Video producer tool using benchmarks in BDV #136
+1,356
−5
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,25 @@ | ||
| # bigdataviewer-core | ||
| [](https://github.com/bigdataviewer/bigdataviewer-core/actions/workflows/build-main.yml) | ||
| [](https://gitter.im/bigdataviewer/bigdataviewer-core?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge) ImgLib2-based viewer for registered SPIM stacks and more | ||
| --- | ||
| Feature added in this fork: **Interactive Video producing using Spline interpolation** | ||
|
|
||
| ### Install: | ||
| `$ ./install.sh` | ||
|
|
||
| ### Run: | ||
| `$ ./bdv INPUT_PATH` | ||
|
|
||
| ### How to use: | ||
|
|
||
| 1- **Video producer panel** can be opened by clicking `F7` or via `Tools -> Produce Movie` | ||
|  | ||
|
|
||
| 2- By opening Video Producer you get this panel | ||
|  | ||
| - `+` To add current frame | ||
| - `-` To delete last frame | ||
| - Preview with a frame down-sampling and sleep time between frames | ||
| - Accel: you select the interpolation: `Slow start` , `slow end` , `Symmetric` ... | ||
| - Export: Can be in `Json` or `PNG sequence` | ||
| - Import saved `Json` | ||
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
Loading
Sorry, something went wrong. Reload?
Sorry, we cannot display this file.
Sorry, this file is invalid so it cannot be displayed.
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,60 @@ | ||
| #!/bin/bash | ||
|
|
||
| # This script is shamelessly adapted from https://github.com/saalfeldlab/n5-utils, thanks @axtimwalde & co! | ||
|
|
||
| VERSION="10.3.2-SNAPSHOT" | ||
| INSTALL_DIR=${1:-$(pwd)} | ||
|
|
||
| echo "" | ||
| echo "Installing into $INSTALL_DIR" | ||
|
|
||
| # check for operating system | ||
| if [[ "$OSTYPE" == "linux-gnu" ]]; then | ||
| echo "Assuming on Linux operating system" | ||
| MEM=$(cat /proc/meminfo | grep MemTotal | sed s/^MemTotal:\\\s*\\\|\\\s\\+[^\\\s]*$//g) | ||
| MEMGB=$(($MEM/1024/1024)) | ||
| MEM=$((($MEMGB/5)*4)) | ||
| elif [[ "$OSTYPE" == "darwin"* ]]; then | ||
| echo "Assuming on MacOS X operating system" | ||
| # sysctl returns total hardware memory size in bytes | ||
| MEM=$(sysctl hw.memsize | grep hw.memsize | sed s/hw.memsize://g) | ||
| MEMGB=$(($MEM/1024/1024/1024)) | ||
| MEM=$((($MEMGB/5)*4)) | ||
| else | ||
| echo "ERROR - Operating system (arg2) must be either linux or osx - EXITING (on windows please run as a normal Java class from e.g. Eclipse)" | ||
| exit | ||
| fi | ||
|
|
||
| echo "Available memory:" $MEMGB "GB, setting Java memory limit to" $MEM "GB" | ||
|
|
||
| mvn clean install | ||
| mvn -Dmdep.outputFile=cp.txt -Dmdep.includeScope=runtime dependency:build-classpath | ||
|
|
||
| echo "" | ||
| echo "Installing 'bdv' command into" $INSTALL_DIR | ||
|
|
||
| echo '#!/bin/bash' > bdv | ||
| echo '' >> bdv | ||
| echo "JAR=\$HOME/.m2/repository/sc/fiji/bigdataviewer-core/${VERSION}/bigdataviewer-core-${VERSION}.jar" >> bdv | ||
| echo 'java \' >> bdv | ||
| echo " -Xmx${MEM}g \\" >> bdv | ||
| echo ' -XX:+UseConcMarkSweepGC \' >> bdv | ||
| echo -n ' -cp $JAR:' >> bdv | ||
| echo -n $(cat cp.txt) >> bdv | ||
| echo ' \' >> bdv | ||
| echo ' bdv.BigDataViewer "$@"' >> bdv | ||
|
|
||
|
|
||
| chmod a+x bdv | ||
|
|
||
| if [ $(pwd) == "$INSTALL_DIR" ]; then | ||
| echo "Installation directory equals current directory, we are done." | ||
| else | ||
| echo "Creating directory $INSTALL_DIR and moving files..." | ||
| mkdir -p $INSTALL_DIR | ||
| mv bdv $INSTALL_DIR/ | ||
| fi | ||
|
|
||
| rm cp.txt | ||
|
|
||
| echo "Installation finished." |
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -28,41 +28,6 @@ | |
