From 941fcd45200cdf9dc1a6fcfe088d5089edae94e0 Mon Sep 17 00:00:00 2001
From: theazgra <theazgra@gmail.com>
Date: Tue, 12 Mar 2019 11:32:25 +0100
Subject: [PATCH] Mapping of signed types to unsigned.
---
czi-format/czi-parser/custom_types.h | 2 +-
czi-format/czi-parser/czi_file.cpp | 29 +++++++-
czi-format/czi-parser/main.cpp | 2 +-
czi-format/czi-parser/utilities/type_mapper.h | 69 ++++++++++++++++++
.../czi-parser/utilities/vector_utilities.h | 50 +++++++++++++
.../DS_ZISRAW-FileFormat.pdf | Bin
.../XmlSchemas/CommonTypes.xsd | 0
.../XmlSchemas/Dimensions.xsd | 0
.../XmlSchemas/DisplaySetting.xsd | 0
.../XmlSchemas/ImageAnalysisSetting.xsd | 0
.../XmlSchemas/ImageMetadata.xsd | 0
.../XmlSchemas/Information.xsd | 0
.../XmlSchemas/Instrument.xsd | 0
.../XmlSchemas/Layers.xsd | 0
.../XmlSchemas/PhysiologySetting.xsd | 0
.../XmlSchemas/Scaling.xsd | 0
.../XmlSchemas/Timeline.xsd | 0
.../XmlSchemas/Views.xsd | 0
18 files changed, 146 insertions(+), 6 deletions(-)
create mode 100644 czi-format/czi-parser/utilities/type_mapper.h
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/DS_ZISRAW-FileFormat.pdf (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/CommonTypes.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/Dimensions.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/DisplaySetting.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/ImageAnalysisSetting.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/ImageMetadata.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/Information.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/Instrument.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/Layers.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/PhysiologySetting.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/Scaling.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/Timeline.xsd (100%)
rename czi-format/{czi-doc-zen-2.3 => docs_czi}/XmlSchemas/Views.xsd (100%)
diff --git a/czi-format/czi-parser/custom_types.h b/czi-format/czi-parser/custom_types.h
index 22a8910..d758eb2 100644
--- a/czi-format/czi-parser/custom_types.h
+++ b/czi-format/czi-parser/custom_types.h
@@ -24,7 +24,7 @@ typedef unsigned long ulong;
constexpr uint UINT_MAX = std::numeric_limits<uint>::max();
constexpr ulong ULONG_MAX = std::numeric_limits<ulong>::max();
constexpr short SHORT_MAX = std::numeric_limits<short>::max();
-constexpr short USHORT_MAX = std::numeric_limits<ushort>::max();
+constexpr ushort USHORT_MAX = std::numeric_limits<ushort>::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 0e274fb..be6ff86 100644
--- a/czi-format/czi-parser/czi_file.cpp
+++ b/czi-format/czi-parser/czi_file.cpp
@@ -522,9 +522,14 @@ void CziFile::frames_difference() const
auto framesByChannels = get_subblocks_grouped_by_channels();
+ std::pair<uint, uint> canBeMappedCounts = std::make_pair(0, 0);
+
for (const std::pair<uint, std::vector<uint>> &channelGroup : framesByChannels)
{
printf("Starting channel %u\n", channelGroup.first);
+
+ //#pragma omp parallel for
+
for (size_t i = 1; i < channelGroup.second.size(); i++)
{
// This assertion will fail if pixel type isn't Gray16
@@ -541,17 +546,33 @@ void CziFile::frames_difference() const
std::vector<int> differenceArray = vecUtil::diff_vectors<ushort, int>(prevFrameValues, currentFrameValues);
+ int min = vecUtil::find_min(differenceArray);
+ int max = vecUtil::find_max(differenceArray);
+ long maxMappedValue = (min < 0) ? (abs(min) + max) : (max);
+ bool canBeMappedToUShort = maxMappedValue < USHORT_MAX;
+
