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.loren...@gmail.com> wrote: > Yes, from the vtk tests. I created them with imagemagik > > > On Fri, Nov 14, 2014 at 11:06 AM, Bradley Lowekamp > <blowek...@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.loren...@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.loren...@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.loren...@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 >>>>> <blowek...@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.loren...@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 >>>>>>> <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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.be...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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 <blowek...@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.mccorm...@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 >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> >>>>>>>> _______________________________________________ >>>>>>>> Powered by www.kitware.com >>>>>>>> >>>>>>>> Visit other Kitware open-source projects at >>>>>>>> http://www.kitware.com/opensource/opensource.html >>>>>>>> >>>>>>>> Kitware offers ITK Training Courses, for more information visit: >>>>>>>> http://kitware.com/products/protraining.php >>>>>>>> >>>>>>>> Please keep messages on-topic and check the ITK FAQ at: >>>>>>>> http://www.itk.org/Wiki/ITK_FAQ >>>>>>>> >>>>>>>> Follow this link to subscribe/unsubscribe: >>>>>>>> http://public.kitware.com/mailman/listinfo/insight-developers >>>>>>>> >>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Unpaid intern in BillsBasement at noware dot com >>>>>> >>>>> >>>>> >>>>> >>>>> -- >>>>> Unpaid intern in BillsBasement at noware dot com >>>> >>>> >>>> >>>> -- >>>> Unpaid intern in BillsBasement at noware dot com >>> >>> >>> >>> -- >>> Unpaid intern in BillsBasement at noware dot com >> > > > > -- > Unpaid intern in BillsBasement at noware dot com
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