added type int64 wrapper

kmpaul · May 15, 2019 · b867c7c · b867c7c
1 parent d803a45
commit b867c7c
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Showing 4 changed files with 111 additions and 0 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -2,6 +2,7 @@ cmake_minimum_required(VERSION 3.9)
 project(cz5test C CXX)
 
 message(STATUS "Using C11")
+message(CXX)
 set(CMAKE_C_STANDARD 11)
 
 if (NOT "${CMAKE_CXX_FLAGS}" MATCHES "-std=c\\+\\+17")
@@ -29,6 +30,7 @@ option(WITH_ZLIB ON)
 if(WITH_ZLIB)
     find_package(ZLIB REQUIRED)
     include_directories(ZLIB_INCLUDE_DIRS)
+    message(ZLIB_INCLUDE_DIRS)
     add_definitions(-DWITH_ZLIB)
     SET(COMPRESSION_LIBRARIES "${COMPRESSION_LIBRARIES};${ZLIB_LIBRARIES}")
 endif()

diff --git a/main.c b/main.c
@@ -11,18 +11,23 @@ int main() {
     float data1[10][10][10];
     float data2[10][10][10];
     float rdata[10][10][10];
+    long long int idata1[10][10][10];
+    long long int idata2[10][10][10];
+    long long int irdata[10][10][10];
     unsigned int ndim = 3;
     for (int i = 0; i < chunks[0]; i++){
         for (int j = 0; j < chunks[1]; j++){
             for (int k = 0; k<chunks[2]; k++){ 
                 data1[i][j][k]=rand()%1000+1;
+                idata1[i][j][k]=rand()%1000+1;
             }    
         }
     }
     for (int i = 0; i < chunks[0]; i++){
         for (int j = 0; j < chunks[1]; j++){
             for (int k = 0; k<chunks[2]; k++){ 
                 data2[i][j][k]=rand()%1000+1;
+                idata2[i][j][k]=rand()%1000+1;
             }    
         }
     }
@@ -48,5 +53,30 @@ int main() {
         printf("data2 = %f\n",data2[i][0][0]);
     }
     printf("after assert\n");
+
+    char* iarrayName = "test_c_int64.z5";
+    z5CreateInt64Dataset(iarrayName, ndim, shape, chunks, cusezlib, level);
+    z5WriteInt64Subarray(iarrayName, idata1, ndim, chunks, offset);
+    z5ReadInt64Subarray(iarrayName, irdata, ndim, chunks, offset); 
+    for (int i = 0; i < chunks[0]; i++){
+        for (int j = 0; j < chunks[1]; j++)
+            for (int k = 0; k<chunks[2]; k++) 
+                assert(idata1[i][j][k] == irdata[i][j][k]); 
+        printf("idata1 = %lu\n",idata1[i][0][0]);
+    }
+    z5WriteInt64Subarray(iarrayName, idata2, ndim, chunks, offset2);
+    z5ReadInt64Subarray(iarrayName, irdata, ndim, chunks, offset2); 
+    printf("after read float\n");
+    for (int i = 0; i < chunks[0]; i++){
+        for (int j = 0; j < chunks[1]; j++)
+            for (int k = 0; k<chunks[2]; k++) 
+                assert(idata2[i][j][k] == irdata[i][j][k]); 
+        printf("idata2 = %lu\n",idata2[i][0][0]);
+    }
+    printf("after assert\n");
+    size_t chunkSize0=z5GetFileSize("test_c_int64.z5/0.0.0");
+    size_t chunkSize1=z5GetFileSize("test_c_int64.z5/1.1.1");
+    printf("size = %lu, %lu\n",chunkSize0,chunkSize1);
+    z5Delete("test_c_int64.z5");
     return 0;
 }
diff --git a/z5wrapper.cc b/z5wrapper.cc
@@ -6,6 +6,7 @@
 #include <iostream>
 #include "z5wrapper.h"
 
+namespace fs = boost::filesystem;
 namespace z5 {
     extern "C" {
 
@@ -34,6 +35,30 @@ namespace z5 {
 
     }
 
+    void z5CreateInt64Dataset(char *path, unsigned int ndim, size_t *shape, size_t *chunks, int cuseZlib, int level) {
+        std::string path_s(path);
+        std::vector<std::string> dtype({"long long int"});
+
+        std::vector<size_t> shape_v(shape, shape + ndim);
+        std::vector<size_t> chunks_v(chunks, chunks + ndim);
+        bool asZarr = true;
+
+        DatasetMetadata int64Meta(types::Datatype::int64,shape_v,chunks_v,asZarr);
+        if (cuseZlib) {
+          int64Meta.compressor = types::zlib;
+          int64Meta.compressionOptions["useZlib"] = true;
+          int64Meta.compressionOptions["level"] = level;
+        }
+        handle::Dataset handle_(path_s);
+        handle_.createDir();
+        writeMetadata(handle_, int64Meta);
+    long long int idata1;
+    int64_t data1;
+    long int data2;
+    //std::cout<<"int64 "<<typeid(data1).name()<<" "<<sizeof(int64_t)<<std::endl;
+    //std::cout<<"long int "<<typeid(data2).name()<<" "<<sizeof(long int)<<std::endl;
+    //std::cout<<"long long int "<<typeid(idata1).name()<<" "<<sizeof(long long int)<<std::endl;
+}
 
