/*
* Copyright (C) 2013 Dr. John Lindsay <jlindsay@uoguelph.ca>
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation, either version 3 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program. If not, see <http://www.gnu.org/licenses/>.
*/
package plugins;
import java.io.*;
import java.nio.ByteBuffer;
import java.nio.channels.FileChannel;
import java.util.Date;
import whitebox.geospatialfiles.WhiteboxRaster;
import whitebox.geospatialfiles.WhiteboxRasterBase;
import whitebox.interfaces.WhiteboxPlugin;
import whitebox.interfaces.WhiteboxPluginHost;
import whitebox.interfaces.InteropPlugin;
import whitebox.utilities.BitOps;
import whitebox.utilities.Unsigned;
/**
* This tool can be used to convert SAGA GIS raster grids to Whitebox GAT raster files.
*
* @author Dr. John Lindsay email: jlindsay@uoguelph.ca
*/
public class ImportSagaGrid implements WhiteboxPlugin, InteropPlugin {
private WhiteboxPluginHost myHost = null;
private String[] args;
/**
* Used to retrieve the plugin tool's name. This is a short, unique name
* containing no spaces.
*
* @return String containing plugin name.
*/
@Override
public String getName() {
return "ImportSagaGrid";
}
/**
* Used to retrieve the plugin tool's descriptive name. This can be a longer
* name (containing spaces) and is used in the interface to list the tool.
*
* @return String containing the plugin descriptive name.
*/
@Override
public String getDescriptiveName() {
return "Import SAGA Grid";
}
/**
* Used to retrieve a short description of what the plugin tool does.
*
* @return String containing the plugin's description.
*/
@Override
public String getToolDescription() {
return "Imports a SAGA GIS raster.";
}
/**
* Used to identify which toolboxes this plugin tool should be listed in.
*
* @return Array of Strings.
*/
@Override
public String[] getToolbox() {
String[] ret = {"IOTools"};
return ret;
}
/**
* Sets the WhiteboxPluginHost to which the plugin tool is tied. This is the
* class that the plugin will send all feedback messages, progress updates,
* and return objects.
*
* @param host The WhiteboxPluginHost that called the plugin tool.
*/
@Override
public void setPluginHost(WhiteboxPluginHost host) {
myHost = host;
}
/**
* Used to communicate feedback pop-up messages between a plugin tool and
* the main Whitebox user-interface.
*
* @param feedback String containing the text to display.
*/
private void showFeedback(String message) {
if (myHost != null) {
myHost.showFeedback(message);
} else {
System.out.println(message);
}
}
/**
* Used to communicate a return object from a plugin tool to the main
* Whitebox user-interface.
*
* @return Object, such as an output WhiteboxRaster.
*/
private void returnData(Object ret) {
if (myHost != null) {
myHost.returnData(ret);
}
}
private int previousProgress = 0;
private String previousProgressLabel = "";
/**
* Used to communicate a progress update between a plugin tool and the main
* Whitebox user interface.
*
* @param progressLabel A String to use for the progress label.
* @param progress Float containing the progress value (between 0 and 100).
*/
private void updateProgress(String progressLabel, int progress) {
if (myHost != null && ((progress != previousProgress)
|| (!progressLabel.equals(previousProgressLabel)))) {
myHost.updateProgress(progressLabel, progress);
}
previousProgress = progress;
previousProgressLabel = progressLabel;
}
/**
* Used to communicate a progress update between a plugin tool and the main
* Whitebox user interface.
*
* @param progress Float containing the progress value (between 0 and 100).
*/
private void updateProgress(int progress) {
if (myHost != null && progress != previousProgress) {
myHost.updateProgress(progress);
}
previousProgress = progress;
}
/**
* Sets the arguments (parameters) used by the plugin.
*
* @param args An array of string arguments.
*/
@Override
public void setArgs(String[] args) {
this.args = args.clone();
}
private boolean cancelOp = false;
/**
* Used to communicate a cancel operation from the Whitebox GUI.
*
* @param cancel Set to true if the plugin should be canceled.
