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Updates dependencies
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Fix path issue in Windows (dirty)
Fix some intellij 'raw' class usage, let's hope it doesn't break anything
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@NicoKiaru
NicoKiaru committed May 21, 2024
1 parent b74e7b2 commit ae9cc8d
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Showing 6 changed files with 59 additions and 27 deletions.
22 changes: 21 additions & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -106,10 +106,30 @@
<package-name>ch.epfl.biop.atlas</package-name>
<license.licenseName>gpl_v3</license.licenseName>
<license.copyrightOwners>EPFL</license.copyrightOwners>
<bigdataviewer-playground.version>0.8.1</bigdataviewer-playground.version>
<bigdataviewer-playground.version>0.10.1</bigdataviewer-playground.version>

<!-- NB: Deploy releases to the SciJava Maven repository. -->
<releaseProfiles>sign,deploy-to-scijava</releaseProfiles>


<n5.version>3.1.1</n5.version>
<n5-hdf5.version>2.1.0</n5-hdf5.version>
<n5-zarr.version>1.2.0</n5-zarr.version>
<n5-ij.version>4.0.1</n5-ij.version>
<n5-universe.version>1.3.1</n5-universe.version>
<n5-zstandard.version>1.0.2</n5-zstandard.version>
<org.janelia.n5-zstandard.version>${n5-zstandard.version}</org.janelia.n5-zstandard.version>

<bigwarp.version>9.1.2</bigwarp.version>
<bigwarp_fiji.version>9.1.2</bigwarp_fiji.version>
<bigdataviewer-core.version>10.4.13</bigdataviewer-core.version>
<bigdataviewer-vistools.version>1.0.0-beta-34</bigdataviewer-vistools.version>
<imglib2-realtransform.version>4.0.2</imglib2-realtransform.version>

<ejml-core.version>0.41</ejml-core.version>
<ejml-ddense.version>0.41</ejml-ddense.version>

<jitk-tps.version>3.0.4</jitk-tps.version>
</properties>

<repositories>
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17 changes: 11 additions & 6 deletions src/main/java/ch/epfl/biop/atlas/mouse/allen/ccfv3/AllenMap.java
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Expand Up @@ -56,9 +56,9 @@ public class AllenMap implements AtlasMap {
final static private int AraSetupId = 2;
final static private int LabelSetupId = 3;

final Map<String,SourceAndConverter> atlasSources = new HashMap<>();
final Map<String,SourceAndConverter<?>> atlasSources = new HashMap<>();

SourceAndConverter labelSource;
SourceAndConverter<?> labelSource;

@Override
public void initialize(String atlasName) {
Expand All @@ -70,6 +70,11 @@ public void initialize(String atlasName) {
address = address.substring(5).replaceAll("%20", " ");
}

// Fix a stupid issue... For some reason the path may contain an extra slash in windows
if (System.getProperty("os.name").startsWith("Windows") && address.startsWith("/")) {
address = address.substring(1);
}

SpimDataFromXmlImporter importer = new SpimDataFromXmlImporter(address);

final List<SourceAndConverter<?>> sacs = SourceAndConverterServices
Expand All @@ -89,14 +94,14 @@ public void initialize(String atlasName) {
}
};

FunctionRealRandomAccessible leftRightSource = new FunctionRealRandomAccessible(3,
FunctionRealRandomAccessible<UnsignedShortType> leftRightSource = new FunctionRealRandomAccessible<>(3,
leftRightIndicator, UnsignedShortType::new);

final Source< UnsignedShortType > s = new RealRandomAccessibleIntervalSource<>( leftRightSource,
FinalInterval.createMinMax( 0, 0, 0, 1000, 1000, 0),
new UnsignedShortType(), new AffineTransform3D(), "Left_Right" );

SourceAndConverter leftRight = SourceAndConverterHelper.createSourceAndConverter(s);
SourceAndConverter<?> leftRight = SourceAndConverterHelper.createSourceAndConverter(s);

atlasSources.put("Left Right", leftRight);

Expand All @@ -123,7 +128,7 @@ public URL getDataSource() {
}

@Override
public Map<String,SourceAndConverter> getStructuralImages() {
public Map<String,SourceAndConverter<?>> getStructuralImages() {
return atlasSources;
}

Expand All @@ -141,7 +146,7 @@ public List<String> getImagesKeys() {
}

@Override
public SourceAndConverter getLabelImage() {
public SourceAndConverter<?> getLabelImage() {
return labelSource;
}

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12 changes: 6 additions & 6 deletions ...in/java/ch/epfl/biop/atlas/rat/waxholm/spraguedawley/v4/WaxholmSpragueDawleyRatV4Map.java
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Expand Up @@ -50,9 +50,9 @@ public class WaxholmSpragueDawleyRatV4Map implements AtlasMap {

public String name;

final Map<String,SourceAndConverter> atlasSources = new HashMap<>();
final Map<String,SourceAndConverter<?>> atlasSources = new HashMap<>();

SourceAndConverter labelSource;
SourceAndConverter<?> labelSource;

@Override
public void setDataSource(URL dataSource) {
Expand Down Expand Up @@ -94,14 +94,14 @@ public void initialize(String atlasName) {
}
};

FunctionRealRandomAccessible leftRightSource = new FunctionRealRandomAccessible(3,
FunctionRealRandomAccessible<UnsignedShortType> leftRightSource = new FunctionRealRandomAccessible<>(3,
leftRightIndicator, UnsignedShortType::new);

final Source< UnsignedShortType > s = new RealRandomAccessibleIntervalSource<>( leftRightSource,
FinalInterval.createMinMax( 0, 0, 0, 1000, 1000, 0),
new UnsignedShortType(), new AffineTransform3D(), "Left_Right" );

