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akramhar
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63 files changed

Lines changed: 514 additions & 511 deletions

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‎src/main/java/edu/umassmed/omega/commons/OmegaLogFileManager.java‎

Lines changed: 7 additions & 7 deletions
Original file line numberDiff line numberDiff line change
@@ -16,7 +16,7 @@
1616
import java.util.Map;
1717

1818
import edu.umassmed.omega.commons.constants.OmegaGenericConstants;
19-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
19+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
2020
import edu.umassmed.omega.commons.utilities.OmegaFileUtilities;
2121

2222
public class OmegaLogFileManager implements UncaughtExceptionHandler {
@@ -33,7 +33,7 @@ public class OmegaLogFileManager implements UncaughtExceptionHandler {
3333
private final File logsDir;
3434

3535
private final File awtLogFile, generalUnhandledException, generalLogFile;
36-
private final Map<OmegaPlugin, File> pluginLogFileMap;
36+
private final Map<OmegaPluginArchetype, File> pluginLogFileMap;
3737

3838
static {
3939
OmegaLogFileManager.instance = new OmegaLogFileManager();
@@ -86,12 +86,12 @@ private OmegaLogFileManager(final OmegaGenericApplication app,
8686
Thread.currentThread().setUncaughtExceptionHandler(this);
8787
}
8888

89-
public static void markPluginsNewRun(final List<OmegaPlugin> plugins) {
89+
public static void markPluginsNewRun(final List<OmegaPluginArchetype> plugins) {
9090
final List<File> files = new ArrayList<>();
9191
final List<String> messages = new ArrayList<>();
9292
final String msg = "Application started!";
9393
messages.add(msg);
94-
for (final OmegaPlugin plugin : plugins) {
94+
for (final OmegaPluginArchetype plugin : plugins) {
9595
final File f = OmegaLogFileManager.instance
9696
.createNewLogFile(plugin);
9797
OmegaLogFileManager.instance.pluginLogFileMap.put(plugin, f);
@@ -214,7 +214,7 @@ public static void handleUncaughtException(final Throwable t,
214214
}
215215
}
216216

217-
public static void handlePluginException(final OmegaPlugin plugin,
217+
public static void handlePluginException(final OmegaPluginArchetype plugin,
218218
final Throwable t, final boolean isShowStopper) {
219219
final List<String> messages = new ArrayList<>();
220220
final List<Throwable> throwables = new ArrayList<>();
@@ -276,13 +276,13 @@ private void terminateApplication() {
276276
}
277277
}
278278

279-
private File createNewLogFile(final OmegaPlugin plugin) {
279+
private File createNewLogFile(final OmegaPluginArchetype plugin) {
280280
final String logFileName = OmegaLogFileManager.PLUGIN_LOG_NAME
281281
+ plugin.getName().replace(" ", "") + ".log";
282282
return new File(this.logsDir.getPath() + File.separator + logFileName);
283283
}
284284

285-
public static void appendToPluginLog(final OmegaPlugin plugin,
285+
public static void appendToPluginLog(final OmegaPluginArchetype plugin,
286286
final String msg) {
287287
final List<String> messages = new ArrayList<>();
288288
messages.add(msg);

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEvent.java‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -27,21 +27,21 @@
2727
*******************************************************************************/
2828
package edu.umassmed.omega.commons.eventSystem.events;
2929

30-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
30+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3131

3232
public class OmegaPluginEvent {
3333

34-
private final OmegaPlugin source;
34+
private final OmegaPluginArchetype source;
3535

3636
public OmegaPluginEvent() {
3737
this(null);
3838
}
3939

40-
public OmegaPluginEvent(final OmegaPlugin source) {
40+
public OmegaPluginEvent(final OmegaPluginArchetype source) {
4141
this.source = source;
4242
}
4343

44-
public OmegaPlugin getSource() {
44+
public OmegaPluginArchetype getSource() {
4545
return this.source;
4646
}
4747
}

