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ekatrukhaekatrukha
committed
v.0.8.3
1 parent 65b467e commit f763e7c

13 files changed

Lines changed: 53 additions & 51 deletions

‎pom.xml‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,7 @@
1111

1212
<groupId>nl.uu.science.cellbiology</groupId>
1313
<artifactId>bigtrace</artifactId>
14-
<version>0.8.2</version>
14+
<version>0.8.3</version>
1515

1616
<name>BigTrace</name>
1717
<description>Tracing of curvilinear structures in 3D</description>

‎src/main/java/bigtrace/BigTrace.java‎

Lines changed: 3 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -114,7 +114,9 @@ public class BigTrace < T extends RealType< T > & NativeType< T > > implements P
114114
/** Frame of BigVolumeViewer **/
115115
public VolumeViewerFrame bvvFrame;
116116

117-
/** flag to check if user interface is frozen **/
117+
/** flag to check if user interface is frozen.
118+
* It should be modified only in the main thread (or in done() of SwingWorker,
119+
* since when running in macro mode main thread becomes EDT => problems! **/
118120
public volatile boolean bInputLock = false;
119121

120122
/** visualization of coordinates origin axes **/

‎src/main/java/bigtrace/BigTraceControlPanel.java‎

Lines changed: 11 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -682,8 +682,8 @@ public void extractClippedView()
682682

683683
GBCHelper.alighLeft(cd);
684684

685-
cd.gridx=0;
686-
cd.gridy=0;
685+
cd.gridx = 0;
686+
cd.gridy = 0;
687687
String[] sExtractClippedTime = { "current time point", "range (specify below)" };
688688
JComboBox<String> extractClippedTimeList = new JComboBox<>(sExtractClippedTime);
689689
int [] nRange = new int [2];
@@ -697,16 +697,16 @@ public void extractClippedView()
697697
cd.gridx++;
698698
clipExtractSettings.add(extractClippedTimeList,cd);
699699
cd.gridy++;
700-
cd.gridx=0;
700+
cd.gridx = 0;
701701
//cd.gridx++;
702702

703-
cd.gridwidth=2;
703+
cd.gridwidth = 2;
704704
clipExtractSettings.add(timeRange,cd);
705-
cd.gridwidth=1;
705+
cd.gridwidth = 1;
706706
cd.gridy++;
707707
}
708708

709-
cd.gridx=0;
709+
cd.gridx = 0;
710710
clipExtractSettings.add(new JLabel("Output:"),cd);
711711
cd.gridx++;
712712
String[] sExtractClippedOutput = { "show in ImageJ", "save as TIF" };
@@ -717,7 +717,7 @@ public void extractClippedView()
717717
if(bt.bApplyLLSTransform)
718718
{
719719
cd.gridy++;
720-
cd.gridx=0;
720+
cd.gridx = 0;
721721
clipExtractSettings.add(new JLabel("Intensity interpolation:"),cd);
722722
cd.gridx++;
723723
String[] sIntInterpolationType = { "Nearest Neighbor", "Linear", "Lanczos" };
@@ -751,7 +751,10 @@ public void extractClippedView()
751751

752752
nExtractClippedOutput = extractClippedOutputList.getSelectedIndex();
753753
Prefs.set("BigTrace.nExtractClippedOutput", nExtractClippedOutput);
754-
754+
755+
//lock interaction
756+
bt.bInputLock = true;
757+
bt.setLockMode(true);
755758
//run in a separate thread
756759
ExtractClip<T> extractClippedBG = new ExtractClip<>(bt, nTimePointMin, nTimePointMax, nExtractClippedOutput);
757760

‎src/main/java/bigtrace/BigTraceData.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -32,7 +32,7 @@ public class BigTraceData < T extends RealType< T > & NativeType< T > >
3232
{
3333

3434
/** current plugin version **/
35-
public static String sVersion = "0.8.2";
35+
public static String sVersion = "0.8.3";
3636

