diff --git a/README.md b/README.md
index 12312df8fe3ae32729bd40282fb95bfcc47fa6e9..0597290818f40345530195a300f9259d1f59569a 100644
--- a/README.md
+++ b/README.md
@@ -1,7 +1,7 @@
# Data compression project
### TODO *deadline* 25.2.2019
-- [ ] Tweak Z-Order reordering
+- [x] Tweak Z-Order reordering
- Values, which are stored in more than one byte, must stay together.
- Pixels, which contains more `channels`, can be separeted in final z order. (Try both separeted and not-separated)
- Right now, when we `reorder` bytes we move *whole* pixel (*all channels*), but when pixel's channels will be separated we will move just one channel.
diff --git a/czi-format/czi-parser/custom_types.h b/czi-format/czi-parser/custom_types.h
index d29883dc64bc399aea582e99b1173dabc4714e52..20fb6b06489bcd68416b291165d2a539927ee31f 100644
--- a/czi-format/czi-parser/custom_types.h
+++ b/czi-format/czi-parser/custom_types.h
@@ -10,6 +10,7 @@
#include <memory>
#include <vector>
#include "always_on_assert.h"
+#include <limits>
constexpr bool NOT_IMPLEMENTED_YET = false;
#define MUST_BE_IMPLEMENTED always_assert(false);
@@ -20,6 +21,9 @@ typedef unsigned short ushort;
typedef unsigned int uint;
typedef unsigned long ulong;
+constexpr uint UINT_MAX = std::numeric_limits<uint>::max();
+constexpr ulong ULONG_MAX = std::numeric_limits<ulong>::max();
+
#define TagType std::string, std::string
typedef std::pair<TagType> Tag;
diff --git a/czi-format/czi-parser/czi_file.cpp b/czi-format/czi-parser/czi_file.cpp
index d031a6c0091170df2ee3a01e01cefc8a77856bd3..b28831e970dac2ace6e31d5324b4b9adbcfff9ef 100644
--- a/czi-format/czi-parser/czi_file.cpp
+++ b/czi-format/czi-parser/czi_file.cpp
@@ -345,10 +345,19 @@ std::vector<byte> CziFile::get_image_data(const uint subblockId, const bool ZCur
if (ZCurveOrdered)
{
- auto zIndices = generate_ordered_z_order_indices(entry.width, entry.height);
- always_assert(zIndices.size() == (ulong)(entry.width * entry.height));
+ always_assert((uint)entry.width <= UINT_MAX && (uint)entry.height <= UINT_MAX);
+ uint componentCount = get_count_of_components_of_pixel(entry.pixelType);
+ uint componentSize = get_component_size_of_pixel(entry.pixelType);
+
+ auto zIndices = generate_ordered_z_order_indices(entry.width, entry.height, componentCount);
+ always_assert(zIndices.size() == (ulong)(componentCount * entry.width * entry.height));
+
+ std::vector<byte> zOrderedBytes = reoder_bytes_to_z_order(imageBytes, zIndices, componentSize);
+
+ auto back = reoder_bytes_from_z_order(zOrderedBytes, zIndices, componentSize);
+ bool eq = vecUtil::vector_eq(imageBytes, back);
+ always_assert(eq);
- std::vector<byte> zOrderedBytes = reoder_bytes_to_z_order(imageBytes, zIndices, bytesPerPixel);
return zOrderedBytes;
}
else
diff --git a/czi-format/czi-parser/image/pixel_structures.h b/czi-format/czi-parser/image/pixel_structures.h
index 453249ec05e9e1a0514622cf0c92aa66ac12b299..505a5bb07cc5d28bbf439f4c0f164b9b06df692d 100644
--- a/czi-format/czi-parser/image/pixel_structures.h
+++ b/czi-format/czi-parser/image/pixel_structures.h
@@ -636,4 +636,66 @@ int get_bytes_per_pixel_type(const PixelType &pt)
break;
}
return -1;
+}
+
+// Get number of bytes, by which ByteArray can be reordered in Z-Order.
+uint get_component_size_of_pixel(const PixelType &pt)
+{
+ switch (pt)
+ {
+ case PixelType_Gray8:
+ return 1;
+ case PixelType_Gray16:
+ return 2;
+ case PixelType_Gray32Float:
+ return 4;
+ case PixelType_Bgr24:
+ return 1; // Channels will be separated.
+ case PixelType_Bgr48:
+ return 2; // Channels will be separated.
+ case PixelType_Bgr96Float:
+ return 4; // Channels will be separated.
+ case PixelType_Bgra32:
+ return 1; // Channels will be separated.
+ case PixelType_Gray64ComplexFloat:
+ return 4; // Channels will be separated.
+ case PixelType_Bgr192ComplexFloat:
+ return 4; // Channels will be separated.
+ case PixelType_Gray32:
+ return 4;
+ case PixelType_Gray64:
+ return 8;
+ default:
+ INVALID_CASE;
+ break;
+ }
+ return -1;
+}
+
+// Get number of separable components in specific `PixelType`.
