Commit 90269d56 authored by Michal Dobaczewski's avatar Michal Dobaczewski

various changes to maven building and site (in progress)

parent 9269174b
This diff is collapsed.
mvn install:install-file -Dfile=javabuilder.jar -DgeneratePom=true -DgroupId=com.mathworks -DartifactId=javabuilder -Dversion=1.0.0 -Dpackaging=jar
mvn install:install-file -Dfile=win32/artifact_mbfj.jar -DgeneratePom=true -DgroupId=org.signalml -DartifactId=artifact-mbfj -Dversion=1.0.0 -Dclassifier=win32 -Dpackaging=jar
mvn install:install-file -Dfile=win32/stager_mbfj.jar -DgeneratePom=true -DgroupId=org.signalml -DartifactId=stager-mbfj -Dversion=1.0.0 -Dclassifier=win32 -Dpackaging=jar
<?xml version="1.0" encoding="UTF-8"?>
<assembly>
<id>full</id>
<formats>
<!--
<format>zip</format> <format>tar.gz</format> <format>tar.bz2</format>
-->
<format>dir</format>
</formats>
<dependencySets>
<dependencySet>
<outputDirectory>/lib</outputDirectory>
<outputFileNameMapping>
${artifact.artifactId}.${artifact.extension}
</outputFileNameMapping>
<excludes>
<exclude>org.signalml:artifact-mbfj
</exclude>
<exclude>org.signalml:stager-mbfj</exclude>
</excludes>
</dependencySet>
</dependencySets>
<fileSets>
<fileSet>
<directory>util</directory>
<outputDirectory>.</outputDirectory>
<includes>
<include>*.bat</include>
<include>*.sh</include>
</includes>
</fileSet>
<fileSet>
<directory>lib</directory>
<outputDirectory>lib</outputDirectory>
<includes>
<include>**/*.jar</include>
</includes>
</fileSet>
</fileSets>
</assembly>
......@@ -23,6 +23,8 @@
*/
public abstract class AbstractPresetManager extends AbstractXMLConfiguration implements PresetManager, Serializable {
private static final long serialVersionUID = 1L;
protected static final Logger logger = Logger.getLogger(AbstractPresetManager.class);
protected ArrayList<Preset> presets = new ArrayList<Preset>();
......
......@@ -34,6 +34,8 @@
@XStreamAlias("artifactdata")
public class ArtifactApplicationData extends ArtifactData {
private static final long serialVersionUID = 1L;
@XStreamOmitField
private SignalDocument signalDocument;
......
......@@ -4,8 +4,6 @@
package org.signalml.app.method.ep;
import javax.swing.JOptionPane;
import org.signalml.app.method.ApplicationMethodManager;
import org.signalml.app.method.InitializingMethodResultConsumer;
import org.signalml.exception.SignalMLException;
......
......@@ -30,6 +30,8 @@
*/
public class StagerApplicationData extends StagerData {
private static final long serialVersionUID = 1L;
private SignalDocument signalDocument;
private float pageSize;
......
......@@ -7,7 +7,6 @@
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import javax.crypto.spec.IvParameterSpec;
import javax.swing.JCheckBox;
import javax.swing.JLabel;
import javax.swing.JPanel;
......
......@@ -37,7 +37,6 @@
import org.signalml.app.action.ExportSignalAction;
import org.signalml.app.action.ExportTagAction;
import org.signalml.app.action.HelpContentsAction;
import org.signalml.app.action.ImportTagAction;
import org.signalml.app.action.IterateMethodAction;
import org.signalml.app.action.NewTagAction;
import org.signalml.app.action.OpenDocumentAction;
......
/* BookPlot.java created 2008-02-23
*
*/
package org.signalml.app.view.book;
import java.awt.BasicStroke;
......@@ -1035,7 +1031,7 @@ private void paintReconstruction(Graphics2D gOrig, double[] samples, Rectangle a
}
int relX = areaToRepaint.x - area.x;
int relEndX = relX + areaToRepaint.width - 1;
// int relEndX = relX + areaToRepaint.width - 1;
int level = area.y + area.height / 2;
g.setColor( Color.BLUE );
......
