added handling reference attributes. Beginning handling enum datasets

HDF-NI · Jun 20, 2018 · a7793cc · a7793cc
1 parent 48b6916
commit a7793cc
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Showing 16 changed files with 288 additions and 53 deletions.
diff --git a/binding.gyp b/binding.gyp
@@ -27,6 +27,7 @@
                     'src/methods.cc',
                     'src/h5_file.cc',
                     'src/h5_group.cc',
+                    'src/reference.cc'
                 ],
                 'link_settings': {
                     'libraries': [
@@ -57,6 +58,7 @@
                     'src/methods.cc',
                     'src/h5_file.cc',
                     'src/h5_group.cc',
+                    'src/reference.cc'
                 ],
                 'msbuild_toolset': 'v120',
                 "configurations": {
@@ -109,6 +111,7 @@
                     'src/methods.cc',
                     'src/h5_file.cc',
                     'src/h5_group.cc',
+                    'src/reference.cc'
                 ],
                 'link_settings': {
                     'libraries': [
@@ -137,7 +140,9 @@
                     "/usr/include/hdf5/serial"
                 ],
                 'sources': [
-                    'src/h5lt.cc'
+                    'src/int64.cc',
+                    'src/h5lt.cc',
+                    'src/reference.cc'
                 ],
                 'link_settings': {
                     'libraries': [
@@ -161,7 +166,9 @@
                     'C:/Program Files/Microsoft SDKs/Windows/v7.1/Include'
                 ],
                 'sources': [
-                    'src/h5lt.cc'
+                    'src/int64.cc',
+                    'src/h5lt.cc',
+                    'src/reference.cc'
                 ],
                 'msbuild_toolset': 'v120',
                 "configurations": {
@@ -205,7 +212,9 @@
                     '<(hdf5_home_mac)/include'
                 ],
                 'sources': [
-                    'src/h5lt.cc'
+                    'src/int64.cc',
+                    'src/h5lt.cc',
+                    'src/reference.cc'
                 ],
                 'link_settings': {
                     'libraries': [

diff --git a/lib/globals.d.ts b/lib/globals.d.ts
@@ -132,7 +132,15 @@ export declare enum H5Type {
     H5T_NATIVE_UINT8,
 }
 
+export declare enum H5RType {
+  H5R_BADTYPE         = -1,     /*invalid Reference Type                     */
+  H5R_OBJECT          = 0,      /*Object reference                           */
+  H5R_DATASET_REGION  = 1,      /*Dataset Region Reference                   */
+  H5R_MAXTYPE         = 2       /*highest type (Invalid as true type)	     */
+}
+
+
 export declare enum Interlace {
     INTERLACE_PIXEL,
     INTERLACE_PLANE
-}
+}
diff --git a/lib/globals.js b/lib/globals.js
@@ -123,6 +123,13 @@ module.exports.H5Type = {
   H5T_NATIVE_UINT8   : 315
 }
 
+module.exports.H5RType ={
+  H5R_BADTYPE         : (-1),   /*invalid Reference Type                     */
+  H5R_OBJECT          : 0,      /*Object reference                           */
+  H5R_DATASET_REGION  : 1,      /*Dataset Region Reference                   */
+  H5R_MAXTYPE         : 2       /*highest type (Invalid as true type)	     */
+}
+
 module.exports.Interlace = {
   INTERLACE_PIXEL : "INTERLACE_PIXEL",
   INTERLACE_PLANE : "INTERLACE_PLANE"

diff --git a/readme.md b/readme.md
@@ -41,6 +41,7 @@ var group = file.openGroup('bar');
 ### Notes on Recent Releases
 
 * Note: Release v0.3.4 
+  * Reference attributes on datasets and groups are now available properties.
   * Reserved propeties such as type, rank, rows etc. are now settable in options for dataset functions.  
   * Typescript definition files now available. 
   * For static native linkng, link_type command line switch is provided in binding.gyp(darwin,win untested).

diff --git a/src/attributes.cc b/src/attributes.cc
@@ -2,6 +2,7 @@
 #include "hdf5.h"
 #include "hdf5_hl.h"
 
