From 098581e93cdf277d2e059cfd7a057ecb477ca09e Mon Sep 17 00:00:00 2001
From: theazgra <theazgra@gmail.com>
Date: Fri, 8 Feb 2019 11:10:10 +0100
Subject: [PATCH] Saving ImageMatrix.
---
czi-format/czi-parser/czi_file.cpp | 26 +--
czi-format/czi-parser/czi_file.h | 3 +-
czi-format/czi-parser/image.cpp | 63 ------
czi-format/czi-parser/{ => image}/CImg.h | 0
czi-format/czi-parser/image/cimg_wrapper.h | 73 +++++++
czi-format/czi-parser/image/image_matrix.cpp | 211 +++++++++++++++++++
czi-format/czi-parser/image/image_matrix.h | 199 +++--------------
czi-format/czi-parser/image_writer.h | 27 ---
czi-format/czi-parser/main.cpp | 7 +-
9 files changed, 333 insertions(+), 276 deletions(-)
delete mode 100644 czi-format/czi-parser/image.cpp
rename czi-format/czi-parser/{ => image}/CImg.h (100%)
create mode 100644 czi-format/czi-parser/image/cimg_wrapper.h
create mode 100644 czi-format/czi-parser/image/image_matrix.cpp
delete mode 100644 czi-format/czi-parser/image_writer.h
diff --git a/czi-format/czi-parser/czi_file.cpp b/czi-format/czi-parser/czi_file.cpp
index 5c9a9bd..ad0f063 100644
--- a/czi-format/czi-parser/czi_file.cpp
+++ b/czi-format/czi-parser/czi_file.cpp
@@ -322,19 +322,19 @@ ImageMatrix CziFile::get_image(const uint subblockId)
return image;
}
-void CziFile::extract_images(const std::string &baseName) const
-{
- BinaryFileStream cziStream(fileName);
- int imageIndex = 0;
- for (const DirectoryEntryDV &entry : subBlockDirectory.entries)
- {
- always_assert(entry.width > 0 && entry.height > 0);
-
- auto imageBytes = cziStream.move_and_consume_bytes(entry.subBlock.dataLocation, entry.subBlock.dataSize);
- std::string imageFileName = baseName + std::to_string(imageIndex++) + ".pnm";
- create_image_file(imageFileName.c_str(), imageBytes, entry.pixelType, entry.width, entry.height);
- }
-}
+// void CziFile::extract_images(const std::string &baseName) const
+// {
+// BinaryFileStream cziStream(fileName);
+// int imageIndex = 0;
+// for (const DirectoryEntryDV &entry : subBlockDirectory.entries)
+// {
+// always_assert(entry.width > 0 && entry.height > 0);
+
+// auto imageBytes = cziStream.move_and_consume_bytes(entry.subBlock.dataLocation, entry.subBlock.dataSize);
+// std::string imageFileName = baseName + std::to_string(imageIndex++) + ".pnm";
+// create_image_file(imageFileName.c_str(), imageBytes, entry.pixelType, entry.width, entry.height);
+// }
+// }
void CziFile::dump_image_data(const std::string &baseName) const
{
diff --git a/czi-format/czi-parser/czi_file.h b/czi-format/czi-parser/czi_file.h
index 407f6b3..0951831 100644
--- a/czi-format/czi-parser/czi_file.h
+++ b/czi-format/czi-parser/czi_file.h
@@ -3,7 +3,6 @@
#include "czi_parts/segments.h"
#include "utilities/vector_utilities.h"
#include "stream/binary_file_stream.h"
-#include "image_writer.h"
#include "image/image_matrix.h"
//TODO: Handle multi-file scenarios.
