Diff_next, but bugged, need to switch to smart pointers.

czi-format/czi-parser/czi_file.cpp

@@ -322,6 +322,30 @@ ImageMatrix CziFile::get_image(const uint subblockId)
     return image;
 }
 
+void CziFile::differences_between_next(const std::string baseName)
+{
+    if (subBlockDirectory.entries.size() <= 1)
+    {
+        printf("There aren't 2 different images in this CZI file.\n");
+        return;
+    }
+
+    std::string fName;
+    for (size_t i = 1; i < subBlockDirectory.entries.size(); i++)
+    {
+        fName = baseName + "diff_" + std::to_string(i - 1) + "_" + std::to_string(i) + ".ppm";
+
+        ImageMatrix ref = get_image(i - 1);
+        ImageMatrix next = get_image(i);
+
+        ImageMatrix diff_ref_next = ref.create_difference_matrix(next);
+
+        diff_ref_next.save_as_ppm(fName.c_str());
+
+        printf("Saved %s\n", fName.c_str());
+    }
+}
+
 // void CziFile::extract_images(const std::string &baseName) const
 // {
 //     BinaryFileStream cziStream(fileName);

czi-format/czi-parser/czi_file.h

@@ -31,6 +31,8 @@ public:
   ImageMatrix get_image(const uint subblockId);
   void dump_image_data(const std::string &baseName) const;
   //void extract_images(const std::string &baseName) const;
+  // Save differences between next images, so 0x1;1x2;...
+  void differences_between_next(const std::string baseName);
 };
 
 #include "czi_file.cpp"
\ No newline at end of file

czi-format/czi-parser/image/image_matrix.cpp

@@ -114,8 +114,8 @@ ImageMatrix::ImageMatrix(const uint width, const uint height, const PixelType pi
 {
     always_assert(width > 0 && height > 0 && pixelType != PixelType_None);
 
-    this->rowCount = rowCount;
-    this->colCount = colCount;
+    this->rowCount = height;
+    this->colCount = width;
     this->pixelType = pixelType;
 
     // Allocate memory.
@@ -142,10 +142,13 @@ ImageMatrix::ImageMatrix(const uint width, const uint height, const PixelType pi
 
 ImageMatrix::~ImageMatrix()
 {
+    //TODO: This is bonkers bad. Let's use either std::shared_ptr or std::unique_ptr...
     printf("ImageMatrix destructor...\n");
     for (size_t i = 0; i < data.size(); i++)
     {
-        if (data[i])
+        printf("Trying to delete data[%lu]\n", i);
+
+        if (data[i] && !data[i]->isEmpty)
         {
             delete data[i];
         }
@@ -190,11 +193,10 @@ bool ImageMatrix::operator!=(const ImageMatrix &other) const
     return (!equals(other));
 }
 
-void ImageMatrix::save_as_ppm(std::string baseFileName) const
+void ImageMatrix::save_as_ppm(const char *fName) const
 {
     always_assert((this->pixelType == PixelType_Gray8 || this->pixelType == PixelType_Bgr24) && "Currently only those pixel types are supported.");
 
-    std::string fName = baseFileName + ".ppm";
     if (this->pixelType == PixelType_Gray8)
     {
         auto bwImage = cimg_wrapper::create_grayscale_image(colCount, rowCount);
@@ -206,7 +208,7 @@ void ImageMatrix::save_as_ppm(std::string baseFileName) const
                 cimg_wrapper::set_grayscale_pixel(bwImage, row, col, ((Gray8Pixel *)data[index++])->value);
             }
         }
-        bwImage.save_pnm(fName.c_str());
+        bwImage.save_pnm(fName);
     }
     else if (this->pixelType == PixelType_Bgr24)
     {
@@ -221,7 +223,7 @@ void ImageMatrix::save_as_ppm(std::string baseFileName) const
                 cimg_wrapper::set_color_pixel(colorImage, row, col, *px);
             }
         }
-        colorImage.save_pnm(fName.c_str());
+        colorImage.save_pnm(fName);
     }
 }
 
