mergew with sz v3.2.0

szcompressor · Aug 27, 2024 · 751f41e · 751f41e
1 parent dc2b5ea
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diff --git a/include/SZ3/api/impl/SZAlgoBioMD.hpp b/include/SZ3/api/impl/SZAlgoBioMD.hpp
@@ -0,0 +1,59 @@
+#ifndef SZ3_SZ_BIOMD_HPP
+#define SZ3_SZ_BIOMD_HPP
+
+#include "SZ3/quantizer/IntegerQuantizer.hpp"
+#include "SZ3/decomposition/SZBioMDXtcDecomposition.hpp"
+#include "SZ3/decomposition/SZBioMDDecomposition.hpp"
+#include "SZ3/encoder/XtcBasedEncoder.hpp"
+#include "SZ3/lossless/Lossless_zstd.hpp"
+#include "SZ3/lossless/Lossless_bypass.hpp"
+#include "SZ3/utils/Statistic.hpp"
+#include "SZ3/utils/Config.hpp"
+#include "SZ3/def.hpp"
+
+namespace SZ3 {
+
+    template<class T, uint N>
+    size_t SZ_compress_bioMD(Config &conf, T *data, uchar *cmpData, size_t cmpCap) {
+        assert(N == conf.N);
+        assert(conf.cmprAlgo == ALGO_BIOMD);
+        calAbsErrorBound(conf, data);
+
+        auto quantizer = LinearQuantizer<T>(conf.absErrorBound, conf.quantbinCnt / 2);
+        auto sz = make_compressor_sz_generic<T, N>(make_decomposition_biomd<T, N>(conf, quantizer), HuffmanEncoder<int>(),
+                                                   Lossless_zstd());
+        return sz->compress(conf, data, cmpData, cmpCap);
+    }
+
+    template<class T, uint N>
+    void SZ_decompress_bioMD(const Config &conf, const uchar *cmpData, size_t cmpSize, T *decData) {
+        assert(conf.cmprAlgo == ALGO_BIOMD);
+
+        LinearQuantizer<T> quantizer;
+        auto sz = make_compressor_sz_generic<T, N>(make_decomposition_biomd<T, N>(conf, quantizer),
+                                                   HuffmanEncoder<int>(), Lossless_zstd());
+        sz->decompress(conf, cmpData, cmpSize, decData);
+    }
+
+    template<class T, uint N>
+    size_t SZ_compress_bioMDXtcBased(Config &conf, T *data, uchar *cmpData, size_t cmpCap) {
+        assert(N == conf.N);
+        assert(conf.cmprAlgo == ALGO_BIOMDXTC);
+        calAbsErrorBound(conf, data);
+
+        auto sz = make_compressor_sz_generic<T, N>(SZBioMDXtcDecomposition<T, N>(conf), XtcBasedEncoder<int>(),
+                                                   Lossless_bypass());
+        return sz->compress(conf, data, cmpData, cmpCap);
+    }
+
+    template<class T, uint N>
+    void SZ_decompress_bioMDXtcBased(const Config &conf, const uchar *cmpData, size_t cmpSize, T *decData) {
+        assert(conf.cmprAlgo == ALGO_BIOMDXTC);
+
+        auto sz = make_compressor_sz_generic<T, N>(SZBioMDXtcDecomposition<T, N>(conf),
+                                                   XtcBasedEncoder<int>(), Lossless_bypass());
+        sz->decompress(conf, cmpData, cmpSize, decData);
+    }
+
+}
+#endif
diff --git a/include/SZ3/api/impl/SZBioMD.hpp b/include/SZ3/api/impl/SZBioMD.hpp
diff --git a/include/SZ3/api/impl/SZDispatcher.hpp b/include/SZ3/api/impl/SZDispatcher.hpp
@@ -7,7 +7,7 @@
 #include "SZ3/api/impl/SZAlgoInterp.hpp"
 #include "SZ3/api/impl/SZAlgoLorenzoReg.hpp"
 #include "SZ3/api/impl/SZAlgo.hpp"
-#include "SZ3/api/impl/SZBioMD.hpp"
+#include "SZ3/api/impl/SZAlgoBioMD.hpp"
 #include <cmath>
 
 namespace SZ3 {
@@ -30,9 +30,9 @@ namespace SZ3 {
         } else if (conf.cmprAlgo == ALGO_NOPRED) {
             return SZ_compress_nopred<T, N>(conf, data, cmpData, cmpCap);
         } else if (conf.cmprAlgo == ALGO_BIOMD) {
-            cmpData = (char *) SZ_compress_bioMD<T, N>(conf, data, outSize);
+            return SZ_compress_bioMD<T, N>(conf, data, cmpData, cmpCap);
         } else if (conf.cmprAlgo == ALGO_BIOMDXTC) {
-            cmpData = (char *) SZ_compress_bioMDXtcBased<T, N>(conf, data, outSize);
+            return SZ_compress_bioMDXtcBased<T, N>(conf, data, cmpData, cmpCap);
         }
         return 0;
 //        return cmpData;

diff --git a/...ude/SZ3/decomposition/SZBioMDFrontend.hpp → ...Z3/decomposition/SZBioMDDecomposition.hpp b/...ude/SZ3/decomposition/SZBioMDFrontend.hpp → ...Z3/decomposition/SZBioMDDecomposition.hpp
@@ -4,31 +4,31 @@
 /**
  */
 
