v1.5

jeanollion · Feb 22, 2018 · a27235d · a27235d
1 parent 8078e8e
commit a27235d
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Showing 7 changed files with 14 additions and 15 deletions.
diff --git a/pom.xml b/pom.xml
@@ -7,7 +7,7 @@
 
     <groupId>ljp</groupId>
     <artifactId>functional-bioimage_core</artifactId>
-    <version>1.4.7-SNAPSHOT</version>
+    <version>1.5-SNAPSHOT</version>
 
     <name>functional-bioimage-core</name>
     <description>Bacteria Analyzer</description>

diff --git a/src/main/java/boa/core/generateXP/GenerateMutationDynamicsXP.java b/src/main/java/boa/core/generateXP/GenerateMutationDynamicsXP.java
@@ -60,7 +60,7 @@
 import boa.plugins.plugins.processing_scheme.SegmentAndTrack;
 import boa.plugins.plugins.processing_scheme.SegmentThenTrack;
 import boa.plugins.plugins.segmenters.BacteriaIntensity;
-import boa.plugins.plugins.segmenters.MicroChannelFluo2D;
+import boa.plugins.plugins.segmenters.MicrochannelFluo2D;
 import boa.plugins.plugins.segmenters.MutationSegmenter;
 import boa.plugins.plugins.trackers.MutationTracker;
 import boa.plugins.plugins.trackers.MicrochannelTracker;
@@ -172,7 +172,7 @@ public static Experiment generateXPFluo(String name, String outputDir, boolean s
         Structure mutation = new Structure("Mutation", 0, mutChan); // parent structure 1 segParentStructure 0
         xp.getStructures().insert(mc, bacteria, mutation);
 
-        mc.setProcessingScheme(new SegmentAndTrack(new MicrochannelTracker().setSegmenter(new MicroChannelFluo2D())));
+        mc.setProcessingScheme(new SegmentAndTrack(new MicrochannelTracker().setSegmenter(new MicrochannelFluo2D())));
         //bacteria.setProcessingScheme(new SegmentAndTrack(new BacteriaClosedMicrochannelTrackerLocalCorrections(new BacteriaFluo()).setCostParameters(0.1, 0.5)));
         bacteria.setProcessingScheme(new SegmentThenTrack(new BacteriaIntensity(), new BacteriaClosedMicrochannelTrackerLocalCorrections().setCostParameters(0.1, 0.5)));
         mutation.setProcessingScheme(new SegmentAndTrack(

diff --git a/src/main/java/boa/core/generateXP/GenerateXP.java b/src/main/java/boa/core/generateXP/GenerateXP.java
@@ -66,7 +66,7 @@
 import boa.plugins.plugins.processing_scheme.SegmentOnly;
 import boa.plugins.plugins.processing_scheme.SegmentThenTrack;
 import boa.plugins.plugins.segmenters.BacteriaIntensity;
-import boa.plugins.plugins.segmenters.MicroChannelFluo2D;
+import boa.plugins.plugins.segmenters.MicrochannelFluo2D;
 import boa.plugins.plugins.segmenters.MicrochannelPhase2D;
 import boa.plugins.plugins.segmenters.MutationSegmenter;
 import boa.plugins.plugins.thresholders.IJAutoThresholder;
@@ -479,8 +479,7 @@ public static void setParametersFluo(Experiment xp, boolean processing, boolean
         mutation.setSegmentationParentStructure(1);
         if (processing) {
             mc.setProcessingScheme(new SegmentAndTrack(
-                    new MicrochannelTracker().setSegmenter(
-                            new MicroChannelFluo2D()
+                    new MicrochannelTracker().setSegmenter(new MicrochannelFluo2D()
                     ).setTrackingParameters(40, 0.5).setYShiftQuantile(0.05)
                     ).addTrackPostFilters(new RemoveMicrochannelsTouchingBackgroundOnSides(2),
                             new RemoveMicrochannelsWithOverexpression(99, 5).setTrim(true),

diff --git a/src/main/java/boa/plugins/PluginFactory.java b/src/main/java/boa/plugins/PluginFactory.java
@@ -46,7 +46,7 @@ public class PluginFactory {
 
     private final static TreeMap<String, Class> plugins = new TreeMap<>();
     private final static Logger logger = LoggerFactory.getLogger(PluginFactory.class);
-    private final static Map<String, String> refactoredNamesOldMapNew = new HashMap<String, String>(){{put("BacteriaFluo", "BacteriaIntensity");}};
+    private final static Map<String, String> refactoredNamesOldMapNew = new HashMap<String, String>(){{put("BacteriaFluo", "BacteriaIntensity");put("MicroChannelFluo2D", "MicrochannelFluo2D");put("LAPTracker", "MutationTracker");put("MutationSegmenter", "MutationSegmenter");}};
 
     public static void findPlugins(String packageName) {
         logger.info("looking for plugin in package: {}", packageName);

diff --git a/...lugins/segmenters/MicroChannelFluo2D.java → ...lugins/segmenters/MicrochannelFluo2D.java b/...lugins/segmenters/MicroChannelFluo2D.java → ...lugins/segmenters/MicrochannelFluo2D.java
@@ -55,7 +55,7 @@
  *
  * @author jollion
  */
-public class MicroChannelFluo2D implements MicrochannelSegmenter, TrackParametrizable<MicroChannelFluo2D>, ToolTip {
+public class MicrochannelFluo2D implements MicrochannelSegmenter, TrackParametrizable<MicrochannelFluo2D>, ToolTip {
 
