[219] | 1 | #include "nc4_data_input.hpp" |
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| 2 | |
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[599] | 3 | #include "context.hpp" |
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| 4 | #include "context_server.hpp" |
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[775] | 5 | #include "context_client.hpp" |
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| 6 | #include "domain.hpp" |
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| 7 | #include "axis.hpp" |
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[599] | 8 | |
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[335] | 9 | namespace xios |
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[219] | 10 | { |
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[599] | 11 | CNc4DataInput::CNc4DataInput(const StdString& filename, MPI_Comm comm_file, bool multifile, bool isCollective /*= true*/) |
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| 12 | : SuperClass() |
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| 13 | , SuperClassWriter(filename, &comm_file, multifile) |
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| 14 | , comm_file(comm_file) |
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| 15 | , filename(filename) |
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| 16 | , isCollective(isCollective) |
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[775] | 17 | , readMetaDataDomains_(), readValueDomains_() |
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| 18 | , readMetaDataAxis_(), readValueAxis_() |
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[599] | 19 | { |
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| 20 | SuperClass::type = multifile ? MULTI_FILE : ONE_FILE; |
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| 21 | } |
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[219] | 22 | |
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[599] | 23 | CNc4DataInput::~CNc4DataInput(void) |
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| 24 | { /* Nothing more to do */ } |
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[219] | 25 | |
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[599] | 26 | StdSize CNc4DataInput::getFieldNbRecords_(CField* field) |
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| 27 | { |
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[770] | 28 | StdString fieldId = field->getFieldOutputName(); |
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[599] | 29 | |
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| 30 | if (SuperClassWriter::isTemporal(fieldId)) |
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| 31 | { |
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| 32 | return SuperClassWriter::getDimensions(&fieldId)[SuperClassWriter::getUnlimitedDimensionName()]; |
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| 33 | } |
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| 34 | |
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| 35 | return 1; |
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| 36 | } |
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| 37 | |
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| 38 | void CNc4DataInput::readFieldData_(CField* field) |
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| 39 | { |
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| 40 | CContext* context = CContext::getCurrent(); |
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| 41 | CContextServer* server = context->server; |
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| 42 | |
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| 43 | CGrid* grid = field->grid; |
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| 44 | |
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| 45 | if (!grid->doGridHaveDataToWrite()) |
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| 46 | if (SuperClass::type==MULTI_FILE || !isCollective) return; |
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| 47 | |
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[770] | 48 | StdString fieldId = field->getFieldOutputName(); |
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[599] | 49 | |
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| 50 | CArray<double,1> fieldData(grid->getWrittenDataSize()); |
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| 51 | if (!field->default_value.isEmpty()) fieldData = field->default_value; |
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| 52 | |
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| 53 | switch (SuperClass::type) |
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| 54 | { |
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| 55 | case MULTI_FILE: |
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| 56 | SuperClassWriter::getData(fieldData, fieldId, isCollective, field->getNStep() - 1); |
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| 57 | break; |
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| 58 | case ONE_FILE: |
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| 59 | { |
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[765] | 60 | /* |
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[599] | 61 | std::vector<int> nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal(); |
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| 62 | std::vector<int> nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer(); |
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| 63 | std::vector<int> nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer(); |
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| 64 | |
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| 65 | int ssize = nZoomBeginGlobal.size(); |
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| 66 | |
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| 67 | std::vector<StdSize> start(ssize); |
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| 68 | std::vector<StdSize> count(ssize); |
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| 69 | |
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| 70 | for (int i = 0; i < ssize; ++i) |
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| 71 | { |
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| 72 | start[i] = nZoomBeginServer[ssize - i - 1] - nZoomBeginGlobal[ssize - i - 1]; |
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| 73 | count[i] = nZoomSizeServer[ssize - i - 1]; |
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| 74 | } |
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[765] | 75 | */ |
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[599] | 76 | |
