Skip to content

Commit

Permalink
Merge pull request #161 from saalfeldlab/refactor/delete-minimaltilespec
Browse files Browse the repository at this point in the history 
Delete MinimalTileSpec
  • Loading branch information
@trautmane
trautmane authored Nov 27, 2023
2 parents e88a417 + 03063c9 commit f9d6160
Show file tree
Hide file tree
Showing 31 changed files with 447 additions and 599 deletions.
33 changes: 33 additions & 0 deletions render-app/src/main/java/org/janelia/alignment/spec/TileSpec.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -55,6 +55,7 @@
*/
public class TileSpec implements Serializable {

public static String RESTART_LABEL = "restart";
private String tileId;
private LayoutData layout;
private String groupId;
Expand Down Expand Up @@ -886,6 +887,38 @@ public CoordinateTransformList<CoordinateTransform> getPostMatchingTransformList
return ctl;
}

/**
* Get the path to the image file for this tile spec.
*
* @return path to image file or null if this tile spec does not have an image.
*/
@JsonIgnore
public String getImagePath() {
final ImageAndMask imageAndMask = this.getFirstMipmapEntry().getValue();
return imageAndMask.hasImage() ? imageAndMask.getImageFilePath() : null;
}

/**
* Get the path to the mask file for this tile spec.
*
* @return path to mask file or null if this tile spec does not have a mask.
*/
@JsonIgnore
public String getMaskPath() {
final ImageAndMask imageAndMask = this.getFirstMipmapEntry().getValue();
return imageAndMask.hasMask() ? imageAndMask.getMaskFilePath() : null;
}

/**
* Get the URL to the image file for this tile spec.
*
* @return URL to image file or null if this tile spec does not have an image.
*/
public String getTileImageUrl() {
final ImageAndMask imageAndMask = this.getFirstMipmapEntry().getValue();
return imageAndMask.hasImage() ? imageAndMask.getImageUrl() : null;
}

@Override
public String toString() {
return tileId;
Expand Down
98 changes: 41 additions & 57 deletions ...r-ws-java-client/src/main/java/org/janelia/render/client/intensityadjust/AdjustBlock.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,6 @@
import org.janelia.render.client.RenderDataClient;
import org.janelia.render.client.intensityadjust.intensity.IntensityMatcher;
import org.janelia.render.client.intensityadjust.virtual.OnTheFlyIntensity;
import org.janelia.render.client.solver.MinimalTileSpec;
import org.janelia.render.client.solver.visualize.RenderTools;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
Expand Down Expand Up @@ -65,34 +64,20 @@

public class AdjustBlock {

public static List< MinimalTileSpecWrapper > wrapTileSpecs(final ResolvedTileSpecCollection resolvedTiles)
{
final List< MinimalTileSpecWrapper > data = new ArrayList<>(resolvedTiles.getTileCount());
public static List<TileSpec> sortTileSpecs(final ResolvedTileSpecCollection resolvedTiles) {
// tile order changes adjustment results, so sort tiles by id to ensure (somewhat) consistent results
final List<TileSpec> sortedTileSpecs = resolvedTiles.getTileSpecs()
return resolvedTiles.getTileSpecs()
.stream()
.sorted(Comparator.comparing(TileSpec::getTileId))
.collect(Collectors.toList());
for ( final TileSpec tileSpec : sortedTileSpecs )
{
//final AffineModel2D lastTransform = SolveTools.loadLastTransformFromSpec( tileSpec );
//data.add( new ValuePair<>( lastTransform, new MinimalTileSpec( tileSpec ) ) );
data.add( new MinimalTileSpecWrapper( tileSpec ) );
}

return data;
}

/**
* Fits a quadratic function along X and removes the difference, independently for each image
*
* @param imp
* @param debug
* @return
*/
public static FloatProcessor correct( final ImageProcessorWithMasks imp, final boolean debug )
{
double[] avg = new double[ imp.ip.getWidth() ];
final double[] avg = new double[ imp.ip.getWidth() ];
final ArrayList< Point > points = new ArrayList<>();

