/usr/share/pyshared/libtiff/tiff_file.py is in python-libtiff 0.3.0~svn78-2.
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Provides TIFFfile class.
"""
# Author: Pearu Peterson
# Created: June 2010
from __future__ import division
__all__ = ['TIFFfile', 'TiffFile']
import os
import sys
import numpy
from numpy.testing.utils import memusage
from .tiff_data import type2name, name2type, type2bytes, type2dtype, tag_value2name, tag_name2value
from .tiff_data import LittleEndianNumpyDTypes, BigEndianNumpyDTypes, default_tag_values, sample_format_map
from .utils import bytes2str
from .tiff_base import TiffBase
from .tiff_sample_plane import TiffSamplePlane
from .tiff_array import TiffArray
import lsm
import tif_lzw
IFDEntry_init_hooks = []
IFDEntry_finalize_hooks = []
class TIFFfile(TiffBase):
"""
Hold a TIFF file image stack that is accessed via memmap.
To access image, use get_tiff_array method.
Attributes
----------
filename : str
data : memmap
IFD : IFD-list
See also
--------
TiffFiles, TiffChannelsAndFiles
"""
def close(self):
if hasattr(self, 'data'):
if self.verbose:
sys.stdout.write('Closing TIFF file %r\n' % (self.filename)); sys.stdout.flush()
del self.data
__del__ = close
def __init__(self, filename, mode='r', first_byte = 0, verbose=False):
if verbose:
sys.stdout.write ('Opening file %r\n' % (filename)); sys.stdout.flush()
self.verbose = verbose
self.filename = filename
if mode!='r':
raise NotImplementedError(`mode`)
if not os.path.isfile (filename):
raise ValueError ('file does not exists')
if not os.stat(filename).st_size:
raise ValueError ('file has zero size')
self.first_byte = first_byte
try:
self.data = numpy.memmap(filename, dtype=numpy.ubyte, mode=mode)
except IOError, msg:
if 'Too many open files' in str (msg):
print '''\
======================================================================
An exception was raised with message:
%s
Ubuntu Linux users:
Check `ulimit -n`.
To increase the number of open files limits, add the following lines
* hard nofile 16384
* soft nofile 16384
to /etc/security/limits.conf and run `sudo start procps`
======================================================================
''' % (msg)
raise IOError ('%s' % (msg))
if 'Operation not permitted' in str (msg):
print '''\
======================================================================
An exception was raised with message:
%s
The exception may be due to unsufficient access rights or due to
opening too many files for the given file system.
======================================================================
''' % (msg)
raise IOError ('%s' % (msg))
raise
self.memory_usage = [(self.data.nbytes, self.data.nbytes, 'eof')]
byteorder = self.data[first_byte:first_byte+2].view(dtype=numpy.uint16)[0]
if byteorder==0x4949:
self.endian = 'little'
self.dtypes = LittleEndianNumpyDTypes
elif byteorder==0x4d4d:
self.endian = 'big'
self.dtypes = BigEndianNumpyDTypes
else:
raise ValueError('unrecognized byteorder: %s' % (hex(byteorder)))
magic = self.get_uint16(first_byte+2)
if magic!=42:
raise ValueError('wrong magic number for TIFF file: %s' % (magic))
self.IFD0 = IFD0 = first_byte + self.get_uint32(first_byte+4)
self.memory_usage.append((first_byte, first_byte+8, 'file header'))
n = self.get_uint16(IFD0)
IFD_list = []
IFD_offset = IFD0
while IFD_offset:
n = self.get_uint16(IFD_offset)
ifd = IFD(self)
for i in range(n):
entry = IFDEntry(ifd, self, IFD_offset + 2 + i*12)
ifd.append(entry)
ifd.finalize()
IFD_list.append(ifd)
self.memory_usage.append((IFD_offset, IFD_offset + 2 + n*12 + 4, 'IFD%s entries (%s)' % (len(IFD_list), len(ifd))))
IFD_offset = self.get_uint32(IFD_offset + 2 + n*12)
if verbose:
sys.stdout.write('\rIFD information read: %s..' % (len (IFD_list))); sys.stdout.flush()
self.IFD = IFD_list
if verbose:
sys.stdout.write(' done\n'); sys.stdout.flush()
self.time = None
def set_time (self, time):
self.time = time
def __repr__(self):
return '%s(%r)' % (self.__class__.__name__, self.filename)
def get_uint16(self, offset):
return self.data[offset:offset+2].view(dtype=self.dtypes.uint16)[0]