......@@ -28,6 +28,8 @@
*/
public abstract class AbstractFilterDialog extends AbstractDialog {
private static final long serialVersionUID = 1L;
private JTextField nameTextField;
private JPanel namePanel;
......
......@@ -26,6 +26,8 @@
*/
public abstract class AbstractMessageDialog extends AbstractDialog {
private static final long serialVersionUID = 1L;
private JCheckBox dontShowAgainCheckBox;
private JPanel messagePanel;
private JLabel messageLabel;
......
......@@ -23,6 +23,8 @@
*/
public abstract class AbstractSignalSpaceAwarePresetDialog extends AbstractPresetDialog {
private static final long serialVersionUID = 1L;
private JCheckBox includeSpaceCheckBox;
public AbstractSignalSpaceAwarePresetDialog(MessageSourceAccessor messageSource, PresetManager presetManager, Window w, boolean isModal) {
......
......@@ -11,6 +11,8 @@
public class AutoSpinnerWithSliderPanel extends AutoSpinnerPanel {
private static final long serialVersionUID = 1L;
private JSlider slider;
private boolean lock = false;
......
......@@ -2,6 +2,8 @@
public class CodecException extends Exception {
private static final long serialVersionUID = 1L;
/**
*
*/
......
......@@ -8,9 +8,6 @@
import java.util.HashMap;
import org.apache.log4j.Logger;
import org.signalml.codec.generator.xml.XMLCodecException;
import org.signalml.codec.precompiled.EASYS;
import org.signalml.codec.precompiled.RAW;
/** SignalMLCodecReader
*
......
......@@ -19,6 +19,8 @@
@XStreamAlias("bookfilter")
public abstract class AbstractAtomFilter implements AtomFilter, Serializable, MessageSourceResolvable {
private static final long serialVersionUID = 1L;
private String name;
private boolean enabled;
......@@ -71,7 +73,6 @@ public void setBlocking(boolean blocking) {
this.blocking = blocking;
}
@SuppressWarnings("unused")
public void initialize() throws SignalMLException {
// do nothing, subclasses may override
}
......
......@@ -13,6 +13,8 @@
*/
public abstract class AverageReferenceMontageGenerator implements MontageGenerator {
private static final long serialVersionUID = 1L;
protected transient Channel[] refChannels;
protected AverageReferenceMontageGenerator( Channel[] refChannels ) {
......
......@@ -15,6 +15,8 @@
*/
public abstract class BipolarReferenceMontageGenerator implements MontageGenerator {
private static final long serialVersionUID = 1L;
protected transient Channel[][] definition;
protected BipolarReferenceMontageGenerator( Channel[][] definition ) {
......
......@@ -13,6 +13,8 @@
*/
public abstract class SingleReferenceMontageGenerator implements MontageGenerator {
private static final long serialVersionUID = 1L;
protected transient Channel refChannel;
protected SingleReferenceMontageGenerator( Channel refChannel ) {
......
......@@ -15,6 +15,8 @@
*/
public abstract class SampleFilterDefinition implements MessageSourceResolvable, Serializable {
private static final long serialVersionUID = 1L;
protected String description;
public String getDescription() {
......
......@@ -14,6 +14,8 @@
*/
public abstract class TimeDomainSampleFilter extends SampleFilterDefinition {
private static final long serialVersionUID = 1L;
private final static Object[] ARGUMENTS = new Object[0];
// these must be built by the constructor
......
......@@ -77,7 +77,6 @@ public final void initialize() throws SignalMLException {
}
}
@SuppressWarnings("unused")
@Override
public final void dispose() throws SignalMLException {
if( solver != null ) {
......@@ -263,7 +262,7 @@ public boolean isRequestingAbort() {
String optimizationType = "";
solver.taguj_wrapper(eegd, wylKanTab, wektorProc, wekAnal, ".tag", projectPath, pacjent, referenceTag, optimizationType);
solver.taguj_wrapper(1, eegd, wylKanTab, wektorProc, wekAnal, ".tag", projectPath, pacjent, referenceTag, optimizationType);
} catch (MWException e) {
throw new ComputationException("Taguj failed",e);
}
......
