/usr/lib/python2.7/dist-packages/fabio/tifimage.py is in python-fabio 0.1.3-3.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
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 | #!/usr/bin/env python
#-*- coding: utf8 -*-
"""
FabIO class for dealing with TIFF images.
In facts wraps TiffIO from V. Armando Solé (available in PyMca) or falls back to PIL
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:
European Synchrotron Radiation Facility;
Grenoble (France)
License: GPLv3+
"""
__authors__ = ["Jérôme Kieffer", "Henning O. Sorensen", "Erik Knudsen"]
__date__ = "11/07/2011"
__license__ = "GPLv3+"
__copyright__ = "ESRF, Grenoble & Risoe National Laboratory"
__status__ = "stable"
import time, logging, struct
logger = logging.getLogger("tifimage")
try:
from PIL import Image
except ImportError:
logger.warning("PIL is not installed ... trying to do without")
Image = None
import numpy
from fabioimage import fabioimage
from TiffIO import TiffIO
PIL_TO_NUMPY = { "I;16": numpy.uint16,
"F": numpy.float32,
"1": numpy.bool,
"I": numpy.int32,
"L": numpy.uint8,
}
LITTLE_ENDIAN = 1234
BIG_ENDIAN = 3412
TYPES = {0:'invalid', 1:'byte', 2:'ascii', 3:'short', 4:'long', 5:'rational', 6:'sbyte', 7:'undefined', 8:'sshort', 9:'slong', 10:'srational', 11:'float', 12:'double'}
TYPESIZES = {0:0, 1:1, 2:1, 3:2, 4:4, 5:8, 6:1, 7:1, 8:2, 9:4, 10:8, 11:4, 12:8}
baseline_tiff_tags = {
256:'ImageWidth',
257:'ImageLength',
306:'DateTime',
315:'Artist',
258:'BitsPerSample',
265:'CellLength',
264:'CellWidth',
259:'Compression',
262:'PhotometricInterpretation',
296:'ResolutionUnit',
282:'XResolution',
283:'YResolution',
278:'RowsPerStrip',
273:'StripOffset',
279:'StripByteCounts',
270:'ImageDescription',
271:'Make',
272:'Model',
320:'ColorMap',
305:'Software',
339:'SampleFormat',
33432:'Copyright'
}
class tifimage(fabioimage):
"""
Images in TIF format
Wraps TiffIO
"""
_need_a_seek_to_read = True
def __init__(self, *args, **kwds):
""" Tifimage constructor adds an nbits member attribute """
self.nbits = None
fabioimage.__init__(self, *args, **kwds)
self.lib = None
def _readheader(self, infile):
"""
Try to read Tiff images header...
"""
# try:
# self.header = { "filename" : infile.name }
# except AttributeError:
# self.header = {}
#
# t = Tiff_header(infile.read())
# self.header = t.header
# try:
# self.dim1 = int(self.header['ImageWidth'])
# self.dim2 = int(self.header['ImageLength'])
# except (KeyError):
# logger.warning("image dimensions could not be determined from header tags, trying to go on anyway")
# read the first 32 bytes to determine size
header = numpy.fromstring(infile.read(64), numpy.uint16)
self.dim1 = int(header[9])
self.dim2 = int(header[15])
# nbits is not a fabioimage attribute...
self.nbits = int(header[21]) # number of bits
def read(self, fname, frame=None):
"""
Wrapper for TiffIO.
"""
infile = self._open(fname, "rb")
self._readheader(infile)
infile.seek(0)
self.lib = None
try:
tiffIO = TiffIO(infile)
if tiffIO.getNumberOfImages() > 0:
#No support for now of multi-frame tiff images
self.data = tiffIO.getImage(0)
self.header = tiffIO.getInfo(0)
except Exception, error:
logger.warning("Unable to read %s with TiffIO due to %s, trying PIL" % (fname, error))
else:
if self.data.ndim == 2:
self.dim2, self.dim1 = self.data.shape
elif self.data.ndim == 3:
self.dim2, self.dim1, ncol = self.data.shape
logger.warning("Third dimension is the color")
else:
logger.warning("dataset has %s dimensions (%s), check for errors !!!!", self.data.ndim, self.data.shape)
self.lib = "TiffIO"
if (self.lib is None):
if Image:
try:
infile.seek(0)
self.pilimage = Image.open(infile)
except Exception:
logger.error("Error in opening %s with PIL" % fname)
self.lib = None
infile.seek(0)
else:
self.lib = "PIL"
self.dim1, self.dim2 = self.pilimage.size
if self.pilimage.mode in PIL_TO_NUMPY:
self.data = numpy.fromstring(self.pilimage.tostring(), PIL_TO_NUMPY[self.pilimage.mode])
else: #probably RGB or RGBA images: rely on PIL to convert it to greyscale float.
self.data = numpy.fromstring(self.pilimage.convert("F").tostring(), numpy.float32)
self.data.shape = (self.dim2, self.dim1)
else:
logger.error("Error in opening %s: no tiff reader managed to read the file.", fname)
self.lib = None
infile.seek(0)
self.bpp = len(numpy.zeros(1, dtype=self.data.dtype).tostring())
self.bytecode = self.data.dtype.name
self.resetvals()
return self
def write(self, fname):
"""
Overrides the fabioimage.write method and provides a simple TIFF image writer.