@@ -31,7 +30,7 @@ public:
void report() const;
ImageMatrix get_image(const uint subblockId);
void dump_image_data(const std::string &baseName) const;
- void extract_images(const std::string &baseName) const;
+ //void extract_images(const std::string &baseName) const;
};
#include "czi_file.cpp"
\ No newline at end of file
diff --git a/czi-format/czi-parser/image.cpp b/czi-format/czi-parser/image.cpp
deleted file mode 100644
index 6d4600e..0000000
--- a/czi-format/czi-parser/image.cpp
+++ /dev/null
@@ -1,63 +0,0 @@
-#define cimg_display 0
-#include "CImg.h"
-#include "image/pixel_structures.h"
-
-// struct RgbPixel
-// {
-// byte R;
-// byte G;
-// byte B;
-
-// RgbPixel()
-// {
-// R = 0;
-// G = 0;
-// B = 0;
-// }
-
-// RgbPixel(byte r, byte g, byte b)
-// {
-// R = r;
-// G = g;
-// B = b;
-// }
-
-// RgbPixel(byte value)
-// {
-// R = value;
-// G = value;
-// B = value;
-// }
-// };
-
-inline void set_pixel(cimg_library::CImg<byte> &img, const uint &row, const uint &col, const Bgr24Pixel &bgr)
-{
- img(col, row, 0) = bgr.r;
- img(col, row, 1) = bgr.g;
- img(col, row, 2) = bgr.b;
-}
-
-inline void set_pixel(cimg_library::CImg<byte> &img, const uint &row, const uint &col, const byte &px)
-{
- img(col, row, 0) = px;
-}
-
-inline Bgr24Pixel get_pixel(cimg_library::CImg<byte> &img, const uint &row, const uint &col)
-{
- Bgr24Pixel rgb(img(col, row, 2), img(col, row, 1), img(col, row, 0));
- return rgb;
-}
-
-cimg_library::CImg<byte> create_grayscale_image(const uint width, const uint height)
-{
- cimg_library::CImg<byte> image(width, height, 1, 1);
- image.fill(0);
- return image;
-}
-
-cimg_library::CImg<byte> create_color_image(const uint width, const uint height)
-{
- cimg_library::CImg<byte> image(width, height, 1, 3);
- image.fill(0);
- return image;
-}
\ No newline at end of file
diff --git a/czi-format/czi-parser/CImg.h b/czi-format/czi-parser/image/CImg.h
similarity index 100%
rename from czi-format/czi-parser/CImg.h
rename to czi-format/czi-parser/image/CImg.h
diff --git a/czi-format/czi-parser/image/cimg_wrapper.h b/czi-format/czi-parser/image/cimg_wrapper.h
new file mode 100644
index 0000000..4c74f56
--- /dev/null
+++ b/czi-format/czi-parser/image/cimg_wrapper.h
@@ -0,0 +1,73 @@
+#pragma once
+#define cimg_display 0
+
+#include "CImg.h"
+#include "pixel_structures.h"
+
+namespace cimg_wrapper
+{
+
+// Set color pixel at row, col in image.
+inline void set_color_pixel(cimg_library::CImg<byte> &img, const uint &row, const uint &col, const Bgr24Pixel &bgr)
+{
+ img(col, row, 0) = bgr.r;
+ img(col, row, 1) = bgr.g;
+ img(col, row, 2) = bgr.b;
+}
+
+// Set grayscale pixel at row, col in image.
+inline void set_grayscale_pixel(cimg_library::CImg<byte> &img, const uint &row, const uint &col, const byte &px)
+{
+ img(col, row, 0) = px;
+}
+// Get grayscale pixel at row, col from image.
+inline Bgr24Pixel get_color_pixel(cimg_library::CImg<byte> &img, const uint &row, const uint &col)
+{
+ Bgr24Pixel rgb(img(col, row, 2), img(col, row, 1), img(col, row, 0));
+ return rgb;
+}
+// Get grayscale pixel at row, col from image.
