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DylanMuir/TIFFStack

  • TS_UnitTest(strFilename)
    TS_UnitTest - FUNCITON Unit test for TIFFStack
  • tiffread31_header(file_name)
    set defaults values :
  • tiffread31_readimage(TIF,...
    - Preallocate data block
  • TIFFStack
    TIFFStack - Manipulate a TIFF file like a tensor
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DylanMuir/TIFFStack

by

Dylan Muir (view profile)

 

01 Jul 2011 (Updated )

Read a TIFF stack as a memory-mapped tensor. Handles a large range of internal TIFF formats.

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File Information
Description

See also http://dylan-muir.com/articles/tiffstack/
If this code is useful to your academic work, please cite the publication in lieu of thanks:
Muir and Kampa, "FocusStack and StimServer: A new open source MATLAB toolchain for visual stimulation and analysis of two-photon calcium neuronal imaging data". Frontiers in Neuroinformatics (accepted).
Usage: tsStack = TIFFStack(strFilename <, bInvert>)
A TIFFStack object behaves like a read-only memory mapped TIF file. The entire image stack is treated as a matlab tensor. Each frame of the file must have the same dimensions. Reading the image data is optimised to the extent possible; the header information is only read once.
  
This class attempts to use the version of tifflib built-in to recent versions of Matlab, if available. Otherwise this class uses a modified version of tiffread [1, 2] to read data. Code is included (but disabled) to use the matlab imread function, but imread returns invalid data for some TIFF formats.
permute, ipermute and transpose are now transparantly supported. Note that to read a pixel, the entire frame containing that pixel is read. So reading a Z-slice of the stack will read in the entire stack.
Construction:
>> tsStack = TIFFStack('test.tiff'); % Construct a TIFF stack associated with a file
>> tsStack = TIFFStack('test.tiff', true); % Indicate that the image data should be inverted
tsStack =
  TIFFStack handle
  Properties:
         bInvert: 0
     strFilename: [1x9 char]
      sImageInfo: [5x1 struct]
    strDataClass: 'uint16'
Usage:
>> tsStack(:, :, 3); % Retrieve the 3rd frame of the stack, all planes
>> tsStack(:, :, 1, 3); % Retrieve the 3rd plane of the 1st frame
>> size(tsStack) % Find the size of the stack (rows, cols, frames, planes per pixel)
ans =
   128 128 5 1
>> tsStack(4); % Linear indexing is supported
>> tsStack.bInvert = true; % Turn on data inversion

Support for de-interleaving of channels and slices into the frame axis is also supported (see help text for TIFFStack).

References:
[1] Francois Nedelec, Thomas Surrey and A.C. Maggs. Physical Review Letters 86: 3192-3195; 2001. DOI: 10.1103/PhysRevLett.86.3192
[2] http://www.cytosim.org/misc/

Required Products MATLAB
MATLAB release MATLAB 7.11 (R2010b)
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Comments and Ratings (12)
11 Feb 2016 Sébastien MAILFERT

Hi Dylan,
You are right, the path was not correcly defined.

Now, my questions is how can I use the mex compiler please?
Best regards.

Comment only
10 Feb 2016 Dylan Muir

Dylan Muir (view profile)

Hi Sébastien,

The warning indicates that matlab can't use the mex compiler, which is required by TIFFStack for accelerated reading.

The error indicates that matlab can't find the file 'tiffread31_header.m', which is the 'private' subdirectory of TIFFStack. The TIFFStack directory needs to be added to the matlab path; perhaps you could check that.

I just downloaded the latest version, and can't reproduce the problem, even if I force TIFFStack to use the non-MEX versions of the access functions.

If you have further problems, please start an issue on github.

Best regards,
Dylan.

Comment only
10 Feb 2016 Sébastien MAILFERT

Hello,

I tried your function and I saw this error:

Warning: --- TIFFStack: Using slower non-TiffLib access.
> In TIFFStack (line 187)
Warning: --- TIFFStack: Could not compile MEX functions. Using slow matlab versions.
> In TIFFStack>GetMexFunctionHandles (line 1354)
In TIFFStack (line 192)
Error using TIFFStack (line 390)
*** TIFFStack: Could not open file
[T:\dark0.tif].