......@@ -60,7 +60,6 @@
private XStream streamer;
@SuppressWarnings("unused")
public MP5Method() throws SignalMLException {
super();
}
......
......@@ -15,6 +15,8 @@
*/
public class StagerData extends AbstractData {
private static final long serialVersionUID = 1L;
private String projectPath;
private String patientName;
private String signalPath;
......
-----
Documentation
-----
Micha³ Dobaczewski
-----
2009-02-22
-----
Documentation
Unfortunately not much documentation is available at this moment.
{{{apidocs/index.html}API docs}} are available, but actual documentation is rather scarse.
\ No newline at end of file
The initial development of Svarog was..... blah blah.
-----
Home
-----
Micha³ Dobaczewski
-----
2009-02-22
-----
Welcome to Svarog
Thanks for visiting Svarog's site. We hope you will find the software
usefull and the information provided sufficient. If you have any questions
do not hesitate to ask someone from the team.
What is Svarog
Blah blah blah.
Please keep in mind that Svarog is still under development
and not a finished product (as indicated by the 0.x version number ;) ).
Feedback is very much appreciated.
What is avaliable
* What is Svarog?
* a signal viewer with an abbility to "annotate" (mark) parts of the signal
Svarog is a <multivariate time series> viewer, annotator, analyzer and recorder.
Unless you want to impress your friends with funny incomprehensible names,
you usually call it a <(multichannel) signal> viewer. The
simplest example of a signal is a
sound signal, for example a <wav> file, and there are quite a few applications
allowing you to view sound files. Svarog aims to handle far more complex
signals which are common in neuroscience. These include EEG and MEG signals which
can contain dozens of channels and be up to many hours in length. See the
{{{screenshots.html}screenshot}} section for a better idea.
* dasdas
* dadsads
Svarog stands for <<S>>ignal <<V>>iever, <<A>>nalyzer and <<R>>ecorder
<<o>>n <<G>>PL. This is also the name of a god (or deity) of the Sun, fire (and
of the smithy) in the religion of the ancient Slavic peoples.
Svarog used to be a prominent deity in central and eastern Europe prior to
christianization in the VIII-X'th century.
Svarog is still under development and not a finished product
(as indicated by the 0.x version number). Feedback is very much appreciated.
Some areas of what Svarog intends to be are still left untouched, for example the
whole aspect of recording signals. In short: if you want to participate, there's
a lot of things that you could do.
-----
Screenshots
-----
Micha Dobaczewski
-----
2009-02-22
-----
Screenshots
Below you will find a few screenshots from the current version of Svarog.
* The main window
[images/app_screen_full.png] The main window
-----
Wiki
-----
Micha Dobaczewski
-----
2009-02-22
-----
Svarog wiki
Svarog wiki is located at the same place where the SignalML wiki is located.
For now, Svarog wiki is located at the same place where the SignalML wiki is located.
