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Projection mode changer #73

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merged 12 commits into from
Jan 21, 2020
Merged

Projection mode changer #73

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c2a24dd
Implement SacProjectionModeChangerCommand
tischi Jan 18, 2020
e28606f
Merge latest master
tischi Jan 18, 2020
ec713cd
Merge latest master
tischi Jan 18, 2020
b39780d
Remove the SourceAndConverterDisplayService interface
tischi Jan 18, 2020
2d72754
Use getSourceAndConverterFromSource in AccumulateMixedProjectorARGB
tischi Jan 18, 2020
d19a88d
Remove instance of TransformedSource
tischi Jan 20, 2020
df97e5d
Add bdvHandle to AccumulateMixedProjectorARGB
tischi Jan 20, 2020
4ada17d
merge master and solve conflicts
NicoKiaru Jan 20, 2020
cdc40b4
modifies the Service API to use only setter and getter
NicoKiaru Jan 20, 2020
b5e6efb
replaces .equals by == in comparison : tests only the memory location…
NicoKiaru Jan 21, 2020
3c4b5b5
solves issue finding sourceandconverter from source + changes the int…
NicoKiaru Jan 21, 2020
5056954
revert failed refactoring
NicoKiaru Jan 21, 2020
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63 changes: 36 additions & 27 deletions src/main/java/sc/fiji/bdvpg/bdv/projector/AccumulateMixedProjectorARGB.java
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Original file line number Diff line number Diff line change
Expand Up @@ -10,14 +10,15 @@
import net.imglib2.RandomAccessible;
import net.imglib2.RandomAccessibleInterval;
import net.imglib2.type.numeric.ARGBType;
import sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterService;
import sc.fiji.bdvpg.services.BdvService;
import sc.fiji.bdvpg.services.SourceAndConverterServices;

import java.util.ArrayList;
import java.util.Map;
import java.util.Set;
import java.util.List;
import java.util.concurrent.ExecutorService;

import static sc.fiji.bdvpg.bdv.projector.Projection.PROJECTION_MODE;
import static sc.fiji.bdvpg.bdv.projector.Projection.PROJECTION_MODE_SUM;

public class AccumulateMixedProjectorARGB extends AccumulateProjector< ARGBType, ARGBType >
{
public static AccumulateProjectorFactory< ARGBType > factory = new AccumulateProjectorFactory< ARGBType >()
Expand All @@ -41,7 +42,7 @@ public AccumulateMixedProjectorARGB createAccumulateProjector(
}
};

private final ArrayList< Source< ? > > sourceList;
private final String[] projectionModes;

public AccumulateMixedProjectorARGB(
final ArrayList< VolatileProjector > sourceProjectors,
Expand All @@ -52,7 +53,7 @@ public AccumulateMixedProjectorARGB(
final ExecutorService executorService )
{
super( sourceProjectors, sourceScreenImages, target, numThreads, executorService );
this.sourceList = sources;
projectionModes = getProjectionModes( sources );
}

@Override
Expand All @@ -65,8 +66,6 @@ protected void accumulate(

int sourceIndex = 0;

final Map< SourceAndConverter, Map< String, Object > > sourceAndConverterToMetadata = BdvService.getSourceAndConverterService().getSourceAndConverterToMetadata();

for ( final Cursor< ? extends ARGBType > access : accesses )
{
final int value = access.get().get();
Expand All @@ -80,16 +79,14 @@ protected void accumulate(
continue;
}

String projectionMode = getProjectionMode( sourceIndex, sourceAndConverterToMetadata );

if ( projectionMode.equals( "Sum" ) )
if ( projectionModes[sourceIndex].equals( Projection.PROJECTION_MODE_SUM ) )
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{
aAccu += a;
rAccu += r;
gAccu += g;
bAccu += b;
}
else if ( projectionMode.equals( "Avg" ))
else if ( projectionModes[sourceIndex].equals( Projection.PROJECTION_MODE_AVG ))
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{
aAvg += a;
rAvg += r;
Expand Down Expand Up @@ -127,26 +124,38 @@ else if ( projectionMode.equals( "Avg" ))

