These are chat archives for fiji/fiji

28th
Aug 2015
Docpit
@Docpit
Aug 28 2015 08:49
HI. My name is Pietro. I am an MD trying to use Fiji to analyze some electrocardiographic traces. Anyone I could ask for help or am I in the wrong channel?
Docpit
@Docpit
Aug 28 2015 10:08
?
Johannes Schindelin
@dscho
Aug 28 2015 12:08
According to http://fiji.sc/Help:Contents the best way to get help is to use the mailing list.
Curtis Rueden
@ctrueden
Aug 28 2015 15:40
@Docpit This is the right channel to ask for live chat, as mentioned on that link. However, there are many fewer people here.
But you can feel free to ask, and someone might answer you as time and knowledge allow! :wink:
@hinerm @dscho Do you foresee any problems with removing jdom.jar and jdom-contrib.jar from the Fiji update site? We also ship jars/jdom2.jar and this is what Fiji plugins (e.g., TrackMate) declare they are using.
Nothing declares deps on jdom or jdom-contrib, and unfortunately jdom overlaps with jdom2 on key classes.
Johannes Schindelin
@dscho
Aug 28 2015 15:57
I guess TrackMate was our jdom user.
OpenSPIM might be jdom user, too.
Curtis Rueden
@ctrueden
Aug 28 2015 16:07
@dscho Which repo? Not SPIMAcquisition, fusion-pipeline or openspim-app. Am I missing one?
Johannes Schindelin
@dscho
Aug 28 2015 16:08
Sorry, Micro-Manager.
But that's only a hunch.
I currently have exactly 0 time to look it up.
Curtis Rueden
@ctrueden
Aug 28 2015 16:28
No worries at all @dscho—not your job to look it up! I'll check right now quickly. I appreciate the tip.
~/code/openspim/micromanager $ git grep jdom
plugins/Magellan/bdv/XMLIOMagellanImageLoader16Bit.java:   public org.jdom2.Element toXml(MagellanImgLoader16Bit loader, File basePath) {
plugins/Magellan/bdv/XMLIOMagellanImageLoader16Bit.java:   public MagellanImgLoader16Bit fromXml(org.jdom2.Element elmnt, File file, AbstractSequenceDescription<?, ?, ?> asd) {
plugins/Magellan/bdv/XMLIOMagellanImageLoader8Bit.java:   public org.jdom2.Element toXml(MagellanImgLoader8Bit loader, File basePath) {
plugins/Magellan/bdv/XMLIOMagellanImageLoader8Bit.java:   public MagellanImgLoader8Bit fromXml(org.jdom2.Element elmnt, File file, AbstractSequenceDescription<?, ?, ?> asd) {
So I am guessing we are OK with jdom2 and not jdom anymore.
Curtis Rueden
@ctrueden
Aug 28 2015 16:37
Heh, it appears I thought I removed jdom in February, but I guess I didn't actually do it properly. I have now obsoleted jdom and jdom-contrib, and updated fiji/fiji#37 accordingly.