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 _______________________________________________ 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
