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Merge remote-tracking branch 'blowekamp/ForSlicerUpdateTiffIO' into slicer-v4.6.0-2014-09-19-554e46a
* blowekamp/ForSlicerUpdateTiffIO: (24 commits) COMP: Add explicit conversion to const char BUG: Support TIFF tiled image with TIFFReadRGBAImage ENH: Query libtiff to determine compression support ENH: adding TIFFImageIO test for RGB palette images BUG: Adding missing parentheses around boolean expression PERF: Refactor color table lookup ENH: Refactor per pixel conversion function to per scan-line method ENH: RGBA read images should stay unchanged. ENH: Remove support for TIFF tile as 3D and dead code BUG: Address Coverity warning about null pointer dereferences ENH: Reduce code duplicate in TIFFImageIO::ReadCurrentPage ENH: add arbitrary TIFF TAGs to meta-data dictionary BUG: Use array delete operator for array new allocations STYLE: Fix minor kwstyle defects in test and test results ENH: Include TIFF tags in the MetaDataDictionary BUG: Remove dead separated plannar code, add test BUG: Fix right oriented tiff images ENH: Refactor duplicated code to read a page ENH: Refactor method to convert RGBA image to output buffer BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO ) ...
2 parents 56fae27 + 48a677f commit 8012ade

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‎Documentation/Migration/TIFFZeiss2Channel.xml‎

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<?xml version="1.0" encoding="UTF-8"?>
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<!DOCTYPE Change SYSTEM "http://itk.org/migrationv4/ITKMigration.dtd">
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<!--**
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**
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** TIFFZeiss2Channel.xml
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**
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** >>>>>>>>>>>>>>>>>>>>>>>>>>>>
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** THIS FILE HAS BEEN AUTOMATICALLY GENERATED. EDIT IT BEFORE COMMITING
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** <<<<<<<<<<<<<<<<<<<<<<<<<<<
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**
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** Please, make sure this file validates the following w3c test before committing it: http://validator.w3.org
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**-->
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<Change>
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<!--**
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** Title for the online migration page
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**-->
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<Title>
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TIFF Zeiss 2-Channel
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</Title>
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<!--**
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** The author of the change
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**-->
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<Author>
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Bradley Lowekamp
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</Author>
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<!--**
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** Date of creation for the XML document
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**-->
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<Date>
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2014-09-18
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</Date>
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<!--**
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** Plain text description of the change
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** Extracted from git commit messages
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**-->
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<Description>
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<![CDATA[
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BUG: Remove Zeiss 2-channel support code in TIFFImageIO ( and LSMImageIO )
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There are no tests for this branch of code. It only works in 3D under
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certain cases. There are apparent bugs in the code such as not setting
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all of the input image, and logically dead branches. Some downloaded
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test images for similar described format do not load. This may effect
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files with the extensions tif, tiff, or lsm.
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Removal of this code will enable expansion of the current code to more
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generically support multi-sample per pixel images.
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For more robust reading of this type of image the SCIFIO remote
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module should be used.
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]]>
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</Description>
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<!--**
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** Sample code snippets
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** Extracted from git diff of changed files in Examples and Testing
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**-->
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<SampleCode>
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<Old>
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<![CDATA[
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]]>
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</Old>
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<New>
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<![CDATA[
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]]>
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</New>
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</SampleCode>
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<!--**
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** The change-ids for all commits in the topic branch
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**-->
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<Gerrit-ChangeId>
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Idb98d69538db3bc8520881ea4a5e22476238c41e
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</Gerrit-ChangeId>
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<!--**
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** List of all changed files from the topic branch
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**-->
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<FileList>
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Modules/IO/TIFF/include/itkTIFFImageIO.h
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Modules/IO/TIFF/src/itkTIFFImageIO.cxx
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</FileList>
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</Change>

‎Modules/IO/TIFF/include/itkTIFFImageIO.h‎

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/** Reads 3D data from multi-pages tiff. */
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virtual void ReadVolume(void *buffer);
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/** Reads 3D data from tiled tiff. */
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virtual void ReadTiles(void *buffer);
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/*-------- This part of the interfaces deals with writing data. ----- */
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/** Determine the file type. Returns true if this ImageIO can read the
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void InitializeColors();
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void ReadGenericImage(void *out,
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unsigned int itkNotUsed(width),
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unsigned int width,
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unsigned int height);
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// To support Zeiss images
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void ReadTwoSamplesPerPixelImage(void *out,
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unsigned int itkNotUsed(width),
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unsigned int width,
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unsigned int height);
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int EvaluateImageAt(void *out, void *in);
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unsigned int GetFormat();
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void GetColor(int index, unsigned short *red,
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void GetColor(unsigned int index, unsigned short *red,
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unsigned short *green, unsigned short *blue);
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// Check that tag t can be found
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TIFFReaderInternal *m_InternalImage;
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void ReadTIFFTags();
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int m_Compression;
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int m_JPEGQuality;
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private:
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TIFFImageIO(const Self &); //purposely not implemented
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void operator=(const Self &); //purposely not implemented
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void ReadCurrentPage(void *out, size_t pixelOffset);
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template <typename TComponent>
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void ReadGenericImage(void *out,
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unsigned int width,
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unsigned int height);
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template <typename TComponent>
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void RGBAImageToBuffer( void *out, const uint32_t *tempImage );
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template <typename TType>
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void PutGrayscale( TType *to, TType * from,
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unsigned int xsize, unsigned int ysize,
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unsigned int toskew, unsigned int fromskew );
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template <typename TType>
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void PutRGB_( TType *to, TType * from,
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unsigned int xsize, unsigned int ysize,
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unsigned int toskew, unsigned int fromskew );
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template <typename TType, typename TFromType>
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void PutPaletteGrayscale( TType *to, TFromType * from,
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unsigned int xsize, unsigned int ysize,
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unsigned int toskew, unsigned int fromskew );
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template <typename TType, typename TFromType>
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void PutPaletteRGB( TType *to, TFromType * from,
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unsigned int xsize, unsigned int ysize,
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unsigned int toskew, unsigned int fromskew );
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unsigned short *m_ColorRed;
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unsigned short *m_ColorGreen;
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unsigned short *m_ColorBlue;

‎Modules/IO/TIFF/src/CMakeLists.txt‎

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set(ITKIOTIFF_SRC
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itkTIFFImageIO.cxx
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itkTIFFReaderInternal.cxx
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itkTIFFImageIOFactory.cxx
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)
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