Merge pull request #1 from weilewei/master

add supports for writing file and attributes

CMakeLists.txt

@@ -43,6 +43,9 @@ target_link_libraries(test_cpp LINK_PUBLIC ${TEST_LIBS} ${COMPRESSION_LIBRARIES}
 add_executable(test_c main.c z5wrapper.cc)
 target_link_libraries(test_c LINK_PUBLIC ${TEST_LIBS} ${COMPRESSION_LIBRARIES})
 
+add_executable(test_attributes test_attributes.c z5wrapper.cc)
+target_link_libraries(test_attributes LINK_PUBLIC ${TEST_LIBS} ${COMPRESSION_LIBRARIES})
+
 
 install(FILES "${CMAKE_CURRENT_SOURCE_DIR}/z5wrapper.h"
   DESTINATION "${CMAKE_INSTALL_PREFIX}/include")

test_attributes.c

@@ -0,0 +1,109 @@
+#include <stdlib.h>
+#include <assert.h>
+#include "z5wrapper.h"
+
+void my_create_dataset(char* arrayName)
+{
+    size_t shape[] = {20, 20, 20};
+    size_t chunks[] = {10, 10, 10};
+    size_t offset[] = {0, 0, 0};
+    size_t offset2[] = {10, 10, 10};
+    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;
+            }
+        }
+    }
+    //char* arrayName = "test_c.z5";
+    int cusezlib = 1;
+    int level = 1;
+    z5CreateFloatDataset(arrayName, ndim, shape, chunks, cusezlib, level);
+    z5WriteFloatSubarray(arrayName, data1, ndim, chunks, offset);
+    z5ReadFloatSubarray(arrayName, rdata, 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(data1[i][j][k] == rdata[i][j][k]);
+        printf("data1 = %f\n",data1[i][0][0]);
+    }
+    z5WriteFloatSubarray(arrayName, data2, ndim, chunks, offset2);
+    z5ReadFloatSubarray(arrayName, rdata, 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(data2[i][j][k] == rdata[i][j][k]);
+        printf("data2 = %f\n",data2[i][0][0]);
+    }
+    z5writeAttributesString(arrayName, "time", "noon");
+
+    float floatval = 42.0;
+    z5writeAttributesfloat(arrayName, "float", &floatval);
+
+    double doubleval = 42.0;
+    z5writeAttributesdouble(arrayName, "double", &doubleval);
+
+    int intval = 42;
+    z5writeAttributesint(arrayName, "int", &intval);
+
+    long int longval = 42;
+    z5writeAttributeslong(arrayName, "long", &longval);
+
+    long long longlongval = 42;
+    z5writeAttributeslonglong(arrayName, "longlong", &longlongval);
+
+    unsigned long long ulonglongval = 42;
+    z5writeAttributesulonglong(arrayName, "ulonglong", &ulonglongval);
+
+    unsigned short ushortval = 42;
+    z5writeAttributesushort(arrayName, "unshort", &ushortval);
+
+    unsigned int uint = 42;
+    z5writeAttributesuint(arrayName, "uint", &uint);
+
+    unsigned short usint = 42;
+    z5writeAttributesusint(arrayName, "usint", &usint);
+
+    short shortint = 42;
+    z5writeAttributesshort(arrayName, "short", &shortint);
+
+    printf("after assert\n");
+}
+
+void test_create_file()
+{
+    // create a group
+    char* fileName = "new_file";
+    z5CreateFile(fileName);
+    char* groupName1 = "new_file/group1";
+    z5CreateGroup(groupName1);
+    char* groupName2 = "new_file/group2";
+    z5CreateGroup(groupName2);
+    char* arrayName = "new_file/group1/array1";
+    my_create_dataset(arrayName);
+
+}
+
+
+int main()
+{
+	test_create_file();
+	return 0;
+}

z5wrapper.cc

@@ -2,6 +2,7 @@
 // Created by Kevin Paul on 2019-04-24.
 //
 #include <string>
+#include <stdint.h>
 #include <vector>
 #include <iostream>
 #include "z5wrapper.h"
@@ -10,6 +11,14 @@ namespace fs = boost::filesystem;
 namespace z5 {
     extern "C" {
 