}

private String getProjectionMode( int sourceIndex, Map< SourceAndConverter, Map< String, Object > > sourceAndConverterToMetadata )
private String[] getProjectionModes( ArrayList< Source< ? > > sources )
{
Source< ? > source = sourceList.get( sourceIndex );
if ( source instanceof TransformedSource )
source = (( TransformedSource )source).getWrappedSource();
final List< SourceAndConverter > sacs = SourceAndConverterServices.getSourceAndConverterService().getSourceAndConverters();
final String[] projectionModes = new String[ sources.size() ];

String projectionMode = "Sum";
int sourceIndex = 0;

for ( SourceAndConverter sac : sourceAndConverterToMetadata.keySet() )
for ( Source<?> source : sources )
{
if ( sac.getSpimSource().equals( source ) )
{
final Set< String > metadata = sourceAndConverterToMetadata.get( sac ).keySet();
if ( metadata.contains( "ProjectionMode" ) )
{
projectionMode = (String) sourceAndConverterToMetadata.get( sac ).get( "ProjectionMode" );
}
}
if ( source instanceof TransformedSource )
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source = ( ( TransformedSource ) source ).getWrappedSource();

SourceAndConverter sac = SourceAndConverterServices.getSourceAndConverterService().getSourceAndConverterFromSource( source );
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This could fail because a Source can have different converters and thus exists in different flavors. One Source -> 2 SourceAndConverters, one with a gray LUT and one with a completely different LUT, for instance.

We have to think about that, but that's a major issue. I had to deal with this in the remove(SourceAndConverter, BdvHandle) function from the display service, you should have a look at it and then let's rediscuss this. Maybe there's no better way...

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Agreed! See conversations below.


final String projectionMode = (String) SourceAndConverterServices.getSourceAndConverterService().getMetadata( sac, PROJECTION_MODE );
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if ( projectionMode == null )
projectionModes[sourceIndex++] = PROJECTION_MODE_SUM;
else
projectionModes[sourceIndex++] = projectionMode;

}
return projectionMode;

return projectionModes;
}

private SourceAndConverter getSourceAndConverter( List< SourceAndConverter > sacs, Source< ? > source )
{
for ( SourceAndConverter sac : sacs )
if ( sac.getSpimSource().equals( source ) )
return sac;

return null;
}
}
7 changes: 6 additions & 1 deletion .../bdvpg/bdv/projector/ProjectionTypes.java → .../fiji/bdvpg/bdv/projector/Projection.java
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@@ -1,8 +1,13 @@
package sc.fiji.bdvpg.bdv.projector;

public class ProjectionTypes
public class Projection
{
public static final String PROJECTION_MODE = "Projection Mode";
public static final String PROJECTION_MODE_SUM = "Sum";
public static final String PROJECTION_MODE_AVG = "Avg";

public static final String MIXED_PROJECTOR = "Mixed Projector";
public static final String SUM_PROJECTOR = "Sum Projector";
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cf comment above, maybe change this to int to fasten the computation

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@tischi tischi Jan 20, 2020 •
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Ok. I could do this, but long term I think an enum would be the cleanest.
The only reason I was choosing String constants was because this is the only thing that works in Command choices. Thus, using ints not would make it more complicated because we have to implement the constants twice.

