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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 299 300 301 302 303 304 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 326 327 328 329 330 331
|
# 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.
"""Compression and decompression algorithm for Esperanto format
Authors: Jérôme Kieffer, ESRF email:jerome.kieffer@esrf.fr
Florian Plaswig
Inspired by C++ code: https://git.3lp.cx/dyadkin/cryio/src/branch/master/src/esperantoframe.cpp
Fortran code: https://svn.debroglie.net/debroglie/Oxford/trunk/diamond2crysalis/bitfield.F90
"""
__author__ = ["Florian Plaswig", "Jérôme Kieffer"]
__contact__ = "jerome.kieffer@esrf.eu"
__license__ = "MIT"
__date__ = "13/11/2020"
__copyright__ = "European Synchrotron Radiation Facility, Grenoble, France"
import logging
from io import BytesIO
from struct import pack, unpack as unpack_
try:
from ..ext._agi_bitfield import get_fieldsize as _get_fieldsize, compress_row as _compress_row, compress as _compress
except ImportError:
_get_fieldsize = None
_compress_row = None
_compress = None
logger = logging.getLogger(__name__)
import numpy
unpack = lambda fmt, buff: unpack_(fmt, buff)[0]
MASK = [(1 << i) - 1 for i in range(9)]
def compress(frame):
"""compress a frame using the agi_bitfield algorithm
:param frame: numpy.ndarray
:returns bytes
"""
dim = frame.shape
buffer = BytesIO()
row_start = numpy.zeros(dim[0], dtype=numpy.uint32)
for row_index in range(0, dim[0]):
row_start[row_index] = buffer.tell()
_compress_row(frame[row_index], buffer)
data_size = pack("<I", buffer.tell())
if numpy.little_endian:
buffer.write(row_start.tobytes())
else:
buffer.write(row_start.byteswap.tobytes())
return data_size + buffer.getvalue()
def compress_row(data, buffer):
"""compress a single row
:arg data numpy.array
:arg buffer io.BytesIO
"""
first_pixel = data[0]
pixel_diff = data[1:] - data[:-1]
write_escaped(first_pixel, buffer)
n_fields = len(pixel_diff) // 16
n_restpx = len(pixel_diff) % 16
for _ in range(0, n_fields):
fielda = pixel_diff[:8]
fieldb = pixel_diff[8:16]
len_a = _get_fieldsize(fielda)
len_b = _get_fieldsize(fieldb)
len_byte = (len_b << 4) | len_a
buffer.write(pack("B", len_byte))
of_buff = BytesIO()
compressed_fielda = compress_field(fielda, len_a, of_buff)
compressed_fieldb = compress_field(fieldb, len_b, of_buff)
buffer.write(compressed_fielda + compressed_fieldb + of_buff.getvalue())
pixel_diff = pixel_diff[16:]
for restpx in range(0, n_restpx):
write_escaped(pixel_diff[restpx], buffer)
if _compress_row is None:
_compress_row = compress_row
def decompress(comp_frame, dimensions):
"""decompresses a frame that was compressed using the agi_bitfield algorithm
:param comp_frame: bytes
:param dimensions: tuple
:return numpy.ndarray
"""
row_count, col_count = dimensions
# read data components (row indices are ignored)
data_size = unpack("I", comp_frame[:4])
data_block = BytesIO(comp_frame[4:])
logger.debug("Size of binary data block: %d with image size: %s, compression ratio: %.3fx", data_size, dimensions, 4 * row_count * col_count / data_size)
output = numpy.zeros(dimensions, dtype=numpy.int32)
for row_index in range(row_count):
output[row_index] = decompress_row(data_block, col_count)
return output.cumsum(axis=1)
def decompress_row(buffer, row_length):
"""decompress a single row
:param buffer: io.BytesIO
:param row_length: int
:returns list
"""
first_pixel = read_escaped(buffer)
n_fields = (row_length - 1) // 16
n_restpx = (row_length - 1) % 16
pixels = [first_pixel]
for field in range(n_fields):
lb = unpack("B", buffer.read(1))
len_b, len_a = read_len_byte(lb)
field_a = decode_field(buffer.read(len_a))
field_b = decode_field(buffer.read(len_b))
