Add matlab/export folder
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56
matlab/export/catalog2csv.m
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56
matlab/export/catalog2csv.m
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% -----------------
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% Copyright © 2022 ACK Cyfronet AGH, Poland.
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% -----------------
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function catalog2csv(catalog, csvFileName)
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fieldNames = getFieldNames(catalog);
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fieldTypes = getFieldTypes(catalog);
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lineFormat = getLineFormat(fieldTypes);
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M = prepareCellMatrix(catalog);
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fid = fopen(csvFileName, 'w+');
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fprintf(fid, '%s\n', strjoin(fieldNames', ','));
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for k=1:size(M,1)
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fprintf(fid, lineFormat, M{k, :});
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end
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fclose(fid);
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end
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function fieldNames = getFieldNames(catalog)
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fieldNames = [];
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for i=1:length(catalog)
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fieldNames{i} = catalog(i).field;
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end
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end
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function fieldTypes = getFieldTypes(catalog)
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fieldTypes = [];
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for i=1:length(catalog)
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fieldTypes{i} = catalog(i).type;
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end
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end
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function M = prepareCellMatrix(catalog)
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M = {};
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for i=1:length(catalog)
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val = catalog(i).val;
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type = catalog(i).type;
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if iscell(val)
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M(:,i) = val;
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elseif isTime(type)
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M(:,i) = formatCatalogTime(val, type);
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else
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M(:,i) = num2cell(val);
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end
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end
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end
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function timeStrVector = formatCatalogTime(timeVector, fieldType)
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if iscell(timeVector)
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timeVector = cell2mat(timeVector);
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end
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emptyIndexes = isnan(timeVector);
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timeStrVector(~emptyIndexes, 1) = cellstr(datestr(timeVector(~emptyIndexes), 'yyyy-mm-dd HH:MM:SS.FFF'));
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timeStrVector(emptyIndexes, 1) = { 'NaN' };
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end
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16
matlab/export/extractGdfFields.m
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16
matlab/export/extractGdfFields.m
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%
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% -----------------
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% Copyright © 2020 ACK Cyfronet AGH, Poland.
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%
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% This work was partially funded by EPOS Project funded in frame of PL-POIR4.2
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% --------------
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%
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function [varargout] = extractGdfFields(gdf, fieldNames)
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for i = 1:length(fieldNames)
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fieldName = fieldNames{i};
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assert(isfield(gdf.d, fieldName), ['gdf has no field with name: ' fieldName])
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varargout{i} = getfield(gdf.d, fieldName);
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end
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end
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46
matlab/export/formatTime.m
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46
matlab/export/formatTime.m
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% -----------------
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% Copyright © 2022 ACK Cyfronet AGH, Poland.
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% -----------------
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%
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% Get string format for the time values provided in timeVector. Format is based
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% on numeric 'FieldType' (GDF) or 'type' (catalog) field
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% see https://docs.cyfronet.pl/display/ISEPOS/GDF+v2.2+-+description
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function timeStrVector = formatTime(timeVector, fieldType)
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% if we have '5a' and '5b', the date value is a string instead of a number)
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if (ischar(fieldType) && (strcmp(fieldType, '5a') || strcmp(fieldType, '5b')))
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timeStrVector = timeVector;
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return;
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end
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if iscell(timeVector)
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timeVector = cell2mat(timeVector);
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end
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emptyIndexes = isnan(timeVector);
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timeFormat = getTimeFormat(fieldType);
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timeStrVector(~emptyIndexes, 1) = cellstr(datestr(timeVector(~emptyIndexes), timeFormat));
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timeStrVector(emptyIndexes, 1) = { 'NaN' };
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end
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function timeFormat = getTimeFormat(fieldType)
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if (fieldType == 5)
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timeFormat = 'yyyy mmm dd HH:MM:SS.FFF';
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else
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timeFormat = arrayfun(@changeToMatlabFormat, fieldType(2:end));
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end
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end
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% Matlab uses different specification of the format than the one used in GDF files (based on Java format) - e.g., 'M' is
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% used in GDF for month, while in Matlab it is used for minutes
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function correctedFormatId = changeToMatlabFormat(javaTimeFormatId)
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switch javaTimeFormatId
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case 'M'
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correctedFormatId = 'm';
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case 'm'
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correctedFormatId = 'M';
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case 's'
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correctedFormatId = 'S';
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case 'S'
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correctedFormatId = 'F';
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otherwise
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correctedFormatId = javaTimeFormatId;
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end
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end
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142
matlab/export/gdf2csv.m
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142
matlab/export/gdf2csv.m
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% -----------------
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% Copyright © 2020 ACK Cyfronet AGH, Poland.
