Make commands visible as per #174

morphonets · Jun 11, 2023 · 9ad2b61 · 9ad2b61
1 parent 94a1e10
commit 9ad2b61
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Showing 33 changed files with 33 additions and 34 deletions.
diff --git a/src/main/java/sc/fiji/snt/analysis/PathProfiler.java b/src/main/java/sc/fiji/snt/analysis/PathProfiler.java
@@ -68,7 +68,7 @@
  * @author Tiago Ferreira
  * @author Cameron Arshadi
  */
-@Plugin(type = Command.class, visible = false, label = "Path Profiler", initializer = "init")
+@Plugin(type = Command.class, label = "Path Profiler", initializer = "init")
 public class PathProfiler extends CommonDynamicCmd {
 
 	public static final String CIRCLE = "Circle (Hollow)";

diff --git a/src/main/java/sc/fiji/snt/gui/SaveMeasurementsCmd.java b/src/main/java/sc/fiji/snt/gui/SaveMeasurementsCmd.java
@@ -61,7 +61,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(initializer = "init", type = Command.class, visible = false, label = "Save Tables & Analysis Plots...")
+@Plugin(initializer = "init", type = Command.class, label = "Save Tables & Analysis Plots...")
 public class SaveMeasurementsCmd extends CommonDynamicCmd {
 
 	private static final int MAX_N = 5;

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/AnnotationGraphGeneratorCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/AnnotationGraphGeneratorCmd.java
@@ -43,7 +43,7 @@
 
 import java.util.*;
 
-@Plugin(type = Command.class, visible = false, label = "Create Annotation Diagram(s)")
+@Plugin(type = Command.class, label = "Create Annotation Diagram(s)")
 public class AnnotationGraphGeneratorCmd extends CommonDynamicCmd {
 
 	@Parameter(required = false, visibility = ItemVisibility.MESSAGE)

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/ChooseDatasetCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/ChooseDatasetCmd.java
@@ -48,7 +48,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(initializer = "init", type = Command.class, visible = false,
+@Plugin(initializer = "init", type = Command.class,
 	label = "Change Tracing Image")
 public class ChooseDatasetCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/ColorMapReconstructionCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/ColorMapReconstructionCmd.java
@@ -51,7 +51,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Tree Color Coder",
+@Plugin(type = Command.class, label = "Tree Color Coder",
 	initializer = "init")
 public class ColorMapReconstructionCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/CommonDynamicCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/CommonDynamicCmd.java
@@ -43,7 +43,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false)
+@Plugin(type = Command.class)
 public class CommonDynamicCmd extends DynamicCommand {
 
 	protected static final String HEADER_HTML = "<html><body><div style='font-weight:bold;'>";

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/ComputeSecondaryImg.java b/src/main/java/sc/fiji/snt/gui/cmds/ComputeSecondaryImg.java
@@ -81,7 +81,7 @@
  * @author Tiago Ferreira
  * @author Cameron Arshadi
  */
-@Plugin(type = Command.class, visible = false, initializer = "init")
+@Plugin(type = Command.class, initializer = "init")
 public class ComputeSecondaryImg<T extends RealType<T> & NativeType<T>, U extends RealType<U> & NativeType<U>>
 		extends CommonDynamicCmd implements Interactive, SigmaPaletteListener
 {

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/DistributionBPCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/DistributionBPCmd.java
@@ -51,7 +51,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false,
+@Plugin(type = Command.class,
 	label = "Distribution Analysis (Branch Properties)", initializer = "init")
 public class DistributionBPCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/DistributionCPCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/DistributionCPCmd.java
@@ -49,7 +49,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false,
+@Plugin(type = Command.class,
 	label = "Distribution Analysis (Multiple Cells)", initializer = "init")
 public class DistributionCPCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/DuplicateCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/DuplicateCmd.java
@@ -41,7 +41,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Duplicate Path...", initializer = "init")
+@Plugin(type = Command.class, label = "Duplicate Path...", initializer = "init")
 public class DuplicateCmd extends CommonDynamicCmd {
 
 	private final String CHOICE_LENGTH = "Use % specified below";

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/GraphGeneratorCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/GraphGeneratorCmd.java
@@ -38,7 +38,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Create Dendrogram", initializer = "init")
+@Plugin(type = Command.class, label = "Create Dendrogram", initializer = "init")
 public class GraphGeneratorCmd extends CommonDynamicCmd {
 
 	@Parameter(required = false)