// use only 70% of the pixels in the middle
Expand Down Expand Up @@ -126,7 +111,7 @@ public static FloatProcessor correct( final ImageProcessorWithMasks imp, final b

if ( debug )
{
ImagePlus line = ImageJFunctions.wrapFloat( Views.addDimension( ArrayImgs.doubles( avg, avg.length ), 0, 0 ), "" );
final ImagePlus line = ImageJFunctions.wrapFloat(Views.addDimension(ArrayImgs.doubles(avg, avg.length), 0, 0), "");
line.setRoi(new Line(0,0,avg.length,0));
new ProfilePlot( line ).createWindow();
}
Expand All @@ -149,12 +134,12 @@ public static FloatProcessor correct( final ImageProcessorWithMasks imp, final b
*/

//HigherOrderPolynomialFunction q = new HigherOrderPolynomialFunction( 3 );
QuadraticFunction q = new QuadraticFunction();
final QuadraticFunction q = new QuadraticFunction();
q.fitFunction(points);

double avgFit = 0.0;

double[] fit = new double[ avg.length ];
final double[] fit = new double[avg.length];

for ( int x = 0; x < avg.length; ++x )
{
Expand All @@ -165,7 +150,7 @@ public static FloatProcessor correct( final ImageProcessorWithMasks imp, final b

avgFit /= (double)fit.length;

double[] correctedAvg = new double[ avg.length ];
final double[] correctedAvg = new double[avg.length];
final FloatProcessor corrected = new FloatProcessor( imp.ip.getWidth(), imp.ip.getHeight() );

for ( int x = 0; x < avg.length; ++x )
Expand All @@ -180,45 +165,44 @@ public static FloatProcessor correct( final ImageProcessorWithMasks imp, final b

if ( debug )
{
ImagePlus fitImp = ImageJFunctions.wrapFloat( Views.addDimension( ArrayImgs.doubles( fit, fit.length ), 0, 0 ), "" );
final ImagePlus fitImp = ImageJFunctions.wrapFloat(Views.addDimension(ArrayImgs.doubles(fit, fit.length), 0, 0), "");
fitImp.setRoi(new Line(0,0,avg.length,0));
new ProfilePlot( fitImp ).createWindow();

ImagePlus correctedImp = ImageJFunctions.wrapFloat( Views.addDimension( ArrayImgs.doubles( correctedAvg, correctedAvg.length ), 0, 0 ), "" );
final ImagePlus correctedImp = ImageJFunctions.wrapFloat(Views.addDimension(ArrayImgs.doubles(correctedAvg, correctedAvg.length), 0, 0), "");
correctedImp.setRoi(new Line(0,0,avg.length,0));
new ProfilePlot( correctedImp ).createWindow();
}

return corrected;
}
catch (Exception e) {
// TODO Auto-generated catch block
e.printStackTrace();
catch (final Exception e) {
LOG.error("correct: caught exception ", e);
}

return null;
}

public static HashMap< Integer, double[] > computeAdjustments(
final List<Pair<AffineModel2D,MinimalTileSpec>> data,
final List<Pair<AffineModel2D, TileSpec>> data,
final List<Pair<ByteProcessor, FloatProcessor>> corrected )
{
// we need to go from inside to outside adjusting avg and stdev of the overlapping areas
ArrayList< Pair< Integer, Integer > > inputOrder = new ArrayList<>();
final ArrayList<Pair<Integer, Integer>> inputOrder = new ArrayList<>();

for ( int i = 0; i < data.size(); ++i )
inputOrder.add( new ValuePair<>( data.get( i ).getB().getImageCol(), i ) );
inputOrder.add(new ValuePair<>(data.get(i).getB().getLayout().getImageCol(), i));

// sort by column order
Collections.sort( inputOrder, (o1, o2 ) -> o1.getA().compareTo( o2.getA() ) );
inputOrder.sort(Comparator.comparing(Pair::getA));

ArrayList< Integer > order = new ArrayList<>();
final ArrayList<Integer> order = new ArrayList<>();