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEventAlgorithm.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@
3030

3131
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaParameter;
3232
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
33-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
33+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3434

3535
public class OmegaPluginEventAlgorithm extends OmegaPluginEvent {
3636

@@ -43,7 +43,7 @@ public OmegaPluginEventAlgorithm(final List<OmegaElement> selections,
4343
this(null, selections, element, params);
4444
}
4545

46-
public OmegaPluginEventAlgorithm(final OmegaPlugin source,
46+
public OmegaPluginEventAlgorithm(final OmegaPluginArchetype source,
4747
final List<OmegaElement> selections, final OmegaElement element,
4848
final List<OmegaParameter> params) {
4949
super(source);

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEventDataChanged.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -30,7 +30,7 @@
3030
import java.util.List;
3131

3232
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
33-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
33+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3434

3535
public class OmegaPluginEventDataChanged extends OmegaPluginEvent {
3636

@@ -40,13 +40,13 @@ public OmegaPluginEventDataChanged() {
4040
this(null);
4141
}
4242

43-
public OmegaPluginEventDataChanged(final OmegaPlugin source) {
43+
public OmegaPluginEventDataChanged(final OmegaPluginArchetype source) {
4444
super(source);
4545

4646
this.selectedData = null;
4747
}
4848

49-
public OmegaPluginEventDataChanged(final OmegaPlugin source,
49+
public OmegaPluginEventDataChanged(final OmegaPluginArchetype source,
5050
final List<OmegaElement> selectedData) {
5151
super(source);
5252
this.selectedData = selectedData;

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEventGateway.java‎

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -28,7 +28,7 @@
2828
package edu.umassmed.omega.commons.eventSystem.events;
2929

3030
import edu.umassmed.omega.commons.data.coreElements.OmegaExperimenter;
31-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
31+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3232

3333
public class OmegaPluginEventGateway extends OmegaPluginEvent {
3434
public static final int STATUS_CREATED = 1;
@@ -40,11 +40,11 @@ public class OmegaPluginEventGateway extends OmegaPluginEvent {
4040

4141
private final OmegaExperimenter experimenter;
4242

43-
public OmegaPluginEventGateway(final OmegaPlugin source, final int status) {
43+
public OmegaPluginEventGateway(final OmegaPluginArchetype source, final int status) {
4444
this(source, status, null);
4545
}
4646

47-
public OmegaPluginEventGateway(final OmegaPlugin source, final int status,
47+
public OmegaPluginEventGateway(final OmegaPluginArchetype source, final int status,
4848
final OmegaExperimenter experimenter) {
4949
super(source);
5050
this.status = status;

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEventPreviewParticleDetection.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@
3232
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
3333
import edu.umassmed.omega.commons.data.coreElements.OmegaPlane;
3434
import edu.umassmed.omega.commons.data.trajectoryElements.OmegaROI;
35-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
35+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3636

3737
public class OmegaPluginEventPreviewParticleDetection extends
3838
OmegaPluginEventAlgorithm {
@@ -47,7 +47,7 @@ public OmegaPluginEventPreviewParticleDetection(
4747
this(null, selections, element, params, frame, resultingParticles);
4848
}
4949

50-
public OmegaPluginEventPreviewParticleDetection(final OmegaPlugin source,
50+
public OmegaPluginEventPreviewParticleDetection(final OmegaPluginArchetype source,
5151
final List<OmegaElement> selections, final OmegaElement element,
5252
final List<OmegaParameter> params, final OmegaPlane frame,
5353
final List<OmegaROI> resultingParticles) {

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEventResultsParticleDetection.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@
3333
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
3434
import edu.umassmed.omega.commons.data.coreElements.OmegaPlane;
3535
import edu.umassmed.omega.commons.data.trajectoryElements.OmegaROI;
36-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
36+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3737