*/
@Override
public void setCancelOp(boolean cancel) {
cancelOp = cancel;
}
private void cancelOperation() {
showFeedback("Operation cancelled.");
updateProgress("Progress: ", 0);
}
private boolean amIActive = false;
/**
* Used by the Whitebox GUI to tell if this plugin is still running.
*
* @return a boolean describing whether or not the plugin is actively being
* used.
*/
@Override
public boolean isActive() {
return amIActive;
}
/**
* Used to execute this plugin tool.
*/
@Override
public void run() {
amIActive = true;
try {
String inputFilesString = "";
String sagaHeaderFile = "";
String sagaDataFile = "";
int i = 0;
int row, col, rows = 0, cols = 0;
double north = 0, south = 0, east = 0, west = 0, cellSize = 0;
long dataFileOffset = 0;
double zFactor = 1.0;
String description = "";
String xyUnit = "not specified";
String dataFormat = "";
boolean topToBottom = false;
int rowStart = 0;
int rowIncrement = 1;
java.nio.ByteOrder byteorder = java.nio.ByteOrder.BIG_ENDIAN;
String[] imageFiles;
int numImages = 0;
double noData = -32768;
String returnHeaderFile = "";
DataInputStream in = null;
BufferedReader br = null;
if (args.length <= 0) {
showFeedback("Plugin parameters have not been set.");
return;
}
inputFilesString = args[0];
// check to see that the inputHeader and outputHeader are not null.
if ((inputFilesString == null)) {
showFeedback("One or more of the input parameters have not been set properly.");
return;
}
imageFiles = inputFilesString.split(";");
numImages = imageFiles.length;
for (i = 0; i < numImages; i++) {
int progress = (int) (100f * i / (numImages - 1));
if (numImages > 1) {
updateProgress("Loop " + (i + 1) + " of " + numImages + ":", progress);
}
String inputFile = imageFiles[i];
// check to see if the file exists.
File file = new File(inputFile);
if (!file.exists()) {
showFeedback("Image file does not exist.");
break;
}
String fileExtension = whitebox.utilities.FileUtilities.getFileExtension(inputFile).toLowerCase();
// the user can specify the name of either the header or the data file.
if (fileExtension.equals("sgrd")) {
sagaHeaderFile = inputFile;
sagaDataFile = inputFile.replace(fileExtension, "sdat");
if (!new File(sagaDataFile).exists()) {
showFeedback("Image file does not exist.");
break;
}
} else {
sagaDataFile = inputFile;
sagaHeaderFile = inputFile.replace(fileExtension, "sgrd");
if (!new File(sagaHeaderFile).exists()) {
showFeedback("Image file does not exist.");
break;
}
}
// read the header file
FileInputStream fstream = new FileInputStream(sagaHeaderFile);
in = new DataInputStream(fstream);
br = new BufferedReader(new InputStreamReader(in));
String delimiter = "\t";
String line;
String[] str;
//Read File Line By Line
while ((line = br.readLine()) != null) {
str = line.split(delimiter);
if (str.length <= 1) {
delimiter = " ";
str = line.split(delimiter);
if (str.length <= 1) {
delimiter = ",";
str = line.split(delimiter);
}
}
if (str[0].toLowerCase().contains("description")) {
description = str[str.length - 1].replace("=", "").trim();
} else if (str[0].toLowerCase().contains("unit")) {
if (!str[str.length - 1].replace("=", "").trim().isEmpty()) {