     void z5WriteFloatSubarray(char *path, float *array, unsigned int ndim, size_t *shape, size_t *offset) {
         std::string path_s(path);
@@ -47,6 +72,21 @@ namespace z5 {
         multiarray::writeSubarray<float>(ds,adp_array,offset_v.begin());
     }
 
+    void z5WriteInt64Subarray(char *path, long long int *array, unsigned int ndim, size_t *shape, size_t *offset) {
+        std::string path_s(path);
+        auto ds =openDataset(path_s);
+        using vec_type = std::vector<long int>;
+        size_t size = 1;
+        std::vector<std::size_t> shape_v(shape,shape + ndim); 
+        for (std::vector<size_t>::const_iterator i = shape_v.begin(); i != shape_v.end(); ++i)
+            size=size*(*i);
+        using shape_type = std::vector<vec_type::size_type>;
+        shape_type s(shape,shape+ndim);
+        std::vector<size_t> offset_v(offset,offset + ndim);
+        auto adp_array=xt::adapt(array,size,xt::no_ownership(),s);
+        multiarray::writeSubarray<long int>(ds,adp_array,offset_v.begin());
+    }
+
     void z5ReadFloatSubarray(char *path, float *array, unsigned int ndim, size_t *shape, size_t *offset) {
         std::string path_s(path);
         auto ds = openDataset(path_s);
@@ -61,6 +101,35 @@ namespace z5 {
         auto adp_array=xt::adapt(array,size,xt::no_ownership(),s);
         multiarray::readSubarray<float>(ds,adp_array,offset_v.begin()); 
     }
+    void z5ReadInt64Subarray(char *path, long long int *array, unsigned int ndim, size_t *shape, size_t *offset) {
+        std::string path_s(path);
+        auto ds = openDataset(path_s);
+        using vec_type = std::vector<long int>;
+        size_t size = 1;
+        std::vector<std::size_t> shape_v(shape,shape + ndim); 
+        for (std::vector<size_t>::const_iterator i = shape_v.begin(); i != shape_v.end(); ++i)
+            size*=(*i);
+        using shape_type = std::vector<vec_type::size_type>;
+        shape_type s(shape,shape+ndim);
+        std::vector<size_t> offset_v(offset,offset + ndim);
+        auto adp_array=xt::adapt(array,size,xt::no_ownership(),s);
+        multiarray::readSubarray<long int>(ds,adp_array,offset_v.begin()); 
+    }
+    size_t z5GetFileSize(char *path){
+        std::string path_s(path);
+	fs::ifstream file(path_s, std::ios::binary);
+	file.seekg(0, std::ios::end);
+	const std::size_t fileSize = file.tellg();
+	file.seekg(0, std::ios::beg);
+	file.close();
+        return fileSize;
+    }
+    void z5Delete(char *path ){
+        std::string path_s(path);
+        fs::path filename(path_s);
+        fs::remove_all(filename);
+    }
+
 }
 
 }
diff --git a/z5wrapper.h b/z5wrapper.h
@@ -22,12 +22,22 @@ namespace z5 {
 #endif
 
         void z5CreateGroup(char* path);
+
         void z5CreateFloatDataset(char *path, unsigned int ndim, size_t *shape, size_t *chunks, int cuseZlib, int level);
 
         void z5WriteFloatSubarray(char *path, float *array, unsigned int ndim, size_t *shape, size_t *offset);
 
         void z5ReadFloatSubarray(char *path, float *array, unsigned int ndim, size_t *shape, size_t *offset);
 
+        void z5CreateInt64Dataset(char *path, unsigned int ndim, size_t *shape, size_t *chunks, int cuseZlib, int level);
+
+        void z5WriteInt64Subarray(char *path, long long int *array, unsigned int ndim, size_t *shape, size_t *offset);
+
+        void z5ReadInt64Subarray(char *path, long long int *array, unsigned int ndim, size_t *shape, size_t *offset);
+
+        size_t z5GetFileSize(char *path);
+
+        void z5Delete(char *path );
 #ifdef __cplusplus
     }
 }