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NicoKiaruNicoKiaru
committed
Homogeneize capitalisation
Rm spurious println
1 parent 4f1f692 commit 5214ca4

4 files changed

Lines changed: 25 additions & 38 deletions

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‎src/main/java/ch/epfl/biop/atlas/aligner/command/ExportSlicesToQuickNIIDatasetCommand.java‎

Lines changed: 0 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -119,7 +119,6 @@ public void run() {
119119
pt.setPosition(mp.getROI()[0]+margin,0);
120120
pt.setPosition(mp.getROI()[1]+margin,1);
121121
pt.setPosition(slicesToExport.get(idx).getSlicingAxisPosition(), 2);
122-
System.out.println("pto "+pt);
123122

124123
double oxi = getSourceValueAt(xSource, pt).get();
125124
double oyi = getSourceValueAt(ySource, pt).get();
@@ -128,14 +127,12 @@ public void run() {
128127
pt.setPosition(mp.getROI()[0]+mp.getROI()[2]-margin,0);
129128
pt.setPosition(mp.getROI()[1]+margin,1);
130129

131-
System.out.println("ptu "+pt);
132130
double uxi = getSourceValueAt(xSource, pt).get();
133131
double uyi = getSourceValueAt(ySource, pt).get();
134132
double uzi = getSourceValueAt(zSource, pt).get();
135133

136134
pt.setPosition(mp.getROI()[0]+margin,0);
137135
pt.setPosition(mp.getROI()[1]+mp.getROI()[3]-margin,1);
138-
System.out.println("ptv"+pt);
139136
double vxi = getSourceValueAt(xSource, pt).get();
140137
double vyi = getSourceValueAt(ySource, pt).get();
141138
double vzi = getSourceValueAt(zSource, pt).get();

‎src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/ABBABdvViewPrefs.java‎

Lines changed: 1 addition & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -5,6 +5,7 @@
55
public class ABBABdvViewPrefs {
66
public static Font slice_info_font;// = new Font("TimesRoman", Font.BOLD, 16);
77
public static Font action_font;
8+
public static String default_font; // Not used, just to prevent warning
89
public static Color slice_info_color;// = new Color(32, 125, 49, 220); // When slice info is shown
910
public static Color done; // = new Color(0, 255, 0, 200);
1011
public static Color done_export;

‎src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/ABBATheme.java‎

Lines changed: 0 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,13 @@
11
package ch.epfl.biop.atlas.aligner.gui.bdv;
22

3-
import javax.swing.SwingUtilities;
4-
import javax.swing.UIManager;
53
import java.awt.BasicStroke;
64
import java.awt.Font;
75
import java.awt.Color;
8-
import java.awt.Window;
96
import java.lang.reflect.Field;
107
import java.lang.reflect.Modifier;
118
import java.util.HashMap;
129
import java.util.HashSet;
1310
import java.util.Map;
14-
import java.util.Random;
1511
import java.util.Set;
1612

1713
public class ABBATheme {

‎src/main/java/ch/epfl/biop/atlas/aligner/gui/bdv/BdvMultislicePositionerView.java‎

Lines changed: 24 additions & 31 deletions
Original file line numberDiff line numberDiff line change
@@ -169,8 +169,8 @@ public class BdvMultislicePositionerView implements MultiSlicePositioner.SliceCh
169169
final public static String NAME_CARD_DISPLAY_NAVIGATION = "Display & Navigation"; //"Atlas Display";
170170
final public static String NAME_CARD_EDIT_SLICES = "Edit Selected Slices";
171171
final public static String NAME_CARD_ATLAS_SLICING = "Atlas Slicing";
172-
final public static String NAME_CARD_DEFINE_ROI = "Define region of interest for registration";
173-
final public static String NAME_CARD_CURRENT_SLICE_INFO = "Current slice info";
172+
final public static String NAME_CARD_DEFINE_ROI = "Define Region Of Interest";
173+
final public static String NAME_CARD_CURRENT_SLICE_INFO = "Current Slice Info";
174174
final public static String NAME_CARD_SLICES_DISPLAY = "Slices Display";
175175

176176
public MultiSlicePositioner msp; // TODO : make accessor
@@ -354,7 +354,6 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
354354
// Load and Save state
355355
BdvScijavaHelper.addActionToBdvHandleMenu(bdvh,"File>Save State (+View)",0, () -> new Thread(this::saveState).start(), "/graphics/SaveState.png", "Save ABBA state file");
356356
BdvScijavaHelper.addActionToBdvHandleMenu(bdvh,"File>Load State (+View)",0, () -> new Thread(this::loadState).start(), "/graphics/LoadState.png", "Load ABBA state file");
357-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "File>Import Demo Sections", ABBAImportDemoSlicesCommand.class, "mp", msp );
358357

