[ITK] [ITK-users] [ITK-dev] TIFFImageIO refactoring, please test
Bill Lorensen
bill.lorensen at gmail.com
Fri Nov 14 12:44:14 EST 2014
I added that compression option to the possibilities
On Fri, Nov 14, 2014 at 12:08 PM, Bradley Lowekamp
<blowekamp at mail.nih.gov> wrote:
> Bill,
>
> Your images have an odd compression:
>
> $ tiffinfo
> /scratch/blowekamp/build/VTK/ExternalData/Testing/Data/libtiff/tiled_64x64_tiff_example.tif
> TIFF Directory at offset 0x81f6 (33270)
> Image Width: 256 Image Length: 256
> Tile Width: 64 Tile Length: 64
> Bits/Sample: 8
> Compression Scheme: AdobeDeflate
> Photometric Interpretation: min-is-black
> FillOrder: msb-to-lsb
> Orientation: row 0 top, col 0 lhs
> Samples/Pixel: 1
> Rows/Strip: 256
> Planar Configuration: single image plane
> Page Number: 0-1
> DocumentName: foo.tif
> White Point: 0.3127-0.329
> PrimaryChromaticities:
> 0.640000,0.330000,0.300000,0.600000,0.150000,0.060000
> Predictor: horizontal differencing 2 (0x2)
>
> This "AdobeDeflate" is not supported by the
> itk::TIFFImageIOInternal::CanRead method. This is what is causing the usage
> of TIFFRGBARead and not the fact that it's a tiled image.
>
> How is VTK handling this odd compression?
>
> Brad
>
> On Nov 14, 2014, at 11:09 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>
> Yes, from the vtk tests. I created them with imagemagik
>
>
> On Fri, Nov 14, 2014 at 11:06 AM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
>
> Actually further reading the TIFFReadScanline documentation says that should
> not work for tiled images. So I guess it must be using the RGBA read method,
> but I am not sure how that is happening either.
>
> Are you used the tiled tiff images from the VTK tests?
>
> Brad
>
>
> On Nov 14, 2014, at 10:46 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>
> Meant to say:
> Wow. The new itk tiff reader read my tiled images.
>
>
> On Fri, Nov 14, 2014 at 10:45 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>
> Wow. The new itk tiff reader sad my tiled images.
>
> On Fri, Nov 14, 2014 at 10:25 AM, Bill Lorensen <bill.lorensen at gmail.com>
> wrote:
>
> There is a TIFFReadTile call in lib tiff. I some tiled images I will
> try with the updated itk reader. I'll be really syprised if it works
> since reading tiled images is tricky and took quite a bit of code.
>
> I'll keep you posted.
>
> Bill
>
> On Fri, Nov 14, 2014 at 10:19 AM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
>
> Bill,
>
> There was a tile block of code before, but that was not covered, looked
> unreachable and was removed.
>
> Currently there are two ways that a tiff page can be read with the
> TIFFReadRGBAImageOriented, and with the TIFFReadScanline. The RGBA method
> from libtiff is fairly robust but reads the image into an RGBA buffer so is
> not memory efficient. Our custom method uses the scanline method [1], which
> should work with both stripped and tiled pages.
>
> But please test, and add a test? I'm not 100% if there is a test image for
> tiled images.
>
> Where the difference between stripped and tiled images would really matter
> is streaming, but that is not there...yet.
>
> Brad
>
> [1] http://www.remotesensing.org/libtiff/libtiff.html#scanlines
>
>
> On Nov 14, 2014, at 10:04 AM, Bill Lorensen <bill.lorensen at gmail.com> wrote:
>
> Brad,
>
> I recently added tiled image reading to VTK's tiff reader. Do you
> think that would be useful in IUTK. I don't know how often tiled tiff
> images are encountered.
>
> BTW I do not mean tiled pyramid tiff images.
>
> Bill
>
> On Fri, Nov 14, 2014 at 9:53 AM, Bradley Lowekamp
> <blowekamp at mail.nih.gov> wrote:
>
> Greetings,
>
> I have recently refactored ITK's TIFFImageIO to remove a significant amount
> of dead code, and improve performance up to 3-5X. A number of bug related to
> reading BigTIFF files have been addressed. Additionally, Tiff tags are now
> place into the Meta-DataDictionary to allow access to additional TIFF fields
> such as OME-XML tags ( Originally contributed by Richard Beare
> http://www.insight-journal.org/browse/publication/728 ).