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%
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% This work was partially funded by EPOS Project funded in frame of PL-POIR4.2
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% -----------------
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function csvFiles = gdf2csv(gdfFilePath)
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csvFiles = {};
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load(gdfFilePath);
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[~, resultFileNameBase] = fileparts(gdfFilePath);
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fieldNames = fieldnames(d);
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fieldTypes = getFieldTypes(FieldType, fieldNames);
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if (hasSingleData(d, fieldNames))
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if (length(d) > 1)
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M = prepareCellMatrixFromStructArrayWithScalars(d, fieldTypes);
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else
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M = prepareCellMatrixFromSingleStructWithVectors(d, fieldTypes, fieldNames);
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end
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resultFileName = [resultFileNameBase, '.csv'];
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saveCsvFile(M, fieldTypes, fieldNames, resultFileName);
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csvFiles = { resultFileName };
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else
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for i = 1:length(d)
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resultFileName = [resultFileNameBase, '-', num2str(i), '.csv'];
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M = prepareCellMatrixFromSingleStructWithVectors(d(i), fieldTypes, fieldNames);
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saveCsvFile(M, fieldTypes, fieldNames, resultFileName);
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csvFiles{i} = resultFileName;
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end
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end
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end
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function isSingle = hasSingleData(d, fieldNames)
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isSingle = length(d) == 1 || ~hasAnyVectors(d, fieldNames);
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end
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function hasVector = hasAnyVectors(d, fieldNames)
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hasVector = false;
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for i = 1:length(d)
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vectorValue = findFirstVectorValue(d(i), fieldNames);
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if ~isempty(vectorValue)
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hasVector = true;
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return;
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end
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end
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end
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function vectorValue = findFirstVectorValue(d, fieldNames)
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vectorValue = [];
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for i = 1:length(fieldNames)
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value = d.(fieldNames{i});
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if ~ischar(value) && ~isscalar(value)
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vectorValue = value;
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return;
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end
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end
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end
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function saveCsvFile(M, fieldTypes, fieldNames, filename)
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lineFormat = getLineFormat(fieldTypes);
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fid = fopen(filename, 'w+');
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fprintf(fid, '%s\n', strjoin(fieldNames', ','));
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for k=1:size(M,1)
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fprintf(fid, lineFormat, M{k, :});
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end
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fclose(fid);
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end
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function M = prepareCellMatrixFromSingleStructWithVectors(d, fieldTypes, fieldNames)
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% some structures might contain vectors mixed with scalars, in that case we want to repeat the scalar values in the csv file
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d = convertScalarsToVectors(d, fieldNames);
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M = cell(length(d.(fieldNames{1})), length(fieldNames));
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for f = 1:length(fieldTypes)
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fieldType = fieldTypes{f};
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field = d.(fieldNames{f});
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if (isTime(fieldType))
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M(:, f) = formatTime(field, fieldType);
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elseif isnumeric(field)
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if (isrow(field))
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field = field';
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end
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M(:, f) = num2cell(field);
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else
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if (isrow(field))
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field = field';
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end
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M(:, f) = field;
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end
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end
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end
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function M = prepareCellMatrixFromStructArrayWithScalars(d, fieldTypes)
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M = squeeze(struct2cell(d))';
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M = cellfun(@handleEmptyArray, M, 'UniformOutput', false);
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for f = 1:length(fieldTypes)
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fieldType = fieldTypes{f};
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if (isTime(fieldType))
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M(:, f) = formatTime(M(:, f), fieldType);
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end
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end
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end
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function struct = convertScalarsToVectors(d, fieldNames)
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struct = d;
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firstVectorValue = findFirstVectorValue(d, fieldNames);
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if isempty(firstVectorValue)
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return;
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end
