Commit 2819d44e authored by gonciarz's avatar gonciarz
Browse files

IA - drawing particles is not using calibration from images now (IA is pixel based)

parent aa238d7a
......@@ -87,26 +87,21 @@
<parent>
<groupId>org.scijava</groupId>
<artifactId>pom-scijava</artifactId>
<version>27.0.1</version>
<version>29.2.1</version>
<relativePath />
</parent>
<repositories>
<repository>
<id>imagej.public</id>
<url>http://maven.imagej.net/content/groups/public</url>
</repository>
<!-- temporary (but remotely accessible repository for not available otherwise jars -->
<!-- <repository>
<id>mosaic.public</id>
<url>http://mosaic.mpi-cbg.de/maven/</url>
</repository> -->
<!-- use instead above mosaic repository local one embedded in source tree -->
<!-- local repository with jars which are not available online -->
<repository>
<id>local-repo</id>
<name>repo</name>
<url>file://${project.basedir}/repo</url>
</repository>
<repository>
<id>scijava.public</id>
<url>https://maven.scijava.org/content/groups/public</url>
</repository>
<repository>
<id>clij</id>
<url>http://dl.bintray.com/haesleinhuepf/clij</url>
......@@ -117,7 +112,11 @@
<dependencies>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>ij</artifactId>
<artifactId>imagej</artifactId>
</dependency>
<dependency>
<groupId>net.imagej</groupId>
<artifactId>imagej-deprecated</artifactId>
</dependency>
<dependency>
<groupId>net.imglib2</groupId>
......@@ -198,10 +197,6 @@
<artifactId>commons-io</artifactId>
<version>2.4</version>
</dependency>
<dependency>
<groupId>org.apache.commons</groupId>
<artifactId>commons-lang3</artifactId>
</dependency>
<dependency>
<groupId>log4j</groupId>
<artifactId>log4j</artifactId>
......@@ -216,6 +211,12 @@
<groupId>net.sf.dozer</groupId>
<artifactId>dozer</artifactId>
<version>5.5.1</version>
<exclusions>
<exclusion>
<groupId>org.slf4j</groupId>
<artifactId>jcl-over-slf4j</artifactId>
</exclusion>
</exclusions>
</dependency>
<dependency>
<groupId>net.sf.supercsv</groupId>
......@@ -223,11 +224,11 @@
<version>2.4.0</version>
</dependency>
<dependency>
<groupId>com.github.rwl</groupId>
<groupId>edu.emory.mathcs</groupId>
<artifactId>jtransforms</artifactId>
<version>2.4.0</version>
<version>2.4</version>
<!-- <scope>runtime</scope>-->
</dependency>
<!-- Exclude com.google.android.tools since it conflicts with same symbols from junit -->
<dependency>
<groupId>net.haesleinhuepf</groupId>
......@@ -257,26 +258,6 @@
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-shade-plugin</artifactId>
<version>2.4.3</version>
<executions>
<execution>
<id>generate-allIn1-jar</id>
<phase>package</phase>
<goals>
<goal>shade</goal>
</goals>
<configuration>
<outputFile>target/${project.artifactId}-${project.version}_Full.jar</outputFile>
<!-- Intentionally not 'true' - removes too much
from destination jar (like org.apache.commons.beanutils.ConvertUtils) -->
<minimizeJar>false</minimizeJar>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<executions>
......
......@@ -641,7 +641,6 @@ public class FeaturePointDetector {
iUseCLIJ = aUseClij;
logger.info("Detection options: radius=" + iRadius + " cutoff=" + iCutoff + " percentile=" + iPercentile + " threshold=" + iAbsIntensityThreshold + " mode=" + (absolute ? "THRESHOLD" : "PERCENTILE") + " useCLIJ=" + iUseCLIJ);
System.out.println("Detection options: radius=" + iRadius + " cutoff=" + iCutoff + " percentile=" + iPercentile + " threshold=" + iAbsIntensityThreshold + " mode=" + (absolute ? "THRESHOLD" : "PERCENTILE") + " useCLIJ=" + iUseCLIJ);
// create Mask for Dilation with the user defined radius
generateDilationMasks(iRadius);
......
......@@ -98,9 +98,11 @@ public class DistanceCalculationsImage extends DistanceCalculations {
// Show input image
aInputImg.show();
// Get parameters from user
// Create point detector with set range of values
final StackStatistics imgStatistics = new StackStatistics(aInputImg);
final FeaturePointDetector featurePointDetector = new FeaturePointDetector((float) imgStatistics.max, (float) imgStatistics.min);
// Get parameters from user
final GenericDialog gd = new GenericDialog("Particle Detection...", IJ.getInstance());
GUIhelper.addUserDefinedParametersDialog(gd, featurePointDetector);
gd.showDialog();
......@@ -118,7 +120,8 @@ public class DistanceCalculationsImage extends DistanceCalculations {
// Draw dots on the positions of the detected particles on the frame and shows it
final Img<T> background = ImagePlusAdapter.wrap(aInputImg);
final Img<ARGBType> detected = frame.createImage(background, aInputImg.getCalibration());
// Do not use calibration since we detect particles based on image pixel positions and not a real values.
final Img<ARGBType> detected = frame.createImage(background, null /* no calibration */);
ImageJFunctions.show(detected);
return frame.getParticles();
......
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