@param fname: name of the file to save the image to
@tag_type fname: string or unicode (file?)...
"""
tiffIO = TiffIO(fname, mode="w")
tiffIO.writeImage(self.data, info=self.header, software="fabio.tifimage", date=time.ctime())
#define a couple of helper classes here:
class Tiff_header(object):
def __init__(self, string):
if string[:4] == "II\x2a\x00":
self.byteorder = LITTLE_ENDIAN
elif string[:4] == 'MM\x00\x2a':
self.byteorder = BIG_ENDIAN
else:
logger.warning("Warning: This does not appear to be a tiff file")
#the next two bytes contains the offset of the oth IFD
offset_first_ifd = struct.unpack_from("h", string[4:])[0]
self.ifd = [Image_File_Directory()]
offset_next = self.ifd[0].unpack(string, offset_first_ifd)
while (offset_next != 0):
self.ifd.append(Image_File_Directory())
offset_next = self.ifd[-1].unpack(string, offset_next)
self.header = {}
#read the values of the header items into a dictionary
for entry in self.ifd[0].entries:
if entry.tag in baseline_tiff_tags.keys():
self.header[baseline_tiff_tags[entry.tag]] = entry.val
else:
self.header[entry.tag] = entry.val
class Image_File_Directory(object):
def __init__(self, instring=None, offset= -1):
self.entries = []
self.offset = offset
self.count = None
def unpack(self, instring, offset= -1):
if (offset == -1): offset = self.offset
strInput = instring[offset:]
self.count = struct.unpack_from("H", strInput[:2])[0]
#0th IFD contains count-1 entries (count includes the adress of the next IFD)
for i in range(self.count - 1):
e = Image_File_Directory_entry().unpack(strInput[2 + 12 * (i + 1):])
if (e != None):
self.entries.append(e)
#extract data associated with tags
for e in self.entries:
if (e.val == None):
e.extract_data(instring)
#do we have some more ifds in this file
offset_next = struct.unpack_from("L", instring[offset + 2 + self.count * 12:])[0]
return offset_next
class Image_File_Directory_entry(object):
def __init__(self, tag=0, tag_type=0, count=0, offset=0):
self.tag = tag
self.tag_type = tag_type
self.count = count
self.val_offset = offset
self.val = None
def unpack(self, strInput):
idfentry = strInput[:12]
################################################################################
# # TOFIX: How is it possible that HHL (2+2+4 bytes has a size of )
################################################################################
(tag, tag_type, count) = struct.unpack_from("HHL", idfentry)
self.tag = tag
self.count = count
self.tag_type = tag_type
self.val = None
if (count <= 0):
logger.warning("Tag # %s has an invalid count: %s. Tag is ignored" % (tag, count))
return
if(count * TYPESIZES[tag_type] <= 4):
self.val_offset = 8
self.extract_data(idfentry)
self.val_offset = None
else:
self.val_offset = struct.unpack_from("L", idfentry[8:])[0]
return self
def extract_data(self, full_string):
tag_type = self.tag_type
if (TYPES[tag_type] == 'byte'):
self.val = struct.unpack_from("B", full_string[self.val_offset:])[0]
elif (TYPES[tag_type] == 'short'):
self.val = struct.unpack_from("H", full_string[self.val_offset:])[0]
elif (TYPES[tag_type] == 'long'):
self.val = struct.unpack_from("L", full_string[self.val_offset:])[0]
elif (TYPES[tag_type] == 'sbyte'):
self.val = struct.unpack_from("b", full_string[self.val_offset:])[0]
elif (TYPES[tag_type] == 'sshort'):
self.val = struct.unpack_from("h", full_string[self.val_offset:])[0]
elif (TYPES[tag_type] == 'slong'):
self.val = struct.unpack_from("l", full_string[self.val_offset:])[0]
elif (TYPES[tag_type] == 'ascii'):
self.val = full_string[self.val_offset:self.val_offset + max(self.count, 4)]
elif (TYPES[tag_type] == 'rational'):
if self.val_offset != None:
(num, den) = struct.unpack_from("LL", full_string[self.val_offset:])
print self.val_offset
self.val = float(num) / den
elif (TYPES[tag_type] == 'srational'):
if self.val_offset != None:
(num, den) = struct.unpack_from("ll", full_string[self.val_offset:])
self.val = float(num) / den,
elif (TYPES[tag_type] == 'float'):
self.val = struct.unpack_from("f", full_string[self.val_offset:])[0]
elif (TYPES[tag_type] == 'double'):
if self.val_offset != None:
self.val = struct.unpack_from("d", full_string[self.val_offset:])[0]
else:
logger.warning("unrecognized type of strInputentry self: %s tag: %s type: %s TYPE: %s" % (self, baseline_tiff_tags[self.tag], self.tag_type, TYPES[tag_type]))
|