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/InsectBrainImporterCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/InsectBrainImporterCmd.java
@@ -49,7 +49,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false,
+@Plugin(type = Command.class,
 	label = "Import InsectBrain Data", initializer = "init")
 public class InsectBrainImporterCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/JSONImporterCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/JSONImporterCmd.java
@@ -47,7 +47,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false,
+@Plugin(type = Command.class,
 	label = "Import ML JSON Data")
 public class JSONImporterCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/LoadReconstructionCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/LoadReconstructionCmd.java
@@ -48,7 +48,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, initializer = "init",
+@Plugin(type = Command.class, initializer = "init",
 	label = "Load Reconstruction(s)...")
 public class LoadReconstructionCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/MLImporterCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/MLImporterCmd.java
@@ -56,7 +56,7 @@
  * @see MouseLightLoader
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false,
+@Plugin(type = Command.class,
 	label = "Import MouseLight Reconstructions", initializer = "init")
 public class MLImporterCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/NDFImporterCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/NDFImporterCmd.java
@@ -41,7 +41,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, initializer = "init", label = "Import NeuronJ NDF")
+@Plugin(type = Command.class, initializer = "init", label = "Import NeuronJ NDF")
 public class NDFImporterCmd extends CommonDynamicCmd {
 
 	@Parameter(label = "File")

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/OpenDatasetCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/OpenDatasetCmd.java
@@ -41,7 +41,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, initializer = "init", visible = false,
+@Plugin(type = Command.class, initializer = "init",
 	label = "Change Tracing Image")
 public class OpenDatasetCmd extends CommonDynamicCmd implements Command {
 

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/PrefsCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/PrefsCmd.java
@@ -70,7 +70,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, initializer="init", label="SNT Preferences")
+@Plugin(type = Command.class, initializer="init", label="SNT Preferences")
 public class PrefsCmd extends ContextCommand {
 
 	@Parameter

diff --git a/src/main/java/sc/fiji/snt/gui/cmds/RemoteSWCImporterCmd.java b/src/main/java/sc/fiji/snt/gui/cmds/RemoteSWCImporterCmd.java
@@ -57,7 +57,7 @@
  * @see FlyCircuitLoader
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, initializer = "init")
+@Plugin(type = Command.class, initializer = "init")
 public class RemoteSWCImporterCmd extends CommonDynamicCmd {
 
 	@Parameter(required = true, persist = true,

diff --git a/src/main/java/sc/fiji/snt/plugin/AnalyzerCmd.java b/src/main/java/sc/fiji/snt/plugin/AnalyzerCmd.java
@@ -55,7 +55,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label="Measure...", initializer = "init")
+@Plugin(type = Command.class, label="Measure...", initializer = "init")
 @Deprecated
 public class AnalyzerCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/plugin/BrainAnnotationCmd.java b/src/main/java/sc/fiji/snt/plugin/BrainAnnotationCmd.java
@@ -46,7 +46,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Distribution Analysis of Brain Areas", initializer = "init")
+@Plugin(type = Command.class, label = "Distribution Analysis of Brain Areas", initializer = "init")
 public class BrainAnnotationCmd extends CommonDynamicCmd {
 
 	@Parameter(label = "Type of distribution:", choices = { "Cable Length", "No. of Tips",

diff --git a/src/main/java/sc/fiji/snt/plugin/GroupAnalyzerCmd.java b/src/main/java/sc/fiji/snt/plugin/GroupAnalyzerCmd.java
@@ -61,7 +61,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label="Compare Groups...", initializer = "init")
+@Plugin(type = Command.class, label="Compare Groups...", initializer = "init")
 public class GroupAnalyzerCmd extends CommonDynamicCmd {
 
 	private static final String COMMON_DESC_PRE = "<HTML><div WIDTH=500>Path to directory containing Group ";

diff --git a/src/main/java/sc/fiji/snt/plugin/LocalThicknessCmd.java b/src/main/java/sc/fiji/snt/plugin/LocalThicknessCmd.java
@@ -44,7 +44,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, initializer = "init", visible = false,
+@Plugin(type = Command.class, initializer = "init",
 label = "Estimate Radii (Local Thickness)")
 public class LocalThicknessCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/plugin/MultiTreeMapperCmd.java b/src/main/java/sc/fiji/snt/plugin/MultiTreeMapperCmd.java
@@ -56,7 +56,7 @@
  * @author Tiago Ferreira
  * @author Cameron Arshadi
  */
-@Plugin(type = Command.class, visible = false, label = "Multi Tree Color Mapper",
+@Plugin(type = Command.class, label = "Multi Tree Color Mapper",
         initializer = "init")
 public class MultiTreeMapperCmd extends CommonDynamicCmd {
 