+#pragma omp critical
+ {
+ if (canBeMappedToUShort)
+ canBeMappedCounts.first++;
+ else
+ canBeMappedCounts.second++;
+ }
+
ByteArray intBytes = int_array_to_bytes(differenceArray);
auto frameCompResult = test_compression_method(currentFrameData, CompressionMethod_BZIP2, 6);
auto diffCompResult = test_compression_method(intBytes, CompressionMethod_BZIP2, 6);
- float diffSizeDif = ((float)diffCompResult.compressedSize / (float)frameCompResult.compressedSize) * 100.0f;
+ float diffSizeDif = ((float)diffCompResult.compressedSize / (float)frameCompResult.compressedSize);
- printf("Frame [%u | %u]: Size %7lu Compression ratio: %7f\n",
- channelGroup.second[i - 1], channelGroup.second[i], frameCompResult.compressedSize, frameCompResult.compressionRatio);
+ printf("========================\nFrame [%u vs %u]\n\tCR frame: %10.5f\n\tCR diff: %10.5f\n\tSizeDiff: %10.5f\n\tMin: %10i\n\tMax: %10i\n\tMax mapped value: %10li\n\tCan be mapped to ushort: %s\n",
+ channelGroup.second[i - 1], channelGroup.second[i], frameCompResult.compressionRatio, diffCompResult.compressionRatio, diffSizeDif,
+ min, max, maxMappedValue, canBeMappedToUShort ? "YES" : "NO");
- printf(" Diff: Size %7lu Compression ratio: %7f\n Size: %f\n\n", diffCompResult.compressedSize, diffCompResult.compressionRatio, diffSizeDif);
+ //printf("Max value: %7i Min value: %7i #of values: %7li\n", max, min, rangeSize);
}
}
+
+ printf("%u can be mapped to short difference value.\n%u can not be mapped.\n", canBeMappedCounts.first, canBeMappedCounts.second);
}
\ No newline at end of file
diff --git a/czi-format/czi-parser/main.cpp b/czi-format/czi-parser/main.cpp
index 55655b2..8a71617 100644
--- a/czi-format/czi-parser/main.cpp
+++ b/czi-format/czi-parser/main.cpp
@@ -1,7 +1,7 @@
#include "czi_parser.h"
#include "compression/benchmark.h"
#include "utilities/args.hxx"
-
+#include "utilities/type_mapper.h"
int main(int argc, char **argv)
{
args::ArgumentParser argParser("CZI file tools", "Optional arguments are in `[]` necessary in `<>`.");
diff --git a/czi-format/czi-parser/utilities/type_mapper.h b/czi-format/czi-parser/utilities/type_mapper.h
new file mode 100644
index 0000000..a7f4087
--- /dev/null
+++ b/czi-format/czi-parser/utilities/type_mapper.h
@@ -0,0 +1,69 @@
+#pragma once
+#include "../custom_types.h"
+#include "vector_utilities.h"
+
+// Provide mapping utilites from signed types to big enaugh unsigned types.
+template <typename SourceType, typename TargetType>
+class TypeMapper
+{
+ private:
+ public:
+ // Map `SourceType` vector to `TargetType` vector. Saving mapping point as first element.
+ std::vector<TargetType> map(std::vector<SourceType> &data)
+ {
+ auto limits = vecUtil::find_min_max(data);
+ SourceType min = limits.first;
+ SourceType max = limits.second;
+
+ TargetType targetMaxValue = std::numeric_limits<TargetType>::max();
+ always_assert(max < targetMaxValue);
+ always_assert((abs(min) + max) < targetMaxValue);
+
+ TargetType mappingPoint = max;
+
+ std::vector<TargetType> result;
+ result.resize(data.size() + 1);
+
+ // Save mapping point as first value.
+ result[0] = mappingPoint;
+
+ for (size_t i = 0; i < data.size(); i++)
+ {
+ if (data[i] >= 0)
+ {
+ result[i + 1] = (TargetType)data[i];
+ }
+ else
+ {
+ result[i + 1] = mappingPoint + abs(data[i]);
+ }
+ }
+
+ return result;
+ }
+
+ // Map back `TargetType` vector to `SourceType` vector.
+ std::vector<SourceType> map_back(std::vector<TargetType> &data)
+ {
+ std::vector<SourceType> result;
+ result.resize(data.size() - 1);
+
+ // Retrieve mapping point.