| */ | ||
| package bdv; | ||
|
|
||
| import bdv.cache.CacheControl; | ||
| import bdv.export.ProgressWriter; | ||
| import bdv.export.ProgressWriterConsole; | ||
|
|
@@ -82,22 +47,51 @@ | |
| import bdv.tools.brightness.RealARGBColorConverterSetup; | ||
| import bdv.tools.brightness.SetupAssignments; | ||
| import bdv.tools.crop.CropDialog; | ||
| import bdv.tools.movie.ProduceMovieDialog; | ||
| import bdv.tools.transformation.ManualTransformation; | ||
| import bdv.tools.transformation.ManualTransformationEditor; | ||
| import bdv.tools.transformation.TransformedSource; | ||
| import bdv.viewer.ConverterSetups; | ||
| import bdv.viewer.NavigationActions; | ||
| import bdv.viewer.SourceAndConverter; | ||
| import bdv.viewer.ViewerFrame; | ||
| import bdv.viewer.ViewerOptions; | ||
| import bdv.viewer.ViewerPanel; | ||
| import bdv.viewer.ViewerState; | ||
| import mpicbg.spim.data.SpimDataException; | ||
| import mpicbg.spim.data.generic.AbstractSpimData; | ||
| import mpicbg.spim.data.generic.sequence.AbstractSequenceDescription; | ||
| import mpicbg.spim.data.generic.sequence.BasicViewSetup; | ||
| import mpicbg.spim.data.sequence.Angle; | ||
| import mpicbg.spim.data.sequence.Channel; | ||
| import net.imglib2.Volatile; | ||
| import net.imglib2.converter.Converter; | ||
| import net.imglib2.display.ColorConverter; | ||
| import net.imglib2.display.RealARGBColorConverter; | ||
| import net.imglib2.display.ScaledARGBConverter; | ||
| import net.imglib2.type.numeric.ARGBType; | ||
| import net.imglib2.type.numeric.NumericType; | ||
| import net.imglib2.type.numeric.RealType; | ||
| import net.imglib2.type.volatiles.VolatileARGBType; | ||
| import org.jdom2.Document; | ||
| import org.jdom2.Element; | ||
| import org.jdom2.JDOMException; | ||
| import org.jdom2.input.SAXBuilder; | ||
| import org.jdom2.output.Format; | ||
| import org.jdom2.output.XMLOutputter; | ||
| import org.scijava.ui.behaviour.io.InputTriggerConfig; | ||
| import org.scijava.ui.behaviour.io.yaml.YamlConfigIO; | ||
| import org.scijava.ui.behaviour.util.Actions; | ||
|
|
||
| import javax.swing.*; | ||
|
There was a problem hiding this comment. Are we doing wildcards in the imports now? |
||
| import javax.swing.filechooser.FileFilter; | ||
| import java.io.File; | ||
| import java.io.FileNotFoundException; | ||
| import java.io.FileWriter; | ||
| import java.io.IOException; | ||
| import java.util.ArrayList; | ||
| import java.util.List; | ||
|
|
||
| public class BigDataViewer | ||
| { | ||
| protected final ViewerFrame viewerFrame; | ||
|
|
@@ -116,6 +110,8 @@ public class BigDataViewer | |
|
|
||
| protected final RecordMovieDialog movieDialog; | ||
|
|
||
| protected final ProduceMovieDialog produceMovieDialog; | ||
|
|
||
| protected final RecordMaxProjectionDialog movieMaxProjectDialog; | ||
|
|
||
| protected final VisibilityAndGroupingDialog activeSourcesDialog; | ||
|
|
@@ -373,6 +369,8 @@ public BigDataViewer( | |
| cropDialog = ( spimData == null ) ? null : new CropDialog( viewerFrame, viewer, spimData.getSequenceDescription() ); | ||
|
|
||
| movieDialog = new RecordMovieDialog( viewerFrame, viewer, progressWriter ); | ||
|
|
||
| produceMovieDialog = new ProduceMovieDialog( viewerFrame, viewer, progressWriter ); | ||
| // this is just to get updates of window size: | ||
| viewer.getDisplay().overlays().add( movieDialog ); | ||
|
|
||
|
|
@@ -458,6 +456,10 @@ public boolean accept( final File f ) | |
| miMovie.setText( "Record Movie" ); | ||
| menu.add( miMovie ); | ||
|
|
||
| final JMenuItem miMovieProducer = new JMenuItem( actionMap.get( BigDataViewerActions.PRODUCE_MOVIE ) ); | ||
