Updated to MIA v1.3.0

mianalysis · Aug 9, 2023 · 5b581ae · 5b581ae
1 parent 7553d48
commit 5b581ae
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Showing 6 changed files with 15 additions and 41 deletions.
diff --git a/MATLAB/StackMatcher/matchImageInStack.asv b/MATLAB/StackMatcher/matchImageInStack.asv
diff --git a/pom.xml b/pom.xml
@@ -144,9 +144,10 @@
 
         <dependency>
             <groupId>io.github.mianalysis</groupId>
-            <artifactId>MIA</artifactId>
-            <version>1.2.10-SNAPSHOT</version>
+            <artifactId>mia</artifactId>
+            <version>1.3.0</version>
             <scope>${scp}</scope>
+
         </dependency>
 
         <dependency>

diff --git a/src/main/java/io/github/mianalysis/mia/matlab/module/CoreMATLABModule.java b/src/main/java/io/github/mianalysis/mia/matlab/module/CoreMATLABModule.java
@@ -6,8 +6,8 @@
 import ij.ImageStack;
 import io.github.mianalysis.mia.module.Module;
 import io.github.mianalysis.mia.module.Modules;
-import io.github.sjcross.sjcommon.object.Point;
-import io.github.sjcross.sjcommon.object.volume.Volume;
+import io.github.mianalysis.mia.object.coordinates.Point;
+import io.github.mianalysis.mia.object.coordinates.volume.Volume;
 
 public abstract class CoreMATLABModule extends Module {
 

diff --git a/src/main/java/io/github/mianalysis/mia/matlab/module/FitAlphaSurface.java b/src/main/java/io/github/mianalysis/mia/matlab/module/FitAlphaSurface.java
@@ -17,6 +17,10 @@
 import io.github.mianalysis.mia.object.Obj;
 import io.github.mianalysis.mia.object.Objs;
 import io.github.mianalysis.mia.object.Workspace;
+import io.github.mianalysis.mia.object.coordinates.Point;
+import io.github.mianalysis.mia.object.coordinates.volume.PointOutOfRangeException;
+import io.github.mianalysis.mia.object.coordinates.volume.Volume;
+import io.github.mianalysis.mia.object.coordinates.volume.VolumeType;
 import io.github.mianalysis.mia.object.image.Image;
 import io.github.mianalysis.mia.object.parameters.ChoiceP;
 import io.github.mianalysis.mia.object.parameters.InputObjectsP;
@@ -33,11 +37,7 @@
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
 import io.github.mianalysis.mia.object.units.SpatialUnit;
-import io.github.sjcross.sjcommon.mathfunc.Indexer;
-import io.github.sjcross.sjcommon.object.Point;
-import io.github.sjcross.sjcommon.object.volume.PointOutOfRangeException;
-import io.github.sjcross.sjcommon.object.volume.Volume;
-import io.github.sjcross.sjcommon.object.volume.VolumeType;
+import io.github.mianalysis.mia.process.math.Indexer;
 import net.imagej.ImageJ;
 
 @Plugin(type = Module.class, priority = Priority.LOW, visible = true)

diff --git a/src/main/java/io/github/mianalysis/mia/matlab/module/SortStack.java b/src/main/java/io/github/mianalysis/mia/matlab/module/SortStack.java
@@ -32,7 +32,7 @@
 import io.github.mianalysis.mia.object.refs.collections.ParentChildRefs;
 import io.github.mianalysis.mia.object.refs.collections.PartnerRefs;
 import io.github.mianalysis.mia.object.system.Status;
-import io.github.sjcross.sjcommon.mathfunc.Indexer;
+import io.github.mianalysis.mia.process.math.Indexer;
 import net.imagej.ImageJ;
 
 /**

diff --git a/src/main/java/io/github/mianalysis/mia/matlab/module/ZDriftCorrection.java b/src/main/java/io/github/mianalysis/mia/matlab/module/ZDriftCorrection.java
@@ -120,6 +120,8 @@ protected Status process(Workspace workspace) {
             return Status.FAIL;
         }
 
+        int count = 0;
+        int total = inputIpl.getNFrames();
         int[] bestSlices = new int[inputIpl.getNFrames()];
         Image substack = null;
         for (int t = 1; t <= inputIpl.getNFrames(); t++) {
@@ -153,14 +155,15 @@ protected Status process(Workspace workspace) {
             try {
                 Object[] output = stackMatcher.matchImageInStack(1, substackArray, refArray);
                 bestSlices[t - 1] = ((MWNumericArray) output[0]).getInt();
-                System.out.println(bestSlices[t - 1]);
             } catch (MWException e) {
                 MIA.log.writeError(e);
                 return Status.FAIL;
             }
 
             substackArray.dispose();
 
+            writeProgressStatus(++count, total, "frames");
+
         }
 
         // Applying temporal smoothing of best focus slice index