<commit_before>/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         https://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkIOTestHelper_h
#define itkIOTestHelper_h
#include "ITKIOImageBaseExport.h"
#include <string>

#include "itksys/SystemTools.hxx"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "vnl/vnl_random.h"
namespace itk
{
class IOTestHelper
{
public:
  template <typename TImage>
  static typename TImage::Pointer
  ReadImage(const std::string &           fileName,
            const bool                    zeroOrigin = false,
            typename ImageIOBase::Pointer imageio = nullptr)
  {
    using ReaderType = itk::ImageFileReader<TImage>;

    auto reader = ReaderType::New();
    {
      if (imageio)
      {
        reader->SetImageIO(imageio);
      }
      reader->SetFileName(fileName.c_str());
      try
      {
        reader->Update();
      }
      catch (const itk::ExceptionObject & err)
      {
        std::cout << "Caught an exception: " << std::endl;
        std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
        throw;
      }
      catch (...)
      {
        std::cout << "Error while reading in image for patient " << fileName << std::endl;
        throw;
      }
    }
    typename TImage::Pointer image = reader->GetOutput();
    if (zeroOrigin)
    {
      double origin[TImage::ImageDimension];
      for (unsigned int i = 0; i < TImage::ImageDimension; ++i)
      {
        origin[i] = 0;
      }
      image->SetOrigin(origin);
    }
    return image;
  }

  template <typename ImageType, typename ImageIOType>
  static void
  WriteImage(typename ImageType::Pointer & image,
             const std::string &           filename,
             typename ImageIOType::Pointer imageio = nullptr)
  {

    using WriterType = itk::ImageFileWriter<ImageType>;
    auto writer = WriterType::New();

    if (imageio.IsNull())
    {
      imageio = ImageIOType::New();
    }

    writer->SetImageIO(imageio);

    writer->SetFileName(filename.c_str());

    writer->SetInput(image);

    try
    {
      writer->Update();
    }
    catch (const itk::ExceptionObject & err)
    {
      std::cerr << "Exception Object caught: " << std::endl << err << std::endl;
      throw;
    }
  }

  //
  // generate random pixels of various types
  static void
  RandomPix(vnl_random & randgen, itk::RGBPixel<unsigned char> & pix)
  {
    for (unsigned int i = 0; i < 3; ++i)
    {
      pix[i] = randgen.lrand32(itk::NumericTraits<unsigned char>::max());
    }
  }

  template <typename TPixel>
  static void
  RandomPix(vnl_random & randgen, TPixel & pix)
  {
    pix = randgen.lrand32(itk::NumericTraits<TPixel>::max());
  }<commit_msg>ENH: Force test failure on bad file writing<commit_after>/*=========================================================================
 *
 *  Copyright NumFOCUS
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         https://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkIOTestHelper_h
#define itkIOTestHelper_h
#include "ITKIOImageBaseExport.h"
#include <string>

#include "itksys/SystemTools.hxx"
#include "itkImageFileWriter.h"
#include "itkImageFileReader.h"
#include "vnl/vnl_random.h"
namespace itk
{
class IOTestHelper
{
public:
  template <typename TImage>
  static typename TImage::Pointer
  ReadImage(const std::string &           fileName,
            const bool                    zeroOrigin = false,
            typename ImageIOBase::Pointer imageio = nullptr)
  {
    using ReaderType = itk::ImageFileReader<TImage>;

    auto reader = ReaderType::New();
    {
      if (imageio)
      {
        reader->SetImageIO(imageio);
      }
      reader->SetFileName(fileName.c_str());
      try
      {
        reader->Update();
      }
      catch (const itk::ExceptionObject & err)
      {
        std::cout << "Caught an exception: " << std::endl;
        std::cout << err << " " << __FILE__ << " " << __LINE__ << std::endl;
        throw;
      }
      catch (...)
      {
        std::cout << "Error while reading in image for patient " << fileName << std::endl;
        throw;
      }
    }
    typename TImage::Pointer image = reader->GetOutput();
    if (zeroOrigin)
    {
      double origin[TImage::ImageDimension];
      for (unsigned int i = 0; i < TImage::ImageDimension; ++i)
      {
        origin[i] = 0;
      }
      image->SetOrigin(origin);
    }
    return image;
  }

  template <typename ImageType, typename ImageIOType>
  static void
  WriteImage(typename ImageType::Pointer & image,
             const std::string &           filename,
             typename ImageIOType::Pointer imageio = nullptr)
  {

    using WriterType = itk::ImageFileWriter<ImageType>;
    auto writer = WriterType::New();

    if (imageio.IsNull())
    {
      imageio = ImageIOType::New();
    }

    writer->SetImageIO(imageio);

    writer->SetFileName(filename.c_str());

    writer->SetInput(image);

    try
    {
      writer->Update();
    }
    catch (const itk::ExceptionObject & err)
    {
      std::cerr << "Exception Object caught: " << std::endl << err << std::endl;
      throw;
    }

    // Test if writing to an invalid location causes exception to be thrown:
    const std::string bad_root_path{ "/a_blatantly_obvious/bad_file_path/that/should/never/exist/on/the/computer/" };
    const std::string bad_filename{ bad_root_path + filename };
    try
    {
      writer->SetFileName(bad_filename);
      writer->Update();
    }
    catch (const itk::ExceptionObject & err)
    {
      // This is the correct behavior
      std::cout << "Correctly caught exception for attempting to write to an invalid file." << std::endl;
      return;
    }
    catch (...)
    {
      itkGenericExceptionMacro(<< "IO library exception not converted to an itk::ExceptionObject.");
    }
    itkGenericExceptionMacro(<< "Invalid file writing path did not throw an exception: " << bad_filename << " with "
                             << imageio->GetNameOfClass());
  }

  //
  // generate random pixels of various types
  static void
  RandomPix(vnl_random & randgen, itk::RGBPixel<unsigned char> & pix)
  {
    for (unsigned int i = 0; i < 3; ++i)
    {
      pix[i] = randgen.lrand32(itk::NumericTraits<unsigned char>::max());
    }
  }

  template <typename TPixel>
  static void
  RandomPix(vnl_random & randgen, TPixel & pix)
  {
    pix = randgen.lrand32(itk::NumericTraits<TPixel>::max());
  }
{'fraction_non_alphanumeric': 0.15334207077326342, 'fraction_numerical': 0.003145478374836173, 'mean_word_length': 2.805985037406484, 'pattern_counts': {'":': 0, '<': 99, '<?xml version=': 0, '>': 42, 'https://': 2, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '3392020', 'n_tokens_mistral': 2273, 'n_tokens_neox': 2222, 'n_words': 593}