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[Netcdftools-commit] SF.net SVN: netcdftools:[80] trunk/src/main/java/au/csiro/netcdf/wron/ MdbsyNetCDF2CSVConverter.java
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From: <jde...@us...> - 2010-08-11 02:35:27
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Revision: 80
http://netcdftools.svn.sourceforge.net/netcdftools/?rev=80&view=rev
Author: jdempsey
Date: 2010-08-11 02:35:21 +0000 (Wed, 11 Aug 2010)
Log Message:
-----------
ANDSWRON-703 - Fix up issues reported by checkstyle
Modified Paths:
--------------
trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java
Modified: trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java
===================================================================
--- trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java 2010-07-26 05:51:53 UTC (rev 79)
+++ trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java 2010-08-11 02:35:21 UTC (rev 80)
@@ -61,8 +61,7 @@
/**
* Constant that defines the logger to be used.
*/
- private static final Logger LOG = Logger
- .getLogger(MdbsyNetCDF2CSVConverter.class.getName());
+ private static final Logger LOG = Logger.getLogger(MdbsyNetCDF2CSVConverter.class.getName());
/**
* The latitude variable name used in the netCDF files.
@@ -129,42 +128,40 @@
* A string containing the date column text to be written out as the first column in all the csv files.
*/
private static String DATE_COLUMN_TEXT = null;
-
+
/**
* The attribute name used to store a variable's type.
*/
private static final String UNITS = "units";
/**
- * @param args
+ * Command line entry point for the MdbsyNetCDF2CSVConverter class. Gets the input and output directory names
+ * from the command line and runs a conversion.
+ *
+ * @param args The command line arguments
+ * @throws ParseException If an error occurs when parsing the arguments.
+ * @throws IOException If the files cannot be read or written to.
+ * @throws InvalidRangeException if an invalid range is attempted to be read from a netCDf variable
*/
@SuppressWarnings("static-access")
- public static void main(String[] args) throws ParseException, IOException,
- InvalidRangeException, java.text.ParseException
+ public static void main(String[] args) throws ParseException, IOException, InvalidRangeException
{
Options options = new Options();
try
{
- Option inputDirectoryName = OptionBuilder
- .withArgName("dir")
- .hasArg()
- .withDescription(
- "1. the directory path containing the netCDF files (split by latitude) to be converted into csv.")
+ Option inputDirectoryName = OptionBuilder.withArgName("dir").hasArg().withDescription(
+ "1. the directory path containing the netCDF files (split by latitude) to be converted into csv.")
.isRequired(true).withLongOpt(INPUT_DIR).create("i");
- Option outputDirectoryName = OptionBuilder
- .withArgName("dir")
- .hasArg()
- .withDescription(
- "2: the directory path to place the new csv files.")
- .isRequired(true).withLongOpt(OUTPUT_DIR).create("o");
+ Option outputDirectoryName = OptionBuilder.withArgName("dir").hasArg().withDescription(
+ "2: the directory path to place the new csv files.").isRequired(true).withLongOpt(OUTPUT_DIR)
+ .create("o");
options.addOption(inputDirectoryName);
options.addOption(outputDirectoryName);
// parse the command line arguments
- CommandLine parsedCommandLine = new GnuParser()
- .parse(options, args);
+ CommandLine parsedCommandLine = new GnuParser().parse(options, args);
String inputDir = parsedCommandLine.getOptionValue(INPUT_DIR);
String outputDir = parsedCommandLine.getOptionValue(OUTPUT_DIR);
@@ -187,8 +184,8 @@
StringWriter sw = new StringWriter();
HelpFormatter formatter = new HelpFormatter();
formatter.setOptionComparator(new CommandLineOptionsComparator());
- formatter.printHelp(new PrintWriter(sw), 80, "-", header, options,
- 0, 1, footer);
+ final int lineWidth = 80;
+ formatter.printHelp(new PrintWriter(sw), lineWidth, "-", header, options, 0, 1, footer);
System.out.println(sw.toString());
}
}
@@ -202,10 +199,10 @@
* the directory in which the csv file will be placed.
* @throws InvalidRangeException
* thrown if an invalid range is attempted to be read from a netCDf variable.
- * @throws IOException
+ * @throws IOException
+ * If the files cannot be read or written to.
*/
- public void execute(String inputDir, String outputDir) throws IOException,
- InvalidRangeException
+ public void execute(String inputDir, String outputDir) throws IOException, InvalidRangeException
{
// perform an initial conversion from netCDF to csv, the csv files will look like this:
// Date, 1985-01-01, 1895-01-02, 1985-01-03, ...
@@ -244,21 +241,21 @@
* thrown if an invalid range is attempted to be read from a netCDf variable.