@@ -244,7 +246,7 @@ ImageMatrix ImageMatrix::create_difference_matrix(const ImageMatrix &other)
     ulong diffCounter = 0;
     for (size_t i = 0; i < size; i++)
     {
-        if (!(this->data[i]->equals(other.get(size))))
+        if (!(this->data[i]->equals(other.get(i))))
         {
             diffCounter++;
             diff.set(i, whitePixel);

czi-format/czi-parser/image/image_matrix.h

@@ -6,56 +6,57 @@
 
 class ImageMatrix
 {
-  private:
-    // Number of rows, height of an image.
-    uint rowCount;
-    // Number of columns, width of an image.
-    uint colCount;
-    // Image data.
-    std::vector<BasePixel *> data;
-    // Type of an image pixel.
-    PixelType pixelType = PixelType_None;
+private:
+  // Number of rows, height of an image.
+  uint rowCount;
+  // Number of columns, width of an image.
+  uint colCount;
+  //TODO: Bad.Bad.Bad. Replace with smart pointer.
+  // Image data.
+  std::vector<BasePixel *> data;
+  // Type of an image pixel.
+  PixelType pixelType = PixelType_None;
 
-    // Check equality of two ImageMatrices.
-    bool equals(const ImageMatrix &other) const;
-    // Returns function to parse bytes into corresponding Pixel structure based on `PixelType`
-    std::function<BasePixel *(const std::vector<byte> &, ulong &)> get_pixel_parse_function(const PixelType pixelType);
-    // Get number of bytes needed to encode specific `PixelType`
-    int get_bytes_per_pixel_type(const PixelType &pt) const;
-    // Parse bytes to this matrix.
-    void parse_bytes_to_image(const std::vector<byte> &bytes, const PixelType &pt);
+  // Check equality of two ImageMatrices.
+  bool equals(const ImageMatrix &other) const;
+  // Returns function to parse bytes into corresponding Pixel structure based on `PixelType`
+  std::function<BasePixel *(const std::vector<byte> &, ulong &)> get_pixel_parse_function(const PixelType pixelType);
+  // Get number of bytes needed to encode specific `PixelType`
+  int get_bytes_per_pixel_type(const PixelType &pt) const;
+  // Parse bytes to this matrix.
+  void parse_bytes_to_image(const std::vector<byte> &bytes, const PixelType &pt);
 
-  public:
-    // Default constructor for empty image.
-    ImageMatrix();
-    // Constuctor creating an empty image with allocated space.
-    ImageMatrix(const uint width, const uint height, const PixelType pixelType);
-    // Constuctor creating image matrix from image data.
-    ImageMatrix(const uint width, const uint height, const PixelType pixelType, const std::vector<byte> &imageBytes);
-    ~ImageMatrix();
-    // Get number of rows.
-    uint rows() const;
-    // Get number of cols.
-    uint cols() const;
-    // Get pixel type of an image.
-    PixelType pixel_type() const;
-    // Set pixel at row and col.
-    inline void set(const uint &row, const uint &col, BasePixel *px);
-    // Set pixel at raw index.
-    inline void set(const ulong index, BasePixel *px);
-    // Get pixel at row and col.
-    inline const BasePixel *get(const uint &row, const uint &col) const;
-    // Get pixel at raw index.
-    inline const BasePixel *get(const ulong index) const;
-    // Equal operator.
-    bool operator==(const ImageMatrix &other) const;
-    // Not equal operator.
-    bool operator!=(const ImageMatrix &other) const;
-    // Save Matrix as image, supports pixels: `Bgr24`, `Gray8`
-    void save_as_ppm(std::string baseFileName) const;
-    // Set all pixels to one value of `px`.
-    void fill(BasePixel *px);
-    ImageMatrix create_difference_matrix(const ImageMatrix &other);
+public:
+  // Default constructor for empty image.
+  ImageMatrix();
+  // Constuctor creating an empty image with allocated space.
+  ImageMatrix(const uint width, const uint height, const PixelType pixelType);
+  // Constuctor creating image matrix from image data.
+  ImageMatrix(const uint width, const uint height, const PixelType pixelType, const std::vector<byte> &imageBytes);
+  ~ImageMatrix();
+  // Get number of rows.
+  uint rows() const;
+  // Get number of cols.
+  uint cols() const;
+  // Get pixel type of an image.
+  PixelType pixel_type() const;
+  // Set pixel at row and col.
+  inline void set(const uint &row, const uint &col, BasePixel *px);
+  // Set pixel at raw index.
+  inline void set(const ulong index, BasePixel *px);
+  // Get pixel at row and col.
+  inline const BasePixel *get(const uint &row, const uint &col) const;
+  // Get pixel at raw index.
+  inline const BasePixel *get(const ulong index) const;
+  // Equal operator.
+  bool operator==(const ImageMatrix &other) const;
+  // Not equal operator.
+  bool operator!=(const ImageMatrix &other) const;
+  // Save Matrix as image, supports pixels: `Bgr24`, `Gray8`
+  void save_as_ppm(const char *fName) const;
+  // Set all pixels to one value of `px`.
+  void fill(BasePixel *px);
+  ImageMatrix create_difference_matrix(const ImageMatrix &other);
 };
 
