From aaf65ed8c5be858d8491bc2d8c217bdb5caf44a8 Mon Sep 17 00:00:00 2001
From: Tiago Ferreira <tiago.tferr@gmail.com>
Date: Wed, 25 Oct 2023 14:53:00 -0400
Subject: [PATCH] Code cleanup and minor fixes
- Cleanup pom
- DemoRunner: Remove unimplemented code
- SigmaPalette: Workaround startup NPE on MacOS
- PathManagerUI: Remove legacy option
- Jython Template: Ensure imported classes appear in Ctrl+Space auto-completion
- Script: Remove outdated LUT option
---
pom.xml | 17 +++---
src/main/java/sc/fiji/snt/PathManagerUI.java | 3 --
src/main/java/sc/fiji/snt/gui/DemoRunner.java | 53 ++++++++++---------
.../java/sc/fiji/snt/gui/SigmaPalette.java | 3 +-
.../Neuroanatomy/Boilerplate/PY.py | 4 +-
...ollection_2D_(Skeletonized_Montage).groovy | 2 +-
6 files changed, 39 insertions(+), 43 deletions(-)
diff --git a/pom.xml b/pom.xml
index 8e86f11ae..b3bace0a3 100644
--- a/pom.xml
+++ b/pom.xml
@@ -143,22 +143,18 @@
<sciview.version>906892d</sciview.version>
<scenery.version>db26f01</scenery.version>
<font-awesome.version>6.4.2</font-awesome.version>
- <flatlaf.version>3.2.1</flatlaf.version>
- <flatlaf-jide-oss.version>3.2.2</flatlaf-jide-oss.version>
- <log4j.version>2.20.0</log4j.version>
- <smile-core.version>3.0.2</smile-core.version>
+ <flatlaf.version>3.2.5</flatlaf.version>
+ <flatlaf-jide-oss.version>${flatlaf.version}</flatlaf-jide-oss.version>
+ <log4j.version>2.21.0</log4j.version>
<jide-oss.version>3.7.14</jide-oss.version>
- <annotations.version>13.0</annotations.version>
+ <annotations.version>24.0.1</annotations.version>
<fastutil-core.version>8.5.12</fastutil-core.version>
- <jheaps.version>0.14</jheaps.version>
- <jide-oss.version>3.7.12</jide-oss.version>
- <log4j.version>2.19.0</log4j.version>
<log4j-api.version>${log4j.version}</log4j-api.version>
<log4j-core.version>${log4j.version}</log4j-core.version>
<scenery.version>0.8.0</scenery.version>
<sciview.version>ba959ae644</sciview.version>
- <smile.version>3.0.0</smile.version>
- <smile-base.version>3.0.2</smile-base.version>
+ <smile.version>3.0.2</smile.version>
+ <smile-base.version>${smile.version}</smile-base.version>
<smile-core.version>${smile.version}</smile-core.version>
<!-- NB: Deploy releases to the SciJava Maven repository. -->
@@ -453,7 +449,6 @@
<dependency>
<groupId>org.jheaps</groupId>
<artifactId>jheaps</artifactId>
- <version>${jheaps.version}</version>
</dependency>
<dependency>
<groupId>sc.iview</groupId>
diff --git a/src/main/java/sc/fiji/snt/PathManagerUI.java b/src/main/java/sc/fiji/snt/PathManagerUI.java
index f413f3b92..c8b5d1903 100644
--- a/src/main/java/sc/fiji/snt/PathManagerUI.java
+++ b/src/main/java/sc/fiji/snt/PathManagerUI.java
@@ -2114,9 +2114,6 @@ private void runDistributionAnalysisCmd(final Collection<Tree> trees, final Stri
input.put("calledFromPathManagerUI", true);
if (metric != null) input.put("measurementChoice", metric);
if (polar != null) input.put("polar", polar);
- if (trees.size() == 1) {
- input.put("onlyConnectivitySafeMetrics", false);
- }
cmdService.run(DistributionCPCmd.class, true, input);
}
diff --git a/src/main/java/sc/fiji/snt/gui/DemoRunner.java b/src/main/java/sc/fiji/snt/gui/DemoRunner.java
index 424a797d8..6ad3e5360 100644
--- a/src/main/java/sc/fiji/snt/gui/DemoRunner.java
+++ b/src/main/java/sc/fiji/snt/gui/DemoRunner.java
@@ -65,7 +65,7 @@ public DemoRunner(final SNTUI ui, final SNT snt) {
entries.add(demo7());
entries.add(demo8());
entries.add(demo9());
- entries.add(demo10());
+ //entries.add(demo10());
}
private Demo demo1() {
@@ -73,7 +73,8 @@ private Demo demo1() {
@Override
public ImagePlus getImage() {
final ImagePlus imp = sntService.demoImage("ddaC");
- imp.setRoi(320, 380, 20, 20); // mark soma
+ if (imp != null)
+ imp.setRoi(320, 380, 20, 20); // mark soma
return imp;
}
@@ -254,30 +255,30 @@ public void load() {
return entry;
}
- private Demo demo10() {
- final Demo entry = new Demo(10, "Segmented astrocyte (2D image)") {
- @Override
- public ImagePlus getImage() {
- final ImagePlus imp = ij.IJ.openImage("http://wsr.imagej.net/images/mitosis.tif");
- imp.setPosition(2, 4, 31); // k-fibers channel, mid Z-range, traced time point
- return imp;
- }
-
- @Override
- public void load() {
- super.load();
