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ij-cmp-bia's Introduction

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I have been working in Machine learning and Data science for several years. I have done my Ph.D. in Medical Imaging. I have gained practical experience working for a few IT companies as a consultant, data scientist, or research engineer. I focus on exploring interesting world problems and solving them with state-of-the-art techniques.

Academic track: I have published several journal articles and papers on international conferences such as ISBI, ICIP, ACCV, and MICCAI workshops. I am also a reviewer for these conferences and other IEEE journals. I was the main organizer of the ANHIR challenge.

ORCID ResearchGate

Developer track: I have created several open-source Python packages, and I am a leading contributor to PyTorch-Lightning and other Lightning projects. I also actively participate in other well-known projects like auto-sklearn, yolov5, dipy, etc., with writing code, reporting issues, building CI/CD, and reviewing PRs.

Manager track: I led a small team while developing a video analysis tool. I have been leading & managing the Lightning team responsible for our open-source projects.

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competition dataset notebook discussion

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JirkaBorovec in/jirka-borovec jirkaborovec @jborovec jirka

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ij-cmp-bia's Issues

wavelets package

Hi,

I couldn't find transform package imported in Descriptors2D (sc.fiji.CMP_BIA.transform.wavelets.HaarWavelets). Is it accessible from somewhere else?

JSLIC Superpixels - Java library errors on iMac

Recently, I started to get an error message when I run the JSLIC superpicels 2D plugin for ImageJ, and I think the error is not inside the JSLIC plugin, but rather is some sort of JAVA configuration error on my iMac. The error message is below, if anyone direct me towards a solution, or users group to discuss this error, I will be grateful.

ImageJ/plugins/segmentation/jSLIC segmentation 2D  *error*

(Fiji Is Just) ImageJ 2.0.0-rc-68/1.52i; Java 1.8.0_73 [64-bit]; Mac OS X 10.13.6; 461MB of 6032MB (7%)
java.lang.NoClassDefFoundError: net/miginfocom/layout/ComponentWrapper
	at org.scijava.ui.swing.console.ConsolePanel.initGui(ConsolePanel.java:110)
	at org.scijava.ui.swing.console.ConsolePanel.<init>(ConsolePanel.java:83)
	at org.scijava.ui.swing.console.SwingConsolePane.initLoggingPanel(SwingConsolePane.java:149)
	at org.scijava.ui.swing.console.SwingConsolePane.consolePanel(SwingConsolePane.java:143)
	at org.scijava.ui.swing.console.SwingConsolePane.append(SwingConsolePane.java:112)
	at org.scijava.ui.console.AbstractConsolePane.outputOccurred(AbstractConsolePane.java:60)
	at org.scijava.console.DefaultConsoleService.notifyListeners(DefaultConsoleService.java:131)
	at org.scijava.console.DefaultConsoleService$OutputStreamReporter.publish(DefaultConsoleService.java:227)
	at org.scijava.console.DefaultConsoleService$OutputStreamReporter.write(DefaultConsoleService.java:213)
	at org.scijava.console.MultiOutputStream.write(MultiOutputStream.java:90)
	at java.io.PrintStream.write(PrintStream.java:480)
	at sun.nio.cs.StreamEncoder.writeBytes(StreamEncoder.java:221)
	at sun.nio.cs.StreamEncoder.implFlushBuffer(StreamEncoder.java:291)
	at sun.nio.cs.StreamEncoder.flushBuffer(StreamEncoder.java:104)
	at java.io.OutputStreamWriter.flushBuffer(OutputStreamWriter.java:185)
	at java.io.PrintStream.write(PrintStream.java:527)
	at java.io.PrintStream.print(PrintStream.java:669)
	at java.io.PrintStream.println(PrintStream.java:806)
	at sc.fiji.CMP_BIA.utils.Logging.logMsg(Logging.java:22)
	at sc.fiji.CMP_BIA.segmentation.superpixels.jSLIC.initInternalVaribales(jSLIC.java:110)
	at sc.fiji.CMP_BIA.segmentation.superpixels.jSLIC.<init>(jSLIC.java:95)
	at sc.fiji.CMP_BIA.segmentation.superpixels.jSLICp2D.<init>(jSLICp2D.java:38)
	at sc.fiji.CMP_BIA.plugins.jSLIC_superpixels_.processSelf(jSLIC_superpixels_.java:150)
	at sc.fiji.CMP_BIA.plugins.jSLIC_superpixels_.process(jSLIC_superpixels_.java:129)
	at sc.fiji.CMP_BIA.plugins.jSLIC_superpixels_.run(jSLIC_superpixels_.java:118)
	at ij.plugin.filter.PlugInFilterRunner.processOneImage(PlugInFilterRunner.java:266)
	at ij.plugin.filter.PlugInFilterRunner.<init>(PlugInFilterRunner.java:114)
	at ij.IJ.runUserPlugIn(IJ.java:230)
	at ij.IJ.runPlugIn(IJ.java:192)
	at ij.Executer.runCommand(Executer.java:137)
	at ij.Executer.run(Executer.java:66)
	at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassNotFoundException: net.miginfocom.layout.ComponentWrapper
	at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:331)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
	... 32 more

No ROIs generated while segmenting gray images

The plugin is working great, however, if I open Lena, convert to 8bits gray and process the image using the JSlic plugin, no ROIs show-up into the ROI manager:

run("Lena (68K)");
run("8-bit");
run("jSLIC superpixels 2D", "init.=30 regularisation=0.20 export overlap=none colour indexed");

However, the segmentation happens.

It is not the case if the image is not converted to gray-scale.

Unnecessary info printed to the Log window

When running the jSLIC plugin, there is a bunch of information printed to the Log window:

 Superpixel size: 35
 jSLIC initialisation...
 jSLIC processing...
 jSLIC process took 6.945s
 jSLIC visualisation...
 -> show ROI manager
 jSLIC finished.

It would be great if that is an option, e.g. a 'Details' checkbox.
In https://github.com/Borda/ij-CMP-BIA/blob/master/src/main/java/sc/fiji/CMP_BIA/plugins/jSLIC_superpixels_.java

I think the lines that have:

ij.IJ.log("whatever message");

and also

 printInfo("whatever message");

should be executed if, for example, a variable set in the plugin dialog is checked.

Otherwise running consecutively the plugin fills the Log window with
information that it is often not necessary and makes it difficult to parse other desired output in the Log window.

For example if there were a dialog entry Details checked it should print the message, otherwise it should not:

 if (details)  ij.IJ.log("whatever message");

or similar.
Or, alternatively just avoid the output as it does not really add anything to the procedure.
Info on the sequence of various steps in the process could be output to the status bar, e.g.

IJ.showStatus("Now I am doing this."); or to the progress bar using IJ.showProgress()

Thanks for considering this.

add CI

Add continues integrations such as Travis
EDIT: maybe GH action would be easier as it will all under one food 🐰

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