thorstenwagner / ij-particlesizer Goto Github PK

Hello,

among the examples on the ImageJ plugin page there are only images included, not the generated text files. We want to reference the ParticleSizer in the NanoDefiner e-tool because the user can directly upload text files generated by the ParticleSizer. It would be nice if the user could see an example of such a file without having to install and use the ParticleSizer (e.g. if they want to transform whatever file format they have to a format compatible with the ParticleSizer output).

It always throws an expection:
Rserve>/bin/sh: null: command not found
java.lang.NullPointerException
at de.biomedical_imaging.ij.rplot.HistogramFrame.getNumberOfBins(HistogramFrame.java:381)

Dear Dr. Wagner,
I wonder is it possible to add an option on the GUI to remove smoothing process, just like the option 'Do not apply denoise'. It will be super helpful, since in some case the smoothing process significantly shortens the length of objects. I tried to make changes to the code in two ways, not sure which one is better or easier or correct? May I have some feedback? Thank you so much!

I tried it on the source code of 1.0.9-SNAP

//Try change default smoothing to 0 @line464. Not sure whether this 0 value works
spinnerSmoothingFactorModel.setMinimum(0.0);

or
//try to add option to remove smoothing @line 152
private static final String PREF_NOSMOOTH = "ndef.nosmoothing";

//Try add option @line 458
checkboxNosmoothing = new JCheckBox("");
checkboxNosmoothing.setSelected(false);

//Not sure about this No smoothing option setting @line 1114
JLabel labelnosmoothing= new JLabel("Do not apply smoothing");
c = new GridBagConstraints();
c.weightx = 0.5;
c.fill = GridBagConstraints.HORIZONTAL;
c.gridx = 0;
c.gridy = gridy;
c.insets = new Insets(0, 5, 0, 5);
pane.add(labelNosmoothing, c);

	c = new GridBagConstraints();
	c.weightx = 0.5;
	c.fill = GridBagConstraints.HORIZONTAL;
	c.gridx = 1;
	c.gridy = gridy;
	c.insets = new Insets(0, 5, 0, 5);
	pane.add(checkboxNosmoothing, c);
	gridy++;

// Add no smooth option @line 1214
ij.Prefs.set(PREF_NOSMOOTH, checkboxNosmoothing.isSelected());

//Not sure about this setting@line143
/*
* No smooth checkbox
*/
checkboxNosmoothing.setSelected(Boolean.parseBoolean(ij.Prefs.get(PREF_NOSMOOTH, "false")));