def get_uint32(self, offset):
return self.data[offset:offset+4].view(dtype=self.dtypes.uint32)[0]
def get_int16(self, offset):
return self.data[offset:offset+2].view(dtype=self.dtypes.int16)[0]
def get_int32(self, offset):
return self.data[offset:offset+4].view(dtype=self.dtypes.int32)[0]
def get_float32(self, offset):
return self.data[offset:offset+4].view(dtype=self.dtypes.float32)[0]
def get_float64(self, offset):
return self.data[offset:offset+8].view(dtype=self.dtypes.float64)[0]
get_short = get_uint16
get_long = get_uint32
get_double = get_float64
def get_value(self, offset, typ):
values = self.get_values(offset, typ, 1)
if values is not None:
return values[0]
def get_values(self, offset, typ, count):
if isinstance(typ, numpy.dtype):
dtype = typ
bytes = typ.itemsize
elif isinstance(typ, type) and issubclass(typ, numpy.generic):
dtype = typ
bytes = typ().itemsize
else:
if isinstance(typ, str):
ntyp = typ
typ = name2type.get(typ)
else:
ntyp = str (typ)
dtype = self.dtypes.type2dt.get(typ)
bytes = type2bytes.get(typ)
if dtype is None or bytes is None:
sys.stderr.write('get_values: incomplete info for type=%r [%r]: dtype=%s, bytes=%s\n' % (typ,ntyp, dtype, bytes))
return
return self.data[offset:offset+bytes*count].view(dtype=dtype)
def get_string(self, offset, length = None):
if length is None:
i = 0
while self.data[offset+i]:
i += 1
length = i
string = self.get_values(offset, 'BYTE', length).tostring()
return string
def check_memory_usage(self, verbose=True):
''' Check memory usage of TIFF fields and blocks.
Returns
-------
ok : bool
Return False if unknown or overlapping memory areas have been detected.
'''
l = []
l.extend(self.memory_usage)
for ifd in self.IFD:
l.extend(ifd.memory_usage)
l.sort()
last_end = None
ok = True
for start, end, resource in l:
if last_end:
if last_end!=start:
if verbose:
print '--- unknown %s bytes' % (start-last_end)
ok = False
if start<last_end and verbose:
print '--- overlapping memory area'
if verbose:
print '%s..%s[%s] contains %s' % (start, end,end-start, resource)
last_end = end
return ok
def is_contiguous(self):
for i,ifd in enumerate(self.IFD):
strip_offsets = ifd.get('StripOffsets').value
strip_nbytes = ifd.get('StripByteCounts').value
if not ifd.is_contiguous():
return False
if i==0:
pass
else:
if isinstance(strip_offsets, numpy.ndarray):
start = strip_offsets[0]
else:
start = strip_offsets
if end!=start:
return False
if isinstance(strip_offsets, numpy.ndarray):
end = strip_offsets[-1] + strip_nbytes[-1]
else:
end = strip_offsets + strip_nbytes
return True
def get_contiguous(self):
""" Return memmap of a stack of images.
"""
if not self.is_contiguous ():
raise ValueError('Image stack data not contiguous')
ifd0 = self.IFD[0]
ifd1 = self.IFD[-1]
width = ifd0.get ('ImageWidth').value
length = ifd0.get ('ImageLength').value
assert width == ifd1.get ('ImageWidth').value
assert length == ifd1.get ('ImageLength').value
depth = len(self.IFD)
compression = ifd.get('Compression').value
if compression!=1:
raise ValueError('Unable to get contiguous image stack from compressed data')
bits_per_sample = ifd0.get('BitsPerSample').value
photo_interp = ifd0.get('PhotometricInterpretation').value
planar_config = ifd0.get('PlanarConfiguration').value
strip_offsets0 = ifd0.get('StripOffsets').value
strip_nbytes0 = ifd0.get('StripByteCounts').value
strip_offsets1 = ifd1.get('StripOffsets').value
strip_nbytes1 = ifd1.get('StripByteCounts').value
samples_per_pixel = ifd1.get('SamplesPerPixel').value
assert samples_per_pixel==1,`samples_per_pixel`
if isinstance (bits_per_sample, numpy.ndarray):
dtype = getattr (self.dtypes, 'uint%s' % (bits_per_sample[i]))
else:
dtype = getattr (self.dtypes, 'uint%s' % (bits_per_sample))
if isinstance(strip_offsets0, numpy.ndarray):
start = strip_offsets0[0]
end = strip_offsets1[-1] + strip_nbytes1[-1]
else:
start = strip_offsets0
end = strip_offsets1 + strip_nbytes1
return self.data[start:end].view (dtype=dtype).reshape ((depth, width, length))
def get_subfile_types(self):
""" Return a list of subfile types.