* @throws IOException
*/
- private void writeCSVFiles(String inputDir, String outputDir)
- throws IOException, InvalidRangeException
+ private void writeCSVFiles(String inputDir, String outputDir) throws IOException, InvalidRangeException
{
File dir = new File(inputDir);
File[] files = dir.listFiles();
- if(files == null)
+ if (files == null)
{
System.out.println("The input directory does not exist: " + inputDir);
LOG.error("The input directory does not exist: " + inputDir);
return;
}
-
+
for (int fileIndex = 0; fileIndex < files.length; fileIndex++)
{
- if (files[fileIndex].isFile() && NETCDF_FILE_EXTENSION.equals(Util.getFileExtension(files[fileIndex].getName())))
+ if (files[fileIndex].isFile()
+ && NETCDF_FILE_EXTENSION.equals(Util.getFileExtension(files[fileIndex].getName())))
{
NetcdfFile nc = null;
try
@@ -268,43 +265,35 @@
Array latitudes = getLatitudeValues(nc);
Array longitudes = getLongitudeValues(nc);
- LOG.info("latitude coordinate variable size: "
- + latitudes.getSize());
- LOG.info("longitude coordinate variable size: "
- + longitudes.getSize());
+ LOG.info("latitude coordinate variable size: " + latitudes.getSize());
+ LOG.info("longitude coordinate variable size: " + longitudes.getSize());
for (int latIndex = 0; latIndex < latitudes.getSize(); latIndex++)
{
- for (int longIndex = 0; longIndex < longitudes
- .getSize(); longIndex++)
+ for (int longIndex = 0; longIndex < longitudes.getSize(); longIndex++)
{
- String fileName = createFileNameBasedOnLatLong(nc,
- latIndex, longIndex);
- String filePath = outputDir
- + System.getProperty("file.separator")
- + fileName + ".csv";
-
+ String fileName = createFileNameBasedOnLatLong(nc, latIndex, longIndex);
+ String filePath = outputDir + System.getProperty("file.separator") + fileName + ".csv";
+
LOG.info("\tWorking on file: " + filePath);
// if the csv file already exists, then append the next variable.
if (Util.fileExists(filePath))
{
File file = new File(filePath);
- PrintWriter out = new PrintWriter(
- new BufferedWriter(new FileWriter(file,
- true /* append mode */)));
+ PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(file, true /*
+ * append
+ * mode
+ */)));
List<String> variablesAlreadyWrittenOut = getVariablesAlreadyWrittenOut(file);
List<String> variablesThatCanBeWrittenOut = getVariablesThatCanBeWrittenOut(nc);
- variablesThatCanBeWrittenOut
- .removeAll(variablesAlreadyWrittenOut);
-
+ variablesThatCanBeWrittenOut.removeAll(variablesAlreadyWrittenOut);
+
try
{
- writeOutVariable(nc, out,
- variablesThatCanBeWrittenOut,
- latIndex, longIndex);
+ writeOutVariable(nc, out, variablesThatCanBeWrittenOut, latIndex, longIndex);
}
finally
{
@@ -315,19 +304,17 @@
else
// if the csv file does not exist, create a new csv file and write all available variables.
{
- PrintWriter out = new PrintWriter(new BufferedWriter(
- new FileWriter(new File(filePath),
- false /* append mode */)));
+ PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(new File(filePath),
+ false /* append mode */)));
List<String> variablesThatCanBeWrittenOut = getVariablesThatCanBeWrittenOut(nc);
try
{
- out.println(writeOutDateColumn(nc)); // note: we only write out the date column when a new csv file is created.
-
- writeOutVariable(nc, out,
- variablesThatCanBeWrittenOut,
- latIndex, longIndex);
+ out.println(writeOutDateColumn(nc)); // note: we only write out the date column when
+ // a new csv file is created.
+
+ writeOutVariable(nc, out, variablesThatCanBeWrittenOut, latIndex, longIndex);
}
finally
{
@@ -359,16 +346,13 @@
* @throws IOException
*
*/
- private void writeOutVariable(NetcdfFile nc, PrintWriter out,
- List<String> variablesThatCanBeWrittenOut, int latIndex,
- int longIndex) throws IOException, InvalidRangeException
+ private void writeOutVariable(NetcdfFile nc, PrintWriter out, List<String> variablesThatCanBeWrittenOut,
+ int latIndex, int longIndex) throws IOException, InvalidRangeException
{
for (String variableName : variablesThatCanBeWrittenOut)
{
- Array subsection = getVariableAcrossTime(nc, variableName,
- latIndex, longIndex);
- out.println(variableName + ","
- + subsection.toString().replaceAll(" ", ","));
+ Array subsection = getVariableAcrossTime(nc, variableName, latIndex, longIndex);
+ out.println(variableName + "," + subsection.toString().replaceAll(" ", ","));
}
}
@@ -383,7 +367,7 @@
{
File dir = new File(outputDir);
File[] files = dir.listFiles();
- if(files == null)
+ if (files == null)
{
System.out.println("The output directory does not exist: " + outputDir);
LOG.error("The output directory does not exist: " + outputDir);
@@ -392,14 +376,16 @@
for (int fileIndex = 0; fileIndex < files.length; fileIndex++)
{
- if (files[fileIndex].isFile() && CSV_FILE_EXTENSION.equals(Util.getFileExtension(files[fileIndex].getName())))
+ if (files[fileIndex].isFile()
+ && CSV_FILE_EXTENSION.equals(Util.getFileExtension(files[fileIndex].getName())))
{
String[][] matrix = readLookupFile(files[fileIndex]);
// write over-the-top of the csv file.