+ TargetType mappingPoint = data[0];
+
+ for (size_t i = 1; i < data.size(); i++)
+ {
+ if (data[i] <= mappingPoint)
+ {
+ // Positive values
+ result[i - 1] = data[i];
+ }
+ else
+ {
+ // Negative values
+ result[i - 1] = -(data[i] - mappingPoint);
+ }
+ }
+ return result;
+ }
+};
\ No newline at end of file
diff --git a/czi-format/czi-parser/utilities/vector_utilities.h b/czi-format/czi-parser/utilities/vector_utilities.h
index 76482d5..7b08691 100644
--- a/czi-format/czi-parser/utilities/vector_utilities.h
+++ b/czi-format/czi-parser/utilities/vector_utilities.h
@@ -1,6 +1,7 @@
#pragma once
#include <vector>
#include <algorithm>
+#include <limits>
namespace vecUtil
{
@@ -59,4 +60,53 @@ std::vector<DiffType> diff_vectors(const std::vector<T> &a, const std::vector<T>
return result;
}
+template <typename T>
+T find_max(const std::vector<T> &data)
+{
+ T max = std::numeric_limits<T>::min();
+ for (size_t i = 0; i < data.size(); i++)
+ {
+ if (data[i] > max)
+ {
+ max = data[i];
+ }
+ }
+ return max;
+}
+
+template <typename T>
+T find_min(const std::vector<T> &data)
+{
+ T min = std::numeric_limits<T>::max();
+ for (size_t i = 0; i < data.size(); i++)
+ {
+ if (data[i] < min)
+ {
+ min = data[i];
+ }
+ }
+ return min;
+}
+
+template <typename T>
+std::pair<T, T> find_min_max(const std::vector<T> &data)
+{
+ T min = std::numeric_limits<T>::max();
+ T max = std::numeric_limits<T>::min();
+
+ for (size_t i = 0; i < data.size(); i++)
+ {
+ if (data[i] < min)
+ {
+ min = data[i];
+ }
+
+ if (data[i] > max)
+ {
+ max = data[i];
+ }
+ }
+ return std::make_pair(min, max);
+}
+
}; // namespace vecUtil
diff --git a/czi-format/czi-doc-zen-2.3/DS_ZISRAW-FileFormat.pdf b/czi-format/docs_czi/DS_ZISRAW-FileFormat.pdf
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/DS_ZISRAW-FileFormat.pdf
rename to czi-format/docs_czi/DS_ZISRAW-FileFormat.pdf
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/CommonTypes.xsd b/czi-format/docs_czi/XmlSchemas/CommonTypes.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/CommonTypes.xsd
rename to czi-format/docs_czi/XmlSchemas/CommonTypes.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/Dimensions.xsd b/czi-format/docs_czi/XmlSchemas/Dimensions.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/Dimensions.xsd
rename to czi-format/docs_czi/XmlSchemas/Dimensions.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/DisplaySetting.xsd b/czi-format/docs_czi/XmlSchemas/DisplaySetting.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/DisplaySetting.xsd
rename to czi-format/docs_czi/XmlSchemas/DisplaySetting.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/ImageAnalysisSetting.xsd b/czi-format/docs_czi/XmlSchemas/ImageAnalysisSetting.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/ImageAnalysisSetting.xsd
rename to czi-format/docs_czi/XmlSchemas/ImageAnalysisSetting.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/ImageMetadata.xsd b/czi-format/docs_czi/XmlSchemas/ImageMetadata.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/ImageMetadata.xsd
rename to czi-format/docs_czi/XmlSchemas/ImageMetadata.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/Information.xsd b/czi-format/docs_czi/XmlSchemas/Information.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/Information.xsd
rename to czi-format/docs_czi/XmlSchemas/Information.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/Instrument.xsd b/czi-format/docs_czi/XmlSchemas/Instrument.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/Instrument.xsd
rename to czi-format/docs_czi/XmlSchemas/Instrument.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/Layers.xsd b/czi-format/docs_czi/XmlSchemas/Layers.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/Layers.xsd
rename to czi-format/docs_czi/XmlSchemas/Layers.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/PhysiologySetting.xsd b/czi-format/docs_czi/XmlSchemas/PhysiologySetting.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/PhysiologySetting.xsd
rename to czi-format/docs_czi/XmlSchemas/PhysiologySetting.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/Scaling.xsd b/czi-format/docs_czi/XmlSchemas/Scaling.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/Scaling.xsd
rename to czi-format/docs_czi/XmlSchemas/Scaling.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/Timeline.xsd b/czi-format/docs_czi/XmlSchemas/Timeline.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/Timeline.xsd
rename to czi-format/docs_czi/XmlSchemas/Timeline.xsd
diff --git a/czi-format/czi-doc-zen-2.3/XmlSchemas/Views.xsd b/czi-format/docs_czi/XmlSchemas/Views.xsd
similarity index 100%
rename from czi-format/czi-doc-zen-2.3/XmlSchemas/Views.xsd
rename to czi-format/docs_czi/XmlSchemas/Views.xsd
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