{"action":"created","comment":{"url":"https://api.github.com/repos/dafer45/TBTK/pulls/comments/85527295","pull_request_review_id":6230005,"id":85527295,"diff_hunk":"@@ -892,6 +895,245 @@ void FileReader::readAttributes(\n \t}\n }\n \n+//herr_t\n+//attr_info(hid_t loc_id, const char *name, void *opdata)\n+//{\n+//    hid_t attr, atype, aspace;  /* Attribute, datatype, dataspace identifiers */\n+//    char    *string_out=NULL;\n+//    int   rank;\n+//    hsize_t sdim[64];\n+//    herr_t ret;\n+//    int i, j ;\n+//    size_t size, totsize;\n+//    size_t npoints;             /* Number of elements in the array attribute. */\n+//    int point_out;\n+//    float *float_array;         /* Pointer to the array attribute. */\n+//    H5S_class_t  classt;\n+//\n+//    /* avoid warnings */\n+//    opdata = opdata;\n+//\n+//    /*  Open the attribute using its name.  */\n+//    attr = H5Aopen_name(loc_id, name);\n+//\n+//    /*  Display attribute name.  */\n+//    printf(\"\\nName : \");\n+//    puts(name);\n+//\n+//    /* Get attribute datatype, dataspace, rank, and dimensions.  */\n+//    atype  = H5Aget_type(attr);\n+//    aspace = H5Aget_space(attr);\n+//    rank = H5Sget_simple_extent_ndims(aspace);\n+//    ret = H5Sget_simple_extent_dims(aspace, sdim, NULL);\n+//\n+//    /* Get dataspace type */\n+//    classt = H5Sget_simple_extent_type (aspace);\n+//    printf (\"H5Sget_simple_extent_type (aspace) returns: %i\\n\", classt);\n+//\n+//    /* Display rank and dimension sizes for the array attribute.  */\n+//    if(rank > 0) {\n+//       printf(\"Rank : %d \\n\", rank);\n+//       printf(\"Dimension sizes : \");\n+//       for (i=0; i< rank; i++) printf(\"%d \", (int)sdim[i]);\n+//       printf(\"\\n\");\n+//    }\n+//\n+//    if (H5T_INTEGER == H5Tget_class(atype)) {\n+//       printf(\"Type : INTEGER \\n\");\n+//       ret  = H5Aread(attr, atype, &point_out);\n+//       printf(\"The value of the attribute \\\"Integer attribute\\\" is %d \\n\",\n+//               point_out);\n+//    }\n+//\n+//    if (H5T_FLOAT == H5Tget_class(atype)) {\n+//       printf(\"Type : FLOAT \\n\");\n+//       npoints = H5Sget_simple_extent_npoints(aspace);\n+//       float_array = (float *)malloc(sizeof(float)*(int)npoints);\n+//       ret = H5Aread(attr, atype, float_array);\n+//       printf(\"Values : \");\n+//       for( i = 0; i < (int)npoints; i++) printf(\"%f \", float_array[i]);\n+//       printf(\"\\n\");\n+//       free(float_array);\n+//    }\n+//\n+//    if (H5T_STRING == H5Tget_class (atype)) {\n+//      printf (\"Type: STRING \\n\");\n+//      size = H5Tget_size (atype);\n+//      printf (\"Size of Each String is: %i\\n\", size);\n+//      totsize = size*sdim[0]*sdim[1];\n+//      string_out = reinterpret_cast<char*>(calloc (totsize, sizeof(char)));\n+//      ret = H5Aread(attr, atype, string_out);\n+//      printf(\"The value of the attribute with index 2 is:\\n\");\n+//      j=0;\n+//      for (i=0; i<totsize; i++) {\n+//        printf (\"%c\", string_out[i]);\n+//        if (j==3) {\n+//          printf(\" \");\n+//          j=0;\n+//        }\n+//        else j++;\n+//      }\n+//      printf (\"\\n\");\n+//    }\n+//\n+//    ret = H5Tclose(atype);\n+//    ret = H5Sclose(aspace);\n+//    ret = H5Aclose(attr);\n+//\n+//    return 0;\n+//}\n+\n+\n+Util::ParameterSet* FileReader::readParameterSet(\n+    string name,\n+\tstring path\n+){\n+\ttry{\n+\t\tstringstream ss;\n+\t\tss << path;\n+\t\tif(path.back() != '/')\n+\t\t\tss << \"/\";\n+\t\tss << name;\n+\n+\t\tException::dontPrint();\n+\n+        Util::ParameterSet *ps = new Util::ParameterSet();\n+\n+        H5File file(filename, H5F_ACC_RDONLY);\n+\t\tDataSet dataset = file.openDataSet(name + \"Int\");\n+        unsigned int num = dataset.getNumAttrs();\n+\n+\t\tfor(unsigned int n = 0; n < num; n++){\n+\t\t\tAttribute attribute = dataset.openAttribute(n);\n+\t\t\tDataType type = attribute.getDataType();\n+            string nameAttribute;\n+\t\t\tnameAttribute = attribute.getName();\n+\n+\t\t\tTBTKAssert(\n+\t\t\t\ttype == PredType::STD_I64BE,\n+\t\t\t\t\"FileReader::readParameterSet()\",\n+\t\t\t\t\"The attribute '\" << nameAttribute << \"' is not of integer type.