+inline Gray8Pixel get_grayscale_pixel(cimg_library::CImg<byte> &img, const uint &row, const uint &col)
+{
+ Gray8Pixel px(img(col, row, 0));
+ return px;
+}
+
+// Create grayscale image. `Gray8`
+cimg_library::CImg<byte> create_grayscale_image(const uint width, const uint height)
+{
+ cimg_library::CImg<byte> image(width, height, 1, 1);
+ image.fill(0);
+ return image;
+}
+
+// Create color image. `Bgr24`
+cimg_library::CImg<byte> create_color_image(const uint width, const uint height)
+{
+ cimg_library::CImg<byte> image(width, height, 1, 3);
+ image.fill(0);
+ return image;
+}
+
+// void cimg_save_image(const char *fileName, ImageMatrix, const PixelType pixelType, const int width, const int height)
+// {
+// // This is not generally true, because it depends on BitsPerPixelType.
+// // always_assert((width * height) == bytes.size());
+// cimg_library::CImg<byte> img = create_color_image((uint)width, (uint)height);
+
+// // Hard-Coded for uncompressed Bgr24 pixel.
+// ulong current = 0;
+
+// for (int row = 0; row < height; row++)
+// {
+// for (int col = 0; col < width; col++)
+// {
+// Bgr24Pixel px(bytes[current + 1], bytes[current + 2], bytes[current + 3]);
+// current += 3;
+// set_pixel(img, row, col, px);
+// }
+// }
+// printf("Finished painting %s\n", fileName);
+// img.save_pnm(fileName);
+// }
+};
\ 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
new file mode 100644
index 0000000..3dda363
--- /dev/null
+++ b/czi-format/czi-parser/image/image_matrix.cpp
@@ -0,0 +1,211 @@
+#include "image_matrix.h"
+
+bool ImageMatrix::equals(const ImageMatrix &other) const
+{
+ if (pixelType != other.pixelType)
+ return false;
+
+ if ((this->rowCount != other.rows()) || (this->colCount != other.cols()))
+ return false;
+
+ size_t dataSize = this->data.size();
+ for (size_t i = 0; i < dataSize; i++)
+ {
+ if (data[i])
+ {
+ if (!this->data[i]->equals(other.data[i]))
+ return false;
+ }
+ else if (other.data[i])
+ {
+ return false;
+ }
+ }
+ return true;
+}
+
+// Returns function to parse bytes into corresponding Pixel structure based on `PixelType`
+std::function<BasePixel *(const std::vector<byte> &, ulong &)> ImageMatrix::get_pixel_parse_function(const PixelType pixelType)
+{
+ switch (pixelType)
+ {
+ case PixelType_Gray8:
+ return bytes_to_Gray8Pixel;
+ case PixelType_Gray16:
+ return bytes_to_Gray16Pixel;
+ case PixelType_Gray32Float:
+ return bytes_to_Gray32FloatPixel;
+ case PixelType_Bgr24:
+ return bytes_to_Bgr24Pixel;
+ case PixelType_Bgr48:
+ return bytes_to_Bgr48Pixel;
+ case PixelType_Bgr96Float:
+ return bytes_to_Bgr96FloatPixel;
+ case PixelType_Bgra32:
+ return bytes_to_Bgra32Pixel;
+ case PixelType_Gray64ComplexFloat:
+ return bytes_to_Gray64ComplexFloatPixel;
+ case PixelType_Bgr192ComplexFloat:
+ return bytes_to_Bgr192ComplexFloatPixel;
+ case PixelType_Gray32:
+ return bytes_to_Gray32Pixel;
+ case PixelType_Gray64:
+ return bytes_to_Gray64Pixel;
+ default:
+ always_assert(false && "Wrong PixelType!");
+ break;
+ }
+ return nullptr;
+}
+
+// Get number of bytes needed to encode specific `PixelType`
+int ImageMatrix::get_bytes_per_pixel_type(const PixelType &pt) const
+{
+ switch (pt)
+ {
+ case PixelType_Gray8:
+ return 1;
+ case PixelType_Gray16:
+ return 2;
+ case PixelType_Gray32Float:
+ return 4;
+ case PixelType_Bgr24:
+ return 3;
+ case PixelType_Bgr48:
+ return 6;
+ case PixelType_Bgr96Float:
+ return 12;
+ case PixelType_Bgra32:
+ return 4;
+ case PixelType_Gray64ComplexFloat:
+ return 8;
+ case PixelType_Bgr192ComplexFloat:
+ return 24;
+ case PixelType_Gray32:
+ return 4;
+ case PixelType_Gray64:
+ return 8;
+
+ default:
+ always_assert("Bad pixel type." && false);
+ break;
+ }
+ return -1;
+}
+
+void ImageMatrix::parse_bytes_to_image(const std::vector<byte> &bytes, const PixelType &pt)
+{
+ auto pixel_parse_function = get_pixel_parse_function(pt);
+ size_t count = rowCount * colCount;
+ ulong bufferIndex = 0;
+ for (size_t i = 0; i < count; i++)
+ {
+ data[i] = pixel_parse_function(bytes, bufferIndex);
+ }
+}
+
+ImageMatrix::ImageMatrix()
+{
+ this->rowCount = 0;
+ this->colCount = 0;
+}
+
+ImageMatrix::ImageMatrix(const uint width, const uint height, const PixelType pixelType, const std::vector<byte> &imageBytes)
+{
+ always_assert(width > 0 && height > 0 && pixelType != PixelType_None && imageBytes.size() > 0);
+
+ this->rowCount = height;
+ this->colCount = width;
+ this->pixelType = pixelType;
+
+ // Allocate memory.
+ data.resize(rowCount * colCount);
+
+ int bytePerPixel = get_bytes_per_pixel_type(pixelType);
+ ulong requiredByteCount = (ulong)width * (ulong)height * (ulong)bytePerPixel;
+ always_assert(requiredByteCount == imageBytes.size() && "imageBytes size is wrong.");
+
+ parse_bytes_to_image(imageBytes, pixelType);
+}
+
+ImageMatrix::~ImageMatrix()
+{
+ for (size_t i = 0; i < data.size(); i++)
+ {
+ if (data[i])
+ {
+ delete data[i];
+ }
+ }
+}
+
+// Get number of rows.
+uint ImageMatrix::rows() const { return this->rowCount; }
+
+// Get number of cols.
+uint ImageMatrix::cols() const { return this->colCount; }
+
+inline void ImageMatrix::set(const uint &row, const uint &col, BasePixel *px)
+{
+ data[((row * colCount) + col)] = px;
+}
+
+inline const BasePixel *ImageMatrix::get(const uint &row, const uint &col) const
+{
+ return data[((row * colCount) + col)];
+}
+
+inline void ImageMatrix::set(const ulong index, BasePixel *px)
+{
+ data[index] = px;
+}
+
+inline const BasePixel *ImageMatrix::get(const ulong index) const
+{
+ return data[index];
+}
+
+bool ImageMatrix::operator==(const ImageMatrix &other) const
+{
+ return equals(other);
+}
+
+bool ImageMatrix::operator!=(const ImageMatrix &other) const
+{
+ return (!equals(other));
+}
+
+void ImageMatrix::save_as_ppm(std::string baseFileName) 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);
+ ulong index = 0;
+ for (uint row = 0; row < this->rowCount; row++)
+ {
+ for (uint col = 0; col < this->colCount; col++)
+ {
+ cimg_wrapper::set_grayscale_pixel(bwImage, row, col, ((Gray8Pixel *)data[index++])->value);
+ }
+ }
+ bwImage.save_pnm(fName.c_str());
+ }
+ else if (this->pixelType == PixelType_Bgr24)
+ {
+ auto colorImage = cimg_wrapper::create_color_image(colCount, rowCount);
+ ulong index = 0;
+ Bgr24Pixel *px;
+ for (uint row = 0; row < this->rowCount; row++)
+ {
+ for (uint col = 0; col < this->colCount; col++)
+ {
+ px = (Bgr24Pixel *)data[index++];
+ cimg_wrapper::set_color_pixel(colorImage, row, col, *px);
+ }
+ }
+ colorImage.save_pnm(fName.c_str());
+ }
+}
\ No newline at end of file
diff --git a/czi-format/czi-parser/image/image_matrix.h b/czi-format/czi-parser/image/image_matrix.h
index 4ca8143..248d1a4 100644
--- a/czi-format/czi-parser/image/image_matrix.h
+++ b/czi-format/czi-parser/image/image_matrix.h
@@ -1,7 +1,8 @@
+#pragma once
+
#include <functional>
#include "pixel_parse_functions.h"
-
-#pragma once
+#include "cimg_wrapper.h"
class ImageMatrix
{
@@ -16,180 +17,38 @@ class ImageMatrix
PixelType pixelType = PixelType_None;
// Check equality of two ImageMatrices.