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count = length(firstVectorValue);
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for i = 1:length(fieldNames)
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field = struct.(fieldNames{i});
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if (isempty(field))
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field = nan;
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end
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if ischar(field) || isscalar(field)
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[vectorValue{1:count}] = deal(field);
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struct.(fieldNames{i}) = vectorValue';
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end
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end
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end
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function value = handleEmptyArray(value)
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if (isempty(value))
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value = nan;
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end
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end
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% creates a vector of field types written as in FieldType, but preserving the same order of fields as in the 'd'
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% structure (fallback for a situation when the types in FieldType are in different order than fieldnames(d) or when
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% FieldType contains more entries than fieldnames(d)
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function fieldTypes = getFieldTypes(fieldTypeCell, fieldNames)
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fieldTypes = cell(1, length(fieldNames));
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for i = 1:length(fieldNames)
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for j = 1:size(fieldTypeCell, 1)
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if strcmp(fieldNames{i}, fieldTypeCell{j, 1})
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fieldTypes{i} = fieldTypeCell{j, 2};
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end
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end
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end
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end
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54
matlab/export/getLineFormat.m
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54
matlab/export/getLineFormat.m
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% -----------------
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% Copyright © 2022 ACK Cyfronet AGH, Poland.
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% -----------------
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%
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% Get string format specification used for fpritf, based on numeric 'FieldType' (GDF) or 'type' (catalog) field
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% see https://docs.cyfronet.pl/display/ISEPOS/GDF+v2.2+-+description
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function lineFormat = getLineFormat(fieldTypes)
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lineFormat = '';
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for f = 1:length(fieldTypes)
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fieldType = fieldTypes{f};
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formatSpec = getFormatSpec(fieldType);
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lineFormat = [lineFormat ',' formatSpec];
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end
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lineFormat = [lineFormat(2:end) '\n'];
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end
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function formatSpec = getFormatSpec(fieldType)
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if isTime(fieldType)
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formatSpec = '"%s"';
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elseif isnumeric(fieldType)
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if fieldType < 10
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formatSpec = getFormatSpecFromReservedFieldType(fieldType);
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elseif fieldType < 200
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formatSpec = ['%.', num2str(mod(fieldType, 10)), 'f'];
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elseif fieldType < 300
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formatSpec = ['%.', num2str(mod(fieldType, 10)), 'e'];
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else
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error(['Unrecognized fieldType: ', num2str(fieldType)])
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end
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else
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error(['Unrecognized fieldType: ', num2str(fieldType)])
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end
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end
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function formatSpec = getFormatSpecFromReservedFieldType(fieldType)
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switch fieldType
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case 1
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formatSpec = '%f';
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case 2
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formatSpec = '%d';
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case 3
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formatSpec = '"%s"';
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case 4
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formatSpec = '%.1f';
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case 5
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formatSpec = '%s';
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case 6
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formatSpec = '%1.1e';
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case 7
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formatSpec = '%1.2e';
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otherwise
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error(['Unrecognized fieldType: ', num2str(fieldType)])
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end
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end
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10
matlab/export/isTime.m
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10
matlab/export/isTime.m
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% -----------------
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% Copyright © 2022 ACK Cyfronet AGH, Poland.
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% -----------------
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%
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% Check if the format defined in 'fieldType' marks time or other type of field.
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% Based on numeric 'FieldType' (GDF) or 'type' (catalog) field
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% see https://docs.cyfronet.pl/display/ISEPOS/GDF+v2.2+-+description
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function isTime = isTime(fieldType)
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isTime = fieldType == 5 || fieldType(1) == '5';
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end
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