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 _______________________________________________ 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
