Meant to say: Wow. The new itk tiff reader read my tiled images.
On Fri, Nov 14, 2014 at 10:45 AM, Bill Lorensen <[email protected]> wrote: > Wow. The new itk tiff reader sad my tiled images. > > On Fri, Nov 14, 2014 at 10:25 AM, Bill Lorensen <[email protected]> > 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 >> <[email protected]> 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 <[email protected]> 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 >>>> <[email protected]> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> Date: Fri Oct 24 13:42:02 2014 -0400 >>>>> >>>>> BUG: Adding missing parentheses around boolean expression >>>>> >>>>> Change-Id: I669d160ff3ba830f3c33ac87de434db41472eb79 >>>>> >>>>> commit 40afd95161727be3274f8094ce19fe45e2c3aa50 >>>>> Author: Bradley Lowekamp <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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 <[email protected]> >>>>> 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