- PrintWriter out = new PrintWriter(
- new BufferedWriter(new FileWriter(files[fileIndex],
- false /* append mode */)));
+ PrintWriter out = new PrintWriter(new BufferedWriter(new FileWriter(files[fileIndex], false /*
+ * append
+ * mode
+ */)));
// transpose String[][] matrix and write back out to csv
String[][] transposed = transpose(matrix);
@@ -411,7 +397,7 @@
for (int col = 0; col < transposed[0].length; col++)
{
out.print(transposed[row][col]);
- if(col < (transposed[0].length-1))
+ if (col < (transposed[0].length - 1))
{
out.print(", ");
}
@@ -460,8 +446,7 @@
* @return the name of the variables that have already be written out to a csv file.
* @throws IOException
*/
- private List<String> getVariablesAlreadyWrittenOut(File file)
- throws IOException
+ private List<String> getVariablesAlreadyWrittenOut(File file) throws IOException
{
List<String> variablesAlreadyWrittenOut = new ArrayList<String>();
@@ -487,15 +472,11 @@
* @throws InvalidRangeException
* @throws IOException
*/
- private String createFileNameBasedOnLatLong(NetcdfFile nc, int latIndex,
- int longIndex) throws IOException, InvalidRangeException
+ private String createFileNameBasedOnLatLong(NetcdfFile nc, int latIndex, int longIndex) throws IOException,
+ InvalidRangeException
{
- return "region_"
- + nc.readSection("lat(" + latIndex + ":" + latIndex + ")")
- .toString().trim()
- + "_"
- + nc.readSection("long(" + longIndex + ":" + longIndex + ")")
- .toString().trim();
+ return "region_" + nc.readSection("lat(" + latIndex + ":" + latIndex + ")").toString().trim() + "_"
+ + nc.readSection("long(" + longIndex + ":" + longIndex + ")").toString().trim();
}
/**
@@ -510,7 +491,7 @@
{
RandomAccessFile raf = new RandomAccessFile(file, "r");
List<String[]> lineList = new ArrayList<String[]>();
-
+
try
{
String line = raf.readLine();
@@ -533,11 +514,12 @@
/**
* Transpose a matrix, e.g. [a][b] -> [b][a]
*
- * @param values a String[][] matrix.
+ * @param values
+ * a String[][] matrix.
*/
private String[][] transpose(String[][] values)
{
- if(values.length == 0)
+ if (values.length == 0)
{
return new String[0][0];
}
@@ -568,21 +550,19 @@
* @throws IOException
* @throws InvalidRangeException
*/
- private Array getVariableAcrossTime(NetcdfFile nc, String variableName,
- int latIndex, int longIndex) throws IOException,
- InvalidRangeException
+ private Array getVariableAcrossTime(NetcdfFile nc, String variableName, int latIndex, int longIndex)
+ throws IOException, InvalidRangeException
{
try
{
- return nc.readSection(variableName + "(" + latIndex + ":"
- + latIndex + "," + longIndex + ":" + longIndex + ",:)");
+ return nc.readSection(variableName + "(" + latIndex + ":" + latIndex + "," + longIndex + ":" + longIndex
+ + ",:)");
}
catch (InvalidRangeException ire)
{
ire.printStackTrace();
- LOG.error("Could not read section: " + variableName + "("
- + latIndex + ":" + latIndex + "," + longIndex + ":"
- + longIndex + ",:)", ire);
+ LOG.error("Could not read section: " + variableName + "(" + latIndex + ":" + latIndex + "," + longIndex
+ + ":" + longIndex + ",:)", ire);
}
return null;
}
@@ -596,25 +576,21 @@
* @throws IOException
* @throws IllegalArgumentException
*/
- private Array getLongitudeValues(NetcdfFile nc) throws IOException,
- IllegalArgumentException
+ private Array getLongitudeValues(NetcdfFile nc) throws IOException, IllegalArgumentException
{
List<Variable> variables = nc.getVariables();
- if(variables != null)
+ if (variables != null)
{
for (Variable v : variables)
{
- if (v.isCoordinateVariable()
- && LONGITUDE_VARIABLE_NAME.equals(v.getName()))