     NumberParameter channelHeight = new BoundedNumberParameter("Microchannel Height", 0, 430, 5, null).setToolTipText("Height of microchannel in pixels");
     NumberParameter channelWidth = new BoundedNumberParameter("Microchannel Width", 0, 40, 5, null);
@@ -69,9 +69,9 @@ public class MicroChannelFluo2D implements MicrochannelSegmenter, TrackParametri
     + "<ol><li>Rough segmentation of cells using \"Threshold\" computed the whole track prior to segmentation step</li>"
     + "<li>Selection of filled channels: lengh in X direction should be over \"Microchannel Height\" x \"Microchannel filling proportion\"</li>"
     + "<li>Computation of Y start: min value of the min y coordinate of the selected objects at step 2</li></ol></html>";
-    public MicroChannelFluo2D() {}
+    public MicrochannelFluo2D() {}
 
-    public MicroChannelFluo2D(int channelHeight, int channelWidth, int yMargin, double fillingProportion, int minObjectSize) {
+    public MicrochannelFluo2D(int channelHeight, int channelWidth, int yMargin, double fillingProportion, int minObjectSize) {
         this.channelHeight.setValue(channelHeight);
         this.channelWidth.setValue(channelWidth);
         this.yShift.setValue(yMargin);
@@ -105,7 +105,7 @@ public Parameter[] getParameters() {
 
 
     @Override
-    public ApplyToSegmenter<MicroChannelFluo2D> run(int structureIdx, List<StructureObject> parentTrack) {
+    public ApplyToSegmenter<MicrochannelFluo2D> run(int structureIdx, List<StructureObject> parentTrack) {
         double thld = TrackParametrizable.getGlobalThreshold(structureIdx, parentTrack, this.threshold.instanciatePlugin());
         return (p, s)->s.thresholdValue=thld;
     }

diff --git a/src/main/java/boa/plugins/plugins/transformations/CropMicroChannelFluo2D.java b/src/main/java/boa/plugins/plugins/transformations/CropMicroChannelFluo2D.java
@@ -60,7 +60,7 @@
 import boa.utils.Utils;
 import static boa.utils.Utils.plotProfile;
 import boa.plugins.OverridableThresholdMap;
-import boa.plugins.plugins.segmenters.MicroChannelFluo2D;
+import boa.plugins.plugins.segmenters.MicrochannelFluo2D;
 import boa.plugins.MicrochannelSegmenter.Result;
 
 /**
@@ -110,7 +110,7 @@ public BoundingBox getBoundingBox(Image image) {
 
     public BoundingBox getBoundingBox(Image image, ImageInteger thresholdedImage, double threshold) {
         if (debug) testMode = true;
-        Result r = MicroChannelFluo2D.segmentMicroChannels(image, thresholdedImage, 0, 0, this.channelHeight.getValue().intValue(), this.fillingProportion.getValue().doubleValue(), threshold, this.minObjectSize.getValue().intValue(), testMode);
+        Result r = MicrochannelFluo2D.segmentMicroChannels(image, thresholdedImage, 0, 0, this.channelHeight.getValue().intValue(), this.fillingProportion.getValue().doubleValue(), threshold, this.minObjectSize.getValue().intValue(), testMode);
         if (r == null) return null;
         int cropMargin = this.cropMarginY.getValue().intValue();
         int xStart = this.xStart.getValue().intValue();

diff --git a/src/test/java/boa/processing/test/TestProcessMicrochannels.java b/src/test/java/boa/processing/test/TestProcessMicrochannels.java
@@ -38,7 +38,7 @@
 import boa.plugins.PluginFactory;
 import boa.plugins.Segmenter;
 import boa.plugins.plugins.segmenters.BacteriaIntensity;
-import boa.plugins.plugins.segmenters.MicroChannelFluo2D;
+import boa.plugins.plugins.segmenters.MicrochannelFluo2D;
 import boa.plugins.plugins.transformations.CropMicroChannelFluo2D;
 import boa.plugins.OverridableThresholdMap;
 
@@ -64,7 +64,7 @@ public static void testSegMicrochannelsFromXP(String dbName, int fieldNumber, in
         StructureObject root = mDAO.getDao(f.getName()).getRoot(timePoint);
         logger.debug("field name: {}, root==null? {} frame: {}", f.getName(), root==null, root.getFrame());
         Image input = root.getRawImage(0);
-        MicroChannelFluo2D.debug=true;
+        MicrochannelFluo2D.debug=true;
         CropMicroChannelFluo2D.debug=true;
         //ObjectPopulation pop = MicroChannelFluo2D.run(input, 355, 40, 20, 50, 0.6d, 100);
         //ObjectPopulation pop = MicroChannelFluo2D.run2(input, 355, 40, 20);