-#include "Frontend.hpp"
+#include "Decomposition.hpp"
 //#include "SZ3/utils/MemoryUtil.hpp"
 #include "SZ3/utils/Config.hpp"
 #include <list>
 
 namespace SZ3 {
 
     template<class T, uint N, class Quantizer>
-    class SZBioMDFrontend : public concepts::FrontendInterface<T, N> {
+    class SZBioMDDecomposition : public concepts::DecompositionInterface<T, N> {
      public:
-        SZBioMDFrontend(const Config &conf, Quantizer quantizer) :
+        SZBioMDDecomposition(const Config &conf, Quantizer quantizer) :
             quantizer(quantizer),
             conf(conf) {
             if (N != 1 && N != 2 && N != 3) {
                 throw std::invalid_argument("SZBioFront only support 1D, 2D or 3D data");
             }
         }
 
-        ~SZBioMDFrontend() {
-            clear();
+        ~SZBioMDDecomposition() {
+//            clear();
         }
 
         void print() {};
-        
-        std::vector<int> compress(T *data) {
+
+        std::vector<int> compress(const Config &conf, T *data) {
             if (N == 1) {
                 return compress_1d(data);
             } else if (N == 2) {
@@ -37,8 +37,8 @@ namespace SZ3 {
                 return compress_3d(data);
             }
         };
-        
-        T *decompress(std::vector<int> &quant_inds, T *dec_data) {
+
+        T *decompress(const Config &conf, std::vector<int> &quant_inds, T *dec_data) {
             if (N == 1) {
                 return decompress_1d(quant_inds, dec_data);
             } else if (N == 2) {
@@ -56,7 +56,7 @@ namespace SZ3 {
         }
 
         void load(const uchar *&c, size_t &remaining_length) {
-            clear();
+//            clear();
             const uchar *c_pos = c;
             read(site, c, remaining_length);
             read(firstFillFrame_, c, remaining_length);
@@ -65,9 +65,9 @@ namespace SZ3 {
             remaining_length -= c_pos - c;
         }
 
-        void clear() {
-            quantizer.clear();
-        }
+//        void clear() {
+//            quantizer.clear();
+//        }
 
         size_t size_est() {
             return quantizer.size_est(); //unpred
@@ -362,9 +362,9 @@ namespace SZ3 {
     };
 
     template<class T, uint N, class Predictor>
-    SZBioMDFrontend<T, N, Predictor>
-    make_sz_bio_frontend(const Config &conf, Predictor predictor) {
-        return SZBioMDFrontend<T, N, Predictor>(conf, predictor);
+    SZBioMDDecomposition<T, N, Predictor>
+    make_decomposition_biomd(const Config &conf, Predictor predictor) {
+        return SZBioMDDecomposition<T, N, Predictor>(conf, predictor);
     }
 }
 

diff --git a/...decomposition/SZBioMDXtcBasedFrontend.hpp → ...decomposition/SZBioMDXtcDecomposition.hpp b/...decomposition/SZBioMDXtcBasedFrontend.hpp → ...decomposition/SZBioMDXtcDecomposition.hpp
@@ -1,40 +1,40 @@
 /*
- * Based on SZBioMDFrontend.hpp
+ * Based on SZBioMDDecomposition.hpp
  * \author: Magnus Lundborg
  */
 
 #ifndef SZ3_SZBIOMDXTCBASED_FRONTEND
 #define SZ3_SZBIOMDXTCBASED_FRONTEND
 
-#include "Frontend.hpp"
+#include "Decomposition.hpp"
 #include "SZ3/utils/Config.hpp"
 
 #include <list>
 
 namespace SZ3 {
 
     template<class T, uint N>
-    class SZBioMDXtcBasedFrontend : public concepts::FrontendInterface<T, N> {
+    class SZBioMDXtcDecomposition : public concepts::DecompositionInterface<T, N> {
      public:
-        SZBioMDXtcBasedFrontend(const Config &conf) : conf(conf) {
+        SZBioMDXtcDecomposition(const Config &conf) : conf(conf) {
             if (N != 1 && N != 2 && N != 3) {
                 throw std::invalid_argument("SZBioFront only support 1D, 2D or 3D data");
             }
         }
 
-        ~SZBioMDXtcBasedFrontend() { clear(); }
+        // ~SZBioMDXtcDecomposition() { clear(); }
 
         void print() {};
 
-        std::vector<int> compress(T *data) {
+        std::vector<int> compress(const Config &conf, T *data) {
             if (N <= 2) {
                 return compressSingleFrame(data);
             } else {
                 return compressMultiFrame(data);
             }
         };
 
-        T *decompress(std::vector<int> &quantData, T *decData) {
+        T *decompress(const Config &conf, std::vector<int> &quantData, T *decData) {
             if (N <= 2) {
                 return decompressSingleFrame(quantData, decData);
             } else {

diff --git a/include/SZ3/utils/Config.hpp b/include/SZ3/utils/Config.hpp
@@ -11,6 +11,7 @@
 #include <cstdint>
 #include "SZ3/utils/MemoryUtil.hpp"
 #include "SZ3/utils/inih/INIReader.h"
+#include "SZ3/version.hpp"
 
 #define SZ_FLOAT 0
 #define SZ_DOUBLE 1