| 1 | package PIANOS; |
| 2 | |
| 3 | import PIANOS.datastructures.*; |
| 4 | import PIANOS.exceptions.*; |
| 5 | import PIANOS.io.*; |
| 6 | import PIANOS.io.ComputationalModelParser; |
| 7 | import PIANOS.generator.*; |
| 8 | |
| 9 | import java.util.*; |
| 10 | import java.io.*; |
| 11 | |
| 12 | /** The PIANOS main class. |
| 13 | Writes Fortran module files for a simulation program that matches the model description files given. |
| 14 | May be run on the command line with 8 or 1 parameters, see the PIANOS manual on the |
| 15 | CD-ROM or in the tar.gz for details. |
| 16 | See writeProgram for the Java way of running PIANOS. |
| 17 | */ |
| 18 | |
| 19 | public class Generator{ |
| 20 | private static ComputationalModel model = null; |
| 21 | private static DistributionFactory factory = null; |
| 22 | private static FortranWriter writer; |
| 23 | |
| 24 | //For testing... |
| 25 | public static void setModel(ComputationalModel modelToSet){ |
| 26 | model = modelToSet; |
| 27 | } |
| 28 | |
| 29 | /** The PIANOS main interface. Writes definitions.f90, input.f90, output.f90, proposal.f90, main.f90. |
| 30 | Note that when compiling the user will also need user_dist.f90 that contains the user-defined |
| 31 | distributions used in the model. |
| 32 | |
| 33 | @param userDistFileName the filename of the user-defined distributions file |
| 34 | @param modelFileName the filename of the model description file |
| 35 | @param initialValueFileName the filename of the simulation initial values file |
| 36 | @param simulationFileName the filename of the simulation parameters file (burn-in, thinning) |
| 37 | @param proposalFileName the filename of the proposal strategies and distributions file |
| 38 | @param updateFileName the filename of the update strategy and iterations file |
| 39 | @param toOutputFileName the filename of the parameters desired as output |
| 40 | @param lastValuesFileName the filename of the file where the last values are to be saved after the simulation |
| 41 | */ |
| 42 | public static void writeProgram(String userDistFileName, String modelFileName, |
| 43 | String initialValueFileName, String simulationFileName, String proposalFileName, |
| 44 | String updateFileName, String toOutputFileName, String lastValueFileName) |
| 45 | throws MissingFunctionException, SyntaxException, InvalidProposalException, IOException, |
| 46 | MissingDistributionException, IllegalParametersException, |
| 47 | InvalidModelException{ |
| 48 | |
| 49 | |
| 50 | |
| 51 | model = null; |
| 52 | factory = new DistributionFactory(userDistFileName); |
| 53 | |
| 54 | |
| 55 | model = ComputationalModelParser.readModel(modelFileName, initialValueFileName, |
| 56 | simulationFileName, proposalFileName, updateFileName, toOutputFileName, factory); |
| 57 | |
| 58 | System.out.print("Writing simulation program..."); |
| 59 | |
| 60 | |
| 61 | model.setLastValuesFileName(lastValueFileName); |
| 62 | |
| 63 | LinkedList<Variable> variables = model.getVariableList(); |
| 64 | |
| 65 | // DEBUG |
| 66 | /* |
| 67 | System.out.println("GENERATOR DEBUG: Generator.java: Global variable list from the parser"); |
| 68 | for (Variable v: variables) |
| 69 | System.out.println(v.getName()); |
| 70 | */ |
| 71 | |
| 72 | String callParameters = setCallParameters(model); |
| 73 | |
| 74 | Definitions.generateDefinitions(model); |
| 75 | |
| 76 | // DEBUG |
| 77 | /* |
| 78 | variables = model.getVariableList(); |