+    void z5CreateFile(char* path)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::File cFile(path_s);
+        createFile(cFile, asZarr);
+    }
+
     void z5CreateGroup(char* path) {
         std::string path_s(path);
         bool asZarr = true;
@@ -124,6 +133,129 @@ namespace z5 {
 	file.close();
         return fileSize;
     }
+
+    void z5writeAttributesString(char *path, const char *name, const char *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+	nlohmann::json j;
+	std::string name_s(name);
+	std::string value_s(value);
+	j[name_s] = value_s;
+	writeAttributes(cHandle, j);	
+    }
+
+    void z5writeAttributesshort(char *path, const char *name, const short *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (int64_t) *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributesint(char *path, const char *name, const int *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (int64_t) *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributeslong(char *path, const char *name, const long *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (int64_t) *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributesfloat(char *path, const char *name, const float *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (double) *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributesdouble(char *path, const char *name, const double *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributesushort(char *path, const char *name, const unsigned short *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (int64_t) *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributesusint(char *path, const char *name, const unsigned short *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (int64_t) *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributeslonglong(char *path, const char *name, const long long *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (int64_t) *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributesulonglong(char *path, const char *name, const unsigned long long *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (int64_t) *value;
+        writeAttributes(cHandle, j);
+    }
+
+    void z5writeAttributesuint(char *path, const char *name, const unsigned int *value)
+    {
+        std::string path_s(path);
+        bool asZarr = true;
+        handle::Handle cHandle(path_s);
+        nlohmann::json j;
+        std::string name_s(name);
+        j[name_s] = (int64_t) *value;
+        writeAttributes(cHandle, j);
+    }	
+
     void z5Delete(char *path ){
         std::string path_s(path);
         fs::path filename(path_s);

z5wrapper.h

@@ -11,7 +11,9 @@
 
 #ifdef __cplusplus
 #include "z5/dataset_factory.hxx"
+#include "z5/file.hxx"
 #include "z5/groups.hxx"
+#include "z5/attributes.hxx"
 #include "z5/compression/zlib_compressor.hxx"
 #include "z5/types/types.hxx"
 #endif
@@ -20,7 +22,8 @@
 namespace z5 {
     extern "C" {
 #endif
-
+	void z5CreateFile(char* path);
+
         void z5CreateGroup(char* path);
 
         void z5CreateFloatDataset(char *path, unsigned int ndim, size_t *shape, size_t *chunks, int cuseZlib, int level);
@@ -37,7 +40,29 @@ namespace z5 {
 
         size_t z5GetFileSize(char *path);
 
-        void z5Delete(char *path );
+	void z5writeAttributesString(char *path, const char *name, const char *value);
+
+	void z5writeAttributesshort(char *path, const char *name, const short *value);
+
+	void z5writeAttributesint(char *path, const char *name, const int *value);
+
+	void z5writeAttributeslong(char *path, const char *name, const long *value);
+
+	void z5writeAttributesfloat(char *path, const char *name, const float *value); 
+
+	void z5writeAttributesdouble(char *path, const char *name, const double *value);
+
+	void z5writeAttributesushort(char *path, const char *name, const unsigned short *value);
+
+	void z5writeAttributesusint(char *path, const char *name, const unsigned short int *value);
+
+	void z5writeAttributeslonglong(char *path, const char *name, const long long *value);
+
+	void z5writeAttributesulonglong(char *path, const char *name, const unsigned long long *value);
+
+	void z5writeAttributesuint(char *path, const char *name, const unsigned int *value);
+
+	void z5Delete(char *path );
 #ifdef __cplusplus
     }
 }