359358
BdvScijavaHelper.addActionToBdvHandleMenu(bdvh,"Edit>Undo [Ctrl+Z]",0, msp::cancelLastAction, "/graphics/ABBAUndo.png", "Undo Last Action");
360359
BdvScijavaHelper.addActionToBdvHandleMenu(bdvh,"Edit>Redo [Ctrl+Shift+Z]",0, msp::redoAction, "/graphics/ABBARedo.png", "Redo Last Action");
@@ -371,8 +370,8 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
371370
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Import>Import QuPath Project", ImportSlicesFromQuPathCommand.class, "mp", msp );
372371
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Import>Import Current ImageJ Window", ImportSliceFromImagePlusCommand.class, "mp", msp );
373372
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Import>Import With Bio-Formats", ImportSlicesFromFilesCommand.class, "mp", msp );
374-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Import>Import Sources", ImportSliceFromSourcesCommand.class, "mp", msp );
375373
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Import>Import QuickNII Project", ImportSlicesFromQuickNIICommand.class, "mp", msp );
374+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Import>Import Sources From BDV-Playground", ImportSliceFromSourcesCommand.class, "mp", msp );
376375
BdvScijavaHelper.addSeparator(bdvh, "Import");
377376
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Import>Import Demo Sections", ABBAImportDemoSlicesCommand.class, "mp", msp );
378377

@@ -404,7 +403,7 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
404403
.filter(SliceSources::isSelected)
405404
.forEach(slice -> new DeleteSliceAction(msp, slice).runRequest())
406405
);
407-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(),"Slices>Re-index Slices channels", ReindexSlicesCommand.class, "mp", msp);
406+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(),"Slices>Re-Index Slices channels", ReindexSlicesCommand.class, "mp", msp);
408407
BdvScijavaHelper.addSeparator(bdvh,"Slices");
409408
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Slices>Set Slices Display Range", SetSlicesDisplayRangeCommand.class, "mp", msp );
410409
BdvScijavaHelper.addSeparator(bdvh,"Slices");
@@ -418,7 +417,7 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
418417
if (DeepSliceHelper.isDeepSliceMouseCompatible(msp.getReslicedAtlas().ba.getName())) {
419418

420419
logger.debug("Installing DeepSlice Command for Mouse");
421-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Edit>Configuration>Set DeepSlice Env path", DeepSlicePrefsSet.class);
420+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Edit>Configuration>Set DeepSlice Env Path", DeepSlicePrefsSet.class);
422421

423422
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Register>DeepSlice>DeepSlice Registration (Web)", RegisterSlicesDeepSliceWebCommand.class, "mp", msp, "model", "mouse");
424423
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Register>DeepSlice>DeepSlice Registration (Local)", RegisterSlicesDeepSliceLocalCommand.class, "mp", msp, "model", "mouse");
@@ -428,7 +427,7 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
428427
if (DeepSliceHelper.isDeepSliceRatCompatible(msp.getReslicedAtlas().ba.getName())) {
429428

430429
logger.debug("Installing DeepSlice Command for Rat");
431-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Edit>Configuration>DeepSlice setup...", DeepSlicePrefsSet.class, 0);
430+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Edit>Configuration>DeepSlice Setup...", DeepSlicePrefsSet.class, 0);
432431

433432
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Register>DeepSlice>DeepSlice Registration (Web)", RegisterSlicesDeepSliceWebCommand.class, "mp", msp, "model", "rat");
434433
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Register>DeepSlice>DeepSlice Registration (Local)", RegisterSlicesDeepSliceLocalCommand.class, "mp", msp, "model", "rat");
@@ -443,8 +442,8 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
443442
// Adds registration plugin commands : discovered via scijava plugin autodiscovery mechanism
444443
installRegistrationPluginUI(hierarchyLevelsSkipped);
445444

446-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Edit>(Experimental)>Raster and cache deformation field", RasterSlicesDeformationCommand.class, "mp", msp);
447-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Edit>(Experimental)>Raster slice", RasterSlicesCommand.class, "mp", msp);
445+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Edit>(Experimental)>Raster And Cache Deformation Field", RasterSlicesDeformationCommand.class, "mp", msp);
446+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Edit>(Experimental)>Raster Slice", RasterSlicesCommand.class, "mp", msp);
448447