"""
s = set()
for ifd in self.IFD:
s.add(ifd.get_value('NewSubfileType'))
return sorted(s)
def get_depth (self, subfile_type=0):
depth = 0
for ifd in self.IFD:
if ifd.get_value('NewSubfileType')==subfile_type:
depth += 1
return depth
def get_first_ifd(self, subfile_type=0):
""" Return the first IFD entry with given subfile type.
Parameters
----------
subfile_type : {0, 1, 2, 4}
Specify subfile type. 0: image, 1: reduced image, 2: single page, 4: transparency mask.
Returns
-------
ifd : IFDEntry
"""
for ifd in self.IFD:
if ifd.get_value('NewSubfileType')==subfile_type:
return ifd
def get_tiff_array(self, sample_index = 0, subfile_type=0):
""" Create array of sample images.
Parameters
----------
sample_index : int
Specify sample within a pixel.
subfile_type : int
Specify TIFF NewSubfileType used for collecting sample images.
Returns
-------
tiff_array : TiffArray
Array of sample images. The array has rank equal to 3.
"""
planes = []
index = 0
time_lst = self.time
for ifd in self.IFD:
if ifd.get_value('NewSubfileType', subfile_type) != subfile_type:
# subfile_type: 0: image, 1: reduced image, 2: single page, 4: transparency mask
continue
plane = TiffSamplePlane(ifd, sample_index=sample_index)
if time_lst is not None:
plane.set_time(time_lst[index])
planes.append(plane)
index += 1
tiff_array = TiffArray(planes)
return tiff_array
def get_samples(self, subfile_type=0, verbose=False):
"""
Return samples and sample names.
Parameters
----------
subfile_type : {0, 1}
Specify subfile type. Subfile type 1 corresponds to reduced resolution image.
verbose : bool
When True the print out information about samples
Returns
-------
samples : list
List of numpy.memmap arrays of samples
sample_names : list
List of the corresponding sample names
"""
l = []
i = 0
step = 0
can_return_memmap = True
ifd_lst = [ifd for ifd in self.IFD if ifd.get_value('NewSubfileType')==subfile_type]
depth = len(ifd_lst)
full_l = []
for ifd in ifd_lst:
if not ifd.is_contiguous():
raise NotImplementedError('none contiguous strips')
strip_offsets = ifd.get_value('StripOffsets')
strip_nbytes = ifd.get_value('StripByteCounts')
l.append((strip_offsets[0], strip_offsets[-1]+strip_nbytes[-1]))
for off, nb in zip (strip_offsets, strip_nbytes):
full_l.append ((off, off+nb))
if i==0:
compression = ifd.get_value('Compression')
if compression!=1:
can_return_memmap = False
#raise ValueError('Unable to get contiguous samples from compressed data (compression=%s)' % (compression))
width = ifd.get_value('ImageWidth')
length = ifd.get_value('ImageLength')
samples_per_pixel = ifd.get_value('SamplesPerPixel')
planar_config = ifd.get_value('PlanarConfiguration')
bits_per_sample = ifd.get_value('BitsPerSample')
sample_format = ifd.get_value('SampleFormat')[0]
photometric_interpretation = ifd.get_value('PhotometricInterpretation')
if self.is_lsm or not isinstance(strip_offsets, numpy.ndarray):
strips_per_image = 1
else:
strips_per_image = len(strip_offsets)
format = sample_format_map.get(sample_format)
if format is None:
print 'Warning(TIFFfile.get_samples): unsupported sample_format=%s is mapped to uint' % (sample_format)
format = 'uint'
dtype_lst = []
bits_per_pixel = 0
for j in range(samples_per_pixel):
bits = bits_per_sample[j]
bits_per_pixel += bits
dtype = getattr (self.dtypes, '%s%s' % (format, bits))
dtype_lst.append(dtype)
bytes_per_pixel = bits_per_pixel // 8
assert 8*bytes_per_pixel == bits_per_pixel,`bits_per_pixel`
bytes_per_row = width * bytes_per_pixel
strip_length = l[-1][1] - l[-1][0]