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Ok, I'll investigate the performance and report back

public static final String AVERAGE_PROJECTOR = "Average Projector";

}
4 changes: 2 additions & 2 deletions src/main/java/sc/fiji/bdvpg/bdv/sourceandconverter/SourceAdder.java
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Expand Up @@ -2,7 +2,7 @@

import bdv.util.BdvHandle;
import bdv.viewer.SourceAndConverter;
import sc.fiji.bdvpg.services.BdvService;
import sc.fiji.bdvpg.services.SourceAndConverterServices;

import java.util.function.Consumer;

Expand All @@ -22,6 +22,6 @@ public void run() {

@Override
public void accept(SourceAndConverter source) {
BdvService.getSourceAndConverterDisplayService().show(bdvh, source);
SourceAndConverterServices.getSourceAndConverterDisplayService().show(bdvh, source);
}
}
6 changes: 3 additions & 3 deletions src/main/java/sc/fiji/bdvpg/bdv/sourceandconverter/SourceRemover.java
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Expand Up @@ -2,7 +2,7 @@

import bdv.util.BdvHandle;
import bdv.viewer.SourceAndConverter;
import sc.fiji.bdvpg.services.BdvService;
import sc.fiji.bdvpg.services.SourceAndConverterServices;

import java.util.function.Consumer;

Expand Down Expand Up @@ -34,10 +34,10 @@ public void run() {
public void accept(SourceAndConverter source) {
if (bdvh==null) {
// Remove from all displays
BdvService.getSourceAndConverterDisplayService().removeFromAllBdvs(source);
SourceAndConverterServices.getSourceAndConverterDisplayService().removeFromAllBdvs(source);
} else {
// Remove from a specific bdvHandle
BdvService.getSourceAndConverterDisplayService().remove(bdvh, source);
SourceAndConverterServices.getSourceAndConverterDisplayService().remove(bdvh, source);
}
}
}
4 changes: 2 additions & 2 deletions src/main/java/sc/fiji/bdvpg/scijava/BdvHandleHelper.java
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Expand Up @@ -3,7 +3,7 @@
import bdv.util.BdvHandle;
import org.scijava.cache.CacheService;
import org.scijava.object.ObjectService;
import sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterDisplayService;
import sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService;

import javax.swing.*;
import java.awt.event.WindowAdapter;
Expand All @@ -13,7 +13,7 @@

public class BdvHandleHelper {

public static void setBdvHandleCloseOperation(BdvHandle bdvh, CacheService cs, BdvSourceAndConverterDisplayService bdvsds, boolean putWindowOnTop) {
public static void setBdvHandleCloseOperation( BdvHandle bdvh, CacheService cs, SourceAndConverterBdvDisplayService bdvsds, boolean putWindowOnTop) {
JFrame topFrame = (JFrame) SwingUtilities.getWindowAncestor(bdvh.getViewerPanel());

topFrame.addWindowListener(new WindowAdapter() {
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/sc/fiji/bdvpg/scijava/command/bdv/BdvSourcesAdderCommand.java
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Expand Up @@ -7,7 +7,7 @@
import org.scijava.plugin.Plugin;
import sc.fiji.bdvpg.bdv.navigate.ViewerTransformAdjuster;
import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
import sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterDisplayService;
import sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService;
import sc.fiji.bdvpg.sourceandconverter.display.BrightnessAutoAdjuster;

@Plugin(type = Command.class, menuPath = ScijavaBdvDefaults.RootMenu+"Bdv>Show Sources")
Expand All @@ -20,7 +20,7 @@ public class BdvSourcesAdderCommand implements Command {
SourceAndConverter[] sacs;

@Parameter
BdvSourceAndConverterDisplayService bsds;
SourceAndConverterBdvDisplayService bsds;

@Parameter
boolean autoContrast;
Expand Down
6 changes: 2 additions & 4 deletions src/main/java/sc/fiji/bdvpg/scijava/command/bdv/BdvSourcesRemoverCommand.java
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Expand Up @@ -5,10 +5,8 @@
import org.scijava.command.Command;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import sc.fiji.bdvpg.bdv.navigate.ViewerTransformAdjuster;
import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
import sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterDisplayService;
import sc.fiji.bdvpg.sourceandconverter.display.BrightnessAutoAdjuster;
import sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService;