{{{http://signalml.org/wiki/}Signalml wiki}}
{{{http://signalml.org/wiki/Svarog}Svarog's article}}
\ No newline at end of file
<?xml version="1.0" encoding="UTF-8"?>
<project name="Svarog">
<bannerLeft>
<name>Svarog</name>
<src>images/svarog.png</src>
<href>http://signalml.org/svarog/</href>
</bannerLeft>
<bannerRight>
<name>Warsaw University</name>
<src>images/orzelekUWsm.gif</src>
<href>http://www.fuw.edu.pl/</href>
</bannerRight>
<skin>
<groupId>org.apache.maven.skins</groupId>
<artifactId>maven-stylus-skin</artifactId>
</skin>
<body>
<breadcrumbs>
<item href="http://signalml.org/" name="SignalML" />
<item name="${project.name}" />
</breadcrumbs>
<links>
<item name="ZFB" href="http://brain.fuw.edu.pl/"/>
</links>
<menu name="${project.name}" collapse="false">
<item name="Overview" href="index.html" />
<item name="FAQ" href="faq.html" />
<item name="Wiki" href="wiki.html" />
</menu>
<menu name="Information" collapse="false">
<item name="History" href="history.html" />
</menu>
<menu ref="reports" collapse="false" />
</body>
<publishDate position="right"/>
<version position="right" />
</project>
<?xml version="1.0" encoding="UTF-8"?>
<project name="Svarog">
<bannerLeft>
<name>Svarog</name>
<src>images/svarog.png</src>
<href>http://signalml.org/svarog/</href>
</bannerLeft>
<bannerRight>
<name>Warsaw University</name>
<src>images/orzelekUWsm.gif</src>
<href>http://www.fuw.edu.pl/</href>
</bannerRight>
<skin>
<groupId>org.apache.maven.skins</groupId>
<artifactId>maven-stylus-skin</artifactId>
</skin>
<body>
<breadcrumbs>
<item href="http://signalml.org/" name="SignalML" />
<item name="${project.name}" />
</breadcrumbs>
<links>
<item name="ZFB" href="http://brain.fuw.edu.pl/"/>
</links>
<menu name="${project.name}" collapse="false">
<item name="Overview" href="index.html" />
<item name="Screenshots" href="screenshots.html" />
<item name="FAQ" href="faq.html" />
<item name="Wiki" href="wiki.html" />
</menu>
<menu name="Information" collapse="false">
<item name="Documentation" href="documentation.html" />
</menu>
<menu ref="reports" collapse="false" />
</body>
<publishDate position="right"/>
<version position="right" />
</project>
......@@ -65,14 +65,14 @@ public void testImportLegacyTags() throws Exception {
Tag tag = sts.getPageTagAt(0);
assertEquals("w", tag.getStyle().getName());
assertEquals(0F, tag.getPosition());
assertEquals(20F, tag.getLength());
assertEquals(0F, tag.getPosition(), 0);
assertEquals(20F, tag.getLength(), 0);
assertEquals(Tag.CHANNEL_NULL, tag.getChannel());
tag = sts.getPageTagAt(724);
assertEquals("r", tag.getStyle().getName());
assertEquals(724*20F, tag.getPosition());
assertEquals(20F, tag.getLength());
assertEquals(724*20F, tag.getPosition(), 0);
assertEquals(20F, tag.getLength(), 0);
assertEquals(Tag.CHANNEL_NULL, tag.getChannel());
style = sts.getStyle("r");
......
......@@ -92,7 +92,7 @@ private void testDefaults() throws Exception {
assertEquals("Stage 1", style.getDescription());
assertEquals(new Color(0x00, 0xCC, 0xCC), style.getOutlineColor());
assertEquals(new Color(0x00, 0xCC, 0xCC), style.getFillColor());
assertEquals(1.0F, style.getOutlineWidth());
assertEquals(1.0F, style.getOutlineWidth(), 0);
assertNull(style.getOutlineDash());
assertEquals(KeyStroke.getKeyStroke("pressed 1"), style.getKeyStroke());
}
......@@ -159,15 +159,15 @@ public void testAddTagsAndSave() throws Exception {
Tag tag = tags.first();
assertEquals("1", tag.getStyle().getName());
assertEquals(120F, tag.getPosition());
assertEquals(20F, tag.getLength());
assertEquals(120F, tag.getPosition(), 0);
assertEquals(20F, tag.getLength(), 0);
assertEquals(Tag.CHANNEL_NULL, tag.getChannel());
assertNull(tag.getAnnotation());
tag = tags.last();
assertEquals("Y", tag.getStyle().getName());
assertEquals(300F, tag.getPosition());
assertEquals(400F, tag.getLength());
assertEquals(300F, tag.getPosition(), 0);
assertEquals(400F, tag.getLength(), 0);
assertEquals(5, tag.getChannel());
assertEquals("test", tag.getAnnotation());
......
@SET PATH=%PATH%;lib
@start javaw -Xmx256M -jar signalml.jar
SET PATH=%PATH%;lib
java -Xmx256M -jar signalml.jar
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