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Merge pull request #58 from PreibischLab/imgloader-fixes
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Imgloader fixes
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@StephanPreibisch
StephanPreibisch authored Sep 26, 2024
2 parents 28aa949 + bb25a94 commit 8dd977d
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Showing 14 changed files with 553 additions and 699 deletions.
41 changes: 21 additions & 20 deletions src/main/java/net/preibisch/mvrecon/fiji/datasetmanager/FileListDatasetDefinition.java
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Original file line number Diff line number Diff line change
Expand Up @@ -115,6 +115,7 @@
import net.preibisch.mvrecon.fiji.spimdata.imgloaders.LegacyFileMapImgLoaderLOCI;
import net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapGettable;
import net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapImgLoaderLOCI2;
import net.preibisch.mvrecon.fiji.spimdata.imgloaders.filemap2.FileMapEntry;
import net.preibisch.mvrecon.fiji.spimdata.intensityadjust.IntensityAdjustments;
import net.preibisch.mvrecon.fiji.spimdata.interestpoints.ViewInterestPoints;
import net.preibisch.mvrecon.fiji.spimdata.pointspreadfunctions.PointSpreadFunctions;
Expand Down Expand Up @@ -443,18 +444,18 @@ public boolean test(Path t)

private static SpimData2 buildSpimData( FileListViewDetectionState state, boolean withVirtualLoader )
{
//final Map< Integer, List< Pair< File, Pair< Integer, Integer > > > > fm = tileIdxMap;

//final Map< Integer, List< FileMapEntry > > fm = tileIdxMap;
//fm.forEach( (k,v ) -> {System.out.println( k ); v.forEach( p -> {System.out.print(p.getA() + ""); System.out.print(p.getB().getA().toString() + " "); System.out.println(p.getB().getB().toString());} );});
Map< Integer, List< Pair< File, Pair< Integer, Integer > > > > tpIdxMap = state.getIdMap().get( TimePoint.class );
Map< Integer, List< Pair< File, Pair< Integer, Integer > > > > channelIdxMap = state.getIdMap().get( Channel.class );
Map< Integer, List< Pair< File, Pair< Integer, Integer > > > > illumIdxMap = state.getIdMap().get( Illumination.class );
Map< Integer, List< Pair< File, Pair< Integer, Integer > > > > tileIdxMap = state.getIdMap().get( Tile.class );
Map< Integer, List< Pair< File, Pair< Integer, Integer > > > > angleIdxMap = state.getIdMap().get( Angle.class );


Map< Integer, List< FileMapEntry > > tpIdxMap = state.getIdMap().get( TimePoint.class );
Map< Integer, List< FileMapEntry > > channelIdxMap = state.getIdMap().get( Channel.class );
Map< Integer, List< FileMapEntry > > illumIdxMap = state.getIdMap().get( Illumination.class );
Map< Integer, List< FileMapEntry > > tileIdxMap = state.getIdMap().get( Tile.class );
Map< Integer, List< FileMapEntry > > angleIdxMap = state.getIdMap().get( Angle.class );


List<Integer> timepointIndexList = new ArrayList<>(tpIdxMap.keySet());
List<Integer> channelIndexList = new ArrayList<>(channelIdxMap.keySet());
List<Integer> illuminationIndexList = new ArrayList<>(illumIdxMap.keySet());
Expand All @@ -477,7 +478,7 @@ private static SpimData2 buildSpimData( FileListViewDetectionState state, boolea
List<ViewId> missingViewIds = new ArrayList<>();
List<TimePoint> timePoints = new ArrayList<>();

HashMap<Pair<Integer, Integer>, Pair<File, Pair<Integer, Integer>>> ViewIDfileMap = new HashMap<>();
Map< Pair< Integer, Integer >, FileMapEntry > ViewIDfileMap = new HashMap<>();
Integer viewSetupId = 0;
for (Integer c = 0; c < nChannels; c++)
for (Integer i = 0; i < nIlluminations; i++)
Expand All @@ -488,8 +489,8 @@ private static SpimData2 buildSpimData( FileListViewDetectionState state, boolea
boolean addedViewSetup = false;
for (Integer tp = 0; tp < nTimepoints; tp++)
{
List< Pair< File, Pair< Integer, Integer > > > viewList;

List< FileMapEntry > viewList;
viewList = FileListDatasetDefinitionUtil.listIntersect( channelIdxMap.get( channelIndexList.get( c ) ), angleIdxMap.get( angleIndexList.get( a ) ) );
viewList = FileListDatasetDefinitionUtil.listIntersect( viewList, tileIdxMap.get( tileIndexList.get( ti ) ) );
viewList = FileListDatasetDefinitionUtil.listIntersect( viewList, illumIdxMap.get( illuminationIndexList.get( i ) ) );
Expand Down Expand Up @@ -520,8 +521,8 @@ else if (viewList.size() > 1)
IOFunctions.println( "Error: more than one View: ch" + c +" a"+ a + " ti" + ti + " tp"+ tp + " i" + i );
else
{
IOFunctions.println( "Found View: ch" + c +" a"+ a + " ti" + ti + " tp"+ tp + " i" + i + " in file " + viewList.get( 0 ).getA().getAbsolutePath());
IOFunctions.println( "Found View: ch" + c +" a"+ a + " ti" + ti + " tp"+ tp + " i" + i + " in file " + viewList.get( 0 ).file().getAbsolutePath());

TimePoint tpI = new TimePoint( tpId );
if (!timePoints.contains( tpI ))
timePoints.add( tpI );
Expand Down Expand Up @@ -610,8 +611,8 @@ else if ( aInfoI.axis == 2 )


SequenceDescription sd = new SequenceDescription( new TimePoints( timePoints ), viewSetups , null, new MissingViews( missingViewIds ));
HashMap<BasicViewDescription< ? >, Pair<File, Pair<Integer, Integer>>> fileMap = new HashMap<>();

Map< BasicViewDescription< ? >, FileMapEntry > fileMap = new HashMap<>();
for (Pair<Integer, Integer> k : ViewIDfileMap.keySet())
{
System.out.println( k.getA() + " " + k.getB() );
Expand Down Expand Up @@ -982,7 +983,7 @@ else if (choice.equals( Z_VARIABLE_CHOICE ))
final double calZ = gd.getNextNumber();
final String calUnit = gd.getNextString();

for (final Pair< File, Pair< Integer, Integer > > key : state.getDimensionMap().keySet())
for (final FileMapEntry key : state.getDimensionMap().keySet())
{
final Pair< Dimensions, VoxelDimensions > pairOld = state.getDimensionMap().get( key );
final Pair< Dimensions, VoxelDimensions > pairNew = new ValuePair< Dimensions, VoxelDimensions >( pairOld.getA(), new FinalVoxelDimensions( calUnit, calX, calY, calZ ) );
Expand Down Expand Up @@ -1093,7 +1094,7 @@ else if (choice.equals( Z_VARIABLE_CHOICE ))
((FileMapGettable)data.getSequenceDescription().getImgLoader() ).getFileMap().values().stream().forEach(
p ->
{
filenames.add( p.getA().getAbsolutePath());
filenames.add( p.file().getAbsolutePath());
});
final File prefixPath;
if (filenames.size() > 1)
Expand Down
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