\",\n+\t\t\t\t\"\"\n+\t\t\t);\n+\t\t\tint value;\n+\t\t\tattribute.read(PredType::NATIVE_INT, &value);\n+\t\t\tps->addInt(nameAttribute, value);\n+\t\t}\n+\n+        dataset = file.openDataSet(name + \"Double\");\n+        num = dataset.getNumAttrs();\n+\n+\t\tfor(unsigned int n = 0; n < num; n++){\n+\t\t\tAttribute attribute = dataset.openAttribute(n);\n+\t\t\tDataType type = attribute.getDataType();\n+            string nameAttribute;\n+\t\t\tnameAttribute = attribute.getName();\n+\n+\t\t\tTBTKAssert(\n+\t\t\t\ttype == PredType::IEEE_F64BE,\n+\t\t\t\t\"FileReader::readParameterSet()\",\n+\t\t\t\t\"The attribute '\" << nameAttribute << \"' is not of double type.\",\n+\t\t\t\t\"\"\n+\t\t\t);\n+\t\t\tdouble value;\n+\t\t\tattribute.read(PredType::NATIVE_DOUBLE, &value);\n+\t\t\tps->addDouble(nameAttribute, value);\n+\t\t}\n+\n+        dataset = file.openDataSet(name + \"Complex\");\n+        num = dataset.getNumAttrs();\n+        const complex<double> one(1,0);\n+        const complex<double> i(0,1);\n+\n+\t\tfor(unsigned int n = 0; n < num; n++){\n+\t\t\tAttribute attribute = dataset.openAttribute(n);\n+\t\t\tDataType type = attribute.getDataType();\n+            string nameAttribute;\n+\t\t\tnameAttribute = attribute.getName();\n+\t\t\tconst hsize_t dimension = 2;\n+\t\t\tArrayType dataTypeComplex(PredType::NATIVE_DOUBLE, 1, &dimension);\n+\n+\t\t\tTBTKAssert(\n+\t\t\t\ttype == dataTypeComplex,\n+\t\t\t\t\"FileReader::readParameterSet()\",\n+\t\t\t\t\"The attribute '\" << nameAttribute << \"' is not of complex type.\",\n+\t\t\t\t\"\"\n+\t\t\t);\n+\t\t\tdouble value[2];\n+\t\t\tattribute.read(dataTypeComplex, value);\n+            complex<double> complexValue = value[0]*one;\n+            complexValue += value[1]*i;\n+            ps->addComplex(nameAttribute, complexValue);\n+\t\t}\n+\n+        dataset = file.openDataSet(name + \"String\");\n+        num = dataset.getNumAttrs();\n+\n+\t\tfor(unsigned int n = 0; n < num; n++){\n+\t\t\tAttribute attribute = dataset.openAttribute(n);\n+\t\t\tDataType type = attribute.getDataType();\n+            string nameAttribute = attribute.getName();\n+\t\t\tunsigned int memLength = attribute.getInMemDataSize();\n+\t\t\tStrType strDataType(PredType::C_S1, memLength);","path":"TBTK/calc/TightBindingLib/src/FileReader.cpp","position":200,"original_position":200,"commit_id":"41c6ede857ef9b2763dab206ddbd5607d0bbeb72","original_commit_id":"41c6ede857ef9b2763dab206ddbd5607d0bbeb72","user":{"login":"dafer45","id":1187144,"avatar_url":"https://avatars.githubusercontent.com/u/1187144?v=3","gravatar_id":"","url":"https://api.github.com/users/dafer45","html_url":"https://github.com/dafer45","followers_url":"https://api.github.com/users/dafer45/followers","following_url":"https://api.github.com/users/dafer45/following{/other_user}","gists_url":"https://api.github.com/users/dafer45/gists{/gist_id}","starred_url":"https://api.github.com/users/dafer45/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/dafer45/subscriptions","organizations_url":"https://api.github.com/users/dafer45/orgs","repos_url":"https://api.github.com/users/dafer45/repos","events_url":"https://api.github.com/users/dafer45/events{/privacy}","received_events_url":"https://api.github.com/users/dafer45/received_events","type":"User","site_admin":false},"body":"Make