strip_length_str = bytes2str(strip_length)
bytes_per_image = length * bytes_per_row
rows_per_strip = bytes_per_image // (bytes_per_row * strips_per_image)
if bytes_per_image % (bytes_per_row * strips_per_image):
rows_per_strip += 1
assert rows_per_strip == ifd.get_value('RowsPerStrip', rows_per_strip), `rows_per_strip, ifd.get_value('RowsPerStrip'), bytes_per_image, bytes_per_row, strips_per_image, self.filename`
else:
assert width == ifd.get_value('ImageWidth', width), `width, ifd.get_value('ImageWidth')`
assert length == ifd.get_value('ImageLength', length),` length, ifd.get_value('ImageLength')`
#assert samples_per_pixel == ifd.get('SamplesPerPixel').value, `samples_per_pixel, ifd.get('SamplesPerPixel').value`
assert planar_config == ifd.get_value('PlanarConfiguration', planar_config)
if can_return_memmap:
assert strip_length == l[-1][1] - l[-1][0], `strip_length, l[-1][1] - l[-1][0]`
else:
strip_length = max (strip_length, l[-1][1] - l[-1][0])
strip_length_str = ' < ' + bytes2str(strip_length)
assert (bits_per_sample == ifd.get_value('BitsPerSample', bits_per_sample)).all(),`bits_per_sample, ifd.get_value('BitsPerSample')`
if i>0:
if i==1:
step = l[-1][0] - l[-2][1]
assert step>=0,`step, l[-2], l[-1]`
else:
if step != l[-1][0] - l[-2][1]:
can_return_memmap = False
#assert step == l[-1][0] - l[-2][1],`step, l[-2], l[-1], (l[-1][0] - l[-2][1]), i`
i += 1
if verbose:
bytes_per_image_str = bytes2str(bytes_per_image)
print '''
width : %(width)s
length : %(length)s
depth : %(depth)s
sample_format : %(format)s
samples_per_pixel : %(samples_per_pixel)s
planar_config : %(planar_config)s
bits_per_sample : %(bits_per_sample)s
bits_per_pixel : %(bits_per_pixel)s
bytes_per_pixel : %(bytes_per_pixel)s
bytes_per_row : %(bytes_per_row)s
bytes_per_image : %(bytes_per_image_str)s
strips_per_image : %(strips_per_image)s
rows_per_strip : %(rows_per_strip)s
strip_length : %(strip_length_str)s
''' % (locals ())
if photometric_interpretation==2:
assert samples_per_pixel==3, `samples_per_pixel`
sample_names = ['red', 'green', 'blue']
else:
sample_names = ['sample%s' % (j) for j in range (samples_per_pixel)]
depth = i
if not can_return_memmap:
if planar_config==1:
if samples_per_pixel==1:
i = 0
arr = numpy.empty(depth * bytes_per_image, dtype=self.dtypes.uint8)
bytes_per_strip = rows_per_strip * bytes_per_row
for start, end in full_l:
#sys.stdout.write ("%s:%s," % (start, end)); sys.stdout.flush ()
if compression==1: # none
d = self.data[start:end]
elif compression==5: # lzw
d = self.data[start:end]
d = tif_lzw.decode(d, bytes_per_strip)
arr[i:i+d.nbytes] = d
i += d.nbytes
arr = arr.view(dtype=dtype_lst[0]).reshape((depth, length, width))
return [arr], sample_names
else:
i = 0
arr = numpy.empty(depth * bytes_per_image, dtype=self.dtypes.uint8)
bytes_per_strip = rows_per_strip * bytes_per_row
for start, end in full_l:
sys.stdout.write ("%s:%s," % (start, end)); sys.stdout.flush ()
if compression==1: # none
d = self.data[start:end]
elif compression==5: # lzw
d = self.data[start:end]
d = tif_lzw.decode(d, bytes_per_strip)
arr[i:i+d.nbytes] = d
i += d.nbytes
dt = numpy.dtype(dict(names=sample_names, formats=dtype_lst))
arr = arr.view(dtype=dt).reshape((depth, length, width))
return [arr[n] for n in arr.dtype.names], arr.dtype.names
raise NotImplementedError(`depth, bytes_per_image, samples_per_pixel`)
else:
raise NotImplementedError (`planar_config`)
start = l[0][0]
end = l[-1][1]
if start > step:
arr = self.data[start - step: end].reshape((depth, strip_length + step))
