tferr / asa Goto Github PK

Here is the Exception:

(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51g; Java 1.8.0_102 [64-bit]; Mac OS X 10.9.5; 763MB of 5714MB (13%)

java.lang.NullPointerException
    at sholl.Sholl_Analysis.removeOverlayShells(Sholl_Analysis.java:2221)
    at sholl.Sholl_Analysis.overlayShells(Sholl_Analysis.java:2236)
    at sholl.Sholl_Analysis.run(Sholl_Analysis.java:691)
    at ij.IJ.runUserPlugIn(IJ.java:217)
    at ij.IJ.runPlugIn(IJ.java:181)
    at ij.Executer.runCommand(Executer.java:137)
    at ij.Executer.run(Executer.java:66)
    at java.lang.Thread.run(Thread.java:745)

had a z-stack that was converted to a max projection z-project. After thresholding and converting to binary, setting up a sholl analysis with step size = 0 resulted in a sholl mask of one color. Increasing the step size showed a more accurate sholl mask, but did not stop at the ending radius. Appreciate any help on the matter.

When I updated the pom-fiji (25f2c2e7), the jenkins job for Sholl Analysis failed. It seems that pom-fiji-21.1.0 and later have set the jdk to version 1.8. Yet, the jenkins job is set to Java 1.6. Is this correct?

@ctrueden, @hinerm:
How would I change the jenkins job to allow compilation with the latest pom-fiji? Using and outdated pom does not seem to be practical, and it already caused me to miss some recent IJ1changes (36f7fd0f).

With IJ1.49t plot labels are missing from the Plot canvas. It is likely due to changes introduced in the new Plot class in 1.49t5.

The sholl profile table doesn't have buttons, such as File > Save As. So the table can't be export or save directly. While the Deprecated command-Sholl Analysis can do it.

There is this really cool feature by GitHub and Jenkins that you can tell GitHub to notify a Jenkins instance whenever there were updates to branches/tags. You configure it by directing your browser to the Settings>Service Hooks, clicking on the Jenkins (Git plugin) entry, typing http://jenkins.imagej.net/ into the Jenkins URL input box, checking the Active checkbox and hitting the Update settings button.

Once you do that, no need to wait for me to start Jenkins builds anymore: as soon as you push to GitHub (well, a minute after that, at most), Jenkins will know about it and start building and deploying!

Requested here. We could implement it here or through SNT.

Hello,

The Group Sholl Profiles command seems to have stopped working with the latest FIJI release. I was using the command without problem, I updated FIJI (which hadn't been done since early this year), and it immediately stopped working. FIJI says command finished, but nothing happens.

I went back to the May 29th release of FIJI with Sholl 3.6.13 and Group Sholl Profiles works again. Hooray!

I re-installed a fresh version of the newest FIJI release (1.51p) in case something was wrong with mine specifically, and Group Sholl didn't work. I also tried going back to Sholl 3.6.12 with 1.51p and it still didn't work. So I'm pretty sure there is some issue between 1.51p and the command itself.

Sara

First release after moving to Travis CI. It failed:

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-deploy-plugin:2.8.2:deploy (default-deploy) on project Sholl_Analysis: Failed to deploy artifacts: Could not transfer artifact ca.mcgill:Sholl_Analysis:jar:sources:3.6.13 from/to imagej.releases (dav:http://maven.imagej.net/content/repositories/releases): Failed to transfer file: http://maven.imagej.net/content/repositories/releases/ca/mcgill/Sholl_Analysis/3.6.13/Sholl_Analysis-3.6.13-sources.jar. Return code is: 400 -> [Help 1]

@ctrueden Why is that? Presumably because I haven't set up upload credentials anywhere?
However I do find the new version on http://maven.imagej.net/content/repositories/releases/ca/mcgill/Sholl_Analysis/3.6.13/. Any thoughts?

On January 25, 2020 at 2:33 PM CST, @imagejan wrote:

I discovered an issue with two Commands in Sholl_Analysis (@tferr):

[ERROR] java.lang.IllegalStateException: java.lang.InstantiationException: sholl.math.Comparator
    at org.scijava.command.CommandModuleItem.getDefaultValue(CommandModuleItem.java:179)
    at org.scijava.module.AbstractModuleItem.toString(AbstractModuleItem.java:80)

and

[ERROR] java.lang.IllegalStateException: java.lang.InstantiationException: sholl.parsers.ImageParser
    at org.scijava.command.CommandModuleItem.getDefaultValue(CommandModuleItem.java:179)
    at org.scijava.module.AbstractModuleItem.toString(AbstractModuleItem.java:80)

I guess these two should simply not be annotated with ContextCommand, since they’re visible=false anyway.

The @Plugin annotation on Comparator and on ImageParser should probably be removed. (Tangentially: the plugin type should probably be type = Command.class rather than type = ContextCommand.class—the latter is merely a concrete base class implementing Command for convenience, not intended to be used as its own plugin type.)

It seems that SNT never really implemented macro options for use_3d and use_three_pane, therefore those are ignored in Call_SNT. We will need to implement them in SNT.

With profiles that are highly skewed or contain plateaus, Nav is not accurate (v3.4.4). The following macro demonstrates this:

run("ddaC Neuron (84K)");
run("Sholl Analysis...", "starting=200 ending=300 radius_step=0 fit linear polynomial=[8th degree]");

Retrieved: Nav = -139230.813. Expected: ~ 58.315

It would be useful if we could help users to bypass "Invalid Image Type" errors as it does not seem clear at the moment. We could improve error messages (that are already quite detailed), or provide "Pro tips" somewhere in the interface

Right now the unit of the analysis is stored under the "Label" column e.g. ddaC_Neuron (µm). The problem is that other headings in that table also use brackets. As such it is not that straightforward to extract the unit in a spreadsheet program without disrupting other columns.
Anyway, it is not a good idea to store multiple info in the same cell. We had a series of miscalibrated images that we missed just because of this.

net.imagej.table is deprecated and should be replaced with org.scijava.table.
This plugin does not compile with imagej-common 0.27.0 or later, which indicates it will encounter issues with the next version of pom-scijava.

Exception below, reported here:

(Fiji Is Just) ImageJ 2.0.0-rc-54/1.51g; Java 1.8.0_66 [64-bit]; Windows 10 10.0; 42MB of 2956MB (1%)

java.lang.IllegalArgumentException: character to be escaped is missing
at java.util.regex.Matcher.appendReplacement(Matcher.java:809)
at java.util.regex.Matcher.replaceAll(Matcher.java:955)
at java.lang.String.replaceAll(String.java:2223)
at sholl.Call_SNT.normalizedPath(Call_SNT.java:379)
at sholl.Call_SNT.dialogItemChanged(Call_SNT.java:268)
at sholl.Call_SNT.showDialog(Call_SNT.java:211)
at sholl.Call_SNT.run(Call_SNT.java:89)
at ij.IJ.runUserPlugIn(IJ.java:217)
at ij.IJ.runPlugIn(IJ.java:181)
at ij.Executer.runCommand(Executer.java:137)
at ij.Executer.run(Executer.java:66)
at java.lang.Thread.run(Thread.java:745)