xyUnit = str[str.length - 1].replace("=", "").trim();
}
} else if (str[0].toLowerCase().contains("datafile_offset")) {
dataFileOffset = Long.parseLong(str[str.length - 1].replace("=", "").trim());
} else if (str[0].toLowerCase().contains("dataformat")) {
dataFormat = str[str.length - 1].replace("=", "").trim().toLowerCase();
} else if (str[0].toLowerCase().contains("byteorder_big")) {
if (str[str.length - 1].toLowerCase().contains("f")) {
byteorder = java.nio.ByteOrder.LITTLE_ENDIAN;
} else {
byteorder = java.nio.ByteOrder.BIG_ENDIAN;
}
} else if (str[0].toLowerCase().contains("position_xmin")) {
west = Double.parseDouble(str[str.length - 1].replace("=", "").trim());
} else if (str[0].toLowerCase().contains("position_ymin")) {
south = Double.parseDouble(str[str.length - 1].replace("=", "").trim());
} else if (str[0].toLowerCase().contains("cellcount_x")) {
cols = Integer.parseInt(str[str.length - 1].replace("=", "").trim());
} else if (str[0].toLowerCase().contains("cellcount_y")) {
rows = Integer.parseInt(str[str.length - 1].replace("=", "").trim());
} else if (str[0].toLowerCase().contains("cellsize")) {
cellSize = Double.parseDouble(str[str.length - 1].replace("=", "").trim());
} else if (str[0].toLowerCase().contains("z_factor")) {
zFactor = Double.parseDouble(str[str.length - 1].replace("=", "").trim());
} else if (str[0].toLowerCase().contains("nodata_value")) {
noData = Double.parseDouble(str[str.length - 1].replace("=", "").trim());
} else if (str[0].toLowerCase().contains("toptobottom")) {
topToBottom = !str[str.length - 1].toLowerCase().contains("f");
}
}
north = south + cellSize * rows;
east = west + cellSize * cols;
if (!topToBottom) {
rowStart = rows - 1;
rowIncrement = -1;
}
// Close the input stream
in.close();
br.close();
// Figure out the output data type
WhiteboxRasterBase.DataType outputDataType;
switch (dataFormat) {
case "bit":
case "byte_unsigned":
case "byte":
case "shortint_unsigned":
case "shortint":
// Notice, although there is support for a byte data type,
// it is not used because of the major limitation of Java's
// signed byte.
outputDataType = WhiteboxRasterBase.DataType.INTEGER;
break;
case "float":
outputDataType = WhiteboxRasterBase.DataType.FLOAT;
break;
//case "integer":
//case "integer_unsigned":
//case "double":
default:
outputDataType = WhiteboxRasterBase.DataType.DOUBLE;
break;
}
if (zFactor < 1.0 && outputDataType == WhiteboxRasterBase.DataType.INTEGER) {
outputDataType = WhiteboxRasterBase.DataType.FLOAT;
}
String whiteboxHeaderFile = imageFiles[i].replace(fileExtension, "dep");
if (i == 0) {
returnHeaderFile = whiteboxHeaderFile;
}
WhiteboxRaster output = new WhiteboxRaster(whiteboxHeaderFile,
north, south, east, west, rows, cols,
WhiteboxRasterBase.DataScale.CONTINUOUS,
outputDataType, noData, noData);
file = new File(sagaDataFile);
int fileLength = (int) file.length();
RandomAccessFile rIn = null;
FileChannel inChannel = null;
ByteBuffer buf = ByteBuffer.allocate(fileLength);
rIn = new RandomAccessFile(sagaDataFile, "r");
inChannel = rIn.getChannel();
inChannel.position(0);
inChannel.read(buf);
// Check the byte order.