@Plugin(type = Command.class, menuPath = ScijavaBdvDefaults.RootMenu+"Bdv>Remove Sources From Bdv")
public class BdvSourcesRemoverCommand implements Command {
Expand All @@ -20,7 +18,7 @@ public class BdvSourcesRemoverCommand implements Command {
SourceAndConverter[] srcs_in;

@Parameter
BdvSourceAndConverterDisplayService bsds;
SourceAndConverterBdvDisplayService bsds;

@Override
public void run() {
Expand Down
10 changes: 5 additions & 5 deletions src/main/java/sc/fiji/bdvpg/scijava/command/bdv/BdvWindowCreatorCommand.java
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Expand Up @@ -8,7 +8,7 @@
import sc.fiji.bdvpg.bdv.BdvCreator;
import sc.fiji.bdvpg.bdv.projector.AccumulateAverageProjectorARGB;
import sc.fiji.bdvpg.bdv.projector.AccumulateMixedProjectorARGB;
import sc.fiji.bdvpg.bdv.projector.ProjectionTypes;
import sc.fiji.bdvpg.bdv.projector.Projection;
import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;

@Plugin(type = Command.class, menuPath = ScijavaBdvDefaults.RootMenu+"Bdv>Create Empty BDV Frame",
Expand All @@ -30,7 +30,7 @@ public class BdvWindowCreatorCommand implements Command {
@Parameter(type = ItemIO.OUTPUT)
public BdvHandle bdvh;

@Parameter(choices = { ProjectionTypes.MIXED_PROJECTOR, ProjectionTypes.SUM_PROJECTOR, ProjectionTypes.AVERAGE_PROJECTOR})
@Parameter(choices = { Projection.MIXED_PROJECTOR, Projection.SUM_PROJECTOR, Projection.AVERAGE_PROJECTOR})
public String projector;

@Override
Expand All @@ -40,12 +40,12 @@ public void run() {
if (is2D) opts = opts.is2D();

switch (projector) {
case ProjectionTypes.MIXED_PROJECTOR:
case Projection.MIXED_PROJECTOR:
opts = opts.accumulateProjectorFactory(AccumulateMixedProjectorARGB.factory);
case ProjectionTypes.SUM_PROJECTOR:
case Projection.SUM_PROJECTOR:
// Default projector
break;
case ProjectionTypes.AVERAGE_PROJECTOR:
case Projection.AVERAGE_PROJECTOR:
opts = opts.accumulateProjectorFactory(AccumulateAverageProjectorARGB.factory);
break;
default:
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/sc/fiji/bdvpg/scijava/command/bdv/ViewSynchronizerCommand.java
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Expand Up @@ -8,7 +8,7 @@
import sc.fiji.bdvpg.bdv.navigate.ViewerTransformSyncStopper;
import sc.fiji.bdvpg.scijava.BdvHandleHelper;
import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
import sc.fiji.bdvpg.services.BdvService;
import sc.fiji.bdvpg.services.SourceAndConverterServices;

import javax.swing.*;
import java.awt.*;
Expand Down Expand Up @@ -36,7 +36,7 @@ public class ViewSynchronizerCommand implements Command {
public void run() {
// Starting synchronnization of selected bdvhandles
sync = new ViewerTransformSyncStarter(bdvhs);
sync.setBdvHandleInitialReference(BdvService.getSourceAndConverterDisplayService().getActiveBdv());
sync.setBdvHandleInitialReference( SourceAndConverterServices.getSourceAndConverterDisplayService().getActiveBdv());
sync.run();

// JFrame serving the purpose of stopping synchronization when it is being closed
Expand Down
4 changes: 2 additions & 2 deletions src/main/java/sc/fiji/bdvpg/scijava/command/source/BigWarpLauncherCommand.java
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Expand Up @@ -8,7 +8,7 @@
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
import sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterDisplayService;
import sc.fiji.bdvpg.scijava.services.SourceAndConverterBdvDisplayService;
import sc.fiji.bdvpg.sourceandconverter.register.BigWarpLauncher;

import java.util.Arrays;
Expand All @@ -35,7 +35,7 @@ public class BigWarpLauncherCommand implements Command {
BdvHandle bdvhP;