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[765] | 77 | std::vector<int> nZoomBeginGlobal = grid->getDistributionServer()->getZoomBeginGlobal(); |
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| 78 | std::vector<int> nZoomBeginServer = grid->getDistributionServer()->getZoomBeginServer(); |
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| 79 | std::vector<int> nZoomSizeServer = grid->getDistributionServer()->getZoomSizeServer(); |
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| 80 | |
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| 81 | std::vector<StdSize> start, count; |
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| 82 | |
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| 83 | CArray<bool,1> axisDomainOrder = grid->axis_domain_order; |
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| 84 | std::vector<StdString> domainList = grid->getDomainList(); |
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| 85 | std::vector<StdString> axisList = grid->getAxisList(); |
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| 86 | int numElement = axisDomainOrder.numElements(); |
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| 87 | int idxDomain = domainList.size() - 1, idxAxis = axisList.size() - 1; |
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| 88 | int idx = nZoomBeginGlobal.size() - 1; |
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| 89 | |
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| 90 | start.reserve(nZoomBeginGlobal.size()); |
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| 91 | count.reserve(nZoomBeginGlobal.size()); |
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| 92 | |
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| 93 | for (int i = numElement - 1; i >= 0; --i) |
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| 94 | { |
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| 95 | if (axisDomainOrder(i)) |
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| 96 | { |
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| 97 | CDomain* domain = CDomain::get(domainList[idxDomain]); |
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| 98 | if ((domain->type) != CDomain::type_attr::unstructured) |
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| 99 | { |
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| 100 | start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]); |
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| 101 | count.push_back(nZoomSizeServer[idx]); |
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| 102 | } |
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| 103 | --idx ; |
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| 104 | start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]); |
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| 105 | count.push_back(nZoomSizeServer[idx]); |
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| 106 | --idx ; |
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| 107 | --idxDomain; |
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| 108 | } |
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| 109 | else |
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| 110 | { |
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| 111 | start.push_back(nZoomBeginServer[idx] - nZoomBeginGlobal[idx]); |
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| 112 | count.push_back(nZoomSizeServer[idx]); |
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| 113 | --idx; |
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| 114 | } |
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| 115 | } |
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[777] | 116 | |
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[599] | 117 | SuperClassWriter::getData(fieldData, fieldId, isCollective, field->getNStep() - 1, &start, &count); |
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| 118 | break; |
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| 119 | } |
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| 120 | } |
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| 121 | |
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| 122 | field->inputField(fieldData); |
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| 123 | |
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| 124 | if (!field->scale_factor.isEmpty() || !field->add_offset.isEmpty()) |
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| 125 | { |
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| 126 | double scaleFactor = 1.0, addOffset = 0.0; |
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| 127 | if (!field->scale_factor.isEmpty()) scaleFactor = field->scale_factor; |
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| 128 | if (!field->add_offset.isEmpty()) addOffset = field->add_offset; |
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| 129 | field->invertScaleFactorAddOffset(scaleFactor, addOffset); |
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| 130 | } |
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| 131 | } |
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| 132 | |
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[775] | 133 | void CNc4DataInput::readFieldAttributes_(CField* field, bool readAttributeValues) |
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| 134 | { |
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[777] | 135 | StdString fieldId = field->getFieldOutputName(); |
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[775] | 136 | |
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| 137 | CGrid* grid = field->grid; |
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| 138 | |
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| 139 | std::vector<CDomain*> domainP = grid->getDomains(); |
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| 140 | std::vector<CAxis*> axisP = grid->getAxis(); |
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| 141 | int gridDim = domainP.size() * 2 + axisP.size(); |
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| 142 | |
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| 143 | // Verify the compatibility of dimension of declared grid and real grid in file |
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| 144 | int realGridDim = 1; |
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| 145 | std::map<StdString, StdSize> dimSizeMap = SuperClassWriter::getDimensions(&fieldId); |
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| 146 | realGridDim = SuperClassWriter::isTemporal(fieldId) ? dimSizeMap.size() - 1 : dimSizeMap.size(); |
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| 147 | |
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| 148 | if (gridDim != realGridDim) |
