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Pearu Peterson edited this page Aug 5, 2015
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PyLibTiff is a package that provides:
- a wrapper to the libtiff library to Python using ctypes.
- a pure Python module for reading and writing TIFF and LSM files. The images are read as numpy.memmap objects so that it is possible to open images that otherwise would not fit to computers RAM. Both TIFF strips and tiles are supported for low-level data storage.
There exists many Python packages such as PIL, FreeImagePy that support reading and writing TIFF files. The PyLibTiff project was started to have an efficient and direct way to read and write TIFF files using the libtiff library without the need to install any unnecessary packages or libraries. The pure Python module was created for reading "broken" TIFF files such as LSM files that in some places use different interpretation of TIFF tags than what specified in the TIFF specification document. The libtiff library would just fail reading such files. In addition, the pure Python module is more memory efficient as the arrays are returned as memory maps. Support for compressed files is not implemented yet.
tifffile.py by Christoph Gohlke is an excellent module for reading TIFF as well as LSM files, it is as fast as libtiff.py by using numpy.
>>> from libtiff import TIFF
>>> # to open a tiff file for reading:
>>> tif = TIFF.open('filename.tif', mode='r')
>>> # to read an image in the currect TIFF directory and return it as numpy array:
>>> image = tif.read_image()
>>> # to read all images in a TIFF file:
>>> for image in tif.iter_images(): # do stuff with image
>>> # to open a tiff file for writing:
>>> tif = TIFF.open('filename.tif', mode='w')
>>> # to write a image to tiff file
>>> tif.write_image(image)
>>> from libtiff import TIFFfile, TIFFimage
>>> # to open a tiff file for reading
>>> tif = TIFFfile('filename.tif')
>>> # to return memmaps of images and sample names (eg channel names, SamplesPerPixel>=1)
>>> samples, sample_names = tiff.get_samples()
>>> # to create a tiff structure from image data
>>> tiff = TIFFimage(data, description='')
>>> # to write tiff structure to file
>>> tiff.write_file('filename.tif', compression='none') # or 'lzw'
>>> del tiff # flushes data to disk
$ libtiff.info -i result_0.tif --no-gui
IFDEntry(tag=ImageWidth, value=512, count=1, offset=None)
IFDEntry(tag=ImageLength, value=512, count=1, offset=None)
IFDEntry(tag=BitsPerSample, value=32, count=1, offset=None)
IFDEntry(tag=Compression, value=1, count=1, offset=None)
IFDEntry(tag=PhotometricInterpretation, value=1, count=1, offset=None)
IFDEntry(tag=StripOffsets, value=8, count=1, offset=None)
IFDEntry(tag=Orientation, value=6, count=1, offset=None)
IFDEntry(tag=StripByteCounts, value=1048576, count=1, offset=None)
IFDEntry(tag=PlanarConfiguration, value=1, count=1, offset=None)
IFDEntry(tag=SampleFormat, value=3, count=1, offset=None)
Use --ifd to see the rest of 31 IFD entries
data is contiguous: False
memory usage is ok: True
sample data shapes and names:
width : 512
length : 512
samples_per_pixel : 1
planar_config : 1
bits_per_sample : 32
strip_length : 1048576
[('memmap', (32, 512, 512), dtype('float32'))] ['sample0']
$ libtiff.info --no-gui -i psf_1024_z5_airy1_set1.lsm
IFDEntry(tag=NewSubfileType, value=0, count=1, offset=None)
IFDEntry(tag=ImageWidth, value=1024, count=1, offset=None)
IFDEntry(tag=ImageLength, value=1024, count=1, offset=None)
IFDEntry(tag=BitsPerSample, value=8, count=1, offset=None)
IFDEntry(tag=Compression, value=1, count=1, offset=None)
IFDEntry(tag=PhotometricInterpretation, value=1, count=1, offset=None)