k = step
elif end <= self.data.size - step:
arr = self.data[start: end+step].reshape((depth, strip_length + step))
k = 0
else:
raise NotImplementedError (`start, end, step`)
sys.stdout.flush()
if planar_config==2:
if self.is_lsm:
# LSM510: one strip per image plane channel
if subfile_type==0:
sample_names = self.lsminfo.get('data channel name')
elif subfile_type==1:
sample_names = ['red', 'green', 'blue']
assert samples_per_pixel==3,`samples_per_pixel`
else:
raise NotImplementedError (`subfile_type`)
samples = []
for j in range(samples_per_pixel):
bytes = bits_per_sample[j] // 8 * width * length
tmp = arr[:,k:k+bytes]
tmp = tmp.view(dtype=dtype_lst[j])
tmp = tmp.reshape((depth, length, width))
samples.append(tmp)
k += bytes
return samples, sample_names
raise NotImplementedError (`planar_config, self.is_lsm`)
elif planar_config==1:
samples = []
bytes = sum(bits_per_sample[:samples_per_pixel]) // 8 * width * length
bytes_per_sample = bits_per_sample // 8
for j in range(samples_per_pixel):
i0 = k+j*bytes_per_sample[j]
#print j, i0, i0+bytes, samples_per_pixel, arr.shape
tmp = arr[:,i0:i0+bytes:samples_per_pixel]
tmp = numpy.array(tmp.reshape((tmp.size,)))
tmp = tmp.view(dtype=dtype_lst[j])
tmp = tmp.reshape((depth, length, width))
samples.append(tmp)
#k += bytes
return samples, sample_names
else:
raise NotImplementedError (`planar_config`)
def get_info (self):
""" Return basic information about the file.
"""
l = []
subfile_types = self.get_subfile_types()
l.append ('Number of subfile types: %s' % (len (subfile_types)))
for subfile_type in subfile_types:
ifd = self.get_first_ifd(subfile_type=subfile_type)
l.append ('-'*50)
l.append('Subfile type: %s' % (subfile_type))
l.append('Number of images: %s' % (self.get_depth(subfile_type = subfile_type)))
for tag in ['ImageLength',
'ImageWidth',
'SamplesPerPixel','ExtraSamples',
'SampleFormat',
'Compression','Predictor',
'PhotometricInterpretation',
'Orientation',
'PlanarConfiguration',
'MinSampleValue', 'MaxSampleValue',
'XResolution', 'YResolution','ResolutionUnit',
'XPosition','YPosition',
'DocumentName',
'Software',
'HostComputer',
'Artist',
'DateTime',
'Make','Model','Copyright',
'ImageDescription',
]:
v = ifd.get_value(tag, human=True)
if v is None:
continue
if tag=='ImageDescription' and subfile_type==0:
if v.startswith ('<?xml') or v[:4].lower()=='<ome':
try:
import lxml.etree
tree = lxml.etree.fromstring(v)
v = lxml.etree.tostring (tree, pretty_print=True)
except Exception, msg:
print '%s.get_info: failed to parse xml in ImageDescription: %s' % (self.__class__.__name__, msg)
l.append ('%s:\n"""%s"""' % (tag, v))
else:
l.append ('%s:\n"""%s"""' % (tag, v))
else:
l.append ('%s: %s' % (tag, v))
if self.is_lsm and subfile_types==0:
l.append ('LSM info:\n"""%s"""' % (self.lsminfo))
return '\n'.join(l)
TiffFile = TIFFfile
class IFD:
""" Image File Directory data structure.
Attributes
----------
entries : IFDEntry-list
"""
def __init__(self, tiff):
self.tiff = tiff
self.entries = []
self.entries_dict = {}
def __len__ (self):
return len (self.entries)
def append(self, entry):
self.entries.append(entry)
self.entries_dict[entry.tag_name] = entry
@property
def memory_usage(self):
l = []
for entry in self.entries:
l.extend(entry.memory_usage)
return l
def __str__(self):
l = []
for entry in self.entries:
l.append(str (entry))
return '\n'.join(l)
def human (self):
l = []
for entry in self.entries:
l.append(entry.human ())
return '\n'.join(l)
def get(self, tag_name):
"""Return IFD entry with given tag name.