Caused by:
Undefined function 'tiffread31_header' for input arguments of type 'char'.

Could you help me please?

Comment only
15 Jul 2015 Dylan Muir

Dylan Muir (view profile)

Hi HCYU, Please pull the latest version and try again. There was a referencing bug for older versions of matlab -- I think this may have been your issue.
Best regards, Dylan.

Comment only
15 Jul 2015 HCYU

HCYU (view profile)

new error message below:

Error using TIFFStack>TS_read_data_Tiff (line 761)
*** TIFFStack: Could not read data from image file.

Error in TIFFStack/subsref (line 438)
tfData = TS_read_data_Tiff(oStack, S.subs, bLinearIndexing);

Error in testvaa3d (line 6)
img = iStack(:, :, i);

Caused by:
Error using tifflib
Directory numbers must be greater than or equal to 1.

Comment only
15 Jul 2015 Dylan Muir

Dylan Muir (view profile)

Hi HCYU, thanks for your bug report. I have fixed the bug in the latest commit of TIFFStack. You can pull it immediately from github; the file exchange version takes a day to update.
Best regards, Dylan.

Comment only
14 Jul 2015 HCYU

HCYU (view profile)

note that: "tfData = oStack.sImageInfo(1).MaxSampleValue - (tfData - oStack.sImageInfo(1).MinSampleValue);"

error info:"Error using -
Integers can only be combined with integers of the same class, or scalar doubles."

Comment only
24 Apr 2015 Dylan Muir

Dylan Muir (view profile)

Hi David, thanks for your message. I'm sorry about that regression. I've uploaded a new version which fixes the problem.
Best regards, Dylan,

Comment only
24 Apr 2015 David

David (view profile)

With the most recent version getting errors when accessing object properties like strDataClass

Error using cellfun
Input #2 expected to be a cell array, was char instead.

Error in TIFFStack/subsref (line 289)
cellfun(@isvalidsubscript, S.subs);

Comment only
09 Mar 2015 Dylan Muir

Dylan Muir (view profile)

Hi Jana, the class has documentation available if you type `help TIFFStack`. What seems to be the problem?

Comment only
09 Mar 2015 Jana Katharina Wrosch

Can't get this to work. Is there a documentation on how to use it?

Comment only
24 Jul 2011 Federico

Best way, to my knowledge, to work with TIFF stacks on Matlab. Recommended.

Updates
24 Jul 2011 1.1

Fixed a bug when indexing non-square TIFF files.

27 Jul 2011 1.2

Fixed a bug when referencing slice 58 of a stack.

16 Aug 2011 1.3

Updated screenshot

30 Sep 2011 1.4

Updated link to Francois Nedelec

07 Nov 2011 1.5

Updated description

05 Sep 2013 1.6

Dramatic acceleration by using tifflib when possible. Added support for permute and transpose.

05 Mar 2014 1.7

Updated description

26 Mar 2014 1.8

Updated description

17 Jun 2014 1.9

Updated description

23 Oct 2014 1.10

Fixed a bug in indexing into an image file

04 Nov 2014 1.11

Fixed bugs where tifflib would cause a crash when TIFFStack was not called with a valid filename.

09 Nov 2014 1.12

Fixed a bug where tiffflib would fail to read tiled images correctly.

08 Dec 2014 1.13

Added paper reference.

20 Jan 2015 1.14

Improved efficiency of linear indexing. Removed code to call imread, which was unused in any case.

21 Jan 2015 1.15

Updated usage notes

23 Jan 2015 1.16

Fixed a bug when using TIFFStack to load an entire stack, with ts(:);

23 Apr 2015 1.17

Improved referencing to make it more similar to matlab tensors. Fixed a referencing bug involving a confusion between "58" and ":".

23 Apr 2015 1.18

Improved referencing for edge cases.

24 Apr 2015 1.19

Fixed a regression when referencing object properties

18 Aug 2015 1.20

Moved TIFFStack to github hosting

19 Nov 2015 1.21

Reinstated description

02 Feb 2016 1.21

Added information that de-interleaving is supported

03 Feb 2016 1.21

Added "neuroscience" tag

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