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sjcrosssjcross
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Merge pull request #219 from mianalysis/develop
Moving to v1.7.7
2 parents 25547a4 + a7e9f18 commit 774e3be

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28 files changed

+75
-5922
lines changed

28 files changed

+75
-5922
lines changed

‎mia-algorithms/pom.xml

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@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
9-
<version>1.7.6</version>
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<version>1.7.7</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-algorithms</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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<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

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@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-bonej</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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<packaging>jar</packaging>
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<name>mia-bonej</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-coordinates/pom.xml

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@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-coordinates</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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<packaging>jar</packaging>
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<name>mia-coordinates</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-core/pom.xml

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@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-core</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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<packaging>jar</packaging>
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<name>mia-core</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-deepimagej/pom.xml

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@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-deepimagej</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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<packaging>jar</packaging>
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<name>mia-deepimagej</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-macros/pom.xml

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@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-macros</artifactId>
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<version>1.7.6</version>
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<version>1.7.7</version>
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<packaging>jar</packaging>
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<name>mia-macros</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-modules/pom.xml

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Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
9-
<version>1.7.6</version>
9+
<version>1.7.7</version>
1010
</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-modules</artifactId>
14-
<version>1.7.6</version>
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<version>1.7.7</version>
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<packaging>jar</packaging>
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<name>mia-modules</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-modules/src/main/java/io/github/mianalysis/mia/module/script/RunScript.java

Lines changed: 6 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -214,6 +214,11 @@ public RunScript(Modules modules) {
214214
super("Run script", modules);
215215
}
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217+
// This is just so other modules can extend this class
218+
protected RunScript(String name, Modules modules) {
219+
super(name, modules);
220+
}
221+
217222
@Override
218223
public Category getCategory() {
219224
return Categories.SCRIPT;
@@ -256,7 +261,7 @@ public static String getLanguageExtension(String language) {
256261
* Some imports may have moved since the script was written. This method
257262
* replaces some commonly occurring ones.
258263
*/
259-
String redirectImports(String scriptText, String extension) {
264+
public static String redirectImports(String scriptText, String extension) {
260265
HashMap<String, String> movedClasses = new HashMap<>();
261266

262267
movedClasses.put("io.github.sjcross.sjcommon.exceptions.PointOutOfRangeException",

‎mia-plugin/pom.xml

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Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
9-
<version>1.7.6</version>
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<version>1.7.7</version>
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</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-plugin</artifactId>
14-
<version>1.7.6</version>
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<version>1.7.7</version>
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<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/process/selectors/ObjectSelector.java

Lines changed: 9 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -456,6 +456,7 @@ public void valueChanged(ListSelectionEvent e) {
456456
@Override
457457
public void actionPerformed(ActionEvent e) {
458458
Prefs.set("MIA.ObjectSelector.AutoAccept", (String) autoAcceptMode.getSelectedItem());
459+
Prefs.savePreferences();
459460
}
460461
});
461462
c.gridx++;
@@ -469,7 +470,8 @@ public void actionPerformed(ActionEvent e) {
469470
autoClassMode.addActionListener(new ActionListener() {
470471
@Override
471472
public void actionPerformed(ActionEvent e) {
472-
Prefs.set("MIA.ObjectSelector.AutoClass", (String) autoAcceptMode.getSelectedItem());
473+
Prefs.set("MIA.ObjectSelector.AutoClass", (String) autoClassMode.getSelectedItem());
474+
Prefs.savePreferences();
473475
}
474476
});
475477
c.gridx++;
@@ -542,6 +544,7 @@ protected JPanel createOverlayPanel() {
542544
@Override
543545
public void actionPerformed(ActionEvent e) {
544546
Prefs.set("MIA.ObjectSelector.OverlayMode", (String) overlayMode.getSelectedItem());
547+
Prefs.savePreferences();
545548

546549
boolean showOverlay = !overlayMode.getSelectedItem().equals(OverlayModes.NONE);
547550

@@ -588,6 +591,8 @@ public void actionPerformed(ActionEvent e) {
588591
Prefs.set("MIA.ObjectSelector.ColourModeNoClass", (String) colourMode.getSelectedItem());
589592
else
590593
Prefs.set("MIA.ObjectSelector.ColourModeWithClass", (String) colourMode.getSelectedItem());
594+
595+
Prefs.savePreferences();
591596