| 79 | System.out.println("GENERATOR DEBUG: Generator.java: Global variable list after Definitions"); |
| 80 | for (Variable v: variables) |
| 81 | System.out.println(v.getName()); |
| 82 | */ |
| 83 | |
| 84 | Input.generateInput(callParameters, model); |
| 85 | |
| 86 | // DEBUG |
| 87 | /* |
| 88 | variables = model.getVariableList(); |
| 89 | System.out.println("Generator.java: Global variable list after Input"); |
| 90 | for (Variable v: variables) |
| 91 | System.out.println(v.getName()); |
| 92 | */ |
| 93 | |
| 94 | Output.generateOutput(callParameters, model); |
| 95 | |
| 96 | // DEBUG |
| 97 | /* |
| 98 | variables = model.getVariableList(); |
| 99 | System.out.println("Generator.java: Global variable list after Output"); |
| 100 | for (Variable v: variables) |
| 101 | System.out.println(v.getName()); |
| 102 | */ |
| 103 | |
| 104 | Proposal.generateProposal(model); |
| 105 | |
| 106 | // DEBUG |
| 107 | /* |
| 108 | variables = model.getVariableList(); |
| 109 | System.out.println("Generator.java: Global variable list after Proposal"); |
| 110 | for (Variable v: variables) |
| 111 | System.out.println(v.getName()); |
| 112 | */ |
| 113 | |
| 114 | FortranMain.generateMain(callParameters, model); |
| 115 | |
| 116 | // DEBUG |
| 117 | /* |
| 118 | variables = model.getVariableList(); |
| 119 | System.out.println("GENERATOR DEBUG: Generator.java: Global variable list after FortranMain"); |
| 120 | for (Variable v: variables) |
| 121 | System.out.println(v.getName()); |
| 122 | */ |
| 123 | System.out.println("\t\t\t\t\t[OK]"); |
| 124 | System.out.println("The program completed successfully."); |
| 125 | } |
| 126 | |
| 127 | /** The PIANOS command-line interface. Writes definitions.f90, input.f90, output.f90, proposal.f90, main.f90. |
| 128 | Note that when compiling the user will also need user_dist.f90 that contains the user-defined |
| 129 | distributions used in the model. Command-line parameters specified in order |
| 130 | (choose first 8 or the last one which incorporates the 8): |
| 131 | |
| 132 | @param userDistFileName the filename of the user-defined distributions file |
| 133 | @param modelFileName the filename of the model description file |
| 134 | @param initialValueFileName the filename of the simulation initial values file |
| 135 | @param simulationFileName the filename of the simulation parameters file (burn-in, thinning) |
| 136 | @param proposalFileName the filename of the proposal strategies and distributions file |
| 137 | @param updateFileName the filename of the update strategy and iterations file |
| 138 | @param toOutputFileName the filename of the parameters desired as output |
| 139 | @param lastValuesFileName the filename of the file where the last values are to be saved after the simulation |
| 140 | @param allFilesFileName (mutually exclusive with the parameters above) |
| 141 | A file containing the file names of all the files specified above, in the format: <br> |
| 142 | <i>(begin of file)</i><br> |
| 143 | user distributions: relative/path/to/user_dist.f90 <br> |
| 144 | model: relative/path/to/modelFile<br> |
| 145 | initial values: relative/path/to/initialValuesFile<br> |
| 146 | simulation: relative/path/to/simulationFile<br> |
| 147 | proposals: relative/path/to/proposalsFile<br> |
| 148 | update strategy: relative/path/to/updateFile<br> |
| 149 | to output: relative/path/to/toOutputFile<br> |
| 150 | last values: relative/path/to/lastValuesFile<br> |
| 151 | <i>(end of file)</i><br> |