SourceAndConverter leftRight = SourceAndConverterHelper.createSourceAndConverter(s);
SourceAndConverter<?> leftRight = SourceAndConverterHelper.createSourceAndConverter(s);

atlasSources.put("Left Right", leftRight);

Expand All @@ -121,7 +121,7 @@ public void initialize(String atlasName) {
}

@Override
public Map<String,SourceAndConverter> getStructuralImages() {
public Map<String,SourceAndConverter<?>> getStructuralImages() {
return atlasSources;
}

Expand All @@ -138,7 +138,7 @@ public List<String> getImagesKeys() {
}

@Override
public SourceAndConverter getLabelImage() {
public SourceAndConverter<?> getLabelImage() {
return labelSource;
}

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17 changes: 11 additions & 6 deletions ...ava/ch/epfl/biop/atlas/rat/waxholm/spraguedawley/v4p2/WaxholmSpragueDawleyRatV4p2Map.java
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Original file line number Diff line number Diff line change
Expand Up @@ -50,9 +50,9 @@ public class WaxholmSpragueDawleyRatV4p2Map implements AtlasMap {

public String name;

final Map<String,SourceAndConverter> atlasSources = new HashMap<>();
final Map<String,SourceAndConverter<?>> atlasSources = new HashMap<>();

SourceAndConverter labelSource;
SourceAndConverter<?> labelSource;

@Override
public void setDataSource(URL dataSource) {
Expand All @@ -74,6 +74,11 @@ public void initialize(String atlasName) {
address = address.substring(5).replaceAll("%20", " ");
}

// Fix a stupid issue... For some reason the path may contain an extra slash in windows
if (System.getProperty("os.name").startsWith("Windows") && address.startsWith("/")) {
address = address.substring(1);
}

SpimDataFromXmlImporter importer = new SpimDataFromXmlImporter(address);

final List<SourceAndConverter<?>> sacs = SourceAndConverterServices
Expand All @@ -96,14 +101,14 @@ public void initialize(String atlasName) {
}
};

FunctionRealRandomAccessible leftRightSource = new FunctionRealRandomAccessible(3,
FunctionRealRandomAccessible<UnsignedShortType> leftRightSource = new FunctionRealRandomAccessible<>(3,
leftRightIndicator, UnsignedShortType::new);

final Source< UnsignedShortType > s = new RealRandomAccessibleIntervalSource<>( leftRightSource,
FinalInterval.createMinMax( 0, 0, 0, 1000, 1000, 0),
new UnsignedShortType(), new AffineTransform3D(), "Left_Right" );

SourceAndConverter leftRight = SourceAndConverterHelper.createSourceAndConverter(s);
SourceAndConverter<?> leftRight = SourceAndConverterHelper.createSourceAndConverter(s);

atlasSources.put("Left Right", leftRight);

Expand All @@ -123,7 +128,7 @@ public void initialize(String atlasName) {
}

@Override
public Map<String,SourceAndConverter> getStructuralImages() {
public Map<String,SourceAndConverter<?>> getStructuralImages() {
return atlasSources;
}

Expand All @@ -141,7 +146,7 @@ public List<String> getImagesKeys() {
}

@Override
public SourceAndConverter getLabelImage() {
public SourceAndConverter<?> getLabelImage() {
return labelSource;
}

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4 changes: 4 additions & 0 deletions src/main/java/ch/epfl/biop/atlas/scijava/AtlasChooserCommand.java
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Original file line number Diff line number Diff line change
Expand Up @@ -69,14 +69,18 @@ public void run() {
try {
switch (choice) {
case WaxholmSpragueDawleyRatV4p2Atlas.atlasName:
//System.out.println("RAT (Java)");
atlas = (Atlas) cmd.run(WaxholmSpragueDawleyRatV4p2Command.class, true).get().getOutput("ba");
break;
case AllenBrainAdultMouseAtlasCCF2017v3p1Command.atlasName:
//System.out.println("MOUSE (Java)");
atlas = (Atlas) cmd.run(AllenBrainAdultMouseAtlasCCF2017v3p1Command.class, true).get().getOutput("ba");
break;
default:
if (extraAtlases.containsKey(choice)) {
//System.out.println(choice+" (Python)");
atlas = extraAtlases.get(choice).get();
//System.out.println("Atlas null ? "+(atlas==null));
} else {
System.err.println("Unrecognized atlas named " + choice);
}
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14 changes: 6 additions & 8 deletions src/main/java/ch/epfl/biop/atlas/struct/AtlasMap.java
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Original file line number Diff line number Diff line change
Expand Up @@ -30,15 +30,13 @@

/**
* Interface to define an AtlasMap
*
* <br>
* Pairs with AtlasOntology
*
* <br>
* The Atlas Map contains :
* - 3D images among which there are:
* - structural images, which are different modalities acquired for an atlas (fluorescence, brightfield)
* - a single Label Image
*
*
*/
public interface AtlasMap {

Expand All @@ -50,21 +48,21 @@ public interface AtlasMap {

/**
* Triggers the initialisation of the Atlas
* @param atlasName
* @param atlasName name to give to the atlas
*/
void initialize(String atlasName);

/**
* For convenience
* @return
* @return the original URL of where the data was read from
*/
URL getDataSource();

Map<String,SourceAndConverter> getStructuralImages();
Map<String,SourceAndConverter<?>> getStructuralImages();

List<String> getImagesKeys();

SourceAndConverter getLabelImage();
SourceAndConverter<?> getLabelImage();

Double getAtlasPrecisionInMillimeter();

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