diff --git a/czi-format/czi-parser/czi_file.cpp b/czi-format/czi-parser/czi_file.cpp
index ad0f0633938f85b9966a27c55fe81cccb32f7f2b..44cf40b94b4e9816255d95b12e30d13fb2f001f4 100644
--- a/czi-format/czi-parser/czi_file.cpp
+++ b/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);
diff --git a/czi-format/czi-parser/czi_file.h b/czi-format/czi-parser/czi_file.h
index 09518312be92194eeb6bd42559cc28985ed58849..81537e4b906e007d9faaaba14f532e238aedae33 100644
--- a/czi-format/czi-parser/czi_file.h
+++ b/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
diff --git a/czi-format/czi-parser/image/image_matrix.cpp b/czi-format/czi-parser/image/image_matrix.cpp
index db630c4ac6d94f6fe8cf7aa66d5e434ef78118c5..992fd732cdc4bbca2e93329679a30abf757d577f 100644
--- a/czi-format/czi-parser/image/image_matrix.cpp
+++ b/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);
diff --git a/czi-format/czi-parser/image/image_matrix.h b/czi-format/czi-parser/image/image_matrix.h
index 865fec78cc57ab1b2821f20fe514bd9bc588c058..4b300e7cd4e186fa17d69057376ddeb860702b9b 100644
--- a/czi-format/czi-parser/image/image_matrix.h
+++ b/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
diff --git a/czi-format/czi-parser/main.cpp b/czi-format/czi-parser/main.cpp
index 616eda6170586bd64f1b4a408e691a86a42ac85b..77e7eb7e8690926145ac780aa978bd2ae9b396b5 100644
--- a/czi-format/czi-parser/main.cpp
+++ b/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");