buf.order(byteorder);
buf.rewind();
byte[] ba = new byte[(int) fileLength];
buf.get(ba);
double z;
row = 0;
col = 0;
int pos = (int) dataFileOffset;
int oldProgress = -1;
boolean flag = true;
row = rowStart;
switch (dataFormat) {
case "bit":
byte b;
while (flag) {
b = buf.get(pos);
for (int bit = 0; bit < 8; bit++) {
if (BitOps.checkBit(b, bit)) {
output.setValue(row, col, 1.0);
} else {
output.setValue(row, col, 0.0);
}
col++;
if (col >= cols) {
row += rowIncrement;
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
}
if (row >= rows || row < 0) {
flag = false;
}
}
pos += 1;
if (pos >= fileLength) {
flag = false;
}
}
case "byte_unsigned":
while (flag) {
for (col = 0; col < cols; col++) {
z = (double) (Unsigned.getUnsignedByte(buf, pos)) * zFactor;
output.setValue(row, col, z);
pos += 1;
}
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
row += rowIncrement;
if (row >= rows || row < 0) {
flag = false;
}
}
case "byte":
while (flag) {
for (col = 0; col < cols; col++) {
z = (double) buf.get(pos) * zFactor;
output.setValue(row, col, z);
pos += 1;
}
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
row += rowIncrement;
if (row >= rows || row < 0) {
flag = false;
}
}
case "shortint_unsigned":
while (flag) {
for (col = 0; col < cols; col++) {
z = (double) (Unsigned.getUnsignedShort(buf, pos)) * zFactor;
output.setValue(row, col, z);
pos += 2;
}
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
row += rowIncrement;
if (row >= rows || row < 0) {
flag = false;
}
}
case "shortint":
while (flag) {
for (col = 0; col < cols; col++) {
z = (double) buf.getShort(pos) * zFactor;
output.setValue(row, col, z);
pos += 2;
}
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
row += rowIncrement;
if (row >= rows || row < 0) {
flag = false;
}
}
case "integer":
while (flag) {
for (col = 0; col < cols; col++) {
z = (double) buf.getInt(pos) * zFactor;
output.setValue(row, col, z);
pos += 4;
}
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
row += rowIncrement;
if (row >= rows || row < 0) {
flag = false;
}
}
break;
case "integer_unsigned":
while (flag) {
for (col = 0; col < cols; col++) {
z = (double) (Unsigned.getUnsignedInt(buf, pos)) * zFactor;
output.setValue(row, col, z);
pos += 4;
}
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
row += rowIncrement;
if (row >= rows || row < 0) {
flag = false;
}
}
case "float":
while (flag) {
for (col = 0; col < cols; col++) {
z = (double) buf.getFloat(pos) * zFactor;
output.setValue(row, col, z);
pos += 4;
}
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
row += rowIncrement;
if (row >= rows || row < 0) {
flag = false;
}
}
break;
default: // 64-bit double
while (flag) {
for (col = 0; col < cols; col++) {
z = buf.getDouble(pos) * zFactor;
output.setValue(row, col, z);
pos += 8;
}
progress = (int) (100f * (row - rowStart) / (rows - 1));
if (progress != oldProgress) {
updateProgress("Importing SAGA file...", progress);
oldProgress = progress;
}
row += rowIncrement;
if (row >= rows || row < 0) {
flag = false;
}
}
break;
}
inChannel.close();
output.addMetadataEntry("Created by the "
+ getDescriptiveName() + " tool.");
output.addMetadataEntry("Created on " + new Date());
output.flush();
output.findMinAndMaxVals();
output.writeHeaderFile();
output.close();
}
// returning a header file string displays the image.
returnData(returnHeaderFile);
} catch (OutOfMemoryError oe) {
myHost.showFeedback("An out-of-memory error has occurred during operation.");
} catch (Exception e) {
myHost.showFeedback("An error has occurred during operation. See log file for details.");
myHost.logException("Error in " + getDescriptiveName(), e);
} finally {
updateProgress("Progress: ", 0);
// tells the main application that this process is completed.
amIActive = false;
myHost.pluginComplete();
}
}
/**
* Used to retrieve the necessary extensions.
* @return String containing the extensions.
*/
@Override
public String[] getExtensions() {
return new String[]{ "txt" };
}
/**
* Used to retrieve the file type name.
* @return String containing the file type name.
*/
@Override
public String getFileTypeName() {
return "ArcGIS ASCII Grid";
}
/**
* Used to check if the file is raster format.
* @return Boolean true if file is raster format.
*/
@Override
public boolean isRasterFormat() {
return true;
}
/**
* Used to retrieve the interoperable plugin type.
* @return
*/
@Override
public InteropPlugin.InteropPluginType getInteropPluginType() {
return InteropPlugin.InteropPluginType.exportPlugin;
}
}
// // This method is only used during testing.
// public static void main(String[] args) {
// args = new String[1];
// args[0] = "/Users/johnlindsay/Documents/Data/SAGA Grid/TestData.sgrd";
// //args[0] = "/Users/johnlindsay/Documents/Data/SAGA Grid/TestData.sdat";
//
// ImportSagaGrid isg = new ImportSagaGrid();
// isg.setArgs(args);
// isg.run();
// }