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sjcrosssjcross
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Moving to v1.7.6
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30 files changed

+6004
-47
lines changed

30 files changed

+6004
-47
lines changed

‎mia-algorithms/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.5</version>
9+
<version>1.7.6</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-algorithms</artifactId>
14-
<version>1.7.5</version>
14+
<version>1.7.6</version>
1515
<packaging>jar</packaging>
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<name>mia-algorithms</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-bonej/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.5</version>
9+
<version>1.7.6</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-bonej</artifactId>
14-
<version>1.7.5</version>
14+
<version>1.7.6</version>
1515
<packaging>jar</packaging>
1616
<name>mia-bonej</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-bonej/src/main/java/io/github/mianalysis/mia/module/objects/process/tools/EllipsoidCalculator.java

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,9 +6,7 @@
66
import io.github.mianalysis.mia.MIA;
77
import io.github.mianalysis.mia.object.coordinates.Point;
88
import io.github.mianalysis.mia.object.coordinates.volume.PointOutOfRangeException;
9-
import io.github.mianalysis.mia.object.coordinates.volume.SpatCal;
109
import io.github.mianalysis.mia.object.coordinates.volume.Volume;
11-
import io.github.mianalysis.mia.object.coordinates.volume.VolumeType;
1210
import io.github.mianalysis.mia.process.exceptions.IntegerOverflowException;
1311

1412
public class EllipsoidCalculator {

‎mia-coordinates/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.5</version>
9+
<version>1.7.6</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-coordinates</artifactId>
14-
<version>1.7.5</version>
14+
<version>1.7.6</version>
1515
<packaging>jar</packaging>
1616
<name>mia-coordinates</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-core/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.5</version>
9+
<version>1.7.6</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-core</artifactId>
14-
<version>1.7.5</version>
14+
<version>1.7.6</version>
1515
<packaging>jar</packaging>
1616
<name>mia-core</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-core/src/main/java/io/github/mianalysis/mia/process/ColourFactory.java

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -360,17 +360,17 @@ public static HashMap<Integer, Float> getObjectMetadataHues(Objs objects, String
360360

361361
for (Obj object : objects.values()) {
362362
if (object == null || metadataName == null) {
363-
hues.put(object.getID(), 0f);
363+
hues.put(object.getID(), 0.167f);
364364
continue;
365365
}
366366

367367
ObjMetadata metadataItem = object.getMetadataItem(metadataName);
368368
if (metadataItem == null) {
369-
hues.put(object.getID(), 0f);
369+
hues.put(object.getID(), 0.167f);
370370
continue;
371371
}
372372

373-
hues.put(object.getID(), new Random(metadataItem.getValue().hashCode()*31).nextFloat());
373+
hues.put(object.getID(), new Random(metadataItem.getValue().hashCode()* 2000*31).nextFloat());
374374

375375
}
376376

‎mia-deepimagej/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.5</version>
9+
<version>1.7.6</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-deepimagej</artifactId>
14-
<version>1.7.5</version>
14+
<version>1.7.6</version>
1515
<packaging>jar</packaging>
1616
<name>mia-deepimagej</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-macros/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.5</version>
9+
<version>1.7.6</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-macros</artifactId>
14-
<version>1.7.5</version>
14+
<version>1.7.6</version>
1515
<packaging>jar</packaging>
1616
<name>mia-macros</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-modules/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.5</version>
9+
<version>1.7.6</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-modules</artifactId>
14-
<version>1.7.5</version>
14+
<version>1.7.6</version>
1515
<packaging>jar</packaging>
1616
<name>mia-modules</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/inputoutput/SaveObjectsAsROIs.java

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -16,6 +16,7 @@
1616

1717
import ij.gui.Roi;
1818
import ij.io.RoiEncoder;
19+
import io.github.mianalysis.mia.MIA;
1920
import io.github.mianalysis.mia.module.Categories;
2021
import io.github.mianalysis.mia.module.Category;
2122
import io.github.mianalysis.mia.module.Module;

‎mia-plugin/pom.xml

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
66
<parent>
77
<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.5</version>
9+
<version>1.7.6</version>
1010
</parent>
1111

1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-plugin</artifactId>
14-
<version>1.7.5</version>
14+
<version>1.7.6</version>
1515
<packaging>jar</packaging>
1616
<name>mia-plugin</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-plugin/src/main/java/io/github/mianalysis/mia/module/objects/detect/ManuallyIdentifyObjects.java

Lines changed: 23 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -7,7 +7,6 @@
77
import java.io.FileWriter;
88
import java.io.IOException;
99
import java.lang.reflect.InvocationTargetException;
10-
import java.util.ArrayList;
1110
import java.util.HashSet;
1211
import java.util.List;
1312
import java.util.TreeSet;
@@ -22,7 +21,6 @@
2221