"""
return self.entries_dict.get(tag_name)
def get_value(self, tag_name, default=None, human=False):
""" Return the value of IFD entry with given tag name.
When the entry does not exist, return default.
"""
entry = self.get(tag_name)
if entry is not None:
value = entry.value
else:
if default is None:
if default_tag_values.has_key(tag_name):
value = default_tag_values[tag_name]
else:
value = None
sys.stdout.write ('%s.get_value: no default value defined tiff_data.default_tag_values dict for %r IFD tag\n' % (self.__class__.__name__, tag_name))
else:
value = default
if tag_name in ['StripOffsets', 'StripByteCounts']:
if not isinstance (value, numpy.ndarray):
value = numpy.array([value])
if tag_name in ['BitsPerSample', 'SampleFormat']:
samples_per_pixel = self.get_value ('SamplesPerPixel')
if not isinstance (value, numpy.ndarray):
value = numpy.array([value]*samples_per_pixel)
if tag_name in ['BitsPerSample']:
value = value[:samples_per_pixel]
if tag_name in ['ImageDescription', 'Software', 'Copyright', 'DocumentName', 'Model', 'Make', 'PageName',
'DateTime', 'Artist', 'HostComputer']:
if value is not None:
return ''.join(value.view('|S%s' % (value.nbytes//value.size)))
if human:
if tag_name=='Compression':
value = {1:'Uncompressed', 2:'CCITT1D', 3:'Group3Fax', 4:'Group4Fax',
5:'LZW', 6:'JPEG', 32773:'PackBits'}.get (value, value)
elif tag_name=='Predictor':
value = {1: 'None', 2: 'HorizontalDifferencing'}.get (value,value)
elif tag_name=='PhotometricInterpretation':
value = {0:'WhiteIsZero', 1:'BlackIsZero', 2:'RGB',3:'RGBPalette',
4:'TransparencyMask', 5:'CMYK', 6:'YCbCr', 8:'CIELab'}.get (value, value)
elif tag_name=='PlanarConfiguration':
value = {1:'Chunky', 2:'Planar'}.get (value, value)
elif tag_name=='Orientation':
value = {1:'TopLeft',2:'TopRight', 3:'BottomRight', 4:'BottomLeft',
5:'LeftTop', 6:'RightTop', 7:'RightBottom', 8:'LeftBottom'}.get (value, value)
elif tag_name=='SampleFormat':
new_value = []
for v in value:
new_value.append(type2name.get (v, v))
value = new_value
elif tag_name=='ResolutionUnit':
value = {1: 'Arbitrary', 2: 'Inch', 3: 'Centimeter'}.get (value, value)
elif tag_name=='FillOrder':
pass
return value
def get_sample_names(self):
subfile_type = self.get_value('NewSubfileType')
samples_per_pixel = self.get_value('SamplesPerPixel')
if self.tiff.is_lsm:
if subfile_type==0:
return self.tiff.lsminfo.get('data channel name')
if subfile_type==1 and samples_per_pixel==3:
return ['red', 'green', 'blue']
return ['sample%i' % i for i in range(samples_per_pixel)]
def get_pixel_name(self):
subfile_type = self.get_value('NewSubfileType')
samples_per_pixel = self.get_value('SamplesPerPixel')
if self.tiff.is_lsm:
if subfile_type==0:
return '_'.join(self.tiff.lsminfo.get('data channel name'))
if subfile_type==1 and samples_per_pixel==3:
return 'rgb'
return 'pixel'
def get_sample_dtypes(self):
sample_format = self.get_value('SampleFormat')
bits_per_sample = self.get_value('BitsPerSample')
return [self.tiff.dtypes.get_dtype(f, b) for f,b in zip(sample_format, bits_per_sample)]
def get_pixel_dtype(self):
sample_names = self.get_sample_names ()
sample_dtypes = self.get_sample_dtypes ()
return numpy.dtype (zip(sample_names, sample_dtypes))
def get_pixel_typename(self):
sample_dtypes = self.get_sample_dtypes ()
return '_'.join (map(str, sample_dtypes))
def finalize(self):
for entry in self.entries:
for hook in IFDEntry_finalize_hooks:
hook(entry)
def is_contiguous (self):
strip_offsets = self.get('StripOffsets').value
strip_nbytes = self.get('StripByteCounts').value
if isinstance(strip_offsets, numpy.ndarray):
for i in range (len(strip_offsets)-1):
if strip_offsets[i] + strip_nbytes[i] != strip_offsets[i+1]:
return False
return True
def get_contiguous(self, channel_name=None):
""" Return memmap of an image.