- // apply tags
- ui.getPathManager().applyDefaultTags("Traced Channel");
- ui.getPathManager().applyDefaultTags("Traced Frame");
- }
- };
- entry.summary = "Downloads a Drosophila S2 cell undergoing mitosis in which K-fibers were traced during anaphase.";
- entry.data = "Image (5D; 2-channel, 3D timelapse, 33MB)";
- entry.source = "ImageJ sample image, PMID 19720876";
- entry.online = true;
- entry.tracingsURL = "https://raw.githubusercontent.com/morphonets/SNTmanuscript/718e4b90fb4bb61f382edcf467173b53045b25e0/FigS3_5D-Tracing/traces/mitosis.traces";
- return entry;
- }
+// private Demo demo10() {
+// final Demo entry = new Demo(10, "Segmented astrocyte (2D image)") {
+// @Override
+// public ImagePlus getImage() {
+// final ImagePlus imp = ij.IJ.openImage("http://wsr.imagej.net/images/mitosis.tif");
+// imp.setPosition(2, 4, 31); // k-fibers channel, mid Z-range, traced time point
+// return imp;
+// }
+//
+// @Override
+// public void load() {
+// super.load();
+// // apply tags
+// ui.getPathManager().applyDefaultTags("Traced Channel");
+// ui.getPathManager().applyDefaultTags("Traced Frame");
+// }
+// };
+// entry.summary = "Downloads a Drosophila S2 cell undergoing mitosis in which K-fibers were traced during anaphase.";
+// entry.data = "Image (5D; 2-channel, 3D timelapse, 33MB)";
+// entry.source = "ImageJ sample image, PMID 19720876";
+// entry.online = true;
+// entry.tracingsURL = "https://raw.githubusercontent.com/morphonets/SNTmanuscript/718e4b90fb4bb61f382edcf467173b53045b25e0/FigS3_5D-Tracing/traces/mitosis.traces";
+// return entry;
+// }
private void error(final Throwable ex) {
ui.error("Loading of data failed (" + ex.getMessage() + " error). See Console for details.");
diff --git a/src/main/java/sc/fiji/snt/gui/SigmaPalette.java b/src/main/java/sc/fiji/snt/gui/SigmaPalette.java
index 7bfe615b9..d6536016a 100644
--- a/src/main/java/sc/fiji/snt/gui/SigmaPalette.java
+++ b/src/main/java/sc/fiji/snt/gui/SigmaPalette.java
@@ -568,7 +568,8 @@ private void updateSigmaFromMouseEvent(final MouseEvent e) {
}
}
updateOverlayLabels();
- paletteWindow.repaint(); // call createSubtitle()
+ if (paletteWindow != null)
+ paletteWindow.repaint(); // call createSubtitle()
mouseMovedAcceptedSigmaIndex = -1;
}
}
diff --git a/src/main/resources/script_templates/Neuroanatomy/Boilerplate/PY.py b/src/main/resources/script_templates/Neuroanatomy/Boilerplate/PY.py
index 22cf5c2dd..88214e1f6 100644
--- a/src/main/resources/script_templates/Neuroanatomy/Boilerplate/PY.py
+++ b/src/main/resources/script_templates/Neuroanatomy/Boilerplate/PY.py
@@ -15,7 +15,9 @@
"""
from sc.fiji.snt import Path, PathAndFillManager, SNT, SNTUI, Tree
-from sc.fiji.snt.analysis import *
+from sc.fiji.snt.analysis import GroupedTreeStatistics, MultiTreeStatistics, NodeStatistics, TreeStatistics,\
+ ConvexHullAnalyzer, PersistenceAnalyzer, ShollAnalyzer, StrahlerAnalyzer, NodeColorMapper,\
+ TreeColorMapper, PathProfiler, PathStraightener, RoiConverter, SkeletonConverter, SNTChart, SNTTable
from sc.fiji.snt.analysis.graph import DirectedWeightedGraph
from sc.fiji.snt.analysis.sholl.parsers import TreeParser
from sc.fiji.snt.annotation import AllenCompartment, AllenUtils, VFBUtils, ZBAtlasUtils
diff --git a/src/main/resources/script_templates/Neuroanatomy/Render/Render_Cell_Collection_2D_(Skeletonized_Montage).groovy b/src/main/resources/script_templates/Neuroanatomy/Render/Render_Cell_Collection_2D_(Skeletonized_Montage).groovy
index 34c1440f7..d7bd2311d 100644
--- a/src/main/resources/script_templates/Neuroanatomy/Render/Render_Cell_Collection_2D_(Skeletonized_Montage).groovy
+++ b/src/main/resources/script_templates/Neuroanatomy/Render/Render_Cell_Collection_2D_(Skeletonized_Montage).groovy
@@ -3,7 +3,7 @@
#@ int (label="Number of columns", value=0) columns
#@ int (label="Number of rows", value=0) rows
#@ Float (label="Scale factor for reconstructions", value=1.0) scale
-#@ String (label="Color mapping:", choices={"Ice.lut", "mpl-viridis.lut", "glasbey_on_dark.lut"}, value="glasbey_on_dark.lut") lutName
+#@ String (label="Color mapping:", choices={"mpl-viridis.lut", "glasbey_on_dark.lut"}, value="glasbey_on_dark.lut") lutName
#@ SNTService snt
/**