- bool equals(const ImageMatrix &other)
- {
- if (pixelType != other.pixelType)
- return false;
-
- if ((this->rowCount != other.rows()) || (this->colCount != other.cols()))
- return false;
-
- size_t dataSize = this->data.size();
- for (size_t i = 0; i < dataSize; i++)
- {
- if (data[i])
- {
- if (!this->data[i]->equals(other.data[i]))
- return false;
- }
- else if (other.data[i])
- {
- return false;
- }
- }
- return true;
- }
-
+ 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)
- {
- switch (pixelType)
- {
- case PixelType_Gray8:
- return bytes_to_Gray8Pixel;
- case PixelType_Gray16:
- return bytes_to_Gray16Pixel;
- case PixelType_Gray32Float:
- return bytes_to_Gray32FloatPixel;
- case PixelType_Bgr24:
- return bytes_to_Bgr24Pixel;
- case PixelType_Bgr48:
- return bytes_to_Bgr48Pixel;
- case PixelType_Bgr96Float:
- return bytes_to_Bgr96FloatPixel;
- case PixelType_Bgra32:
- return bytes_to_Bgra32Pixel;
- case PixelType_Gray64ComplexFloat:
- return bytes_to_Gray64ComplexFloatPixel;
- case PixelType_Bgr192ComplexFloat:
- return bytes_to_Bgr192ComplexFloatPixel;
- case PixelType_Gray32:
- return bytes_to_Gray32Pixel;
- case PixelType_Gray64:
- return bytes_to_Gray64Pixel;
- default:
- always_assert(false && "Wrong PixelType!");
- break;
- }
- return nullptr;
- }
-
+ 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
- {
- switch (pt)
- {
- case PixelType_Gray8:
- return 1;
- case PixelType_Gray16:
- return 2;
- case PixelType_Gray32Float:
- return 4;
- case PixelType_Bgr24:
- return 3;
- case PixelType_Bgr48:
- return 6;
- case PixelType_Bgr96Float:
- return 12;
- case PixelType_Bgra32:
- return 4;
- case PixelType_Gray64ComplexFloat:
- return 8;
- case PixelType_Bgr192ComplexFloat:
- return 24;
- case PixelType_Gray32:
- return 4;
- case PixelType_Gray64:
- return 8;
-
- default:
- always_assert("Bad pixel type." && false);
- break;
- }
- return -1;
- }
-
- void parse_bytes_to_image(const std::vector<byte> &bytes, const PixelType &pt)
- {
- auto pixel_parse_function = get_pixel_parse_function(pt);
- size_t count = rowCount * colCount;
- ulong bufferIndex = 0;
- for (size_t i = 0; i < count; i++)
- {
- data[i] = pixel_parse_function(bytes, bufferIndex);
- }
- }
+ 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()
- {
- this->rowCount = 0;
- this->colCount = 0;
- }
+ ImageMatrix();
// Constuctor creating image matrix from image data.