>
> Significant performance improvements were made to both scalar images and
> palette images. Handling of certain orientations are now "better" handled,
> while not changing how the default TOPLEFT orientation is loaded or written.
> There were a number of cases which appear unreachable and illogical such as
> support from Zeiss two-componet types, and support for some type of SGI
> tiled tiff as a 3D image. These were removed.
>
> If you are an active user of TIFF images with ITK, please checkout the
> latest ITK master and test the refactored TIFFImageIO.
>
> Thanks,
> Brad
>
> p.s. Here is the git log for the recent changes.
>
> $git log --no-merges 6791b4a3613aade07e3f11f765f1316faf03b113..
>
> commit 46f4125df47aeff9c42c9f2b3699c06e67ffaca9
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Fri Oct 31 14:25:13 2014 -0400
>
> ENH: adding TIFFImageIO test for RGB palette images
>
> Change-Id: I320acc8beac8225616451d11b291b1d7e12a17d0
>
> commit 9adc54c7f53b4da84a41f500d561ae494cb85158
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Fri Oct 24 13:42:02 2014 -0400
>
> BUG: Adding missing parentheses around boolean expression
>
> Change-Id: I669d160ff3ba830f3c33ac87de434db41472eb79
>
> commit 40afd95161727be3274f8094ce19fe45e2c3aa50
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Wed Oct 22 15:05:39 2014 -0400
>
> PERF: Refactor color table lookup
>
> Change to use a index lookup for the color and gray scale
> palettes. The remove excessive exception checking done on a per pixel
> basis with the GetColor method. Additionally the InitializeColor
> method was change do initialize the color palette variables.
>
> An exception no longer occurs when an index exceeds the number of
> entries in a palette. Instead a module operator is used to prevent
> out of bounds memory access.
>
> Change-Id: Ia62c65cd8b1be0d66c488540709a8fb961190cc9
>
> commit d98cbeb7206f6007f7d0c25fd4a4becad8973053
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Fri Oct 3 09:01:28 2014 -0400
>
> ENH: Refactor per pixel conversion function to per scan-line method
>
> This patch changes the implementation of conversion from the TIFF
> scanline buffer from a function call on each pixel to a function call
> per scanline. The enable efficient copying of similar scanline and
> better reuse of variables for palette look ups.
>
> This can increase the performance of reading grayscale images by up to
> 3X for cached files.
>
> Change-Id: I24bb744fda35629f1c1ed7154e26e5708e912059
>
> commit 8e488f40e8cb7defa046700798b77e3944ac33c9
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Tue Sep 30 08:56:58 2014 -0400
>
> ENH: RGBA read images should stay unchanged.
>
> The image that are read with the TIFFReadRGBAImage should not have
> their pixel types converted. This libtiff method always read images
> into an ABGR uint8 format. When the tiff file is read by this method
> it should report that uint8 and RGBA is the component an pixel type
> for the image. This allows the standard ITK buffer conversion to be
> performed.
>
> This change remove extra cases and template instantiations.
>
> Additionally the RGBAImageToBuffer method was flipping the image along
> the y-axis, this has been more explicitly done with the call to
> TIFFReadRGBAImageOriented.
>
> Change-Id: I022b12921d406edb09730f905213b0db811f1bd4
>
> commit e5834d5b00e4e3fab3255d88e7d8fd917ee722e9
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Fri Sep 26 14:04:09 2014 -0400
>
> ENH: Remove support for TIFF tile as 3D and dead code
>
> This TIFF file format is a file which contains a list of directories,
> if there are no directories in the file it's not a valid tiff. Code
> which supported 3D tiles was conditioned on a file with no directories
> and no data. Additional code was removed related to a private SGI tag
> TIFFTAG_TILEDEPTH, ImageJ specific tag also pre-conditioned on this
> invalid case.
