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Adjust curation presets + minor code cleanup
1 parent 93bc31f commit 4c6636d

7 files changed

Lines changed: 63 additions & 8 deletions

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‎src/main/java/sc/fiji/snt/CurationManager.java‎

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@@ -313,7 +313,6 @@ private JPopupMenu buildTablePopupMenu() {
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}
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});
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popup.add(resetZoomItem);
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popup.addSeparator();
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// Detach / dock table

‎src/main/java/sc/fiji/snt/analysis/curation/PlausibilityCalibrator.java‎

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@@ -150,7 +150,7 @@ public String toTable() {
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sb.append(String.format("Calibration from %d tree(s) | Radii present: %s%n", treeCount, hasRadii));
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sb.append(String.format("%-28s %-22s %10s %8s %10s %10s %6s%n",
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"Check", "Parameter", "Threshold", "N", "Mean", "Std Dev", "Pctl"));
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sb.append("-".repeat(96)).append('\n');
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sb.repeat("-", 96).append('\n');
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for (final CheckSummary s : summaries) {
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sb.append(String.format("%-28s %-22s %10.2f %8d %10.2f %10.2f %5.0f%%%n",
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s.checkName, s.paramLabel, s.computedValue, s.sampleSize,
@@ -448,7 +448,8 @@ private void addSummary(final CalibrationResult result, final String checkName,
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public static final String[] BUILT_IN_PRESETS = {
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"CA1 Dendrites (Mouse, DeFelipe)",
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"CA3 Dendrites (Rat, Amaral)",
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"Eurydendroid Cells (Larval Zebrafish, Baier)",
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"Eurydendroid Cells (Zebrafish, Baier)",
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"Kenyon Cells (Drosophila, Bock)",
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"Martinotti Axons (Mouse, Yuste)",
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"Martinotti Dendrites (Mouse, Yuste)",
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"Purkinje Dendrites (Mouse, Dusart)",

‎src/main/java/sc/fiji/snt/analysis/curation/PlausibilityMonitor.java‎

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@@ -164,7 +164,7 @@ public List<PlausibilityCheck.Warning> onNodeEdited(final Path editedPath, final
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/**
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* Clears the cached fork context. Should be called when tracing is
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* cancelled or a non-forking path is started.
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* canceled or a non-forking path is started.
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*/
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public void clearForkContext() {
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cachedParent = null;
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/*-
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* #%L
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* Fiji distribution of ImageJ for the life sciences.
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* %%
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* Copyright (C) 2010 - 2026 Fiji developers.
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* %%
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* This program is free software: you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as
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* published by the Free Software Foundation, either version 3 of the
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* License, or (at your option) any later version.
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*
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* This program is distributed in the hope that it will be useful,
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* but WITHOUT ANY WARRANTY; without even the implied warranty of
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* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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* GNU General Public License for more details.
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*
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* You should have received a copy of the GNU General Public
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* License along with this program. If not, see
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* <http://www.gnu.org/licenses/gpl-3.0.html>.
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* #L%
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*/
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/**
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* Classes for curation of reconstructions, as implemented by the "Curation Assistant".
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*
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* @author Tiago Ferreira
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*
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*/
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package sc.fiji.snt.analysis.curation;

‎src/main/java/sc/fiji/snt/util/CrossoverFinder.java‎

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@@ -604,8 +604,8 @@ static PairKey of(Path p, Path q) {
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@Override
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public boolean equals(Object o) {
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if (!(o instanceof PairKey k)) return false;
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return a == k.a && b == k.b;
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if (!(o instanceof PairKey(Path a1, Path b1))) return false;
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return a == a1 && b == b1;
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}
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@Override
@@ -650,8 +650,8 @@ private record Cell(int ix, int iy, int iz) {
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@Override
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public boolean equals(Object o) {
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if (!(o instanceof Cell c)) return false;
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return ix == c.ix && iy == c.iy && iz == c.iz;
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if (!(o instanceof Cell(int ix1, int iy1, int iz1))) return false;
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return ix == ix1 && iy == iy1 && iz == iz1;
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}
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}

src/main/resources/curations/Eurydendroid Cells (Larval Zebrafish, Baier).curation renamed to src/main/resources/curations/Eurydendroid Cells (Zebrafish, Baier).curation

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# Kenyon Cells (Drosophila, Bock).curation
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# Computed from 15 reconstructions of Kenyon cells of adult
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# Drosophila melanogaster from NeuroMorpho's Bock archive.
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# https://pubmed.ncbi.nlm.nih.gov/30033368/
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# Curation preset saved from SNT on Sat Apr 25 14:09:54 EDT 2026
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branchAngle.min=30.862120581596685
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branchAngle.max=155.83140862907354
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branchAngle.enabled=true
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directionContinuity.minAlignment=17.131437285277258
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directionContinuity.enabled=true
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radiusContinuity.maxRatio=1.0
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radiusContinuity.enabled=true
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terminalBranchLength.minLength=0.11916375287813273
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terminalBranchLength.enabled=true
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somaDistance.maxDist=500.0
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somaDistance.enabled=true
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tortuosityConsistency.maxDiff=0.4630534803983825
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tortuosityConsistency.enabled=true
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constantRadii.enabled=true
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pathOverlap.proximity=0.1761038196029276
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pathOverlap.enabled=true
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radiusJumps.maxRatio=3.0
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radiusJumps.enabled=true
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radiusMonotonicity.minRun=10
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radiusMonotonicity.enabled=true
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monitor.enabled=true

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