private static String getAllEntries(final ArrayList<ConfigurationParserObject> list) {
String entries = "";
for (final ConfigurationParserObject cpo : list) entries += cpo.getEntry() + "\n";
return entries;
}
private static int findEntry(
final ArrayList<ConfigurationParserObject> list, final String entry) {
int pos = -1;
for (int i = 0; i < list.size() && pos == -1; i++) {
final ConfigurationParserObject cpo = list.get(i);
if (cpo.getEntry().toLowerCase().compareTo(entry.toLowerCase()) == 0) pos = i;
}
return pos;
}
public static SPIMConfiguration parseFile(String confFileName)
throws ConfigurationParserException {
SPIMConfiguration conf = new SPIMConfiguration();
String knownDatatypes[] = {
"int",
"double",
"String",
"boolean",
"float",
"float[]",
"ContainerFactory",
"InterpolatorFactory",
"OutsideStrategyFactory"
};
// convert to unix-style
confFileName = confFileName.replace('\\', '/');
confFileName = confFileName.replaceAll("//", "/");
// get path
String confFilePath;
try {
if (confFileName.indexOf("/") != -1)
confFilePath = confFileName.substring(0, confFileName.lastIndexOf("/") + 1);
else confFilePath = "";
} catch (Exception e) {
throw new ConfigurationParserException(
"Error parsing confFileName-String: '" + e.getMessage() + "'");
}
// open configfile
BufferedReader assignFile = null;
BufferedReader confFile;
try {
confFile = TextFileAccess.openFileReadEx(confFileName);
} catch (IOException e) {
throw new ConfigurationParserException(
"Configuration file not found: '" + confFileName + "'");
}
// open assignment file
try {
while (confFile.ready() && assignFile == null) {
String line = confFile.readLine().trim();
if (line.startsWith("<") && line.endsWith(">")) {
assignFile =
TextFileAccess.openFileRead(confFilePath + line.substring(1, line.length() - 1));
if (assignFile == null)
throw new ConfigurationParserException(
"Variables Assignment file not found: '"
+ confFilePath
+ (line.substring(1, line.length() - 1))
+ "'");
}
}
} catch (Exception e) {
throw new ConfigurationParserException(
"Error finding assignment file entry: '" + e.getMessage() + "'");
}
// load assignments
final ArrayList<ConfigurationParserObject> assignments =
new ArrayList<ConfigurationParserObject>();
Field[] fields = conf.getClass().getDeclaredFields();
int lineCount = 0;
try {
while (assignFile.ready()) {
lineCount++;
String line = assignFile.readLine().trim();
if (!line.startsWith("#") && line.length() > 0) {
String words[] = line.split("=");
if (words.length != 2)
throw new ConfigurationParserException(
"Wrong format in assignment file, should be 'entry = datatype name'");
// entry name
final ConfigurationParserObject cpo = new ConfigurationParserObject();
cpo.setEntry(words[0].trim());
words = words[1].trim().split(" ");
if (words.length != 2)
throw new ConfigurationParserException(
"Wrong format in assignment file, datatype and name on right side MUST have no spaces");
words[0] = words[0].trim();
words[1] = words[1].trim();
// datatype
boolean positiveMatch = false;
for (int i = 0; i < knownDatatypes.length; i++) {
if (words[0].compareTo(knownDatatypes[i]) == 0) positiveMatch = true;
}
if (!positiveMatch) {
String datatypes = "";
for (int i = 0; i < knownDatatypes.length; i++) datatypes += knownDatatypes[i] + " ";
throw new ConfigurationParserException(
"Unknown datatype '" + words[0] + "', available datatypes are: " + datatypes);
}
cpo.setDataType(words[0]);
// variable name
int variablesPosition = -1;
for (int i = 0; i < fields.length; i++) {
if (words[1].compareTo(fields[i].getName()) == 0) variablesPosition = i;
}
if (variablesPosition == -1) {
String variables = "";
for (int i = 0; i < fields.length; i++) variables += fields[i].getName() + "\n";
throw new ConfigurationParserException(
"Unknown variable '" + words[1] + "', available variables are:\n" + variables);
}
cpo.setVariableName(words[1]);
cpo.setVariableFieldPosition(variablesPosition);
assignments.add(cpo);
}
}
} catch (Exception e) {
throw new ConfigurationParserException(
"Error reading/parsing assignment file at line " + lineCount + ":\n" + e.getMessage());
}