@Parameter
BdvSourceAndConverterDisplayService bsds;
SourceAndConverterBdvDisplayService bsds;

public void run() {
List<SourceAndConverter> movingSacs = Arrays.stream(movingSources).collect(Collectors.toList());
Expand Down
6 changes: 3 additions & 3 deletions src/main/java/sc/fiji/bdvpg/scijava/command/source/BrightnessAdjusterCommand.java
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Expand Up @@ -6,7 +6,7 @@
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
import sc.fiji.bdvpg.services.BdvService;
import sc.fiji.bdvpg.services.SourceAndConverterServices;
import sc.fiji.bdvpg.sourceandconverter.display.BrightnessAdjuster;

import java.text.DecimalFormat;
Expand Down Expand Up @@ -66,8 +66,8 @@ public void updateMessage() {

public void init() {
if (sources.length>0) {
double minSource = BdvService.getSourceAndConverterDisplayService().getConverterSetup(sources[0]).getDisplayRangeMin();
double maxSource = BdvService.getSourceAndConverterDisplayService().getConverterSetup(sources[0]).getDisplayRangeMax();
double minSource = SourceAndConverterServices.getSourceAndConverterDisplayService().getConverterSetup(sources[0]).getDisplayRangeMin();
double maxSource = SourceAndConverterServices.getSourceAndConverterDisplayService().getConverterSetup(sources[0]).getDisplayRangeMax();

if (minSource>=0) {
min = 0;
Expand Down
14 changes: 0 additions & 14 deletions src/main/java/sc/fiji/bdvpg/scijava/command/source/ColorSourceCreatorCommand.java
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@@ -1,31 +1,17 @@
package sc.fiji.bdvpg.scijava.command.source;

import bdv.viewer.SourceAndConverter;
import net.imagej.display.ColorTables;
import net.imagej.lut.LUTService;
import net.imglib2.converter.Converter;
import net.imglib2.display.ColorConverter;
import net.imglib2.display.ColorTable;
import net.imglib2.type.numeric.ARGBType;
import org.scijava.ItemIO;
import org.scijava.command.Command;
import org.scijava.command.DynamicCommand;
import org.scijava.convert.ConvertService;
import org.scijava.module.MutableModuleItem;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.util.ColorRGB;
import org.scijava.util.ColorRGBA;
import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
import sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterDisplayService;
import sc.fiji.bdvpg.sourceandconverter.SourceAndConverterUtils;
import sc.fiji.bdvpg.sourceandconverter.display.ConverterChanger;

import java.net.URL;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Map;

@Plugin(type = Command.class, menuPath = ScijavaBdvDefaults.RootMenu+"Sources>Create New Source (Set Color)")
public class ColorSourceCreatorCommand implements Command {

Expand Down
2 changes: 0 additions & 2 deletions src/main/java/sc/fiji/bdvpg/scijava/command/source/LUTSourceCreatorCommand.java
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Expand Up @@ -5,15 +5,13 @@
import net.imagej.lut.LUTService;
import net.imglib2.converter.Converter;
import net.imglib2.display.ColorTable;
import org.scijava.ItemIO;
import org.scijava.command.Command;
import org.scijava.command.DynamicCommand;
import org.scijava.convert.ConvertService;
import org.scijava.module.MutableModuleItem;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import sc.fiji.bdvpg.scijava.ScijavaBdvDefaults;
import sc.fiji.bdvpg.scijava.services.BdvSourceAndConverterDisplayService;
import sc.fiji.bdvpg.sourceandconverter.display.ConverterChanger;

import java.net.URL;
Expand Down
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