3737
/** plugin instance **/
3838
BigTrace<T> bt;

‎src/main/java/bigtrace/BigTraceRenderSettings.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -8,7 +8,7 @@
88
import ij.Prefs;
99

1010

11-
@Plugin(type = Command.class, menuPath = "Plugins>BigTrace 0.8.2>Volume Render Settings")
11+
@Plugin(type = Command.class, menuPath = "Plugins>BigTrace 0.8.3>Volume Render Settings")
1212
public class BigTraceRenderSettings implements Command {
1313

1414

‎src/main/java/bigtrace/gui/ClipPanel.java‎

Lines changed: 5 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -67,7 +67,7 @@ private RangeSliderPanel addRangeSlider(String label, int[] realMinMax, int[] se
6767
c.gridx++;
6868
}
6969
//c.gridx++;
70-
c.gridwidth=3;
70+
c.gridwidth = 3;
7171
c.fill = GridBagConstraints.BOTH;
7272
c.weightx = 1.0;
7373
layout.setConstraints(slider, c);
@@ -142,7 +142,7 @@ public void setBoundingBox(int bbx0, int bby0, int bbz0, int bbx1, int bby1, int
142142

143143
public void setBoundingBox(final long [][] box)
144144
{
145-
for(int d=0;d<3;d++)
145+
for(int d = 0; d < 3; d++)
146146
{
147147
bbAxes[d].setMinAndMax((int)box[0][d], (int)box[1][d]);
148148
}
@@ -152,15 +152,15 @@ public void setBoundingBox(final long [][] box)
152152
public void setBoundingBox(final Interval interval)
153153
{
154154
long [][] box = new long[2][3];
155-
box[0]=interval.minAsLongArray();
156-
box[1]=interval.maxAsLongArray();
155+
box[0] = interval.minAsLongArray();
156+
box[1] = interval.maxAsLongArray();
157157
setBoundingBox(box);
158158
}
159159

160160
public long [][] getBoundingBox()
161161
{
162162
long [][] boxout = new long[2][3];
163-
for(int d=0;d<3;d++)
163+
for(int d = 0; d < 3; d++)
164164
{
165165
boxout[0][d] = bbAxes[d].getMin();
166166
boxout[1][d] = bbAxes[d].getMax();

‎src/main/java/bigtrace/io/ROIsLoadBG.java‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -191,7 +191,7 @@ protected Void doInBackground() throws Exception {
191191
try {
192192
Thread.sleep(1);
193193
} catch (InterruptedException ignore) {}
194-
setProgress((Integer.parseInt(line_array[1])-1)*100/nRoiN);
194+
setProgress((Integer.parseInt(line_array[1])-1) * 100 / nRoiN);
195195
setProgressState("loading ROI #"+line_array[1]+" of "+Integer.toString(nRoiN));
196196
break;
197197

‎src/main/java/bigtrace/measure/RoiMeasure3D.java‎

Lines changed: 26 additions & 15 deletions
Original file line numberDiff line numberDiff line change
@@ -1151,8 +1151,8 @@ public void dialExtractROIBox(final Roi3D roiIn)
11511151
nfBoxExpand.setIntegersOnly(true);
11521152

11531153
GBCHelper.alighLeft(cd);
1154-
cd.gridx=0;
1155-
cd.gridy=0;
1154+
cd.gridx = 0;
1155+
cd.gridy = 0;
11561156
extractROISettings.add(new JLabel("Extract box around:"),cd);
11571157
cd.gridx++;
11581158
final String[] sExtractBoxROIsRange = { "Selected ROI", "All visible ROIs" };
@@ -1161,15 +1161,15 @@ public void dialExtractROIBox(final Roi3D roiIn)
11611161
extractROISettings.add(extractBoxRoiList, cd);
11621162