| 152 | The order of the identifier - file name pairs is arbitrary.<br> |
| 153 | The file may contain comments beginning with a hash '#'<br> |
| 154 | */ |
| 155 | public static void main(String[] args) throws SyntaxException, IOException{ |
| 156 | |
| 157 | model = null; |
| 158 | String userDistFileName = null; |
| 159 | String modelFileName = null; |
| 160 | String initialValueFileName = null; |
| 161 | String simulationFileName = null; |
| 162 | String proposalFileName = null; |
| 163 | String updateFileName = null; |
| 164 | String toOutputFileName = null; |
| 165 | String lastValuesFileName = null; |
| 166 | if (args.length != 8 && args.length != 1) { |
| 167 | System.out.println("Wrong number of command-line arguments. Expected: 1 or 8: either one file with the " + |
| 168 | "filenames (user_dist, model, initial values, simulation, proposal, update, to output, last values) " + |
| 169 | "or these filenames directly."); |
| 170 | System.exit(1); |
| 171 | } |
| 172 | if (args.length == 1){ |
| 173 | Scanner reader = null; |
| 174 | int linenum = 0; |
| 175 | try{ |
| 176 | reader = new Scanner(new File(args[0])); |
| 177 | } catch (FileNotFoundException fnf){ |
| 178 | fnf.printStackTrace(); |
| 179 | System.exit(1); |
| 180 | } |
| 181 | while (reader.hasNextLine()){ |
| 182 | String line = reader.nextLine().trim(); |
| 183 | linenum++; |
| 184 | if (line.length() <= 0 || line.charAt(0) == '#') |
| 185 | continue; |
| 186 | |
| 187 | if (line.startsWith("user distributions:")){ |
| 188 | line = line.substring(19).trim(); |
| 189 | userDistFileName = line; |
| 190 | } else if (line.startsWith("model:")){ |
| 191 | line = line.substring(6).trim(); |
| 192 | modelFileName = line; |
| 193 | } else if (line.startsWith("initial values:")){ |
| 194 | line = line.substring(15).trim(); |
| 195 | initialValueFileName = line; |
| 196 | } else if (line.startsWith("simulation:")){ |
| 197 | line = line.substring(11).trim(); |
| 198 | simulationFileName = line; |
| 199 | } else if (line.startsWith("proposals:")){ |
| 200 | line = line.substring(10).trim(); |
| 201 | proposalFileName = line; |
| 202 | } else if (line.startsWith("update strategy:")){ |
| 203 | line = line.substring(16).trim(); |
| 204 | updateFileName = line; |
| 205 | } else if (line.startsWith("to output:")){ |
| 206 | line = line.substring(10).trim(); |
| 207 | toOutputFileName = line; |
| 208 | } else if (line.startsWith("last values:")){ |
| 209 | line = line.substring(12).trim(); |
| 210 | lastValuesFileName = line; |
| 211 | } else{ |
| 212 | throw new SyntaxException("Invalid line in" + args[0] + ": (line "+ linenum + ")"); |
| 213 | } |
| 214 | } |
| 215 | |
| 216 | |
| 217 | } else { |
| 218 | userDistFileName = args[0]; |
| 219 | modelFileName = args[1]; |
| 220 | initialValueFileName = args[2]; |
| 221 | simulationFileName = args[3]; |
| 222 | proposalFileName = args[4]; |
| 223 | updateFileName = args[5]; |
| 224 | toOutputFileName = args[6]; |
| 225 | lastValuesFileName = args[7]; |
| 226 | } |
| 227 | if (userDistFileName == null) |
| 228 | throw new IOException("Cannot proceed without a good userDistFileName"); |
| 229 | if (modelFileName == null) |
| 230 | throw new IOException("Cannot proceed without a good modelFileName"); |
| 231 | if (initialValueFileName == null) |
| 232 | throw new IOException("Cannot proceed without a good initialValueFileName"); |
| 233 | if (simulationFileName == null) |
| 234 | throw new IOException("Cannot proceed without a good simulationFileName"); |