// read configuration file and assign entry values to assigned variables
lineCount = 0;
try {
while (confFile.ready()) {
lineCount++;
String line = confFile.readLine().trim();
if (!line.startsWith("#") && line.length() > 0) {
String words[] = line.split("=");
if (words.length != 2)
throw new ConfigurationParserException(
"Wrong format in configuration file, should be 'entry = value'");
words[0] = words[0].trim();
words[1] = words[1].trim();
int entryPos = findEntry(assignments, words[0]);
if (entryPos == -1)
throw new ConfigurationParserException(
"Entry '"
+ words[0]
+ "' does not exist!\nFollowing entries are available:\n"
+ getAllEntries(assignments));
final ConfigurationParserObject cpo = assignments.get(entryPos);
final int varFieldPos = cpo.getVariableFieldPosition();
if (cpo.getDataType().compareTo("byte") == 0) {
fields[varFieldPos].setByte(conf, Byte.parseByte(words[1]));
} else if (cpo.getDataType().compareTo("short") == 0) {
fields[varFieldPos].setShort(conf, Short.parseShort(words[1]));
} else if (cpo.getDataType().compareTo("int") == 0) {
fields[varFieldPos].setInt(conf, Integer.parseInt(words[1]));
} else if (cpo.getDataType().compareTo("long") == 0) {
fields[varFieldPos].setLong(conf, Long.parseLong(words[1]));
} else if (cpo.getDataType().compareTo("boolean") == 0) {
fields[varFieldPos].setBoolean(conf, Boolean.parseBoolean(words[1]));
} else if (cpo.getDataType().compareTo("float[]") == 0) {
final String[] entries = words[1].split(",");
if (entries.length < 1)
throw new ConfigurationParserException(
"Cannot parse array, should be 3, 4.3, 2, ... - but is '" + words[1] + "'");
final float[] values = new float[entries.length];
for (int i = 0; i < entries.length; ++i) values[i] = Float.parseFloat(entries[i]);
fields[varFieldPos].set(conf, values);
} else if (cpo.getDataType().compareTo("float") == 0) {
if (words[1].toLowerCase().compareTo("nan") == 0)
fields[varFieldPos].setFloat(conf, Float.NaN);
else fields[varFieldPos].setFloat(conf, Float.parseFloat(words[1]));
} else if (cpo.getDataType().compareTo("double") == 0) {
if (words[1].toLowerCase().compareTo("nan") == 0)
fields[varFieldPos].setDouble(conf, Double.NaN);
else fields[varFieldPos].setDouble(conf, Double.parseDouble(words[1]));
} else if (cpo.getDataType().compareTo("String") == 0) {
if (words[1].equals("null")) fields[varFieldPos].set(conf, null);
else {
if (words[1].startsWith("\"") && words[1].endsWith("\""))
fields[varFieldPos].set(conf, words[1].substring(1, words[1].length() - 1));
else
throw new ConfigurationParserException(
"Strings have to be surrounded by \"\" or be null");
}
} else if (cpo.getDataType().compareTo("ContainerFactory") == 0) {
if (words[1].startsWith("ArrayContainerFactory")) {
ArrayContainerFactory factory = new ArrayContainerFactory();
factory.setParameters(words[1].substring(words[1].indexOf("("), words[1].length()));
fields[varFieldPos].set(conf, factory);
} else if (words[1].startsWith("CellContainerFactory")) {
CellContainerFactory factory = new CellContainerFactory();
factory.setParameters(words[1].substring(words[1].indexOf("("), words[1].length()));
fields[varFieldPos].set(conf, factory);
} else {
throw new ConfigurationParserException(
"Unknown implementation of ContainerFactory '" + words[1] + "'");
}
} else if (cpo.getDataType().compareTo("InterpolatorFactory") == 0) {
if (words[1].startsWith("LinearInterpolatorFactory")) {
LinearInterpolatorFactory<FloatType> factory =
new LinearInterpolatorFactory<FloatType>(null);
factory.setParameters(words[1].substring(words[1].indexOf("("), words[1].length()));
fields[varFieldPos].set(conf, factory);
} else if (words[1].startsWith("NearestNeighborInterpolatorFactory")) {
NearestNeighborInterpolatorFactory<FloatType> factory =
new NearestNeighborInterpolatorFactory<FloatType>(null);
factory.setParameters(words[1].substring(words[1].indexOf("("), words[1].length()));
fields[varFieldPos].set(conf, factory);
} else {
throw new ConfigurationParserException(
"Unknown implementation of FloatInterpolatorFactory '" + words[1] + "'");
}
} else if (cpo.getDataType().compareTo("OutsideStrategyFactory") == 0) {
