Experimental Physics and
Industrial Control System

Mark Rivers <[email protected]> · Wed, 21 Mar 2012 04:11:15 +0000

Folks,

I added the SampleFormat tag to TIFF files written with the areaDetector NDFileTIFF plugin.  I then ran a test with an IDL script that collects 1 image of each supported areaDetector data type (Int8, UInt8, Int16, UInt16, Int32, UInt32, Float32, Float64), and saves the images to TIFF files.  IDL then reads the TIFF file and displays the data type of the array in the file.  Here are the results:

IDL> .run ~/devel/areaDetector/ADApp/pluginSrc/tiff_test
DATA            BYTE      = Array[1024, 1024]
DATA            BYTE      = Array[1024, 1024]
DATA            INT       = Array[1024, 1024]
DATA            UINT      = Array[1024, 1024]
DATA            LONG      = Array[1024, 1024]
DATA            ULONG     = Array[1024, 1024]
DATA            FLOAT     = Array[1024, 1024]
DATA            DOUBLE    = Array[1024, 1024]

This is exactly as expected.  IDL only supports unsigned 8-bit integers, not signed, so it does not distinguish between Int8 and UInt8, but it successfully reads all the TIFF files.

I then tried reading and displaying the files with ImageJ and PIL.

Here are the results with ImageJ:

Int8     OK
UInt8    OK
Int16    OK
UInt16   OK
Int32    OK
UInt32   OK
Float32  OK
Float64  Fail

So ImageJ does not support Float64, but does support all other types.

Here are the results with PIL:

Int8     Fail
UInt8    OK
Int16    OK
UInt16   OK
Int32    OK
UInt32   Fail
Float32  OK
Float64  Fail

So PIL does not support Int8, UInt32, or Float64.  It does support UInt8 and Int32, so it can read 8-bit and 32-bit TIFFs, but not both signed and unsigned.

I've committed these changes to the areaDetector SVN repository (https://subversion.xor.aps.anl.gov/synApps/areaDetector/trunk) and they will be in the upcoming R1-8 release.

Mark

________________________________________
From: Mark Rivers
Sent: Tuesday, March 20, 2012 2:34 PM
To: 'J. Lewis Muir'
Cc: Timothy Madden; [email protected]; Ross Harder; [email protected]
Subject: RE: 32-bit TIFFs and PIL

Hi Lewis,

Thanks very much for tracking that down!

I have added the SampleFormat tag to the areaDetector TIFF files, and now I can read signed 32-bit integer TIFFs with PIL. It will not read unsigned 32-bit TIFFs. By adding the SampleFormat tag I can now also successfully write 32-bit float and 64-bit double TIFF files as well. Those can be read fine with IDL, and the 32-bit float files can also be read by PIL.

I will do testing with each areaDetector data type and report which applications (IDL, ImageJ, PIL) can read which data types.

Thanks again,
Mark

-----Original Message-----
From: J. Lewis Muir [mailto:[email protected]]
Sent: Tuesday, March 20, 2012 11:48 AM
To: Mark Rivers
Cc: Timothy Madden; [email protected]; Ross Harder; [email protected]
Subject: Re: 32-bit TIFFs and PIL

On 3/20/12 11:25 AM, J. Lewis Muir wrote:
> So it seems to be unhappy about the pixel mode.

Looking further, there's a debug level variable in PIL which
sheds more light on things:

===
>>> import PIL.Image
>>> PIL.Image.DEBUG = 1
>>> im = PIL.Image.open("/tmp/im.tif")
tag: ImageWidth (256) - type: short (3) - value: (1023,)
tag: ImageLength (257) - type: short (3) - value: (1023,)
tag: BitsPerSample (258) - type: short (3) - value: (32,)
tag: Compression (259) - type: short (3) - value: (1,)
tag: PhotometricInterpretation (262) - type: short (3) - value: (1,)
tag: Make (271) - type: ascii (2) - value: Unknown
tag: Model (272) - type: ascii (2) - value: Unknown
tag: StripOffsets (273) - type: long (4) - value: (8,)
tag: SamplesPerPixel (277) - type: short (3) - value: (1,)
tag: RowsPerStrip (278) - type: short (3) - value: (1023,)
tag: StripByteCounts (279) - type: long (4) - value: (4186116,)
tag: PlanarConfiguration (284) - type: short (3) - value: (1,)
*** Summary ***
- compression: raw
- photometric_interpretation: 1
- planar_configuration: 1
- fill_order: 1
- size: (1023, 1023)
format key: ('II', 1, 1, 1, (32,), ())
- unsupported format
Traceback (most recent call last):
File "<stdin>", line 1, in <module>
File
"/opt3/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/PIL/Image.py",
line 1980, in open
raise IOError("cannot identify image file")
IOError: cannot identify image file
===

Looking at TiffImagePlugin.py where it generates the "-
unsupported format" message, and comparing the output with an
SLS PILATUS image that works, I see the following difference:

=== /tmp/im.tif (bad) ===
format key: ('II', 1, 1, 1, (32,), ())
===

=== /tmp/sls-im.tif (good) ===
format key: ('II', 1, 2, 1, (32,), ())
===

The third format key value is different. Looking at
TiffImagePlugin.py shows that the third value is the value of
the SAMPLEFORMAT (339) tag. In the bad TIFF, that tag appears
to be missing, but in the good TIFF, it's present and the debug
output shows it:

=== /tmp/sls-im.tif (good) ===
tag: SampleFormat (339) - type: short (3) - value: (2,)
===

Lewis

Experimental Physics and Industrial Control System

Experimental Physics and
Industrial Control System