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| 149 | ERROR("CNc4DataInput::readFieldAttributes_(CField* field, bool readAttributeValues)", |
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| 150 | << "Field '" << fieldId << "' has incorrect dimension " << std::endl |
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| 151 | << "Verify dimension of grid defined by 'grid_ref' or 'domain_ref'/'axis_ref' and dimension of grid in read file."); |
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| 152 | |
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| 153 | // Remove unlimited dimension from the map, we dont need it anymore |
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| 154 | if (SuperClassWriter::isTemporal(fieldId)) dimSizeMap.erase(SuperClassWriter::getUnlimitedDimensionName()); |
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| 155 | int mapSize = dimSizeMap.size() - 1; |
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| 156 | |
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| 157 | // Now process domain and axis |
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| 158 | CArray<bool,1> axisDomainOrder = grid->axis_domain_order; |
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| 159 | int numElement = domainP.size() + axisP.size(); |
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| 160 | int elementPosition = 0; |
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| 161 | int idxDomain = 0, idxAxis = 0; |
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| 162 | |
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| 163 | std::pair<std::set<StdString>::iterator,bool> it; |
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| 164 | for (int i = 0; i < numElement; ++i) |
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| 165 | { |
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| 166 | if(axisDomainOrder(i)) |
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| 167 | { |
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| 168 | if (readAttributeValues) |
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| 169 | { |
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| 170 | it = readValueDomains_.insert(domainP[idxDomain]->getId()); |
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| 171 | if (it.second) readDomainAttributeValueFromFile(domainP[idxDomain], dimSizeMap, mapSize - 1 - elementPosition, fieldId); |
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| 172 | } |
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| 173 | else |
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| 174 | { |
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| 175 | it = readMetaDataDomains_.insert(domainP[idxDomain]->getId()); |
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| 176 | if (it.second) readDomainAttributesFromFile(domainP[idxDomain], dimSizeMap, mapSize - 1 - elementPosition, fieldId); |
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| 177 | } |
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| 178 | ++idxDomain; |
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| 179 | elementPosition += 2; |
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| 180 | } |
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| 181 | else |
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| 182 | { |
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| 183 | if (readAttributeValues) |
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| 184 | { |
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| 185 | it = readValueAxis_.insert(axisP[idxAxis]->getId()); |
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| 186 | if (it.second) readAxisAttributeValueFromFile(axisP[idxAxis], dimSizeMap, mapSize - elementPosition, fieldId); |
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| 187 | } |
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| 188 | else |
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| 189 | { |
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| 190 | it = readMetaDataAxis_.insert(axisP[idxAxis]->getId()); |
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| 191 | if (it.second) readAxisAttributesFromFile(axisP[idxAxis], dimSizeMap, mapSize - elementPosition, fieldId); |
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| 192 | } |
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| 193 | ++idxAxis; |
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| 194 | ++elementPosition; |
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| 195 | } |
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| 196 | } |
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| 197 | } |
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| 198 | |
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| 199 | /*! |
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| 200 | Read attributes of a domain from a file |
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| 201 | \param [in] domain domain whose attributes are read from the file |
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| 202 | \param [in] dimSizeMap Dimensions and and their corresponding names and size read from file |
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| 203 | \param [in] emelentPosition position of domain in grid |
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[782] | 204 | \param [in] fieldId id (or name) associated with the grid |
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[775] | 205 | */ |
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| 206 | void CNc4DataInput::readDomainAttributeValueFromFile(CDomain* domain, std::map<StdString, StdSize>& dimSizeMap, |
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| 207 | int elementPosition, const StdString& fieldId) |
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| 208 | { |
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| 209 | // There are some optional attributes of a domain to retrieve from file // + lon lat? |
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| 210 | std::map<StdString, StdSize>::const_iterator itMapNj = dimSizeMap.begin(), itMapNi, |
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| 211 | iteMap = dimSizeMap.end(); |
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| 212 | |
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| 213 | for (int i = 0; i < elementPosition; ++i, ++itMapNj) {} |
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| 214 | itMapNi = itMapNj; ++itMapNi; |
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| 215 | |
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| 216 | if (this->isRectilinear(fieldId)) |
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| 217 | { |