sure this name convention agrees with that for complexType/complexDataType above (currently dataTypeComplex).","created_at":"2016-10-28T13:14:19Z","updated_at":"2016-10-28T13:14:19Z","html_url":"https://github.com/dafer45/TBTK/pull/4#discussion_r85527295","pull_request_url":"https://api.github.com/repos/dafer45/TBTK/pulls/4","_links":{"self":{"href":"https://api.github.com/repos/dafer45/TBTK/pulls/comments/85527295"},"html":{"href":"https://github.com/dafer45/TBTK/pull/4#discussion_r85527295"},"pull_request":{"href":"https://api.github.com/repos/dafer45/TBTK/pulls/4"}}},"pull_request":{"url":"https://api.github.com/repos/dafer45/TBTK/pulls/4","id":91359651,"html_url":"https://github.com/dafer45/TBTK/pull/4","diff_url":"https://github.com/dafer45/TBTK/pull/4.diff","patch_url":"https://github.com/dafer45/TBTK/pull/4.patch","issue_url":"https://api.github.com/repos/dafer45/TBTK/issues/4","number":4,"state":"open","locked":false,"title":"Read and write TBTK::ParameterSet to hdf5 files","user":{"login":"glaurung24","id":22666580,"avatar_url":"https://avatars.githubusercontent.com/u/22666580?v=3","gravatar_id":"","url":"https://api.github.com/users/glaurung24","html_url":"https://github.com/glaurung24","followers_url":"https://api.github.com/users/glaurung24/followers","following_url":"https://api.github.com/users/glaurung24/following{/other_user}","gists_url":"https://api.github.com/users/glaurung24/gists{/gist_id}","starred_url":"https://api.github.com/users/glaurung24/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/glaurung24/subscriptions","organizations_url":"https://api.github.com/users/glaurung24/orgs","repos_url":"https://api.github.com/users/glaurung24/repos","events_url":"https://api.github.com/users/glaurung24/events{/privacy}","received_events_url":"https://api.github.com/users/glaurung24/received_events","type":"User","site_admin":false},"body":"Added functionality to write a ParamterSet to a hdf5 file with FileWriter::writeParameterSet and read from it with FileReader::readParameterSet.\r\nAlso found and corrected some typos in Parameterset.cpp","created_at":"2016-10-28T10:40:21Z","updated_at":"2016-10-28T13:18:44Z","closed_at":null,"merged_at":null,"merge_commit_sha":"c2d3244665af638b5a53de08891b076325946e17","assignee":null,"assignees":[],"milestone":null,"commits_url":"https://api.github.com/repos/dafer45/TBTK/pulls/4/commits","review_comments_url":"https://api.github.com/repos/dafer45/TBTK/pulls/4/comments","review_comment_url":"https://api.github.com/repos/dafer45/TBTK/pulls/comments{/number}","comments_url":"https://api.github.com/repos/dafer45/TBTK/issues/4/comments","statuses_url":"https://api.github.com/repos/dafer45/TBTK/statuses/41c6ede857ef9b2763dab206ddbd5607d0bbeb72","head":{"label":"glaurung24:readAndWriteParamSet","ref":"readAndWriteParamSet","sha":"41c6ede857ef9b2763dab206ddbd5607d0bbeb72","user":{"login":"glaurung24","id":22666580,"avatar_url":"https://avatars.githubusercontent.com/u/22666580?v=3","gravatar_id":"","url":"https://api.github.com/users/glaurung24","html_url":"https://github.com/glaurung24","followers_url":"https://api.github.com/users/glaurung24/followers","following_url":"https://api.github.com/users/glaurung24/following{/other_user}","gists_url":"https://api.github.com/users/glaurung24/gists{/gist_id}","starred_url":"https://api.github.com/users/glaurung24/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/glaurung24/subscriptions","