>
> Change-Id: Id4ef171c5dbe0c797be206e0059c7488719ef6e6
>
> commit 3ac19a9ffd94e02254900dd0e5e2661c329e3183
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Mon Oct 6 10:01:50 2014 -0400
>
> BUG: Address Coverity warning about null pointer dereferences
>
> The patch addressed the following Coverity warnings:
>
> ** CID 1243373: Explicit null dereferenced (FORWARD_NULL)
> itkTIFFImageIO.cxx:
> 1192 in itk::TIFFImageIO::ReadTIFFTags()()
>
> ** CID 1243372: Dereference null return value (NULL_RETURNS)
> itkTIFFImageIO.cxx:
> 1096 in itk::TIFFImageIO::ReadTIFFTags()()
>
> ** CID 1243371: Dereference before null check (REVERSE_INULL)
> itkTIFFImageIO.cxx:
> 1100 in itk::TIFFImageIO::ReadTIFFTags()()
> Last login: Fri Oct 3 19:47:29 on ttys004
>
> Change-Id: I02c8435628c860ff03889b9b57e9dd1543bf82da
>
> commit 52ce992f3a57ef9f187f9c4b4ebd7ce20db365bd
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Fri Sep 26 11:04:38 2014 -0400
>
> ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage
>
> Refactoring of the pixelOffset to include the number of components
> remove the need for a separate block for RGB multi-component files.
>
> commit 97b33787ec17b76a61fdb43b5f1e1ea708bbac2c
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Wed Sep 24 15:00:54 2014 -0400
>
> ENH: add arbitrary TIFF TAGs to meta-data dictionary
>
> A more general approach to adding custom tiff tags to the meta-data
> dictionary has been used based on the implementation of libtiff's
> PrintDirectory method and the libtiff "Defining New TIFF Tags"
> documentation.
>
> Additionally a new test image was added generated in Photoshop, which
> has a novel pixel layout, and also contains additional tag types such
> as byte, and size specified ascii.
>
> Change-Id: Idb2e669e540cfbe27a932444011f4b9896ca403d
>
> commit 795c71abb8b5c3a09d461ec7b34eefbfdcb460e9
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Mon Sep 22 15:08:36 2014 -0400
>
> BUG: Use array delete operator for array new allocations
>
> Change-Id: Ic9bc3c3792083a1a1b3fd842486a7436a4086150
>
> commit 83e8b6e699b3d9e2da8533dd1ea36dc0692bc9eb
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Tue Sep 23 11:14:15 2014 -0400
>
> STYLE: Fix minor kwstyle defects in test and test results
>
> Change-Id: I4b2641d31acb5c764de4041bb7d21c08b3c99846
>
> commit 869f3275120646829b27d5cd75c23800d9df01cd
> Author: Richard Beare <Richard.Beare at ieee.org>
> Date: Tue Sep 23 11:11:34 2014 -0400
>
> ENH: Include TIFF tags in the MetaDataDictionary
>
> Add contribution from the Insight Journal:
> http://hdl.handle.net/10380/3170
>
> Change-Id: I20b02394d92c421bad75c5d0af496a6e80089ac0
>
> commit c7a76c9acb319862647a651a2060dd3fb16560d7
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Mon Sep 22 14:46:44 2014 -0400
>
> BUG: Remove dead separated plannar code, add test
>
> The PLANARCONFIG_SEPARATE block in TIFFImageIO::ReadGenericImage, was
> preceded by a unreachable due to a conditional and exception
> check. Support for this configuration remains in the TIFFReadRGBAImage
> method. A test for the configuration has been added.
>
> A new input image is added from the from the libTiff test images:
>
> PlanarConfiguration = 2 (separated samples)
> -------------------------------------------
> oxford.tif 601x81 8-bit RGB (lzw) screendump off oxford
>
> Change-Id: Ibb874f80809b70b1aee7a2c9ff1fc8544ed56c04
>
> commit 1b57d75964496dd2cc9e050a4a4425f1163d4b22
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Mon Sep 22 13:32:23 2014 -0400
>
> BUG: Fix right oriented tiff images
>
> The TIFFImageIO::ReadGenericImage method correctly handled top-left
> oriented images, and bottom-right image, however images oriented with
> right were non-correctly handled. These cases are now handled
> correctly by the TIFFRGBAImage generic path.
>
> New test images of the cthead1 image were added which have been
> flipped the to the different orientation, and the matching orientation
> tag specified so that they should all be read as equivalent
> images. These have been added as a test case.