592597
updateOverlay();
593598
}
@@ -628,6 +633,8 @@ public void focusLost(FocusEvent e) {
628633
@Override
629634
public void actionPerformed(ActionEvent e) {
630635
Prefs.set("MIA.ObjectSelector.ShowLabels", labelCheck.isSelected());
636+
Prefs.savePreferences();
637+
631638
Arrays.stream(fontPanel.getComponents()).forEach(v -> v.setEnabled(labelCheck.isSelected()));
632639

633640
updateOverlay();
@@ -994,6 +1001,7 @@ public void processObjectsAndFinish() {
9941001
y0 = (int) Math.round(location.getY());
9951002
Prefs.set("MIA.ObjectSelector.x0", x0);
9961003
Prefs.set("MIA.ObjectSelector.y0", y0);
1004+
Prefs.savePreferences();
9971005

9981006
// If the frame isn't already closed, hide it while we finish processing the
9991007
// objects

‎mia-ptbiop/pom.xml

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Original file line numberDiff line numberDiff line change
@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>pom-mia</artifactId>
9-
<version>1.7.6</version>
9+
<version>1.7.7</version>
1010
</parent>
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<groupId>io.github.mianalysis</groupId>
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<artifactId>mia-ptbiop</artifactId>
14-
<version>1.7.6</version>
14+
<version>1.7.7</version>
1515
<packaging>jar</packaging>
1616
<name>mia-ptbiop</name>
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<url>https://github.com/mianalysis/mia</url>

‎mia-ptbiop/src/main/java/io/github/mianalysis/mia/module/objects/detect/CellposeDetection.java

Lines changed: 37 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -287,17 +287,17 @@ public Status process(Workspace workspace) {
287287
cellpose.setUseClustering(useClustering);
288288
cellpose.setAdditionalFlags(additionalFlags);
289289

290-
Objs outputObjects = null;
291-
int count = 0;
292-
if (dimensionMode.equals(DimensionModes.TWOD) && inputImage.getImagePlus().getNSlices() > 1) {
293-
SpatCal spatCal = SpatCal.getFromImage(inputImage.getImagePlus());
294-
int nFrames = inputImage.getImagePlus().getNFrames();
295-
double frameInterval = inputImage.getImagePlus().getCalibration().frameInterval;
296-
outputObjects = new Objs(outputObjectsName, spatCal, nFrames, frameInterval,
297-
TemporalUnit.getOMEUnit());
298-
299-
for (int z = 0; z < inputImage.getImagePlus().getNSlices(); z++) {
300-
for (int t = 0; t < inputImage.getImagePlus().getNFrames(); t++) {
290+
SpatCal spatCal = SpatCal.getFromImage(inputImage.getImagePlus());
291+
int nFrames = inputImage.getImagePlus().getNFrames();
292+
int nSlices = inputImage.getImagePlus().getNSlices();
293+
double frameInterval = inputImage.getImagePlus().getCalibration().frameInterval;
294+
Objs outputObjects = new Objs(outputObjectsName, spatCal, nFrames, frameInterval, TemporalUnit.getOMEUnit());
295+
296+
if (dimensionMode.equals(DimensionModes.TWOD)) {
297+
int count = 0;
298+
int total = nFrames * nSlices;
299+
for (int z = 0; z < nSlices; z++) {
300+
for (int t = 0; t < nFrames; t++) {
301301
Image currImage = ExtractSubstack.extractSubstack(inputImage, "Timepoint", "1-end",
302302
String.valueOf(z + 1) + "-" + String.valueOf(z + 1),
303303
String.valueOf(t + 1) + "-" + String.valueOf(t + 1));
@@ -306,7 +306,8 @@ public Status process(Workspace workspace) {
306306
cellpose.run();
307307

308308
Image cellsImage = ImageFactory.createImage("Objects", cellpose.getLabels());
309-
Objs currOutputObjects = cellsImage.convertImageToObjects(VolumeType.QUADTREE, outputObjectsName);
309+
Objs currOutputObjects = cellsImage.convertImageToObjects(VolumeType.QUADTREE,
310+
outputObjectsName);
310311