 #include "image_matrix.cpp"
\ No newline at end of file

czi-format/czi-parser/main.cpp

@@ -3,21 +3,17 @@
 
 int main(int argc, char **argv)
 {
-    std::string cziFile;
-    // #if DEBUG
-    //     printf("***DEBUG MODE***\n");
-    //     if (argc == 1)
-    //     {
-    //         argv[1] = (char *)"/home/mor0146/gitlab/data_project/czi-format/data/MultiResolution-Mosaic.czi";
-    //         argv[2] = (char *)"--dump-image-data";
-    //         argv[3] = (char *)"imgdump/";
-    //     }
-    //     argc = 4;
-    //     cziFile = argv[1];
-    // #else
-
-    // #endif
-    cziFile = (argc > 1) ? argv[1] : "/home/mor0146/gitlab/data_project/czi-format/data/CZT-Stack-Anno.czi"; //"/home/mor0146/gitlab/data_project/czi-format/data/m2/exampleSingleChannel.czi";
+
+    std::string cziFile = (argc > 1) ? argv[1] : "/home/mor0146/gitlab/data_project/czi-format/data/CZT-Stack-Anno.czi"; //"/home/mor0146/gitlab/data_project/czi-format/data/m2/exampleSingleChannel.czi";
+    if (cziFile == "-v" || cziFile == "--version")
+    {
+#if DEBUG
+        printf("Running `Debug` version\n.");
+#else
+        printf("Running `Release` version\n.");
+#endif
+        return 0;
+    }
 
     always_assert(is_file(cziFile));
 
@@ -28,6 +24,7 @@ int main(int argc, char **argv)
     bool reportAll = method == "--report-verbose";
     bool dumpRawImageData = method == "--dump-raw-image-data";
     bool dumpImageData = method == "--dump-image-data";
+    bool nextImageDiff = method == "--diff-next";
 
     auto name = get_filename_without_extension(cziFile);
     auto x = get_files_in_parent_directory(cziFile, true);
@@ -45,10 +42,15 @@ int main(int argc, char **argv)
     else if (dumpImageData)
     {
         auto imgMat = parseResult.get_image(0);
-        imgMat.save_as_ppm("matrix");
+        imgMat.save_as_ppm("matrix.ppm");
         //TODO: Re-Enable it.
         //parseResult.extract_images(dumpName);
     }
+    else if (nextImageDiff)
+    {
+        always_assert(dumpName != "");
+        parseResult.differences_between_next(dumpName);
+    }
 
     printf("Finished.\n");