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| 218 | // Ok, try to read some f.. attributes such as longitude and latitude |
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| 219 | domain->latvalue_rectilinear_read_from_file.resize(itMapNj->second); |
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| 220 | std::vector<StdSize> nBeginLat(1, 0), nSizeLat(1, itMapNj->second); |
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| 221 | readFieldVariableValue(domain->latvalue_rectilinear_read_from_file, itMapNj->first, nBeginLat, nSizeLat, true); |
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| 222 | |
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| 223 | domain->lonvalue_rectilinear_read_from_file.resize(itMapNi->second); |
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| 224 | std::vector<StdSize> nBeginLon(1, 0), nSizeLon(1, itMapNi->second); |
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| 225 | readFieldVariableValue(domain->lonvalue_rectilinear_read_from_file, itMapNi->first, nBeginLon, nSizeLon, true); |
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| 226 | domain->fillInRectilinearLonLat(); |
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| 227 | } |
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| 228 | else if (this->isCurvilinear(fieldId)) |
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| 229 | { |
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[782] | 230 | int ni = domain->ni; |
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| 231 | int nj = domain->nj; |
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| 232 | std::vector<StdSize> nBeginLatLon(2), nSizeLatLon(2); |
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| 233 | nBeginLatLon[0] = domain->jbegin.getValue(); nBeginLatLon[1] = domain->ibegin.getValue(); |
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| 234 | nSizeLatLon[0] = nj; nSizeLatLon[1] = ni; |
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[775] | 235 | |
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[782] | 236 | StdString latName = this->getLatCoordName(fieldId); |
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| 237 | domain->latvalue_2d.resize(ni,nj); |
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| 238 | readFieldVariableValue(domain->latvalue_2d, latName, nBeginLatLon, nSizeLatLon); |
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| 239 | StdString lonName = this->getLonCoordName(fieldId); |
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| 240 | domain->lonvalue_2d.resize(ni,nj); |
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| 241 | readFieldVariableValue(domain->lonvalue_2d, lonName, nBeginLatLon, nSizeLatLon); |
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| 242 | |
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| 243 | StdString boundsLatName = this->getBoundsId(latName); |
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| 244 | if (0 == boundsLatName.compare("")) |
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| 245 | ERROR("CNc4DataInput::readDomainAttributeValueFromFile(...)", |
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| 246 | << "Field '" << fieldId << std::endl |
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| 247 | << "Trying to read attributes from curvilinear grid." |
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| 248 | << "Latitude variable " << latName << " does not have bounds."); |
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| 249 | StdString boundsLonName = this->getBoundsId(lonName); |
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| 250 | if (0 == boundsLonName.compare("")) |
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| 251 | ERROR("CNc4DataInput::readDomainAttributeValueFromFile(...)", |
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| 252 | << "Field '" << fieldId << std::endl |
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| 253 | << "Trying to read attributes from curvilinear grid." |
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| 254 | << "Longitude variable " << lonName << " does not have bounds."); |
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| 255 | |
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| 256 | domain->nvertex.setValue(4); |
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| 257 | std::vector<StdSize> nBeginBndsLatLon(3), nSizeBndsLatLon(3); |
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| 258 | nBeginBndsLatLon[0] = domain->jbegin.getValue(); nSizeBndsLatLon[0] = nj; |
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| 259 | nBeginBndsLatLon[1] = domain->ibegin.getValue(); nSizeBndsLatLon[1] = ni; |
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| 260 | nBeginBndsLatLon[2] = 0; nSizeBndsLatLon[2] = 4; |
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| 261 | |
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| 262 | domain->bounds_lat_2d.resize(4,ni,nj); |
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| 263 | readFieldVariableValue(domain->bounds_lat_2d, boundsLatName, nBeginBndsLatLon, nSizeBndsLatLon); |
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| 264 | domain->bounds_lon_2d.resize(4,ni,nj); |
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| 265 | readFieldVariableValue(domain->bounds_lon_2d, boundsLonName, nBeginBndsLatLon, nSizeBndsLatLon); |
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[775] | 266 | } |
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| 267 | else if (this->isUnstructured(fieldId)) |
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| 268 | { |
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| 269 | |
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| 270 | } |
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| 271 | } |
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| 272 | |
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| 273 | /*! |
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[782] | 274 | Read attribute value of a domain from a file |
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[775] | 275 | \param [in] domain domain whose attributes are read from the file |
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| 276 | \param [in] dimSizeMap Dimensions and and their corresponding names and size read from file |
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| 277 | \param [in] emelentPosition position of domain in grid |
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[782] | 278 | \param [in] fieldId id (or name) associated with the grid |
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[775] | 279 | */ |