+#include "reference.hpp"
 #include "attributes.hpp"
 
 namespace NodeHDF5 {

diff --git a/src/attributes.hpp b/src/attributes.hpp
@@ -9,6 +9,7 @@
 #include <cstring>
 #include <vector>
 #include <memory>
+
 #include "H5Tpublic.h"
 #include "int64.hpp"
 #include "uint64.hpp"
@@ -39,6 +40,14 @@ namespace NodeHDF5 {
           hssize_t    numberOfElements = H5Sget_simple_extent_npoints(space);
           H5T_class_t class_id         = H5Tget_class(attr_type);
           switch (class_id) {
+        case H5T_REFERENCE:{
+            std::unique_ptr<char[]> buf(new char[H5Aget_storage_size(attr_id)]);
+            H5Aread(attr_id, attr_type, buf.get());
+            hid_t objectId=((hid_t*)buf.get())[0];
+            v8::Local<v8::Object>&& ref = Reference::Instantiate(objectId, 1);
+            focus->Set(v8::String::NewFromUtf8(v8::Isolate::GetCurrent(), holder[index].c_str()), ref);
+          }
+            break;
             case H5T_ARRAY: {
               hid_t basetype_id = H5Tget_super(attr_type);
               if (H5Tis_variable_str(basetype_id)>0) {

diff --git a/src/file.h b/src/file.h
@@ -12,6 +12,7 @@
 #include "hdf5_hl.h"
 
 #include "exceptions.hpp"
+#include "reference.hpp"
 #include "attributes.hpp"
 #include "methods.hpp"
 

diff --git a/src/h5_lt.hpp b/src/h5_lt.hpp
@@ -1389,7 +1389,7 @@ namespace NodeHDF5 {
             }
             H5Tclose(t);
             H5Dclose(h);
-          } else if (class_id == H5T_INTEGER && bufSize == 2) {
+          } else if ((class_id == H5T_INTEGER || class_id == H5T_ENUM) && bufSize == 2) {
             hid_t h = H5Dopen(idWrap->Value(), *dset_name, H5P_DEFAULT);
             hid_t t = H5Dget_type(h);
             if (H5Tget_sign(H5Dget_type(h)) == H5T_SGN_2) {
@@ -1458,6 +1458,27 @@ namespace NodeHDF5 {
                 options->Set(String::NewFromUtf8(v8::Isolate::GetCurrent(), "rows"), Number::New(v8::Isolate::GetCurrent(), values_dim.get()[0]));
                 break;
             }
+            if(class_id == H5T_ENUM){
+                v8::Local<v8::Object> enumeration = v8::Object::New(v8::Isolate::GetCurrent());
+
+                hid_t h = H5Dopen(idWrap->Value(), *dset_name, H5P_DEFAULT);
+                hid_t t = H5Dget_type(h);
+                int n=H5Tget_nmembers( t );
+                for(unsigned int i=0;i<(unsigned int)n;i++){
+                    char * mname=H5Tget_member_name( t, i );
+                    int idx=H5Tget_member_index(t, (const char *) mname );
+                    unsigned int value;
+                    H5Tget_member_value( t, idx, (void *)&value );
+                    //std::cout<<i<<" "<<value<<std::endl;
+                    hsize_t dvalue=value;
+                    enumeration->Set(String::NewFromUtf8(v8::Isolate::GetCurrent(), mname), Number::New(v8::Isolate::GetCurrent(), dvalue));                    
+                    H5free_memory((void *)mname);
+                }
+                H5Tclose(t);
+                H5Dclose(h);
+                options->Set(String::NewFromUtf8(v8::Isolate::GetCurrent(), "enumeration"), enumeration);
+
+            }
             v8::Local<v8::Value> argv[1] = {options};
             v8::Local<v8::Function>::New(v8::Isolate::GetCurrent(), callback)
                 ->Call(v8::Isolate::GetCurrent()->GetCurrentContext()->Global(), argc, argv);
@@ -1709,56 +1730,11 @@ namespace NodeHDF5 {
           }
           H5Tclose( type_id);
           v8::Local<v8::Object> focus=buffer->ToObject();
+          // Attributes
           refreshAttributes(focus, did);
           H5Dclose(did);
 