// [1,2,3,4] -> 3
// [1,2,4] -> 2
// [1,4] -> 4
// [1] -> 1
while( inputOrder.size() > 0 )
while(!inputOrder.isEmpty())
{
final int index = inputOrder.size() / 2;
order.add( inputOrder.get( index ).getB() ); // just remember the index
Expand All @@ -237,7 +221,7 @@ public static HashMap< Integer, double[] > computeAdjustments(

final AffineModel2D model = data.get( i ).getA();
final AffineTransform2D affine = toImgLib( model );
final MinimalTileSpec tileSpec = data.get( i ).getB();
final TileSpec tileSpec = data.get(i).getB();
final RealInterval boundingBox = boundingBox( 0,0,corrected.get( i ).getB().getWidth() - 1,corrected.get( i ).getB().getHeight() - 1, model );

final RealRandomAccessible<FloatType> interpolant = Views.interpolate( Views.extendValue( (RandomAccessibleInterval<FloatType>)(Object)ImagePlusImgs.from( new ImagePlus("", corrected.get( i ).getB() ) ), new FloatType(-1f) ), new NLinearInterpolatorFactory<>() );
Expand Down Expand Up @@ -349,7 +333,7 @@ public static HashMap< Integer, double[] > computeAdjustments(
adjustments.put( i, new double[] { avgO, mul, avgQ } );

LOG.debug("computeAdjustments: adjustment for column {} is: sub {}, mul {}, add {}",
tileSpec.getImageCol(), avgO, mul, avgQ);
tileSpec.getLayout().getImageCol(), avgO, mul, avgQ);
break;
}
}
Expand All @@ -359,7 +343,7 @@ public static HashMap< Integer, double[] > computeAdjustments(
if ( !adjustments.containsKey( i ) )
{
LOG.warn("computeAdjustments: COULD NOT ADJUST column {}, setting to identity",
tileSpec.getImageCol());
tileSpec.getLayout().getImageCol());
adjustments.put( i, new double[] { 0, 1, 0 } );
}
}
Expand All @@ -369,7 +353,7 @@ public static HashMap< Integer, double[] > computeAdjustments(

public static ImageProcessorWithMasks fuseFinal(
final RenderParameters sliceRenderParameters,
final List<MinimalTileSpecWrapper> data1,
final List<TileSpec> data1,
final ArrayList < OnTheFlyIntensity > corrected1,
final ImageProcessorCache imageProcessorCache )
{
Expand All @@ -380,7 +364,7 @@ public static ImageProcessorWithMasks fuseFinal(
false);

for (int i = 0; i < data1.size(); i++) {
final MinimalTileSpecWrapper wrapper = data1.get(i);
final TileSpec tileSpec = data1.get(i);

// this should be a virtual construct
{
Expand All @@ -392,7 +376,7 @@ public static ImageProcessorWithMasks fuseFinal(
final ByteProcessor correctedSource8Bit = correctedSource.convertToByteProcessor();
*/

preloadedImageProcessorCache.put(wrapper.getTileImageUrl(), corrected1.get( i ).computeIntensityCorrection8BitOnTheFly(imageProcessorCache) );
preloadedImageProcessorCache.put(tileSpec.getTileImageUrl(), corrected1.get(i).computeIntensityCorrection8BitOnTheFly(imageProcessorCache));
}
}
// TODO: this will be bigger than 2^31
Expand All @@ -401,7 +385,7 @@ public static ImageProcessorWithMasks fuseFinal(

public static ImageProcessorWithMasks fuseFinal(
final RenderParameters sliceRenderParameters,
final List<MinimalTileSpecWrapper> data1,
final List<TileSpec> data1,
final List<Pair<ByteProcessor, FloatProcessor>> corrected1 ) // TODO: this will likely cause outofmemory
{
// TODO: pass pre-loaded cache in and clear source data so that masks can be cached and reused across z
Expand All @@ -411,7 +395,7 @@ public static ImageProcessorWithMasks fuseFinal(
false);

for (int i = 0; i < data1.size(); i++) {
final MinimalTileSpecWrapper wrapper = data1.get(i);
final TileSpec wrapper = data1.get(i);
final FloatProcessor correctedSource = corrected1.get(i).getB();