IFDEntry(tag=StripOffsets, value=97770, count=1, offset=None)
IFDEntry(tag=SamplesPerPixel, value=1, count=1, offset=None)
IFDEntry(tag=StripByteCounts, value=1048576, count=1, offset=None)
IFDEntry(tag=PlanarConfiguration, value=2, count=1, offset=None)
IFDEntry(tag=CZ_LSMInfo, value=CZ_LSMInfo276(
MagicNumber=[67127628],
StructureSize=[500],
DimensionX=[1024],
DimensionY=[1024],
DimensionZ=[20],
DimensionChannels=[1],
DimensionTime=[1],
SDataType=[1],
ThumbnailX=[128],
ThumbnailY=[128],
VoxelSizeX=[ 2.79017865e-08],
VoxelSizeY=[ 2.79017865e-08],
VoxelSizeZ=[ 3.60105263e-07],
OriginX=[ -2.22222228e-07],
OriginY=[ 1.90476196e-07],
OriginZ=[ 0.],
ScanType=[0],
SpectralScan=[0],
DataType=[0],
OffsetVectorOverlay->DrawingElement(name='OffsetVectorOverlay', size=200, offset=6560),
OffsetInputLut->LookupTable(name='OffsetInputLut', size=8388, subblocks=6, channels=1, offset=7560),
OffsetOutputLut->LookupTable(name='OffsetOutputLut', size=24836, subblocks=3, channels=3, offset=18638),
OffsetChannelColors->ChannelColors (names=['Ch3'], colors=[(255, 0, 0, 0)]),
TimeInterval=[ 0.],
OffsetChannelDataTypes->None,
OffsetScanInformation->recording[size=3535]
name = 'psf_1024_z5_airy1_set1'
description = ' '
notes = ' '
objective = 'C-Apochromat 63x/1.20 W Korr UV-VIS-IR M27'
special scan mode = 'FocusStep'
scan type = ''
scan mode = 'Stack'
number of stacks = 10
lines per plane = 1024
samples per line = 1024
planes per volume = 20
images width = 1024
images height = 1024
images number planes = 20
images number stacks = 1
images number channels = 1
linescan xy size = 512
scan direction = 0
scan directionz = 0
time series = 0
original scan data = 1
zoom x = 5.0000000000000009
zoom y = 5.0000000000000009
zoom z = 1.0
sample 0x = -0.22200000000000006
sample 0y = 0.19500000000000006
sample 0z = 6.8420000000000014
sample spacing = 0.028000000000000008
line spacing = 0.028000000000000008
plane spacing = 0.3600000000000001
rotation = 0.0
nutation = 0.0
precession = 0.0
sample 0time = 39583.598368055624
start scan trigger in = ''
start scan trigger out = ''
start scan event = 0
start scan time = 0.0
stop scan trigger in = ''
stop scan trigger out = ''
stop scan event = 0
start scan time = 0.0
use rois = 0
use reduced memory rois = 0
user = 'User Name'
usebccorrection = 0
positionbccorrection1 = 0.0
positionbccorrection2 = 0.0
interpolationy = 1
camera binning = 1
camera supersampling = 0
camera frame width = 1388
camera frame height = 1040
camera offsetx = 0.0
camera offsety = 0.0
rt binning = 1
ENTRY0x10000064L = 1
rt frame width = 512
rt frame height = 512
rt region width = 512
rt region height = 512
rt offsetx = 0.0
rt offsety = 0.0
rt zoom = 1.0000000000000004
rt lineperiod = 112.43300000000002
prescan = 0
lasers[size=188]
laser[size=80]
name = 'HeNe633'
acquire = 1
power = 5.0000000000000009
end laser
laser[size=84]
name = 'DPSS 532-75'
acquire = 1
power = 75.000000000000014
end laser
end lasers
tracks[size=2071]
track[size=2047]
pixel time = 1.5980000000000003
time between stacks = 1.0
multiplex type = 1
multiplex order = 1
sampling mode = 2
sampling method = 1
sampling number = 8
acquire = 1
name = 'Track'
collimator1 position = 16
collimator1 name = 'IR/Vis'
collimator2 position = 66
collimator2 name = 'UV/Vis'
is bleach track = 0
is bleach after scan number = 0
bleach scan number = 0
trigger in = ''
trigger out = ''
is ratio track = 0
bleach count = 0
spi center wavelength = 582.53000000000009
id condensor aperture = 'KAB1'
condensor aperture = 0.55000000000000016
id condensor revolver = 'FW2'
condensor filter = 'HF'
id tubelens = 'Tubelens'
id tubelens position = 'Lens LSM'
transmitted light = 0.0
reflected light = -1.0000000000000002
detection channels[size=695]
detection channel[size=671]