449448
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export>Set Slices Thickness", SetSlicesThicknessCommand.class, "mp", msp);
450449
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export>Set Slices Thickness (fill gaps)", SetSlicesThicknessMatchNeighborsCommand.class, "mp", msp);
@@ -453,20 +452,20 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
453452
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> QuPath > Export Registrations To QuPath Project", ExportRegistrationToQuPathCommand.class, "mp", msp);
454453
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Regions To Roi Manager", ExportRegionsToRoiManagerCommand.class, "mp", msp);
455454
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Regions To File", ExportRegionsToRoisetFileCommand.class, "mp", msp);
456-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export > BDV > Export Registered Slices to BDV Json Dataset", ExportSlicesToBDVJsonDatasetCommand.class, "mp", msp);
457-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export > BDV > Export Resampled Slices as BDV Source", ExportResampledSlicesToBDVSourceCommand.class, "mp", msp);
458-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> BigDataViewer > Export Registered Slices to BDV", ExportSlicesToBDVCommand.class, "mp", msp);
459-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Registered Slices to ImageJ", ExportSlicesToImageJCommand.class, "mp", msp);
460-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Original Slices to ImageJ", ExportSlicesOriginalDataToImageJCommand.class, "mp", msp);
461-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Atlas Coordinates of Original Slices to ImageJ", ExportDeformationFieldToImageJCommand.class, "mp", msp);
462-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Atlas to ImageJ", ExportAtlasToImageJCommand.class, "mp", msp);
463-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> QuickNII > Export Registered Slices as Quick NII Dataset", ExportSlicesToQuickNIIDatasetCommand.class, "mp", msp);
455+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export > BDV > Export Registered Slices To BDV Json Dataset", ExportSlicesToBDVJsonDatasetCommand.class, "mp", msp);
456+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export > BDV > Export Resampled Slices As BDV Sources", ExportResampledSlicesToBDVSourceCommand.class, "mp", msp);
457+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> BigDataViewer > Export Registered Slices To BDV", ExportSlicesToBDVCommand.class, "mp", msp);
458+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Registered Slices To ImageJ", ExportSlicesToImageJCommand.class, "mp", msp);
459+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Original Slices To ImageJ", ExportSlicesOriginalDataToImageJCommand.class, "mp", msp);
460+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Atlas Coordinates Of Original Slices To ImageJ", ExportDeformationFieldToImageJCommand.class, "mp", msp);
461+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> ImageJ > Export Atlas To ImageJ", ExportAtlasToImageJCommand.class, "mp", msp);
462+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Export> QuickNII > Export Registered Slices As Quick NII Dataset", ExportSlicesToQuickNIIDatasetCommand.class, "mp", msp);
464463

465464
BdvScijavaHelper.addSeparator(bdvh,"Register");
466465
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Register>Edit Last Registration", RegisterSlicesEditLastCommand.class, "mp", msp);
467466
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Register>Remove Last Registration", RegisterSlicesRemoveLastCommand.class, "mp", msp );
468467
BdvScijavaHelper.addSeparator(bdvh,"Register");
469-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Register>Copy Registrations from model and Apply to selected slices", RegisterSlicesCopyAndApplyCommand.class, "mp", msp );
468+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Register>Copy Registrations From Model And Apply To Selected Slices", RegisterSlicesCopyAndApplyCommand.class, "mp", msp );
470469

471470
final BiConsumer<String,String> guiErrorLogger = this::blockingErrorMessageForUsers;
472471

@@ -484,19 +483,19 @@ private void installBdvMenu(int hierarchyLevelsSkipped) {
484483
addToCleanUpHook(() -> msp.unSubscribeFromInfoMessages(infoLogger));
485484

486485
// Update check
487-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Check for updates", ABBACheckForUpdateCommand.class);
486+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Check For Updates", ABBACheckForUpdateCommand.class);
488487

489488
// Help commands
490-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Ask for help in the forum (web)", ABBAForumHelpCommand.class);
491-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Go to documentation (web)", ABBADocumentationCommand.class);
492-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Give your feedback (web)", ABBAUserFeedbackCommand.class);
489+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Ask For Help In The Forum (web)", ABBAForumHelpCommand.class);
490+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Go To Documentation (web)", ABBADocumentationCommand.class);
491+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>Give Your Feedback (web)", ABBAUserFeedbackCommand.class);
493492
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Help>About DeepSlice (web)", DeepSliceDocumentationCommand.class);
494493

495-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Cite>How to cite ABBA (web)", ABBACiteInfoCommand.class);
496-
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Cite>Generate methods prompt", ABBAGenerateMethodsPrompt.class, "mp", msp);
494+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Cite>How To Cite ABBA (web)", ABBACiteInfoCommand.class);
495+
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Cite>Generate Methods Prompt", ABBAGenerateMethodsPrompt.class, "mp", msp);
497496
BdvScijavaHelper.addSeparator(bdvh,"Cite");
498497
BdvScijavaHelper.addCommandToBdvHandleMenu(bdvh, msp.getContext(), "Cite>About DeepSlice (web)", DeepSliceDocumentationCommand.class);
499-
BdvScijavaHelper.addActionToBdvHandleMenu(bdvh, "Cite>About current atlas (web)", 0, () ->
498+
BdvScijavaHelper.addActionToBdvHandleMenu(bdvh, "Cite>About Current Atlas (web)", 0, () ->
500499
{
501500
try {
502501
(msp.getContext().getService(PlatformService.class)).open(new URL(msp.getAtlas().getURL()));
@@ -532,12 +531,6 @@ private void installRegistrationPluginUI(int hierarchyLevelsSkipped) {
532531
)
533532
);
534533

535-
536-
//logger.debug("Adding interactive transform");
537-
//BdvScijavaHelper.addActionToBdvHandleMenu(bdvh, "Align>ABBA - Interactive Transform", 0, () ->
538-
// (msp.getContext().getService(CommandService.class)).run(SliceAffineTransformCommand.class, true, "mp", msp)
539-
//);
540-
541534
}
542535

543536
private void installBigDataViewerCards() {

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