// Need to reset intensity range back to full 8-bit before converting to byte processor!
Expand All @@ -426,7 +410,7 @@ public static ImageProcessorWithMasks fuseFinal(

public static RandomAccessibleInterval< UnsignedByteType > fuse2d(
final Interval interval,
final List<Pair<AffineModel2D,MinimalTileSpec>> data,
final List<Pair<AffineModel2D, TileSpec>> data,
final List<Pair<ByteProcessor, FloatProcessor>> corrected,
final Map< Integer, double[] > adjustments )
{
Expand Down Expand Up @@ -479,7 +463,7 @@ public static RandomAccessibleInterval< UnsignedByteType > fuse2d(
public static AffineTransform2D toImgLib( final AffineModel2D model )
{
final AffineTransform2D affine = new AffineTransform2D();
double[] array = new double[6];
final double[] array = new double[6];
model.toArray( array );
affine.set( array[0], array[2], array[4], array[1], array[3], array[5] );
return affine;
Expand Down Expand Up @@ -512,7 +496,7 @@ public static RealInterval boundingBox( final int minX, final int minY, final in
}

public static ArrayList<OnTheFlyIntensity> correctIntensitiesForSliceTiles(
final List<MinimalTileSpecWrapper> sliceTiles,
final List<TileSpec> sliceTiles,
final double renderScale,
final Integer zDistance,
final ImageProcessorCache imageProcessorCache,
Expand Down Expand Up @@ -548,7 +532,7 @@ public static ImageProcessorWithMasks renderIntensityAdjustedSliceGlobalPerSlice
final IntensityCorrectionStrategy strategy,
final int numThreads) throws InterruptedException, ExecutionException
{
final List<MinimalTileSpecWrapper> tilesForZ = wrapTileSpecs(resolvedTiles);
final List<TileSpec> tilesForZ = sortTileSpecs(resolvedTiles);
//final HashMap< Integer, double[] > adjustments = new HashMap<>();

//final List<Pair<ByteProcessor, FloatProcessor>> corrected = new IntensityMatcher().match(
Expand Down Expand Up @@ -577,14 +561,14 @@ public static ImageProcessorWithMasks renderIntensityAdjustedSliceGlobalPerSlice
// final double scale = 0.22;
// final double[] sigma = new double[] { 0, 50 };
//
// final List<MinimalTileSpecWrapper> data = getData(z, renderDataClient, stack);
// final List<TileSpec> data = getData(z, renderDataClient, stack);
// final List<Pair<ByteProcessor, FloatProcessor>> corrected = new ArrayList<>();
// final HashMap< Integer, double[] > adjustments = new HashMap<>();
//
// int k = -1;
// for (final Pair<AffineModel2D, MinimalTileSpec> tile : data) {
// for (final Pair<AffineModel2D, TileSpec> tile : data) {
// ++k;
// final MinimalTileSpec minimalTileSpec = tile.getB();
// final TileSpec minimalTileSpec = tile.getB();
//
// //if (minimalTileSpec.getImageCol() != 0 )
// // continue;
Expand Down Expand Up @@ -704,12 +688,12 @@ public static ImageProcessorWithMasks renderIntensityAdjustedSliceGlobalPerSlice
// final int z)
// throws IOException {
//
// final List<MinimalTileSpecWrapper> data = getData(z, renderDataClient, stack);
// final List<TileSpec> data = getData(z, renderDataClient, stack);
// final List<Pair<ByteProcessor, FloatProcessor>> corrected = new ArrayList<>();
//
// for ( final Pair<AffineModel2D,MinimalTileSpec> tile : data )
// for ( final Pair<AffineModel2D,TileSpec> tile : data )
// {
// final MinimalTileSpec minimalTileSpec = tile.getB();
// final TileSpec minimalTileSpec = tile.getB();
//
// LOG.debug("renderIntensityAdjustedSlice: processing tile {} in column {}",
// minimalTileSpec.getTileId(), minimalTileSpec.getImageCol());
Expand All @@ -731,12 +715,12 @@ public static ImageProcessorWithMasks renderIntensityAdjustedSliceGlobalPerSlice
// return fuse2d(interval, data, corrected, adjustments);
// }