11631163
cd.gridy++;
1164-
cd.gridx=0;
1164+
cd.gridx = 0;
11651165
extractROISettings.add(new JLabel("Extract only voxels inside ROI:"),cd);
11661166
cd.gridx++;
11671167
JCheckBox extractVoxelsInsideROI = new JCheckBox();
11681168
extractVoxelsInsideROI.setSelected( Prefs.get("BigTrace.bOnlyVoxelsInsideROI", false) );
11691169
extractROISettings.add(extractVoxelsInsideROI,cd);
11701170

11711171
cd.gridy++;
1172-
cd.gridx=0;
1172+
cd.gridx = 0;
11731173
extractROISettings.add(new JLabel("Box size:"),cd);
11741174
cd.gridx++;
11751175
String[] sExtractRoiType = { "Tight", "Enlarge/shrink below" };
@@ -1179,7 +1179,7 @@ public void dialExtractROIBox(final Roi3D roiIn)
11791179

11801180
nfBoxExpand.setText(Integer.toString((int)Prefs.get("BigTrace.nExpandROIBox", 5)));
11811181
cd.gridy++;
1182-
cd.gridx=0;
1182+
cd.gridx = 0;
11831183
extractROISettings.add(new JLabel("Expand box by (px):"),cd);
11841184
cd.gridx++;
11851185
extractROISettings.add(nfBoxExpand,cd);
@@ -1189,15 +1189,15 @@ public void dialExtractROIBox(final Roi3D roiIn)
11891189
if(bt.btData.nNumTimepoints > 1 )
11901190
{
11911191
cd.gridy++;
1192-
cd.gridx=0;
1192+
cd.gridx = 0;
11931193
extractROISettings.add(new JLabel("Time range per ROI:"),cd);
11941194
extractBoxTimeList.setSelectedIndex((int)Prefs.get("BigTrace.nExtractBoxTime", 0));
11951195
cd.gridx++;
11961196
extractROISettings.add(extractBoxTimeList,cd);
11971197

11981198
}
11991199
cd.gridy++;
1200-
cd.gridx=0;
1200+
cd.gridx = 0;
12011201
extractROISettings.add(new JLabel("Output:"),cd);
12021202
cd.gridx++;
12031203
String[] sExtractBoxOutput = { "show in ImageJ", "save as TIF" };
@@ -1279,7 +1279,11 @@ public void dialExtractROIBox(final Roi3D roiIn)
12791279

12801280
}
12811281
if(roiOut.size() > 0)
1282-
{
1282+
{
1283+
1284+
bt.bInputLock = true;
1285+
bt.setLockMode(true);
1286+
12831287
//run in a separate thread
12841288
ExtractROIBox<T> extractBoxBG = new ExtractROIBox<>(roiOut, bt, nExpandROIBox, nTimeRange, nExtractBoxOutput, bOnlyVoxelsInsideROI, sSaveDir);
12851289
extractBoxBG.addPropertyChangeListener(bt.btPanel);
@@ -1317,8 +1321,8 @@ public void dialStraightenCurve(final AbstractCurve3D curveLine)
13171321

13181322
GBCHelper.alighLeft(cd);
13191323

1320-
cd.gridx=0;
1321-
cd.gridy=0;
1324+
cd.gridx = 0;
1325+
cd.gridy = 0;
13221326
straightenSettings.add(new JLabel("Straighten:"),cd);
13231327
cd.gridx++;
13241328
String[] sStraightenROIsRange = { "Selected ROI", "All visible ROIs" };
@@ -1327,7 +1331,7 @@ public void dialStraightenCurve(final AbstractCurve3D curveLine)
13271331
straightenSettings.add(straightenRoiList,cd);
13281332