detector gain first = 700.00000000000011
detector gain last = 700.00000000000011
amplifier gain first = 1.0000000000000002
amplifier gain last = 1.0000000000000002
amplifier offs first = 0.10000000000000002
amplifier offs last = 0.10000000000000002
pinhole diameter = 144.00000000000003
counting trigger = 5.0
acquire = 1
integration mode = 0
special mode = 0
detector name = 'Pmt3'
amplifier name = 'Amplifier1'
pinhole name = 'PH3'
filter set name = 'EF3'
filter name = 'LP 650'
ENTRY0x70000011L = ''
ENTRY0x70000012L = ''
integrator name = 'Integrator3'
detection channel name = 'Ch3'
detector gain bc1 = 0.0
detector gain bc2 = 0.0
amplifier gain bc1 = 0.0
amplifier gain bc2 = 0.0
amplifier offs bc1 = 0.0
amplifier offs bc2 = 0.0
spectral scan channels = 32
spi wavelength start = 415.0
spi wavelength end = 735.0
ENTRY0x70000024L = 575.0
ENTRY0x70000025L = 575.0
dye name = ''
dye folder = ''
ENTRY0x70000028L = 1.0000000000000004
ENTRY0x70000029L = 0.0
end detection channel
end detection channels
beam splitters[size=330]
beam splitter[size=82]
filter set = 'HT'
filter = 'HFT 405/514/633'
name = 'HT'
end beam splitter
beam splitter[size=75]
filter set = 'NT1'
filter = 'Mirror'
name = 'NT1'
end beam splitter
beam splitter[size=76]
filter set = 'NT2'
filter = 'NFT 565'
name = 'NT2'
end beam splitter
beam splitter[size=73]
filter set = 'FW1'
filter = 'None'
name = 'FW1'
end beam splitter
end beam splitters
illumination channels[size=160]
illumination channel[size=136]
name = '633'
power = 0.30000000000000004
wavelength = 633.0
aquire = 1
power bc1 = 0.0
power bc2 = 0.0
end illumination channel
end illumination channels
data channels[size=338]
data channel[size=314]
name = 'Ch3'
acquire = 1
acquire = 0
color = 255
sampletype = 1
bitspersample = 8
ratio type = 0
ratio track1 = 0
ratio track2 = 0
ratio channel1 = ''
ratio channel2 = ''
ratio const1 = 0.0
ratio const2 = 0.0
ratio const3 = 1.0
ratio const4 = 0.0
ratio const5 = 0.0
ratio const6 = 0.0
end data channel
end data channels
end track
end tracks
timers[size=24]
end timers
markers[size=24]
end markers
end recording,
OffsetKsData->OffsetData(name='OffsetKsData', size=8, offset=48590),
OffsetTimeStamps->TimeStamps(stamps=[ 2335.75582836]),
OffsetEventList->EventList(events=[]),
OffsetRoi->DrawingElement(name='OffsetRoi', size=200, offset=6160),
OffsetBleachRoi->DrawingElement(name='OffsetBleachRoi', size=200, offset=6360),
OffsetNextRecording->None,
DisplayAspectX=[ 1.],
DisplayAspectY=[ 1.],
DisplayAspectZ=[ 1.],
DisplayAspectTime=[ 1.],
OffsetMeanOfRoisOverlay->DrawingElement(name='OffsetMeanOfRoisOverlay', size=200, offset=6760),
OffsetTopoIsolineOverlay->DrawingElement(name='OffsetTopoIsolineOverlay', size=200, offset=7160),
OffsetTopoProfileOverlay->DrawingElement(name='OffsetTopoProfileOverlay', size=200, offset=7360),
OffsetLinescanOverlay->DrawingElement(name='OffsetLinescanOverlay', size=200, offset=6960),
ToolbarFlags=[0],
OffsetChannelWavelength->ChannelWavelength (ranges=[(-1.0, -1.0)]),
OffsetChannelFactors->ChannelFactors(size=36, offset=40836),
ObjectiveSphereCorrection=[ 0.],
OffsetUnmixParameters->OffsetData(name='OffsetUnmixParameters', size=124, offset=48466),
Reserved=[[40896 44726 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0 0 0 0
0 0 0 0 0 0 0 0 0]]))
Use --ifd to see the rest of 39 IFD entries
data is contiguous: False
memory usage is ok: True
sample data shapes and names:
width : 1024
length : 1024
samples_per_pixel : 1
planar_config : 2
bits_per_sample : 8
strip_length : 1048576
[('memmap', (20, 1024, 1024), dtype('uint8'))] ['Ch3']
[((20, 128, 128), dtype('uint8')), ((20, 128, 128), dtype('uint8')), ((20, 128, 128), dtype('uint8'))] ['red', 'green', 'blue']