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[Netcdftools-commit] SF.net SVN: netcdftools:[71] trunk/src/main/java/au/csiro/netcdf/wron/ MdbsyNetCDF2CSVConverter.java
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From: <rob...@us...> - 2010-07-13 00:09:56
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Revision: 71
http://netcdftools.svn.sourceforge.net/netcdftools/?rev=71&view=rev
Author: robertbridle
Date: 2010-07-13 00:09:49 +0000 (Tue, 13 Jul 2010)
Log Message:
-----------
ANDSWRON-703 - Review fix - Modified code to obtain EPOC dateTime from netCDF file instead of from a hard coded constant.
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 2010-07-08 09:35:45 UTC (rev 70)
+++ trunk/src/main/java/au/csiro/netcdf/wron/MdbsyNetCDF2CSVConverter.java 2010-07-13 00:09:49 UTC (rev 71)
@@ -1,3 +1,19 @@
+/**
+ * Copyright 2010, CSIRO Australia.
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
package au.csiro.netcdf.wron;
import java.io.BufferedWriter;
@@ -23,6 +39,7 @@
import ucar.ma2.Array;
import ucar.ma2.InvalidRangeException;
+import ucar.nc2.Attribute;
import ucar.nc2.NetcdfFile;
import ucar.nc2.Variable;
import ucar.nc2.units.DateFormatter;
@@ -41,8 +58,6 @@
*/
public class MdbsyNetCDF2CSVConverter
{
- private static final String EPOC = "1895-01-01";
-
/**
* Constant that defines the logger to be used.
*/
@@ -114,6 +129,11 @@
* 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
@@ -187,18 +207,26 @@
public void execute(String inputDir, String outputDir) throws IOException,
InvalidRangeException
{
- // perform an initial conversion from netCDF to csv, the csv file will look like this:
+ // 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, ...
// APET, 0.1, 0.3, 0.0, ....
// rainfall,0.0, 0.4, 0.1, ...
+ System.out.println("Starting intial convert of NetCDF 2 CSV.");
+ LOG.info("Starting intial convert of NetCDF 2 CSV.");
writeCSVFiles(inputDir, outputDir);
+ System.out.println("Finished intial convert of NetCDF 2 CSV.");
+ LOG.info("Finished intial convert of NetCDF 2 CSV.");
- // transpose the csv files so the will look like this:
+ // transpose the csv files so they will look like this:
// Date, APET, rainfall
// 1895-01-01, 0.1, 0.0
// 1895-01-02, 0.3, 0.4
// 1895-01-03, 0.0, 0.1
+ System.out.println("Started transposition of CSV.");
+ LOG.info("Started transposition of CSV.");
transposeCSVFiles(outputDir);
+ System.out.println("Finished transposition of CSV.");
+ LOG.info("Finished transposition of CSV.");
}
/**
@@ -255,6 +283,8 @@
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))
@@ -293,7 +323,7 @@
try
{
- out.println(writeOutDateColumn(nc));
+ out.println(writeOutDateColumn(nc)); // note: we only write out the date column when a new csv file is created.
writeOutVariable(nc, out,
variablesThatCanBeWrittenOut,
@@ -569,12 +599,16 @@
private Array getLongitudeValues(NetcdfFile nc) throws IOException,
IllegalArgumentException
{
- for (Variable v : nc.getVariables())
+ List<Variable> variables = nc.getVariables();
+ if(variables != null)
{
- if (v.isCoordinateVariable()
- && LONGITUDE_VARIABLE_NAME.equals(v.getName()))
+ for (Variable v : variables)
{
- return v.read();
+ if (v.isCoordinateVariable()
+ && LONGITUDE_VARIABLE_NAME.equals(v.getName()))
+ {
+ return v.read();
+ }
}
}
LOG.error("Could not find coordinate variable: "
@@ -595,12 +629,16 @@
private Array getLatitudeValues(NetcdfFile nc) throws IOException,
IllegalArgumentException
{
- for (Variable v : nc.getVariables())
+ List<Variable> variables = nc.getVariables();
+ if(variables != null)
{
- if (v.isCoordinateVariable()
- && LATITUDE_VARIABLE_NAME.equals(v.getName()))
+ for (Variable v : variables)
{
- return v.read();
+ if (v.isCoordinateVariable()
+ && LATITUDE_VARIABLE_NAME.equals(v.getName()))
+ {
+ return v.read();
+ }
}
}
LOG.error("Could not find coordinate variable: "
@@ -620,12 +658,16 @@
private static Variable getTimeVariable(NetcdfFile nc)
throws IllegalArgumentException
{
- for (Variable v : nc.getVariables())
+ List<Variable> variables = nc.getVariables();
+ if(variables != null)
{
- if (v.isCoordinateVariable()
- && TIME_VARIABLE_NAME.equals(v.getName()))
+ for (Variable v : variables)
{
- return v;
+ if (v.isCoordinateVariable()
+ && TIME_VARIABLE_NAME.equals(v.getName()))
+ {
+ return v;
+ }
}
}
LOG.error("Could not find coordinate variable: " + TIME_VARIABLE_NAME);
@@ -648,16 +690,21 @@
StringBuffer strBuf = new StringBuffer();
DateFormatter dateFormatter = new DateFormatter();
- Date epoc;
+ Date epocDate;
try
{
- epoc = dateFormatter.dateOnlyFormat(EPOC);
+ 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"
+
+ epocDate = dateFormatter.dateOnlyFormat(epocString);
strBuf.append("Date,");
- long timeVariableSize = getTimeVariable(nc).getSize();
+ long timeVariableSize = time.getSize();
for (int i = 0; i < timeVariableSize; i++)
{
- strBuf.append(dateFormatter.toDateOnlyString(new Date(epoc
+ strBuf.append(dateFormatter.toDateOnlyString(new Date(epocDate
.getTime()
+ (i * MILLISECONDS_IN_A_DAY))).trim());
@@ -674,8 +721,34 @@
pe.printStackTrace();
LOG.error("Error parsing date", pe);
}
-
}
return DATE_COLUMN_TEXT;
}
+
+ /**
+ * Finds the string value of the attribute that is used to store a variable's type.
+ *
+ * @param variable
+ * a variable {@link Variable}
+ * @return the string value of the variable's type.
+ */
+ private static String getVariablesUnits(Variable variable)
+ {
+ List<Attribute> attributes = variable.getAttributes();
+ if(attributes != null)
+ {
+ for(Attribute attribute : attributes)
+ {
+ if(UNITS.equals(attribute.getName()))
+ {
+ return attribute.getStringValue();
+ }
+ }
+ }
+ LOG
+ .error("Could not find the value for the variable: " + variable.getName() + " -\"" + UNITS
+ + "\" attribute.");
+ throw new IllegalStateException("Could not find the value for the variable: " + variable.getName() + " -\""
+ + UNITS + "\" attribute.");
+ }
}
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