tmp64b = 0
int64_t tmp64c = 0
int64_t tmp64d = 0
int64_t tmp64e = 0
int64_t tmp64f = 0
int64_t tmp64g = 0
uint8_t key8 = 0x80
uint8_t key0 = 0x00
int csize
int lenStream = < int > len(stream)
uint8_t[::1] cstream = bytearray(stream)
int64_t[::1] data_out
if size is None:
csize = lenStream
else:
csize = < int > size
data_out = numpy.empty(csize, dtype=numpy.int64)
with nogil:
while (i < lenStream) and (j < csize):
if (cstream[i] == key8):
if ((cstream[i + 1] == key0) and (cstream[i + 2] == key8)):
if (cstream[i + 3] == key0) and (cstream[i + 4] == key0) and (cstream[i + 5] == key0) and (cstream[i + 6] == key8):
# Retrieve the interesting Bytes of data
tmp64g = cstream[i + 7]
tmp64f = cstream[i + 8]
tmp64e = cstream[i + 9]
tmp64d = cstream[i + 10]
tmp64c = cstream[i + 11]
tmp64b = cstream[i + 12]
tmp64a = cstream[i + 13]
tmp64 = <int8_t> cstream[i + 14]
# Assemble data into a 64 bits integer
current = (tmp64 << 56) | (tmp64a << 48) | (tmp64b << 40) | (tmp64c << 32) | (tmp64d << 24) | (tmp64e << 16) | (tmp64f << 8) | (tmp64g)
i += 15
else:
# Retrieve the interesting Bytes of data
tmp64c = cstream[i + 3]
tmp64b = cstream[i + 4]
tmp64a = cstream[i + 5]
tmp64 = <int8_t> cstream[i + 6]
# Assemble data into a 64 bits integer
current = (tmp64 << 24) | (tmp64a << 16) | (tmp64b << 8) | (tmp64c)
i += 7
else:
tmp64a = cstream[i + 1]
tmp64 = <int8_t> cstream[i + 2]
current = (tmp64 << 8) | (tmp64a)
i += 3
else:
current = (<int8_t> cstream[i])
i += 1
last += current
data_out[j] = last
j += 1
return data_out[:j]
@cython.boundscheck(False)
def dec_cbf32(bytes stream not None, size=None):
"""
Analyze a stream of char with any length of exception (2 or 4 bytes integers)
Optimized for int32 decompression
:param stream: bytes (string) representing the compressed data
:param size: the size of the output array (of longInts)
:return: int64 ndArrays
"""
cdef:
int i = 0
int j = 0
uint8_t tmp8 = 0
int32_t last = 0
int32_t current = 0
int32_t tmp64 = 0
int32_t tmp64a = 0
int32_t tmp64b = 0
int32_t tmp64c = 0
uint8_t key8 = 0x80
uint8_t key0 = 0x00
int csize
int lenStream = < int > len(stream)
uint8_t[:] cstream = bytearray(stream)
int32_t[::1] data_out
if size is None:
csize = lenStream
else:
csize = < int > size
data_out = numpy.empty(csize, dtype=numpy.int32)
with nogil:
while (i < lenStream) and (j < csize):
if (cstream[i] == key8):
if ((cstream[i + 1] == key0) and (cstream[i + 2] == key8)):
# Retrieve the interesting Bytes of data
tmp64c = cstream[i + 3]
tmp64b = cstream[i + 4]
tmp64a = cstream[i + 5]
tmp64 = <int8_t> cstream[i + 6]
# Assemble data into a 32 bits integer
current = (tmp64 << 24) | (tmp64a << 16) | (tmp64b << 8) | (tmp64c)
i += 7
else:
tmp64a = cstream[i + 1]
tmp64 = <int8_t> cstream[i + 2]
current = (tmp64 << 8) | (tmp64a)
i += 3
else:
current = (<int8_t> cstream[i])
i += 1
last += current
data_out[j] = last
j += 1
return numpy.asarray(data_out[:j])
@cython.boundscheck(False)
def dec_TY5(bytes stream not None, size=None):
"""
Analyze a stream of char with a TY5 compression scheme and exception (2 or 4 bytes integers)
TODO: known broken, FIXME
:param stream: bytes (string) representing the compressed data
:param size: the size of the output array (of longInts)
:return: int32 ndArrays
"""
cdef:
int i = 0
int j = 0
int32_t last = 0
int32_t current = 0
uint8_t key8 = 0xfe # 127+127
int32_t tmp32a = 0
int32_t tmp32b = 0
int csize
int lenStream = len(stream)
uint8_t[::1] cstream = bytearray(stream)
int32_t[::1] data_out
if size is None:
csize = lenStream
else:
csize = < int > size
data_out = numpy.zeros(csize, dtype=numpy.int32)
if True:
while (i < lenStream) and (j < csize):
if (cstream[i] == key8):
tmp32a = cstream[i + 1] - 127
tmp32b = <int16_t>( <int8_t> cstream[i + 2] << 8 )
current = (tmp32b) | (tmp32a)
i += 3
else:
current = <int32_t>(<uint8_t> cstream[i]) - 127
i += 1
last += current
data_out[j] = last
j += 1
return numpy.asarray(data_out[:j])
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