13291333
cd.gridy++;
1330-
cd.gridx=0;
1334+
cd.gridx = 0;
13311335
straightenSettings.add(new JLabel("Curve thickness:"),cd);
13321336
cd.gridx++;
13331337
String[] sStraightenType = { "Use ROI settings", "Override here" };
@@ -1349,7 +1353,7 @@ public void dialStraightenCurve(final AbstractCurve3D curveLine)
13491353
String[] sStraightenAxis = { "X", "Y", "Z" };
13501354
JComboBox<String> cbStraightenAxis = new JComboBox<>(sStraightenAxis);
13511355
cd.gridy++;
1352-
cd.gridx=0;
1356+
cd.gridx = 0;
13531357
straightenSettings.add(new JLabel("Line becomes output axis:"),cd);
13541358
cd.gridx++;
13551359
cbStraightenAxis.setSelectedIndex((int)Prefs.get("BigTrace.nStraightenAxis", 0));
@@ -1358,7 +1362,7 @@ public void dialStraightenCurve(final AbstractCurve3D curveLine)
13581362
String[] sShapeOutput = { "Square", "Round" };
13591363
JComboBox<String> cbStraightenShape = new JComboBox<>(sShapeOutput);
13601364
cd.gridy++;
1361-
cd.gridx=0;
1365+
cd.gridx = 0;
13621366
straightenSettings.add(new JLabel("Shape:"),cd);
13631367
cd.gridx++;
13641368
cbStraightenShape.setSelectedIndex((int)Prefs.get("BigTrace.nStraightenShape", 0));
@@ -1369,7 +1373,7 @@ public void dialStraightenCurve(final AbstractCurve3D curveLine)
13691373
if(bt.btData.nNumTimepoints > 1)
13701374
{
13711375
cd.gridy++;
1372-
cd.gridx=0;
1376+
cd.gridx = 0;
13731377
straightenSettings.add(new JLabel("Time range per ROI:"),cd);
13741378
straightenTimeList.setSelectedIndex((int)Prefs.get("BigTrace.nStraightenTime", 0));
13751379
cd.gridx++;
@@ -1473,8 +1477,11 @@ public void dialStraightenCurve(final AbstractCurve3D curveLine)
14731477
}
14741478

14751479
}
1476-
if(curvesOut.size()>0)
1480+
if(curvesOut.size() > 0)
14771481
{
1482+
//lock interaction
1483+
bt.bInputLock = true;
1484+
bt.setLockMode(true);
14781485
//run in a separate thread
14791486
StraightenCurve<T> straightBG = new StraightenCurve<>(curvesOut, bt, fRadiusStraighted, nStraightenAxis, nStraightenShape, nTimeRange, nStraightenOutput, sSaveDir);
14801487
straightBG.addPropertyChangeListener(bt.btPanel);
@@ -1510,6 +1517,10 @@ public void dialSliceVolume(final CrossSection3D crossSection)
15101517
{
15111518
nSliceType = sliceTypeList.getSelectedIndex();
15121519
Prefs.set("BigTrace.nSliceType", nSliceType);
1520+
1521+
//lock interaction
1522+
bt.bInputLock = true;
1523+
bt.setLockMode(true);
15131524
//run in a separate thread
15141525
SplitVolumePlane<T> splitBG = new SplitVolumePlane<>(crossSection, bt, nSliceType);
15151526
splitBG.addPropertyChangeListener(bt.btPanel);

‎src/main/java/bigtrace/volume/ExtractClip.java‎

Lines changed: 0 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -38,8 +38,6 @@ public ExtractClip( final BigTrace<T> bt_, final int nTimePointMin_, final int n
3838
}
3939
@Override
4040
protected Void doInBackground() throws Exception {
41-
bt.bInputLock = true;
42-
bt.setLockMode(true);
4341

4442
try {
4543
Thread.sleep(1);

‎src/main/java/bigtrace/volume/ExtractROIBox.java‎

Lines changed: 1 addition & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -72,12 +72,7 @@ public void setProgressState(String state_)
7272

7373
@Override
7474
protected Void doInBackground() throws Exception
75-
{
76-
77-
bt.bInputLock = true;
78-
bt.setLockMode(true);
79-
80-
75+
{
8176
try
8277
{
8378
Thread.sleep(1);

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