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