undo_escapes(field_a, len_a, buffer)
undo_escapes(field_b, len_b, buffer)
pixels += field_a
pixels += field_b
pixels += [read_escaped(buffer) for _ in range(n_restpx)]
return pixels
def fortran_fieldsize(nbvalue):
"Direct translation of Fortran"
if(nbvalue < -63):
getfieldsize = 8
elif(nbvalue < -31):
getfieldsize = 7
elif(nbvalue < -15):
getfieldsize = 6
elif(nbvalue < -7):
getfieldsize = 5
elif(nbvalue < -3):
getfieldsize = 4
elif(nbvalue < -1):
getfieldsize = 3
elif(nbvalue < 0):
getfieldsize = 2
elif(nbvalue < 2):
getfieldsize = 1
elif(nbvalue < 3):
getfieldsize = 2
elif(nbvalue < 5):
getfieldsize = 3
elif(nbvalue < 9):
getfieldsize = 4
elif(nbvalue < 17):
getfieldsize = 5
elif(nbvalue < 33):
getfieldsize = 6
elif(nbvalue < 65):
getfieldsize = 7
else:
getfieldsize = 8
return getfieldsize
def get_fieldsize(array):
"""determine the fieldsize to store the given values
:param array numpy.array
:returns int
"""
return max(fortran_fieldsize(array.max()), fortran_fieldsize(array.min()))
if _get_fieldsize is None:
_get_fieldsize = get_fieldsize
def compress_field(ifield, fieldsize, overflow_table):
"""compress a field with given size
:param ifield: numpy.ndarray
:param fieldsize: int
:param overflow_table: io.BytesIO
:returns int
"""
if fieldsize == 8:
# we have to deal offsets but not bitshifts
conv_ = MASK[fieldsize - 1]
tmp = bytearray(8)
for i, elem in enumerate(ifield):
if -127 <= elem < 127:
tmp[i] = elem + conv_
elif -32767 <= elem < 32767:
tmp[i] = 254
overflow_table.write(pack("<h", elem))
else:
tmp[i] = 255
overflow_table.write(pack("<i", elem))
return bytes(tmp)
elif fieldsize > 0:
# we have to deal with bit-shifts but not offsets
conv_ = MASK[fieldsize - 1]
compressed_field = 0
for i, elem in enumerate(ifield):
val = int(elem) + conv_
compressed_field |= val << (i * fieldsize)
try:
res = pack("<Q", compressed_field)
except:
logger.error("Exception in struct.pack: %s %s %s %s", fieldsize, type(fieldsize), ifield, compressed_field)
raise
return res[:fieldsize]
else:
raise AssertionError("fieldsize is between 0 and 8")
def decode_field(field):
"""decodes a field from bytes.
One field always encode for 8 pixels but my be stored on 1 to 8 pixels
(overflow are handeled separately)
:param field: bytes
:returns list
"""
size = len(field)
if size == 8:
return list(unpack_("B"*8, field))
elif size < 8:
field = unpack("<Q", field.ljust(8, b'\x00'))
mask_ = MASK[size]
return [(field >> (size * i)) & mask_ for i in range(8)]
else:
raise RuntimeError("Expected a maximum of 8 bytes, got %s" % size)
def read_len_byte(lb):
"""parses the length byte and returns the sizes of the next twofields
:param lb: int/byte
:returns tuple
"""
return lb >> 4, lb & 0xf
def write_escaped(value, buffer):
"""write an value to the buffer and escape when overflowing one byte
:param value: int
:param buffer: io.BytesIO
"""
if -127 <= value < 127:
buffer.write(pack("B", value + 127))
elif -32767 < value < 32767:
buffer.write(b'\xfe' + pack("<h", value))
else:
buffer.write(b'\xff' + pack("<i", value))
def read_escaped(buffer):
"""reads byte value that might be escaped from a buffer
:param buffer: io.BytesIO
:returns int
"""
byte = buffer.read(1)
if byte == b'\xfe': # two byte overflow
return unpack("<h", buffer.read(2))
elif byte == b'\xff': # four byte overflow
return unpack("<i", buffer.read(4))
else: # no overflow
return unpack("B", byte) - 127
def undo_escapes(field, length, buffer):
"""undo escaping of values in a field
:param field: list
:param length: int
:param buffer: io.BytesIO
"""
conv_ = MASK[length - 1]
for i, val in enumerate(field):
if val == 0xfe:
field[i] = unpack("<h", buffer.read(2))
elif val == 0xff:
field[i] = unpack("<i", buffer.read(4))
else:
field[i] = val - conv_
|