2322
import ij.IJ;
2423
import ij.ImagePlus;
25-
import ij.Prefs;
2624
import ij.gui.Toolbar;
2725
import io.github.mianalysis.mia.MIA;
2826
import io.github.mianalysis.mia.module.Categories;
@@ -97,7 +95,12 @@ public class ManuallyIdentifyObjects extends AbstractSaver {
9795
/**
9896
*
9997
*/
100-
public static final String INPUT_SEPARATOR = "Image/object input";
98+
public static final String IMAGE_INPUT_SEPARATOR = "Image input";
99+
100+
/**
101+
*
102+
*/
103+
public static final String OBJECT_INPUT_SEPARATOR = "Object input";
101104

102105
/**
103106
* Image onto which selections will be drawn. This will be displayed
@@ -115,6 +118,11 @@ public class ManuallyIdentifyObjects extends AbstractSaver {
115118
*/
116119
public static final String INPUT_OBJECTS = "Input objects";
117120

121+
/**
122+
*
123+
*/
124+
public static final String EXISTING_OBJECT_TYPE = "Existing object type";
125+
118126
/**
119127
*
120128
*/
@@ -235,6 +243,8 @@ public class ManuallyIdentifyObjects extends AbstractSaver {
235243
*/
236244
public static final String MESSAGE_ON_IMAGE = "Message on image";
237245

246+
public interface ExistingObjectTypes extends ObjectSelector.ExistingObjectTypes {};
247+
238248
protected HashSet<ManualExtension> extensions = new HashSet<>();
239249
protected ObjectSelector objectSelector = null;
240250

@@ -483,6 +493,7 @@ public Status process(Workspace workspace) {// Local access to this is required
483493
boolean addExistingObjects = parameters.getValue(ADD_EXISTING_OBJECTS, workspace);
484494
String inputObjectsName = parameters.getValue(INPUT_OBJECTS, workspace);
485495
boolean applyExistingClass = parameters.getValue(APPLY_EXISTING_CLASS, workspace);
496+
String existingObjectType = parameters.getValue(EXISTING_OBJECT_TYPE, workspace);
486497
String metadataForClass = parameters.getValue(METADATA_FOR_CLASS, workspace);
487498
String type = parameters.getValue(VOLUME_TYPE, workspace);
488499
boolean outputTracks = parameters.getValue(OUTPUT_TRACKS, workspace);
@@ -545,7 +556,7 @@ public Status process(Workspace workspace) {// Local access to this is required
545556
metadataForClass = null;
546557

547558
if (inputObjects != null) {
548-
objectSelector.addObjects(inputObjects, metadataForClass);
559+
objectSelector.addObjects(inputObjects, existingObjectType, metadataForClass);
549560
objectSelector.updateOverlay();
550561
}
551562
}
@@ -615,10 +626,13 @@ public Status process(Workspace workspace) {// Local access to this is required
615626
protected void initialiseParameters() {
616627
super.initialiseParameters();
617628

618-
parameters.add(new SeparatorP(INPUT_SEPARATOR, this));
629+
parameters.add(new SeparatorP(IMAGE_INPUT_SEPARATOR, this));
619630
parameters.add(new InputImageP(INPUT_IMAGE, this));
631+
632+
parameters.add(new SeparatorP(OBJECT_INPUT_SEPARATOR, this));
620633
parameters.add(new BooleanP(ADD_EXISTING_OBJECTS, this, false));
621634
parameters.add(new CustomInputObjectsP(INPUT_OBJECTS, this));
635+
parameters.add(new ChoiceP(EXISTING_OBJECT_TYPE, this, ExistingObjectTypes.REGIONS, ExistingObjectTypes.ALL));
622636
parameters.add(new BooleanP(ALLOW_MISSING_OBJECTS, this, false));
623637
parameters.add(new BooleanP(APPLY_EXISTING_CLASS, this, false));
624638
parameters.add(new CustomObjectMetadataP(METADATA_FOR_CLASS, this));
@@ -657,11 +671,14 @@ public Parameters updateAndGetParameters() {
657671
Workspace workspace = null;
658672
Parameters returnedParameters = new Parameters();
659673

660-
returnedParameters.add(parameters.get(INPUT_SEPARATOR));
674+
returnedParameters.add(parameters.get(IMAGE_INPUT_SEPARATOR));
661675
returnedParameters.add(parameters.get(INPUT_IMAGE));
676+
677+
returnedParameters.add(parameters.get(OBJECT_INPUT_SEPARATOR));
662678
returnedParameters.add(parameters.get(ADD_EXISTING_OBJECTS));
663679
if ((boolean) parameters.getValue(ADD_EXISTING_OBJECTS, workspace)) {
664680
returnedParameters.add(parameters.get(INPUT_OBJECTS));
681+
returnedParameters.add(parameters.get(EXISTING_OBJECT_TYPE));
665682
returnedParameters.add(parameters.get(ALLOW_MISSING_OBJECTS));
666683
boolean allowMissingObjects = parameters.getValue(ALLOW_MISSING_OBJECTS, workspace);
667684
((CustomInputObjectsP) parameters.get(INPUT_OBJECTS)).setAllowMissingObjects(allowMissingObjects);

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