Bill, There are quite a number of possible compression types which can be used in a tiff file[1]. Some of these are enabled/disable at compilation time based in what external libraries are used. These are defined with preprocessor directives in the tiff configuration file[2]. Ideally CanRead should some how query libtiff about support for this... I am looking for some type of documentation now...
Brad [1] http://www.awaresystems.be/imaging/tiff/tifftags/compression.html [2] https://github.com/InsightSoftwareConsortium/ITK/blob/master/Modules/ThirdParty/TIFF/src/itktiff/tif_config.h.in#L218 On Nov 14, 2014, at 12:44 PM, Bill Lorensen <bill.loren...@gmail.com> wrote: > I added that compression option to the possibilities > > > On Fri, Nov 14, 2014 at 12:08 PM, Bradley Lowekamp > <blowek...@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.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 >> >> > > > > -- > Unpaid intern in BillsBasement at noware dot com _______________________________________________ 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