+uint get_count_of_components_of_pixel(const PixelType &pt)
+{
+ switch (pt)
+ {
+ case PixelType_Gray8:
+ case PixelType_Gray16:
+ case PixelType_Gray32Float:
+ case PixelType_Gray32:
+ case PixelType_Gray64:
+ return 1;
+ case PixelType_Gray64ComplexFloat:
+ return 2;
+ case PixelType_Bgr24:
+ case PixelType_Bgr48:
+ case PixelType_Bgr96Float:
+ return 3;
+ case PixelType_Bgra32:
+ return 4;
+ case PixelType_Bgr192ComplexFloat:
+ return 6;
+ default:
+ INVALID_CASE;
+ break;
+ }
+ return -1;
}
\ No newline at end of file
diff --git a/czi-format/czi-parser/image/z_order.h b/czi-format/czi-parser/image/z_order.h
index ecd4cb0d9583cb615a0612a41817bc9884dcf8e7..29546d1d7c694bbdefc1f3dcd1c1df7887c5ab17 100644
--- a/czi-format/czi-parser/image/z_order.h
+++ b/czi-format/czi-parser/image/z_order.h
@@ -67,54 +67,62 @@ struct PointWithIndex
bool operator>=(const PointWithIndex &other) const { return (z >= other.z); }
};
-std::vector<PointWithIndex> generate_ordered_z_order_indices(const uint width, const uint height)
+std::vector<PointWithIndex> generate_ordered_z_order_indices(const uint colCount, const uint rowCount, const uint componentCount)
{
std::vector<PointWithIndex> result;
- result.resize(width * height);
+ result.resize((colCount * componentCount) * rowCount);
+ // This doesnt count with bytes per pixel
size_t index = 0;
- for (uint y = 0; y < height; y++)
+ for (uint row = 0; row < rowCount; row++)
{
- for (uint x = 0; x < width; x++)
+ for (uint col = 0; col < (colCount * componentCount); col++)
{
- result[index] = PointWithIndex(x, y, index);
+ result[index] = PointWithIndex(col, row, index);
index++;
}
}
+ always_assert(((ulong)(colCount * componentCount) * (ulong)rowCount) == result.size());
std::sort(result.begin(), result.end());
return result;
}
-std::vector<byte> reoder_bytes_to_z_order(const std::vector<byte> &bytes, const std::vector<PointWithIndex> &zIndices, const uint chunkSize)
+std::vector<byte> reoder_bytes_to_z_order(const std::vector<byte> &bytes, const std::vector<PointWithIndex> &zIndices,
+ const uint componentSize)
{
std::vector<byte> zOrderedBytes;
-
+ zOrderedBytes.resize(bytes.size());
+ size_t it = 0;
+ size_t from, pos;
for (const PointWithIndex &index : zIndices)
{
- auto fromIt = bytes.begin() + index.bufferPosition;
- auto toIt = fromIt + chunkSize;
- zOrderedBytes.insert(zOrderedBytes.end(), fromIt, toIt);
+ from = (index.bufferPosition * componentSize);
+ //zOrderedBytes.insert(zOrderedBytes.end(), fromIt, toIt);
+ pos = it * componentSize;
+ vecUtil::vector_insert_at(zOrderedBytes, bytes, pos, from, componentSize);
+ it++;
}
- always_assert(zOrderedBytes.size() == bytes.size());
+ always_assert(zOrderedBytes.size() == bytes.size());
return zOrderedBytes;
}
-std::vector<byte> reoder_bytes_from_z_order(const std::vector<byte> &zOrderedBytes, const std::vector<PointWithIndex> &zIndices, const uint chunkSize)
+std::vector<byte> reoder_bytes_from_z_order(const std::vector<byte> &zOrderedBytes, const std::vector<PointWithIndex> &zIndices,
+ const uint componentSize)
{
std::vector<byte> bytes;
bytes.resize(zOrderedBytes.size());
- ulong iteration = 0;
+ size_t it = 0;
size_t insertAt, copyFrom;
for (const PointWithIndex &index : zIndices)
{
- insertAt = index.bufferPosition;
- copyFrom = iteration * chunkSize;
- vecUtil::vector_insert_at(bytes, zOrderedBytes, insertAt, copyFrom, chunkSize);
- ++iteration;
+ insertAt = index.bufferPosition * componentSize;
+ copyFrom = it * componentSize;
+ vecUtil::vector_insert_at(bytes, zOrderedBytes, insertAt, copyFrom, componentSize);
+ ++it;
}
always_assert(bytes.size() == zOrderedBytes.size());
diff --git a/czi-format/czi-parser/main.cpp b/czi-format/czi-parser/main.cpp
index 024746f2a9a9f813910600dcb8466ffe5c72022d..2f67f8e9865c0d8dc3ca8bce44a8ba196ebe39bb 100644
--- a/czi-format/czi-parser/main.cpp
+++ b/czi-format/czi-parser/main.cpp
@@ -8,7 +8,7 @@ int main(int argc, char **argv)
args::Group cziFileGroup(argParser, "CZI file input - necessary.", args::Group::Validators::All);
args::Group mainMethodGroup(argParser, "Methods:", args::Group::Validators::AtMostOne);
args::Group optionsGroup(argParser, "Program options:", args::Group::Validators::DontCare);
- args::Group compressionGroup(argParser, "Avaible compressions", args::Group::Validators::Xor);
+ args::Group compressionGroup(argParser, "Avaible compressions", args::Group::Validators::AtMostOne);
// Main option, has to be set. Czi file.
args::ValueFlag<std::string> cziFile(cziFileGroup, "czi file", "CZI file to load.", {'i', "input"});
@@ -64,6 +64,14 @@ int main(int argc, char **argv)
parsedFile.test_compression(cm, verboseOption.Matched());
}
+ if (reportMethod)
+ {
+ if (verboseOption.Matched())
+ parsedFile.report_verbose();
+ else
+ parsedFile.report();
+ }
+
/*
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")