This operation is succesful only when image data strips are
contiguous in memory. Return None when unsuccesful.
"""
width = self.get ('ImageWidth').value
length = self.get ('ImageLength').value
strip_offsets = self.get('StripOffsets').value
strip_nbytes = self.get('StripByteCounts').value
bits_per_sample = self.get('BitsPerSample').value
photo_interp = self.get('PhotometricInterpretation').value
planar_config = self.get('PlanarConfiguration').value
compression = self.get('Compression').value
subfile_type = self.get('NewSubfileType').value
if compression != 1:
raise ValueError('Unable to get contiguous image from compressed data')
if not self.is_contiguous ():
raise ValueError('Image data not contiguous')
if self.tiff.is_lsm:
lsminfo = self.tiff.lsminfo
#print lsminfo
if subfile_type==0:
channel_names = lsminfo.get('data channel name')
elif subfile_type==1: # thumbnails
if photo_interp==2:
channel_names = 'rgb'
else:
raise NotImplementedError (`photo_interp`)
else:
raise NotImplementedError (`subfile_type`)
assert planar_config==2,`planar_config`
nof_channels = self.tiff.lsmentry['DimensionChannels'][0]
scantype = self.tiff.lsmentry['ScanType'][0]
assert scantype==0,`scantype` # xyz-scan
r = {}
for i in range (nof_channels):
if isinstance (bits_per_sample, numpy.ndarray):
dtype = getattr (self.dtypes, 'uint%s' % (bits_per_sample[i]))
r[channel_names[i]] = self.tiff.data[strip_offsets[i]:strip_offsets[i]+strip_nbytes[i]].view (dtype=dtype).reshape((width, length))
else:
dtype = getattr (self.dtypes, 'uint%s' % (bits_per_sample))
r[channel_names[i]] = self.tiff.data[strip_offsets:strip_offsets+strip_nbytes].view (dtype=dtype).reshape((width, length))
return r
else:
raise NotImplementedError (`self.tiff`)
def get_voxel_sizes(self):
tiff = self.tiff
if tiff.is_lsm:
sample_spacing = tiff.lsminfo.get('recording sample spacing')[0]
line_spacing = tiff.lsminfo.get('recording line spacing')[0]
plane_spacing = tiff.lsminfo.get('recording plane spacing')[0]
return (plane_spacing, line_spacing, sample_spacing)
descr = self.get_value('ImageDescription', human=True)
if descr is None:
return (1,1,1)
if descr.startswith ('<?xml') or descr[:4].lower()=='<ome':
raise NotImplementedError('getting voxel sizes from OME-XML string')
for vx,vy,vz in [('VoxelSizeX', 'VoxelSizeY', 'VoxelSizeZ'),
('PixelSizeX', 'PixelSizeY', 'PixelSizeZ'),
]:
ix = descr.find(vx)
iy = descr.find(vy)
iz = descr.find(vz)
if ix == -1: x = 1
else: x = float(descr[ix:].split (None, 2)[1].strip())
if iy == -1: y = 1
else: y = float(descr[iy:].split (None, 2)[1].strip())
if iz == -1: z = 1
else: z = float(descr[iz:].split (None, 2)[1].strip())
if -1 not in [ix,iy]:
return (z, y, x)
print 'Could not determine voxel sizes from\n%s' % (descr)
return (z,y,x)
def get_pixel_sizes(self):
tiff = self.tiff
if tiff.is_lsm:
sample_spacing = tiff.lsminfo.get('recording sample spacing')[0]
line_spacing = tiff.lsminfo.get('recording line spacing')[0]
return (line_spacing, sample_spacing)
descr = self.get_value('ImageDescription', human=True)
if descr is None:
return (1,1)
if descr.startswith ('<?xml') or descr[:4].lower()=='<ome':
raise NotImplementedError('getting pixels sizes from OME-XML string')
for vx,vy,vz in [('PixelSizeX', 'PixelSizeY', 'PixelSizeZ'),
('VoxelSizeX', 'VoxelSizeY', 'VoxelSizeZ'),
]:
ix = descr.find(vx)
iy = descr.find(vy)
if ix == -1: x = 1
else: x = float(descr[ix:].split (None, 2)[1].strip())
if iy == -1: y = 1
else: y = float(descr[iy:].split (None, 2)[1].strip())
if -1 not in [ix,iy]:
return (y, x)
print 'Could not determine pixel sizes from\n%s' % (descr)
return (1,1)
class IFDEntry:
""" Entry for Image File Directory data structure.