diff --git a/src/main/java/sc/fiji/snt/plugin/PathAnalyzerCmd.java b/src/main/java/sc/fiji/snt/plugin/PathAnalyzerCmd.java
@@ -48,7 +48,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label="Measure Path(s)...", initializer = "init")
+@Plugin(type = Command.class, label="Measure Path(s)...", initializer = "init")
 public class PathAnalyzerCmd extends CommonDynamicCmd {
 
 	private static final String TABLE_TITLE = "SNT Measurements";

diff --git a/src/main/java/sc/fiji/snt/plugin/PathMatcherCmd.java b/src/main/java/sc/fiji/snt/plugin/PathMatcherCmd.java
@@ -54,7 +54,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label="Match Path(s) Across Time...", initializer = "init")
+@Plugin(type = Command.class, label="Match Path(s) Across Time...", initializer = "init")
 public class PathMatcherCmd extends CommonDynamicCmd {
 
 	private static final String TAG_FORMAT = "{Group %d}";

diff --git a/src/main/java/sc/fiji/snt/plugin/PathSpineAnalysisCmd.java b/src/main/java/sc/fiji/snt/plugin/PathSpineAnalysisCmd.java
@@ -57,7 +57,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Spine/Varicosity Density Profile...", initializer = "init")
+@Plugin(type = Command.class, label = "Spine/Varicosity Density Profile...", initializer = "init")
 public class PathSpineAnalysisCmd extends CommonDynamicCmd {
 
 	@Parameter

diff --git a/src/main/java/sc/fiji/snt/plugin/PathTimeAnalysisCmd.java b/src/main/java/sc/fiji/snt/plugin/PathTimeAnalysisCmd.java
@@ -64,7 +64,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Time Profile Analysis...", initializer = "init")
+@Plugin(type = Command.class, label = "Time Profile Analysis...", initializer = "init")
 public class PathTimeAnalysisCmd extends CommonDynamicCmd {
 
 	private static final String TAG_REGEX_PATTERN = "("+ PathMatcherCmd.TAG_REGEX_PATTERN + ")";

diff --git a/src/main/java/sc/fiji/snt/plugin/ShollAnalysisBulkTreeCmd.java b/src/main/java/sc/fiji/snt/plugin/ShollAnalysisBulkTreeCmd.java
@@ -60,7 +60,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Bulk Sholl Analysis (Tracings)", initializer = "init")
+@Plugin(type = Command.class, label = "Bulk Sholl Analysis (Tracings)", initializer = "init")
 public class ShollAnalysisBulkTreeCmd extends CommonDynamicCmd
 {
 

diff --git a/src/main/java/sc/fiji/snt/plugin/SkeletonConverterCmd.java b/src/main/java/sc/fiji/snt/plugin/SkeletonConverterCmd.java
@@ -58,7 +58,7 @@
  * @author Cameron Arshadi
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Automated Tracing: Tree(s) from Segmented Image...", initializer = "init")
+@Plugin(type = Command.class, label = "Automated Tracing: Tree(s) from Segmented Image...", initializer = "init")
 public class SkeletonConverterCmd extends CommonDynamicCmd {
 
 	private static final String IMG_NONE= "None";

diff --git a/src/main/java/sc/fiji/snt/plugin/SkeletonizerCmd.java b/src/main/java/sc/fiji/snt/plugin/SkeletonizerCmd.java
@@ -53,8 +53,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false,
-	label = "Convert Paths to Topographic Skeletons")
+@Plugin(type = Command.class, label = "Convert Paths to Topographic Skeletons")
 public class SkeletonizerCmd implements Command {
 
 	@Parameter

diff --git a/src/main/java/sc/fiji/snt/plugin/SpineExtractorCmd.java b/src/main/java/sc/fiji/snt/plugin/SpineExtractorCmd.java
@@ -57,7 +57,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label = "Extract Spine/Varicosity Counts from ROI(s)...", initializer = "init")
+@Plugin(type = Command.class, label = "Extract Spine/Varicosity Counts from ROI(s)...", initializer = "init")
 public class SpineExtractorCmd extends CommonDynamicCmd {
 
 	private static final String MSG = "<br>To initiate counts, right-click on image and run \"Count Spine/Varicosities...\"";

diff --git a/src/main/java/sc/fiji/snt/plugin/StrahlerCmd.java b/src/main/java/sc/fiji/snt/plugin/StrahlerCmd.java
@@ -64,7 +64,7 @@
  *
  * @author Tiago Ferreira
  */
-@Plugin(type = Command.class, visible = false, label="Strahler Analysis...")
+@Plugin(type = Command.class, label="Strahler Analysis...")
 public class StrahlerCmd extends ContextCommand {
 
 	@Parameter