3838
public class OmegaPluginEventResultsParticleDetection extends
3939
OmegaPluginEventAlgorithm {
@@ -50,7 +50,7 @@ public OmegaPluginEventResultsParticleDetection(
5050
resultingParticlesValues);
5151
}
5252

53-
public OmegaPluginEventResultsParticleDetection(final OmegaPlugin source,
53+
public OmegaPluginEventResultsParticleDetection(final OmegaPluginArchetype source,
5454
final List<OmegaElement> selections, final OmegaElement element,
5555
final List<OmegaParameter> params,
5656
final Map<OmegaPlane, List<OmegaROI>> resultingParticles,

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEventResultsParticleLinking.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,7 @@
3131
import edu.umassmed.omega.commons.data.analysisRunElements.OmegaParameter;
3232
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
3333
import edu.umassmed.omega.commons.data.trajectoryElements.OmegaTrajectory;
34-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
34+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3535

3636
public class OmegaPluginEventResultsParticleLinking extends
3737
OmegaPluginEventAlgorithm {
@@ -45,7 +45,7 @@ public OmegaPluginEventResultsParticleLinking(
4545
this(null, selections, element, params, resultingTrajectories);
4646
}
4747

48-
public OmegaPluginEventResultsParticleLinking(final OmegaPlugin source,
48+
public OmegaPluginEventResultsParticleLinking(final OmegaPluginArchetype source,
4949
final List<OmegaElement> selections, final OmegaElement element,
5050
final List<OmegaParameter> params,
5151
final List<OmegaTrajectory> resultingTrajectories) {

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEventResultsParticleTracking.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -34,7 +34,7 @@
3434
import edu.umassmed.omega.commons.data.coreElements.OmegaPlane;
3535
import edu.umassmed.omega.commons.data.trajectoryElements.OmegaROI;
3636
import edu.umassmed.omega.commons.data.trajectoryElements.OmegaTrajectory;
37-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
37+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3838

3939
public class OmegaPluginEventResultsParticleTracking extends
4040
OmegaPluginEventAlgorithm {
@@ -53,7 +53,7 @@ public OmegaPluginEventResultsParticleTracking(
5353
resultingTrajectories, resultingParticlesValues);
5454
}
5555

56-
public OmegaPluginEventResultsParticleTracking(final OmegaPlugin source,
56+
public OmegaPluginEventResultsParticleTracking(final OmegaPluginArchetype source,
5757
final List<OmegaElement> selections, final OmegaElement element,
5858
final List<OmegaParameter> params,
5959
final Map<OmegaPlane, List<OmegaROI>> resultingParticles,

‎src/main/java/edu/umassmed/omega/commons/eventSystem/events/OmegaPluginEventResultsSNR.java‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -33,7 +33,7 @@
3333
import edu.umassmed.omega.commons.data.coreElements.OmegaElement;
3434
import edu.umassmed.omega.commons.data.coreElements.OmegaPlane;
3535
import edu.umassmed.omega.commons.data.trajectoryElements.OmegaROI;
36-
import edu.umassmed.omega.commons.plugins.OmegaPlugin;
36+
import edu.umassmed.omega.commons.pluginArchetypes.OmegaPluginArchetype;
3737

3838
public class OmegaPluginEventResultsSNR extends OmegaPluginEventAlgorithm {
3939

@@ -114,7 +114,7 @@ public OmegaPluginEventResultsSNR(final List<OmegaElement> selections,
114114
resultingMinErrorIndexSNR, resultingMaxErrorIndexSNR);
115115
}
116116

117-
public OmegaPluginEventResultsSNR(final OmegaPlugin source,
117+
public OmegaPluginEventResultsSNR(final OmegaPluginArchetype source,
118118
final List<OmegaElement> selections, final OmegaElement element,
119119
final List<OmegaParameter> params,
120120
final Map<OmegaPlane, Double> resultingImageAvgCenterSignal,

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