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Check compression method used in the image (#17) #19

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May 5, 2021
Merged

Check compression method used in the image (#17) #19

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45 changes: 20 additions & 25 deletions cpp/plugins/cucim.kit.cuslide/src/cuslide/cuslide.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -17,21 +17,19 @@

#include "cuslide.h"

#include "cucim/io/format/image_format.h"

#include "cucim/core/framework.h"
#include "cucim/core/plugin_util.h"

#include <memory>
//#include "tiffio.h"
//#include "tif_dir.h"
#include "cucim/io/format/image_format.h"
#include "tiff/tiff.h"
#include <fcntl.h>

#include <fmt/format.h>
#include <nlohmann/json.hpp>

#include <array>
#include <cassert>
#include <cstring>
#include <array>
#include <nlohmann/json.hpp>
// #include <rmm/mr/host/new_delete_resource.hpp>
#include <fcntl.h>
#include <memory>

using json = nlohmann::json;

Expand Down Expand Up @@ -121,7 +119,18 @@ static bool CUCIM_ABI parser_parse(CuCIMFileHandle* handle, cucim::io::format::I
}

// Assume that the image has only one main (high resolution) image.
assert(main_ifd_list.size() == 1);
if (main_ifd_list.size() != 1)
{
throw std::runtime_error(
fmt::format("This format has more than one image with Subfile Type 0 so cannot be loaded!"));
}

// Explicitly forbid loading SVS format (#17)
if (tif->ifd(0)->image_description().rfind("Aperio", 0) == 0)
{
throw std::runtime_error(
fmt::format("cuCIM doesn't support Aperio SVS for now (https://github.com/rapidsai/cucim/issues/17)."));
}

//
// Metadata Setup
Expand Down Expand Up @@ -284,17 +293,3 @@ void fill_interface(cucim::io::format::IImageFormat& iface)
};
// clang-format on
}

//
//
//#include <iostream>
//#include "fmt/format.h"
//
//
//
// CUCIM_API int foo()
//{
// std::cout << "Foo!" << std::endl;
//// std::string a = fmt::format(b.getName());
// return 0;
//}
35 changes: 32 additions & 3 deletions cpp/plugins/cucim.kit.cuslide/src/cuslide/tiff/ifd.cpp
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Original file line number Diff line number Diff line change
Expand Up @@ -173,6 +173,14 @@ bool IFD::read(const TIFF* tiff,
"Cannot handle the out-of-boundary cases for a non-RGB image or a non-Jpeg/Deflate-compressed image."));
}

// Check if the image format is supported or not
if (!is_format_supported())
{
throw std::runtime_error(fmt::format(
"This format (compression: {}, sample_per_pixel: {}, planar_config: {}, photometric: {}) is not supported yet!.",
compression_, samples_per_pixel_, planar_config_, photometric_));
}

if (tif->tif_curdir != ifd_index)
{
TIFFSetDirectory(tif, ifd_index);
Expand Down Expand Up @@ -204,8 +212,20 @@ bool IFD::read(const TIFF* tiff,
}
}
}
else
{
throw std::runtime_error(fmt::format(
"This format (compression: {}, sample_per_pixel: {}, planar_config: {}, photometric: {}) is not supported yet!: {}",
compression_, samples_per_pixel_, planar_config_, photometric_, emsg));
}
TIFFRGBAImageEnd(&img);
}
else
{
throw std::runtime_error(fmt::format(
"This format (compression: {}, sample_per_pixel: {}, planar_config: {}, photometric: {}) is not supported yet!: {}",
compression_, samples_per_pixel_, planar_config_, photometric_, emsg));
}
}

int ndim = 3;
Expand Down Expand Up @@ -308,15 +328,24 @@ const std::vector<uint64_t>& IFD::image_piece_bytecounts() const
return image_piece_bytecounts_;
}

bool IFD::is_read_optimizable() const
bool IFD::is_compression_supported() const
{
return (compression_ == COMPRESSION_ADOBE_DEFLATE || compression_ == COMPRESSION_JPEG ||
compression_ == COMPRESSION_DEFLATE) &&
bits_per_sample_ == 8 && samples_per_pixel_ == 3 && planar_config_ == PLANARCONFIG_CONTIG &&
compression_ == COMPRESSION_DEFLATE);
}
bool IFD::is_read_optimizable() const
{
return is_compression_supported() && bits_per_sample_ == 8 && samples_per_pixel_ == 3 &&
planar_config_ == PLANARCONFIG_CONTIG &&
(photometric_ == PHOTOMETRIC_RGB || photometric_ == PHOTOMETRIC_YCBCR) &&
!tiff_->is_in_read_config(TIFF::kUseLibTiff);
}

bool IFD::is_format_supported() const
{
return is_compression_supported();
}

bool IFD::read_region_tiles(const TIFF* tiff,
const IFD* ifd,
const int64_t sx,
Expand Down
10 changes: 10 additions & 0 deletions cpp/plugins/cucim.kit.cuslide/src/cuslide/tiff/ifd.h
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Original file line number Diff line number Diff line change
Expand Up @@ -121,6 +121,11 @@ class EXPORT_VISIBLE IFD : public std::enable_shared_from_this<IFD>
std::vector<uint64_t> image_piece_offsets_;
std::vector<uint64_t> image_piece_bytecounts_;

/**
* @brief Check if the current compression method is supported or not.
*/
bool is_compression_supported() const;

/**
*
* Note: This method is called by the constructor of IFD and read() method so it is possible that the output of
Expand All @@ -129,6 +134,11 @@ class EXPORT_VISIBLE IFD : public std::enable_shared_from_this<IFD>
* @return
*/
bool is_read_optimizable() const;

/**
* @brief Check if the specified image format is supported or not.
*/
bool is_format_supported() const;
};
} // namespace cuslide::tiff

Expand Down