311312
for (Obj currOutputObject : currOutputObjects.values()) {
312313
Obj outputObject = outputObjects.createAndAddNewObject(VolumeType.QUADTREE);
@@ -315,15 +316,31 @@ public Status process(Workspace workspace) {
315316
outputObject.translateCoords(0, 0, z);
316317
}
317318

318-
writeProgressStatus(++count, inputImage.getImagePlus().getStackSize(), "slices");
319+
writeProgressStatus(++count, total, "slices");
319320

320321
}
321322
}
322323
} else {
323-
cellpose.setImagePlus(inputImage.getImagePlus());
324-
cellpose.run();
325-
Image cellsImage = ImageFactory.createImage("Objects", cellpose.getLabels());
326-
outputObjects = cellsImage.convertImageToObjects(VolumeType.QUADTREE, outputObjectsName);
324+
for (int t = 0; t < inputImage.getImagePlus().getNFrames(); t++) {
325+
Image currImage = ExtractSubstack.extractSubstack(inputImage, "Timepoint", "1-end", "1-end",
326+
String.valueOf(t + 1) + "-" + String.valueOf(t + 1));
327+
328+
cellpose.setImagePlus(currImage.getImagePlus());
329+
cellpose.run();
330+
331+
Image cellsImage = ImageFactory.createImage("Objects", cellpose.getLabels());
332+
Objs currOutputObjects = cellsImage.convertImageToObjects(VolumeType.QUADTREE,
333+
outputObjectsName);
334+
335+
for (Obj currOutputObject : currOutputObjects.values()) {
336+
Obj outputObject = outputObjects.createAndAddNewObject(VolumeType.QUADTREE);
337+
outputObject.setT(t);
338+
outputObject.setCoordinateSet(currOutputObject.getCoordinateSet());
339+
}
340+
341+
writeProgressStatus((t + 1), nFrames, "frames");
342+
343+
}
327344
}
328345

329346
workspace.addObjects(outputObjects);
@@ -528,7 +545,7 @@ public Parameters updateAndGetParameters() {
528545
Prefs.set(keyPrefix + "useFastMode", parameters.getValue(USE_FASTMODE, workspace).toString());
529546

530547
Prefs.savePreferences();
531-
548+
532549
return returnedParameters;
533550

534551
}
@@ -544,8 +561,8 @@ public ObjMeasurementRefs updateAndGetObjectMeasurementRefs() {
544561
}
545562

546563
@Override
547-
public ObjMetadataRefs updateAndGetObjectMetadataRefs() {
548-
return null;
564+
public ObjMetadataRefs updateAndGetObjectMetadataRefs() {
565+
return null;
549566
}
550567

551568
@Override

‎mia-samj/pom.xml

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66
<parent>
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<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.6</version>
9+
<version>1.7.7</version>
1010
</parent>
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<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-samj</artifactId>
14-
<version>1.7.6</version>
14+
<version>1.7.7</version>
1515
<packaging>jar</packaging>
1616
<name>mia-samj</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎mia-stardist/pom.xml

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@@ -6,12 +6,12 @@
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<parent>
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<groupId>io.github.mianalysis</groupId>
88
<artifactId>pom-mia</artifactId>
9-
<version>1.7.6</version>
9+
<version>1.7.7</version>
1010
</parent>
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1212
<groupId>io.github.mianalysis</groupId>
1313
<artifactId>mia-stardist</artifactId>
14-
<version>1.7.6</version>
14+
<version>1.7.7</version>
1515
<packaging>jar</packaging>
1616
<name>mia-stardist</name>
1717
<url>https://github.com/mianalysis/mia</url>

‎pom.xml

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -12,7 +12,7 @@
1212

1313
<groupId>io.github.mianalysis</groupId>
1414
<artifactId>pom-mia</artifactId>
15-
<version>1.7.6</version>
15+
<version>1.7.7</version>
1616
<packaging>pom</packaging>
1717
<name>pom-mia</name>
1818
<url>https://github.com/mianalysis/mia</url>

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