| miMovieProducer.setText( "Produce Movie" ); | ||
| menu.add( miMovieProducer ); | ||
|
|
||
| final JMenuItem miMaxProjectMovie = new JMenuItem( actionMap.get( BigDataViewerActions.RECORD_MAX_PROJECTION_MOVIE ) ); | ||
| miMaxProjectMovie.setText( "Record Max-Projection Movie" ); | ||
| menu.add( miMaxProjectMovie ); | ||
|
|
@@ -744,18 +746,25 @@ public static void main( final String[] args ) | |
| // final String fn = "/Users/pietzsch/Desktop/data/fibsem-remote.xml"; | ||
| // final String fn = "/Users/pietzsch/Desktop/url-valia.xml"; | ||
| // final String fn = "/Users/pietzsch/Desktop/data/clusterValia/140219-1/valia-140219-1.xml"; | ||
| // final String fn = "/Users/pietzsch/workspace/data/111010_weber_full.xml"; | ||
|
There was a problem hiding this comment. Should we keep this for @tpietzsch ? |
||
| // final String fn = "/Volumes/projects/tomancak_lightsheet/Mette/ZeissZ1SPIM/Maritigrella/021013_McH2BsGFP_CAAX-mCherry/11-use/hdf5/021013_McH2BsGFP_CAAX-mCherry-11-use.xml"; | ||
|
|
||
| // final String fn = "/Users/Marwan/Downloads/drosophila_his-yfp/dataset.xml"; | ||
|
|
||
| try | ||
| { | ||
| final String fn = args[0]; | ||
| System.setProperty( "apple.laf.useScreenMenuBar", "true" ); | ||
|
|
||
| final BigDataViewer bdv = open( fn, new File( fn ).getName(), new ProgressWriterConsole(), ViewerOptions.options() ); | ||
|
|
||
| // PanelSnapshot.showPanel(bdv.getViewer()); | ||
| // DumpInputConfig.writeToYaml( System.getProperty( "user.home" ) + "/.bdv/bdvkeyconfig.yaml", bdv.getViewerFrame() ); | ||
| } | ||
| catch ( final Exception e ) | ||
| { | ||
| if (args.length==0) | ||
| System.out.println("Please specify the input"); | ||
| e.printStackTrace(); | ||
| } | ||
| } | ||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,49 @@ | ||
| package bdv.tools.movie; | ||
|
|
||
| import javax.swing.*; | ||
| import java.awt.*; | ||
|
Comment on lines
+3
to
+4
|
||
| import java.awt.image.BufferedImage; | ||
|
|
||
| public class ImagePanel extends JPanel { | ||
| private final BufferedImage image; | ||
|
|
||
| public ImagePanel(BufferedImage image) { | ||
| super(); | ||
| setPreferredSize(new Dimension(90, 90)); | ||
| this.image = scale(image, 90, 90); | ||
| } | ||
|
|
||
| public static ImagePanel snapshotOf(JPanel panel) { | ||
| return new ImagePanel(takeSnapShot(panel)); | ||
| } | ||
|
|
||
| @Override | ||
| protected void paintComponent(Graphics g) { | ||
| super.paintComponent(g); | ||
| g.drawImage(image, 0, 0, this); | ||
| } | ||
|
|
||
| public static BufferedImage scale(BufferedImage src, int w, int h) { | ||
| BufferedImage img = new BufferedImage(w, h, BufferedImage.TYPE_INT_RGB); | ||
| int x, y; | ||
| int ww = src.getWidth(); | ||
| int hh = src.getHeight(); | ||
| int[] ys = new int[h]; | ||
| for (y = 0; y < h; y++) | ||
| ys[y] = y * hh / h; | ||
| for (x = 0; x < w; x++) { | ||
| int newX = x * ww / w; | ||
| for (y = 0; y < h; y++) { | ||
| int col = src.getRGB(newX, ys[y]); | ||
| img.setRGB(x, y, col); | ||
| } | ||
| } | ||
| return img; | ||
| } | ||
|
|
||
| public static BufferedImage takeSnapShot(JPanel panel){ | ||
| BufferedImage bufImage = new BufferedImage(panel.getSize().width, panel.getSize().height,BufferedImage.TYPE_INT_RGB); | ||
| panel.paint(bufImage.createGraphics()); | ||
| return bufImage; | ||
| } | ||
| } | ||
Oops, something went wrong.
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
There was a problem hiding this comment.
Choose a reason for hiding this comment
The reason will be displayed to describe this comment to others. Learn more.
Mention Windows install instructions or recommend WSL2.