- ImageMatrix(const uint width, const uint height, const PixelType pixelType, const std::vector<byte> &imageBytes)
- {
- always_assert(width > 0 && height > 0 && pixelType != PixelType_None && imageBytes.size() > 0);
-
- this->rowCount = height;
- this->colCount = width;
- this->pixelType = pixelType;
-
- // Allocate memory.
- data.resize(rowCount * colCount);
-
- int bytePerPixel = get_bytes_per_pixel_type(pixelType);
- ulong requiredByteCount = (ulong)width * (ulong)height * (ulong)bytePerPixel;
- always_assert(requiredByteCount == imageBytes.size() && "imageBytes size is wrong.");
-
- parse_bytes_to_image(imageBytes, pixelType);
- }
-
- ~ImageMatrix()
- {
- for (size_t i = 0; i < data.size(); i++)
- {
- if (data[i])
- {
- delete data[i];
- }
- }
- }
-
+ ImageMatrix(const uint width, const uint height, const PixelType pixelType, const std::vector<byte> &imageBytes);
+ ~ImageMatrix();
// Get number of rows.
- uint rows() const { return this->rowCount; }
-
+ uint rows() const;
// Get number of cols.
- uint cols() const { return this->colCount; }
-
- inline void set(const uint &row, const uint &col, BasePixel *px)
- {
- data[((row * colCount) + col)] = px;
- }
-
- inline const BasePixel *get(const uint &row, const uint &col)
- {
- return data[((row * colCount) + col)];
- }
-
- inline void set(const ulong index, BasePixel *px)
- {
- data[index] = px;
- }
-
- inline const BasePixel *get(const ulong index)
- {
- return data[index];
- }
-
- bool operator==(const ImageMatrix &other)
- {
- return equals(other);
- }
-
- bool operator!=(const ImageMatrix &other)
- {
- return (!equals(other));
- }
+ uint cols() 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;
};
+
+#include "image_matrix.cpp"
\ No newline at end of file
diff --git a/czi-format/czi-parser/image_writer.h b/czi-format/czi-parser/image_writer.h
deleted file mode 100644
index 8319c7c..0000000
--- a/czi-format/czi-parser/image_writer.h
+++ /dev/null
@@ -1,27 +0,0 @@
-#pragma once
-#include <fstream>
-#include "czi_parts/pixel_type.h"
-#include "image/pixel_structures.h"
-#include "image.cpp"
-
-void create_image_file(const char *fileName, const std::vector<byte> &bytes, const PixelType pixelType, const int width, const int height)
-{
- // This is not generally true, because it depends on BitsPerPixelType.
- // always_assert((width * height) == bytes.size());
- cimg_library::CImg<byte> img = create_color_image((uint)width, (uint)height);
-
- // Hard-Coded for uncompressed Bgr24 pixel.
- ulong current = 0;
-
- for (int row = 0; row < height; row++)
- {
- for (int col = 0; col < width; col++)
- {
- Bgr24Pixel px(bytes[current + 1], bytes[current + 2], bytes[current + 3]);
- current += 3;
- set_pixel(img, row, col, px);
- }
- }
- printf("Finished painting %s\n", fileName);
- img.save_pnm(fileName);
-}
\ No newline at end of file
diff --git a/czi-format/czi-parser/main.cpp b/czi-format/czi-parser/main.cpp
index 0444278..616eda6 100644
--- a/czi-format/czi-parser/main.cpp
+++ b/czi-format/czi-parser/main.cpp
@@ -43,7 +43,12 @@ int main(int argc, char **argv)
else if (dumpRawImageData)
parseResult.dump_image_data(dumpName);
else if (dumpImageData)
- parseResult.extract_images(dumpName);
+ {
+ auto imgMat = parseResult.get_image(0);
+ imgMat.save_as_ppm("matrix");
+ //TODO: Re-Enable it.
+ //parseResult.extract_images(dumpName);
+ }
printf("Finished.\n");
--
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