if (words[1].startsWith("OutsideStrategyMirrorFactory")) {
OutOfBoundsStrategyFactory<FloatType> factory =
new OutOfBoundsStrategyMirrorFactory<FloatType>();
factory.setParameters(words[1].substring(words[1].indexOf("("), words[1].length()));
fields[varFieldPos].set(conf, factory);
} else if (words[1].startsWith("OutsideStrategyValueFactory")) {
OutOfBoundsStrategyFactory<FloatType> factory =
new OutOfBoundsStrategyValueFactory<FloatType>();
factory.setParameters(words[1].substring(words[1].indexOf("("), words[1].length()));
fields[varFieldPos].set(conf, factory);
} else {
throw new ConfigurationParserException(
"Unknown implementation of OutsideStrategyFactory '" + words[1] + "'");
}
} else {
throw new ConfigurationParserException("Unknown datatype '" + cpo.getDataType() + "'");
}
}
}
} catch (Exception e) {
throw new ConfigurationParserException(
"Error reading/parsing configuration file at line " + lineCount + ":\n" + e.getMessage());
}
// variable specific verification
if (conf.numberOfThreads < 1) conf.numberOfThreads = Runtime.getRuntime().availableProcessors();
if (conf.scaleSpaceNumberOfThreads < 1)
conf.scaleSpaceNumberOfThreads = Runtime.getRuntime().availableProcessors();
// check the directory string
conf.inputdirectory = conf.inputdirectory.replace('\\', '/');
conf.inputdirectory = conf.inputdirectory.trim();
if (conf.inputdirectory.length() > 0 && !conf.inputdirectory.endsWith("/"))
conf.inputdirectory = conf.inputdirectory + "/";
if (conf.outputdirectory == null || conf.outputdirectory.length() == 0) {
conf.outputdirectory = conf.inputdirectory;
} else {
conf.outputdirectory = conf.outputdirectory.replace('\\', '/');
conf.outputdirectory = conf.outputdirectory.trim();
if (conf.outputdirectory.length() > 0 && !conf.outputdirectory.endsWith("/"))
conf.outputdirectory = conf.outputdirectory + "/";
}
if (conf.registrationFiledirectory == null || conf.registrationFiledirectory.length() == 0) {
conf.registrationFiledirectory = conf.inputdirectory;
} else {
conf.registrationFiledirectory = conf.registrationFiledirectory.replace('\\', '/');
conf.registrationFiledirectory = conf.registrationFiledirectory.trim();
if (conf.registrationFiledirectory.length() > 0
&& !conf.registrationFiledirectory.endsWith("/"))
conf.registrationFiledirectory = conf.registrationFiledirectory + "/";
}
// check if directories exist
File dir = new File(conf.outputdirectory, "");
if (!dir.exists()) {
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Creating directory '"
+ conf.outputdirectory
+ "'.");
boolean success = dir.mkdirs();
if (!success) {
if (!dir.exists()) {
throw new ConfigurationParserException(
"("
+ new Date(System.currentTimeMillis())
+ "): Cannot create directory '"
+ conf.outputdirectory
+ "', quitting.");
}
}
}
dir = new File(conf.registrationFiledirectory, "");
if (!dir.exists()) {
IOFunctions.println(
"("
+ new Date(System.currentTimeMillis())
+ "): Creating directory '"
+ conf.registrationFiledirectory
+ "'.");
boolean success = dir.mkdirs();
if (!success) {
if (!dir.exists()) {
throw new ConfigurationParserException(
"("
+ new Date(System.currentTimeMillis())
+ "): Cannot create directory '"
+ conf.registrationFiledirectory
+ "', quitting.");
}
}
}
int countTrue = 0;
if (conf.paralellFusion) countTrue++;
if (conf.sequentialFusion) countTrue++;
if (conf.multipleImageFusion) countTrue++;
if (countTrue != 1)
throw new ConfigurationParserException(
"Error reading/parsing configuration file: Only one fusion method must be true!");
if (conf.debugLevel.toUpperCase().equals("DEBUG_ERRORONLY"))
conf.debugLevelInt = ViewStructure.DEBUG_ERRORONLY;
if (conf.debugLevel.toUpperCase().equals("DEBUG_MAIN"))
conf.debugLevelInt = ViewStructure.DEBUG_MAIN;
if (conf.debugLevel.toUpperCase().equals("DEBUG_ALL"))
conf.debugLevelInt = ViewStructure.DEBUG_ALL;
// here all angles, timepoints and channels are parsed from the input strings
conf.getFileNames();
// set interpolator stuff
conf.interpolatorFactorOutput.setOutOfBoundsStrategyFactory(conf.strategyFactoryOutput);
// close files
try {
assignFile.close();
confFile.close();
} catch (Exception e) {
}
;
return conf;
}