-          // Attributes
-/*          uint32_t                 index = 0;
-          hsize_t                  idx   = 0;
-          std::vector<std::string> holder;
-          H5Aiterate_by_name(idWrap->Value(),
-                             *dset_name,
-                             H5_INDEX_CRT_ORDER,
-                             H5_ITER_INC,
-                             &idx,
-                             [](hid_t location_id, const char* attr_name, const H5A_info_t* ainfo, void* operator_data) {
-                               if (ainfo->data_size > 0)
-                                 ((std::vector<std::string>*)operator_data)->push_back(std::string(attr_name));
-                               return (herr_t)((std::vector<std::string>*)operator_data)->size();
-                             },
-                             (void*)&holder,
-                             H5P_DEFAULT);
-          for (index = 0; index < (uint32_t)holder.size(); index++) {
-            hsize_t     values_dim[1] = {1};
-            size_t      bufSize       = 0;
-            H5T_class_t class_id;
-            err = H5LTget_attribute_info(idWrap->Value(), *dset_name, holder[index].c_str(), values_dim, &class_id, &bufSize);
-            if (err >= 0) {
-              switch (class_id) {
-                case H5T_INTEGER:
-                  long long intValue;
-                  H5LTget_attribute_int(idWrap->Value(), *dset_name, holder[index].c_str(), (int*)&intValue);
-                  buffer->Set(String::NewFromUtf8(v8::Isolate::GetCurrent(), holder[index].c_str()),
-                              Int32::New(v8::Isolate::GetCurrent(), intValue));
-                  break;
-                case H5T_FLOAT:
-                  double value;
-                  H5LTget_attribute_double(idWrap->Value(), *dset_name, holder[index].c_str(), &value);
-                  buffer->Set(String::NewFromUtf8(v8::Isolate::GetCurrent(), holder[index].c_str()),
-                              Number::New(v8::Isolate::GetCurrent(), value));
-                  break;
-                case H5T_STRING: {
-                  std::string strValue(bufSize + 1, '\0');
-                  H5LTget_attribute_string(idWrap->Value(), *dset_name, holder[index].c_str(), (char*)strValue.c_str());
-                  buffer->Set(String::NewFromUtf8(v8::Isolate::GetCurrent(), holder[index].c_str()),
-                              String::NewFromUtf8(v8::Isolate::GetCurrent(), strValue.c_str()));
-                } break;
-                case H5T_NO_CLASS:
-                default: break;
-              }
-            }
-          }
-*/
+
           args.GetReturnValue().Set(buffer);
         } break;
         default:

diff --git a/src/h5lt.cc b/src/h5lt.cc
@@ -2,6 +2,7 @@
 #include "file.h"
 #include "group.h"
 #include "h5_lt.hpp"
+#include "reference.hpp"
 
 using namespace v8;
 using namespace NodeHDF5;
@@ -14,7 +15,9 @@ static void init_lt(Handle<Object> target) {
   HandleScope scope(v8::Isolate::GetCurrent());
 
   // initialize wrapped objects
+  Int64::Initialize(target);
   H5lt::Initialize(target);
+  Reference::Init(target);
 }
 
 NODE_MODULE(h5lt, init_lt)

diff --git a/src/hdf5.cc b/src/hdf5.cc
@@ -2,6 +2,7 @@
 #include "file.h"
 #include "group.h"
 #include "filters.hpp"
+#include "reference.hpp"
 #include "hdf5node.hpp"
 
 using namespace v8;
@@ -20,6 +21,7 @@ static void init(Handle<Object> target) {
   // initialize wrapped objects
   File::Initialize(target);
   Filters::Init(target);
+  Reference::Init(target);
   Int64::Initialize(target);
   Uint64::Initialize(target);
 

diff --git a/src/int64.hpp b/src/int64.hpp
@@ -17,6 +17,7 @@ namespace NodeHDF5 {
     friend class Group;
     friend class Filters;
     friend class Attributes;
+    friend class Reference;
     friend class PacketTable;
 
   protected:

diff --git a/src/methods.cc b/src/methods.cc
@@ -2,9 +2,11 @@
 #include "hdf5.h"
 #include "hdf5_hl.h"
 
+#include "reference.hpp"
 #include "attributes.hpp"
 #include "methods.hpp"
 #include "filters.hpp"
+
 #include "H5LTpublic.h"
 #include "H5PTpublic.h"
 #include "H5Lpublic.h"
@@ -343,7 +345,15 @@ namespace NodeHDF5 {
       switch (H5Tget_class(attr_type)) {
         case H5T_BITFIELD:
         case H5T_OPAQUE:
-        case H5T_REFERENCE:
+            break;
+        case H5T_REFERENCE:{
+          std::unique_ptr<char[]> buf(new char[H5Aget_storage_size(attr_id)]);
+          H5Aread(attr_id, attr_type, buf.get());
+          hid_t objectId=((hid_t*)buf.get())[0];
+          v8::Local<v8::Object>&& ref = Reference::Instantiate(objectId, 1);
+          attrs->Set(v8::String::NewFromUtf8(v8::Isolate::GetCurrent(), attrName.c_str()), ref);
+        }
+            break;
         case H5T_ARRAY:
         case H5T_ENUM: break;
         case H5T_COMPOUND: {

diff --git a/src/reference.cc b/src/reference.cc
@@ -0,0 +1,9 @@
+#include <v8.h>
+#include <node.h>
+
+#include "reference.hpp"
+
+namespace NodeHDF5 {
+  v8::Persistent<v8::Function> Reference::Constructor;
+}
+