+ if (v.isCoordinateVariable() && LONGITUDE_VARIABLE_NAME.equals(v.getName()))
{
return v.read();
}
}
}
- LOG.error("Could not find coordinate variable: "
- + LONGITUDE_VARIABLE_NAME);
- throw new IllegalStateException("Could not find coordinate variable: "
- + LONGITUDE_VARIABLE_NAME);
+ LOG.error("Could not find coordinate variable: " + LONGITUDE_VARIABLE_NAME);
+ throw new IllegalStateException("Could not find coordinate variable: " + LONGITUDE_VARIABLE_NAME);
}
/**
@@ -626,25 +602,21 @@
* @throws IOException
* @throws IllegalArgumentException
*/
- private Array getLatitudeValues(NetcdfFile nc) throws IOException,
- IllegalArgumentException
+ private Array getLatitudeValues(NetcdfFile nc) throws IOException, IllegalArgumentException
{
List<Variable> variables = nc.getVariables();
- if(variables != null)
+ if (variables != null)
{
for (Variable v : variables)
{
- if (v.isCoordinateVariable()
- && LATITUDE_VARIABLE_NAME.equals(v.getName()))
+ if (v.isCoordinateVariable() && LATITUDE_VARIABLE_NAME.equals(v.getName()))
{
return v.read();
}
}
}
- LOG.error("Could not find coordinate variable: "
- + LATITUDE_VARIABLE_NAME);
- throw new IllegalStateException("Could not find coordinate variable: "
- + LATITUDE_VARIABLE_NAME);
+ LOG.error("Could not find coordinate variable: " + LATITUDE_VARIABLE_NAME);
+ throw new IllegalStateException("Could not find coordinate variable: " + LATITUDE_VARIABLE_NAME);
}
/**
@@ -655,24 +627,21 @@
* @return the time variable.
* @throws IllegalArgumentException
*/
- private static Variable getTimeVariable(NetcdfFile nc)
- throws IllegalArgumentException
+ private static Variable getTimeVariable(NetcdfFile nc) throws IllegalArgumentException
{
List<Variable> variables = nc.getVariables();
- if(variables != null)
+ if (variables != null)
{
for (Variable v : variables)
{
- if (v.isCoordinateVariable()
- && TIME_VARIABLE_NAME.equals(v.getName()))
+ if (v.isCoordinateVariable() && TIME_VARIABLE_NAME.equals(v.getName()))
{
return v;
}
}
}
LOG.error("Could not find coordinate variable: " + TIME_VARIABLE_NAME);
- throw new IllegalStateException("Could not find coordinate variable: "
- + TIME_VARIABLE_NAME);
+ throw new IllegalStateException("Could not find coordinate variable: " + TIME_VARIABLE_NAME);
}
/**
@@ -694,21 +663,23 @@
try
{
Variable time = getTimeVariable(nc);
-
+
String timeUnits = getVariablesUnits(time);
- String epocString = timeUnits.substring(timeUnits.indexOf("days since") + 11); // we expect the time value to be in units of: "days since yyyy-mm-dd h:m:s"
-
+ String epocString = timeUnits.substring(timeUnits.indexOf("days since") + 11); // we expect the time
+ // value to be in units
+ // of:
+ // "days since yyyy-mm-dd h:m:s"
+
epocDate = dateFormatter.dateOnlyFormat(epocString);
strBuf.append("Date,");
long timeVariableSize = time.getSize();
for (int i = 0; i < timeVariableSize; i++)
{
- strBuf.append(dateFormatter.toDateOnlyString(new Date(epocDate
- .getTime()
- + (i * MILLISECONDS_IN_A_DAY))).trim());
-
- if(i < (timeVariableSize-1))
+ strBuf.append(dateFormatter.toDateOnlyString(
+ new Date(epocDate.getTime() + (i * MILLISECONDS_IN_A_DAY))).trim());
+
+ if (i < (timeVariableSize - 1))
{
strBuf.append(",");
}
@@ -735,11 +706,11 @@
private static String getVariablesUnits(Variable variable)
{
List<Attribute> attributes = variable.getAttributes();
- if(attributes != null)
+ if (attributes != null)
{
- for(Attribute attribute : attributes)
+ for (Attribute attribute : attributes)
{
- if(UNITS.equals(attribute.getName()))
+ if (UNITS.equals(attribute.getName()))
{
return attribute.getStringValue();
}
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