Attributes
----------
ifd : IFD
tiff : TIFFfile
tag : uint16
data tag constant
tag_name : str
data tag name
type : uint16
data type constant
type_name : str
data type name
count : uint32
number of data points
offset : {None, int}
offset of a tag entry in tiff data array
value : array
data array
bytes : int
number of bytes in data array
memory_usage : list of 3-tuples
(start byte, end byte, name of tag)
"""
def __init__(self, ifd, tiff, offset):
self.ifd = ifd
self.tiff = tiff
self.offset = offset
# initialization:
self.tag = tiff.get_uint16(offset)
self.type = tiff.get_uint16(offset+2)
self.count = tiff.get_uint32(offset+4)
for hook in IFDEntry_init_hooks:
hook(self)
self.bytes = bytes = type2bytes.get(self.type,0)
if self.count==1 and 1<=bytes<=4:
self.offset = None
value = tiff.get_value(offset+8, self.type)
else:
self.offset = tiff.get_int32(offset+8)
value = tiff.get_values(self.offset, self.type, self.count)
if value is not None:
self.value = value
tag_name = self.tag_name = tag_value2name.get(self.tag,'TAG%s' % (hex(self.tag),))
self.type_name = type2name.get(self.type, 'TYPE%s' % (self.type,))
self.memory_usage = []
if self.offset is not None:
self.memory_usage.append((self.offset, self.offset + self.bytes*self.count, self.tag_name))
@property
def _value_str(self):
tag_name = self.tag_name
value = self.value
if value is not None:
if tag_name in ['ImageDescription', 'Software']:
return ''.join(value.view('|S%s' % (value.nbytes//value.size)))
return value
def __str__(self):
if hasattr(self, 'str_hook'):
r = self.str_hook(self)
if isinstance (r, str):
return r
if hasattr(self, 'value'):
return 'IFDEntry(tag=%(tag_name)s, value=%(value)r, count=%(count)s, offset=%(offset)s)' % (self.__dict__)
else:
return 'IFDEntry(tag=%(tag_name)s, type=%(type_name)s, count=%(count)s, offset=%(offset)s)' % (self.__dict__)
def human(self):
if hasattr(self, 'str_hook'):
r = self.str_hook(self)
if isinstance (r, str):
return r
if hasattr(self, 'value'):
self.value_str = self._value_str
if self.tag_name=='ImageDescription':
return 'IFDEntry(tag=%(tag_name)s, value="%(value_str)s", count=%(count)s, offset=%(offset)s)' % (self.__dict__)
else:
return 'IFDEntry(tag=%(tag_name)s, value=%(value_str)r, count=%(count)s, offset=%(offset)s)' % (self.__dict__)
else:
return 'IFDEntry(tag=%(tag_name)s, type=%(type_name)s, count=%(count)s, offset=%(offset)s)' % (self.__dict__)
def __repr__(self):
return '%s(%r, %r)' % (self.__class__.__name__, self.tiff, self.offset)
def StripOffsets_hook(ifdentry):
if ifdentry.tag_name=='StripOffsets':
ifd = ifdentry.ifd
counts = ifd.get('StripByteCounts')
if ifdentry.offset is not None:
for i, (count, offset) in enumerate(zip(counts.value, ifdentry.value)):
ifdentry.memory_usage.append((offset, offset+count, 'strip %s' % (i)))
else:
offset = ifdentry.value
ifdentry.memory_usage.append((offset, offset+counts.value, 'strip'))
# todo: TileOffsets_hook
IFDEntry_finalize_hooks.append(StripOffsets_hook)
# Register CZ LSM support:
lsm.register(locals())
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