Update and Bugfixes on arImportPEtab

Author: timo-rachel

arFramework3/ImportExport/arImportPEtab.m

@@ -75,13 +75,13 @@ function arImportPEtab(PEtabName, doPreEq, model, dataFolder, dataFilenames)
  if ~exist(dataFolder, 'dir') % Check if folder does not exist
  mkdir(dataFolder); % Create folder
  end
- dataFilenames = arWriteDataFromPEtab(PEtabName, dataFolder);
+ dataFilenames = writeDataFromPEtab(PEtabName, dataFolder);
  elseif (exist('dataFolder','var') || ~isempty(dataFolder)) & (~exist('dataFilenames','var') || isempty(dataFilenames))
  files = dir(fullfile(dataFolder, '*.xls'));
  dataFilenames = arrayfun(@(f) f.name(1:end-4), files, 'UniformOutput', false);
  elseif (exist('dataFolder','var') || ~isempty(dataFolder)) & (exist('dataFilenames','var') || ~isempty(dataFilenames))
- files = dir(fullfile(dataFolder, dataFilenames,[strrep(PEtabName,'.xls','') '.xls']));
- dataFilenames = arrayfun(@(f) f.name(1:end-4), files, 'UniformOutput', false);
+ dataFilenames = fullfile(dataFolder,strrep(dataFilenames,'.xls',''));
+ dataFilenames = cellfun(@(x) dir([x, '.def']), dataFilenames, 'UniformOutput', false);
  end
 
  %%
@@ -113,8 +113,11 @@ function arImportPEtab(PEtabName, doPreEq, model, dataFolder, dataFilenames)
 arLoadModel(modelname);
 splitedFilenames = split(dataFilenames,filesep);
 for i=1:length(dataFilenames)
- arLoadData(char(splitedFilenames(1,i,2)),[],[],[],'DataPath',char(splitedFilenames(1,i,1)));
+  arLoadData(char(splitedFilenames(1,i,2)),[],[],[],'DataPath',char(splitedFilenames(1,i,1)));
 end
+% for i=1:length(dataFilenames)
+% arLoadData(dataFilenames{i}.name,[],[],[],'DataPath',dataFilenames{i}.folder);
+% end
 arCompileAll;
 ar.config.fiterrors = 1;
 arLoadParsPEtab(PEparas);
@@ -195,6 +198,8 @@ function arImportPEtab(PEtabName, doPreEq, model, dataFolder, dataFilenames)
 % end
 % end
 
+arSave(ar.info.name)
+
 end
 
 function [out,numberOfEls] = extractFromStruct(struct, field)

…ork3/ImportExport/arWriteDataFromPEtab.m …ework3/ImportExport/writeDataFromPEtab.marFramework3/ImportExport/arWriteDataFromPEtab.m renamed to arFramework3/ImportExport/writeDataFromPEtab.m arFramework3/ImportExport/arWriteDataFromPEtab.m renamed to arFramework3/ImportExport/writeDataFromPEtab.m

@@ -1,8 +1,16 @@
-% ToDo:
-% \tC\tau\tconc.\t1\t1\t etc
-% num2str(max(time)*1.2)
+function dataFilenames = writeDataFromPEtab(yamlFile, savePath)
+% writeDataFromPEtab(yamlFile, savePath)
+%
+% This function reads the PEtab files and writes the data to excel (.xls) files and creates the corresponding .def files for each simulation condition.
+%
+% Inputs:
+% yamlFile: string, name of the yaml file in the PEtab folder. If not specified, the function will look for a .yaml file in the PEtab folder. Multiple .yaml files are not allowed.
+% savePath: string, path to the folder where the data files should be saved. [default: 'DataPEtab']
+%
+% Outputs:
+% dataFilenames: cell array of strings, filenames of the data files
+% 
 
-function dataFilenames = arWriteDataFromPEtab(yamlFile, savePath)
 
 %% Filenames
 if ~exist('yamlFile','var') || isempty(yamlFile)
@@ -97,15 +105,18 @@
  end
 
  % only the observableIDs that have uniqueSimConds{i} in their name
- observableIdCond = unique(Tdat.observableId(contains(Tdat.observableId, uniqueSimConds{i}))); % find all occurences of uniqueSimConds{i} in observableIds
- observableId = regexprep(observableIdCond, ['_',uniqueSimConds{i}],'');
+ %observableIdCond = unique(Tdat.observableId(contains(Tdat.observableId, uniqueSimConds{i}))); % find all occurences of uniqueSimConds{i} in observableIds
+ %observableId = regexprep(observableIdCond, ['_',uniqueSimConds{i}],'');
+ 
+ % find observabeles that of simulationConditionId
+ observableId = unique(Tdat.observableId(contains(Tdat.simulationConditionId, uniqueSimConds{i})));
 
- ind = find(contains(Tdat.observableId, uniqueSimConds{i}));
+ ind = find(contains(Tdat.simulationConditionId, uniqueSimConds{i}));
  timeUni = unique(Tdat.time(ind));
  timeMax = [timeUni, NaN(length(timeUni),1)];
 
- for o = 1:length(observableIdCond)
- indObs = find(Tdat.observableId == observableIdCond{o});
+ for o = 1:length(observableId)
+ indObs = intersect(find(Tdat.observableId == observableId{o}),ind); % observableID and simulationConditionId
  tObs = Tdat.time(indObs);
 
  % Compute unique values and counts
@@ -132,8 +143,8 @@
  T.(char(observableId(o))) = NaN(length(time), 1); % Fill with NaN for now
  end
 
- for o=1:length(observableIdCond)
- indObs = find(Tdat.observableId == observableIdCond{o});
+ for o=1:length(observableId)
+ indObs = find(Tdat.observableId == observableId{o});
  for t = 1:length(indObs)
  % find all rows in T where T.time==Tdat.time(indObs(t))
  indT = find(T.time == Tdat.time(indObs(t)));
@@ -169,17 +180,21 @@
 
  % Observables 
  fprintf(fid, '\nOBSERVABLES\n');
- indObs = find(contains(Tobs.observableId, uniqueSimConds{i})); 
+ indObs = find(contains(Tobs.observableId, observableId));
  for j = 1:length(indObs)
  ind = indObs(j);
- fprintf(fid, [Tobs.observableName{ind},'\tC\tau\tconc.\t1\t1\t','"',Tobs.observableFormula{ind},'"\n']);
+ if isfield(Tobs,'observableName')
+ fprintf(fid, [Tobs.observableId{ind},'\tC\tau\tconc.\t1\t1\t','"',Tobs.observableFormula{ind},'"\t"',Tobs.observableName{ind},'"\n']);
+ else
+ fprintf(fid, [Tobs.observableId{ind},'\tC\tau\tconc.\t1\t1\t','"',Tobs.observableFormula{ind},'"\n']);
+ end
  end
 
  % Errors
  fprintf(fid, '\nERRORS\n');
  for j = 1:length(indObs)
  ind = indObs(j);
- fprintf(fid, [Tobs.observableName{ind},'\t','"',Tobs.noiseFormula{ind},'"\n']);
+ fprintf(fid, [Tobs.observableId{ind},'\t','"',Tobs.noiseFormula{ind},'"\n']);
  end
 
  % Conditions 

arFramework3/arLoadData.m

@@ -102,6 +102,10 @@ function arLoadData(name, m, extension, removeEmptyObs, varargin)
 
 global ar
 
+% works also if .xls or .def fileaendings are used
+name = strrep(name,'.xls','');
+name = strrep(name,'.def','');
+
 arFprintf( 3, 'Parsing input arguments...\n' );
 
 if(isempty(ar))