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| 280 | void CNc4DataInput::readDomainAttributesFromFile(CDomain* domain, std::map<StdString, StdSize>& dimSizeMap, |
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| 281 | int elementPosition, const StdString& fieldId) |
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| 282 | { |
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| 283 | // There are some mandatory attributes of a domain to retrieve from file |
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| 284 | // + ni_glo, nj_glo |
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| 285 | std::map<StdString, StdSize>::const_iterator itMapNj = dimSizeMap.begin(), itMapNi, |
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| 286 | iteMap = dimSizeMap.end(); |
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| 287 | for (int i = 0; i < elementPosition; ++i, ++itMapNj) {} |
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| 288 | itMapNi = itMapNj; ++itMapNi; |
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| 289 | |
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[782] | 290 | if (this->isRectilinear(fieldId) || this->isCurvilinear(fieldId)) |
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[775] | 291 | { |
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| 292 | domain->nj_glo.setValue(itMapNj->second); |
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| 293 | domain->ni_glo.setValue((itMapNi)->second); |
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| 294 | } |
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| 295 | else if (this->isUnstructured(fieldId)) |
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| 296 | { |
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| 297 | |
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| 298 | } |
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| 299 | } |
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| 300 | |
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| 301 | /*! |
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| 302 | Read attributes of an axis from a file |
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| 303 | \param [in] axis axis whose attributes are read from the file |
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| 304 | \param [in] dimSizeMap Dimensions and and their corresponding names and size read from file |
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| 305 | \param [in] emelentPosition position of axis in grid |
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[782] | 306 | \param [in] fieldId id (or name) associated with the grid |
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[775] | 307 | */ |
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| 308 | void CNc4DataInput::readAxisAttributesFromFile(CAxis* axis, std::map<StdString, StdSize>& dimSizeMap, |
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| 309 | int elementPosition, const StdString& fieldId) |
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| 310 | { |
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| 311 | std::map<StdString, StdSize>::const_iterator itMapN = dimSizeMap.begin(), |
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| 312 | iteMap = dimSizeMap.end(); |
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| 313 | for (int i = 0; i < elementPosition; ++i, ++itMapN) {} |
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| 314 | axis->n_glo.setValue(itMapN->second); |
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| 315 | } |
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| 316 | |
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| 317 | /*! |
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[782] | 318 | Read attribute value of an axis from a file |
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[775] | 319 | \param [in] axis axis whose attributes are read from the file |
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| 320 | \param [in] dimSizeMap Dimensions and and their corresponding names and size read from file |
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| 321 | \param [in] emelentPosition position of axis in grid |
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[782] | 322 | \param [in] fieldId id (or name) associated with the grid |
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[775] | 323 | */ |
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| 324 | void CNc4DataInput::readAxisAttributeValueFromFile(CAxis* axis, std::map<StdString, StdSize>& dimSizeMap, |
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| 325 | int elementPosition, const StdString& fieldId) |
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| 326 | { |
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| 327 | std::map<StdString, StdSize>::const_iterator itMapN = dimSizeMap.begin(), |
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| 328 | iteMap = dimSizeMap.end(); |
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| 329 | for (int i = 0; i < elementPosition; ++i, ++itMapN) {} |
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| 330 | |
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| 331 | { // Read axis value |
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| 332 | std::vector<StdSize> nBegin(1, 0), nSize(1, itMapN->second); |
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| 333 | CArray<double,1> readAxisValue(itMapN->second); |
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| 334 | readFieldVariableValue(readAxisValue, itMapN->first, nBegin, nSize, true); |
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| 335 | int begin = 0, n = itMapN->second; |
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| 336 | if (!axis->begin.isEmpty()) begin = axis->begin.getValue(); |
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| 337 | if (!axis->n.isEmpty()) n = axis->n.getValue(); |
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| 338 | axis->value.resize(n); |
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| 339 | for (int i = 0; i < n; ++i) axis->value(i) = readAxisValue(begin + i); |
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| 340 | } |
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| 341 | } |
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| 342 | |
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[599] | 343 | void CNc4DataInput::closeFile_(void) |
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| 344 | { |
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| 345 | SuperClassWriter::close(); |
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| 346 | } |
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[335] | 347 | } // namespace xios |
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