organizations_url":"https://api.github.com/users/glaurung24/orgs","repos_url":"https://api.github.com/users/glaurung24/repos","events_url":"https://api.github.com/users/glaurung24/events{/privacy}","received_events_url":"https://api.github.com/users/glaurung24/received_events","type":"User","site_admin":false},"repo":{"id":71365136,"name":"TBTK","full_name":"glaurung24/TBTK","owner":{"login":"glaurung24","id":22666580,"avatar_url":"https://avatars.githubusercontent.com/u/22666580?v=3","gravatar_id":"","url":"https://api.github.com/users/glaurung24","html_url":"https://github.com/glaurung24","followers_url":"https://api.github.com/users/glaurung24/followers","following_url":"https://api.github.com/users/glaurung24/following{/other_user}","gists_url":"https://api.github.com/users/glaurung24/gists{/gist_id}","starred_url":"https://api.github.com/users/glaurung24/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/glaurung24/subscriptions","organizations_url":"https://api.github.com/users/glaurung24/orgs","repos_url":"https://api.github.com/users/glaurung24/repos","events_url":"https://api.github.com/users/glaurung24/events{/privacy}","received_events_url":"https://api.github.com/users/glaurung24/received_events","type":"User","site_admin":false},"private":false,"html_url":"https://github.com/glaurung24/TBTK","description":null,"fork":true,"url":"https://api.github.com/repos/glaurung24/TBTK","forks_url":"https://api.github.com/repos/glaurung24/TBTK/forks","keys_url":"https://api.github.com/repos/glaurung24/TBTK/keys{/key_id}","collaborators_url":"https://api.github.com/repos/glaurung24/TBTK/collaborators{/collaborator}","teams_url":"https://api.github.com/repos/glaurung24/TBTK/teams","hooks_url":"https://api.github.com/repos/glaurung24/TBTK/hooks","issue_events_url":"https://api.github.com/repos/glaurung24/TBTK/issues/events{/number}","events_url":"https://api.github.com/repos/glaurung24/TBTK/events","assignees_url":"https://api.github.com/repos/glaurung24/TBTK/assignees{/user}","branches_url":"https://api.github.com/repos/glaurung24/TBTK/branches{/branch}","tags_url":"https://api.github.com/repos/glaurung24/TBTK/tags","blobs_url":"https://api.github.com/repos/glaurung24/TBTK/git/blobs{/sha}","git_tags_url":"https://api.github.com/repos/glaurung24/TBTK/git/tags{/sha}","git_refs_url":"https://api.github.com/repos/glaurung24/TBTK/git/refs{/sha}","trees_url":"https://api.github.com/repos/glaurung24/TBTK/git/trees{/sha}","statuses_url":"https://api.github.com/repos/glaurung24/TBTK/statuses/{sha}","languages_url":"https://api.github.com/repos/glaurung24/TBTK/languages","stargazers_url":"https://api.github.com/repos/glaurung24/TBTK/stargazers","contributors_url":"https://api.github.com/repos/glaurung24/TBTK/contributors","subscribers_url":"https://api.github.com/repos/glaurung24/TBTK/subscribers","subscription_url":"https://api.github.com/repos/glaurung24/TBTK/subscription","commits_url":"https://api.github.com/repos/glaurung24/TBTK/commits{/sha}","git_commits_url":"https://api.github.com/repos/glaurung24/TBTK/git/commits{/sha}","comments_url":"https://api.github.com/repos/glaurung24/TBTK/comments{/number}","issue_comment_url":"https://api.github.com/repos/glaurung24/TBTK/issues/comments{/number}","contents_url":"https://api.github.com/repos/glaurung24/TBTK/contents/{+path}","compare_url":"https://api.github.com/repos/glaurung24/TBTK/compare/{base}...{head}","merges_url":"https://api.github.com/repos/glaurung24/TBTK/merges","archive_url":"https://api.github.com/repos/glaurung24/TBTK/{archive_format}{/ref}","downloads_url":"https://api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