| 235 | if (proposalFileName == null) |
| 236 | throw new IOException("Cannot proceed without a good proposalFileName"); |
| 237 | if (updateFileName == null) |
| 238 | throw new IOException("Cannot proceed without a good updateFileName"); |
| 239 | if (toOutputFileName == null) |
| 240 | throw new IOException("Cannot proceed without a good toOutputFileName"); |
| 241 | if (lastValuesFileName == null) |
| 242 | throw new IOException("Cannot proceed without a good lastValuesFileName"); |
| 243 | |
| 244 | System.out.println("PIANOS using files:"); |
| 245 | System.out.println("------------------------"); |
| 246 | System.out.println("user distributions:\t\""+ userDistFileName +"\""); |
| 247 | System.out.println("model:\t\t\t\""+ modelFileName +"\""); |
| 248 | System.out.println("initial values:\t\t\""+ initialValueFileName +"\""); |
| 249 | System.out.println("simulation:\t\t\""+ simulationFileName +"\""); |
| 250 | System.out.println("proposals:\t\t\""+ proposalFileName +"\""); |
| 251 | System.out.println("update strategy:\t\""+ updateFileName +"\""); |
| 252 | System.out.println("to output:\t\t\""+ toOutputFileName +"\""); |
| 253 | System.out.println("last values:\t\t\""+ lastValuesFileName +"\""); |
| 254 | System.out.println("------------------------"); |
| 255 | try{ |
| 256 | writeProgram(userDistFileName, modelFileName, initialValueFileName, simulationFileName, |
| 257 | proposalFileName, updateFileName, toOutputFileName, lastValuesFileName); |
| 258 | } catch (Exception e){ |
| 259 | e.printStackTrace(); |
| 260 | System.exit(1); |
| 261 | } |
| 262 | } |
| 263 | |
| 264 | private static String setCallParameters(ComputationalModel model){ |
| 265 | String callParameters = ""; |
| 266 | LinkedList<Variable> variables = model.getVariableList(); |
| 267 | LinkedList<Entity> entities = model.getEntityList(); |
| 268 | boolean first = true; |
| 269 | |
| 270 | for (Variable variableIterator : variables){ |
| 271 | if(first){ |
| 272 | callParameters = variableIterator.getName(); |
| 273 | first = false; |
| 274 | } else |
| 275 | callParameters = callParameters + ", " + variableIterator.getName(); |
| 276 | |
| 277 | } |
| 278 | |
| 279 | for (Entity entityIterator : entities){ |
| 280 | variables = entityIterator.getVariableList(); |
| 281 | for (Variable variableIterator : variables){ |
| 282 | callParameters = callParameters + ", " + variableIterator.getName(); |
| 283 | } |
| 284 | } |
| 285 | |
| 286 | return callParameters; |
| 287 | } |
| 288 | |
| 289 | // introduce parameters |
| 290 | public static ArrayList<String> generateIntroduction(){ |
| 291 | |
| 292 | assert model != null; |
| 293 | |
| 294 | ArrayList<String> toWrite = new ArrayList<String>(); |
| 295 | |
| 296 | for (Variable v : model.getVariableList()){ |
| 297 | if (v.isInteger()) |
| 298 | toWrite.add("TYPE(variables_int), INTENT(INOUT) :: " + v.getName()); |
| 299 | else |
| 300 | toWrite.add("TYPE(variables_real), INTENT(INOUT) :: " + v.getName()); |
| 301 | } |
| 302 | |
| 303 | for (Entity e : model.getEntityList()){ |
| 304 | ArrayList<Variable> variables = new ArrayList<Variable>(e.getVariableList()); |
| 305 | for (Variable v : variables){ |
| 306 | if (v.isInteger()) |
| 307 | toWrite.add("TYPE(variables_int), INTENT(INOUT) :: " + v.getName()); |
| 308 | else |
| 309 | toWrite.add("TYPE(variables_real), INTENT(INOUT) :: " + v.getName()); |
| 310 | } |
| 311 | } |
| 312 | return toWrite; |
| 313 | } |
| 314 | } |
| 315 | |