public static void main( String[] args ) throws IOException, InterruptedException, ExecutionException
public static void main(final String[] args) throws IOException, InterruptedException, ExecutionException
{
String baseUrl = "http://tem-services.int.janelia.org:8080/render-ws/v1";
String owner = "Z0720_07m_BR"; //"flyem";
String project = "Sec39";//"Sec26"; //"Z0419_25_Alpha3";
String stack = "v1_acquire_trimmed_sp1";//"v2_acquire_trimmed_align"; //"v1_acquire_sp_nodyn_v2";
final String baseUrl = "http://tem-services.int.janelia.org:8080/render-ws/v1";
final String owner = "Z0720_07m_BR"; //"flyem";
final String project = "Sec39";//"Sec26"; //"Z0419_25_Alpha3";
final String stack = "v1_acquire_trimmed_sp1";//"v2_acquire_trimmed_align"; //"v1_acquire_sp_nodyn_v2";

final RenderDataClient renderDataClient = new RenderDataClient(baseUrl, owner, project );
final StackMetaData meta = renderDataClient.getStackMetaData( stack );
Expand Down Expand Up @@ -792,7 +776,7 @@ public static void main( String[] args ) throws IOException, InterruptedExceptio

final ImagePlus imp1 = new ImagePlus( project + "_" + stack, stack3d );

Calibration cal = new Calibration();
final Calibration cal = new Calibration();
cal.xOrigin = -(int)interval.min(0);
cal.yOrigin = -(int)interval.min(1);
cal.zOrigin = -minZ;
Expand Down
9 changes: 5 additions & 4 deletions ...ain/java/org/janelia/render/client/intensityadjust/AffineIntensityCorrectionStrategy.java
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,6 +7,7 @@
import mpicbg.models.Model;
import mpicbg.models.Tile;
import mpicbg.models.TranslationModel1D;
import org.janelia.alignment.spec.TileSpec;
import org.janelia.render.client.intensityadjust.intensity.PointMatchFilter;
import org.janelia.render.client.intensityadjust.intensity.RansacRegressionReduceFilter;
import org.janelia.render.client.intensityadjust.virtual.LinearOnTheFlyIntensity;
Expand Down Expand Up @@ -36,12 +37,12 @@ public AffineIntensityCorrectionStrategy(final double lambda1, final double lamb
@Override
// TODO: this code should be computed on-the-fly as a function of the coefficients
public ArrayList<OnTheFlyIntensity> getOnTheFlyIntensities(
final List<MinimalTileSpecWrapper> patches,
final List<TileSpec> patches,
final int numCoefficients,
final Map<MinimalTileSpecWrapper, ArrayList<Tile<? extends Affine1D<?>>>> coefficientsTiles) {
final Map<TileSpec, ArrayList<Tile<? extends Affine1D<?>>>> coefficientsTiles) {

final ArrayList<OnTheFlyIntensity> correctedOnTheFly = new ArrayList<>();
for (final MinimalTileSpecWrapper p : patches) {
for (final TileSpec p : patches) {
/* save coefficients */
final double[][] ab_coefficients = new double[numCoefficients * numCoefficients][2];

Expand All @@ -61,7 +62,7 @@ public ArrayList<OnTheFlyIntensity> getOnTheFlyIntensities(

@Override
@SuppressWarnings("unchecked") // modelTemplate is always of the type given above
public <M extends Model<M>> M getModelFor(final MinimalTileSpecWrapper p) {
public <M extends Model<M>> M getModelFor(final TileSpec p) {
return (M) modelTemplate.copy();
}

Expand Down
Loading

0 comments on commit f9d6160

Please sign in to comment.