>
> Change-Id: I058382d6d2e18341ab87edd165490be2187c1d15
>
> commit 6263f4389026f1bd770054e86c428b56629d705b
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Thu Sep 18 16:20:41 2014 -0400
>
> ENH: Refactor duplicated code to read a page
>
> Created a method to read a single page or sub-image in a tiff
> file. Simular code was both in the ReadVolume method for 3-d and the
> Read method for 2-d. The code block from ReadVolume was used because
> it contained more typed cases. There for this patch does improve the
> 2d reading capabilities for tiffio, so that they are consistent with
> the 3d.
>
> Change-Id: I0fbfb19f04435a703bb3fa09ea4e79179592e443
>
> commit 233571f1e626917bce872e450907bc8e8521e371
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Thu Sep 18 14:59:58 2014 -0400
>
> ENH: Refactor method to convert RGBA image to output buffer
>
> BUG: Address overflow issue when computing page offset with
> TIFFReadRGBAImage method.
>
> Extract repeated code to convert from ReadRGBAImage to output image
> type.
>
> Change-Id: Ia90b5e104f22c77493b8a4cd5bf640fd793b8b4b
>
> commit 1cd59825fa65f1123726a32f67c1a443015b40ec
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Thu Sep 18 11:30:41 2014 -0400
>
> BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO
> )
>
> There are no tests for this branch of code. It only works in 3D under
> certain cases. There are apparent bugs in the code such as not setting
> all of the input image, and logically dead branches. Some downloaded
> test images for similar described format do not load. This may effect
> files with the extensions tif, tiff, or lsm.
>
> Removal of this code will enable expansion of the current code to more
> generically support multi-sample per pixel images.
>
> For more robust reading of this type of image the SCIFIO remote
> module should be used.
>
> Change-Id: Idb98d69538db3bc8520881ea4a5e22476238c41e
>
> commit 690cfdc89343fcc8c7d3cc266d652cfb14de9d41
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Tue Sep 16 15:31:52 2014 -0400
>
> ENH: Refactor GenericReadImage into template function
>
> Reduce code duplication by using template method.
>
> Change-Id: I79411ad6595258d54cbfa5a4152cc55994acd8e0
>
> commit 5f73f24bfb668fa9f33804218c0db05cf5cadb3f
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Tue Sep 16 12:09:59 2014 -0400
>
> ENH: Refactor ReadTwoSamplePerPixelImage into template function
>
> Reduce code duplication by using template method.
>
> Change-Id: I45f417486e60a4d3e67ff31fa967dac069b3ce3e
>
> commit 0b573136d636613217df9683ea846db8039f9312
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Tue Sep 16 11:12:45 2014 -0400
>
> ENH: Extract TiffReaderInternal to separate file
>
> Refactored private class to be in separate private header.
>
> Change-Id: Icb4008c1605a3a0b62c563350cf2e3bbe948ec6d
>
> commit 6791b4a3613aade07e3f11f765f1316faf03b113
> Author: Bradley Lowekamp <blowekamp at mail.nih.gov>
> Date: Mon Sep 15 16:46:26 2014 -0400
>
> BUG: Fix overflows computing size of read tiff image
>
> When multiplying the height and width of an tiff image (32-bits),
> at least one element should be converted to size_t to help prevent
> numeric overflow.
>
> This change enables reading of larger RGB and large 2D image, that
> were previously truncated when reading. This does not address
> potential buffer overflow or resource limits which could occur.
>
> Change-Id: I192370606677c8dc1a903c67c2a0701026256d5a
>
> commit b6fabfeb2a5b8d339b2d459edd3e3c50232b55ff
> Author: Matt McCormick <matt.mccormick at kitware.com>
> Date: Mon Aug 25 00:35:48 2014 -0400
>
> COMP: Do not use _stat64 with MinGW-32.
>
> Unlike MinGW-w64, MinGW-32 aka MinGW, does not define as much of the API
> including _stat64. Do not use use _stat64 in TIFFImageIO when building
> with
> MinGW-32.
>
> Change-Id: I8f13a4500cdadf4f4adae7b5cf8893fe8b8cad55
>
>
>
>
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