20100913T070719: *: <== :rubikcube_work!~rubikcube@134.76.218.177 JOIN :#fiji-devel 20100913T081247: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :Good morning, I have two questions: Do you know if there's a standalone plugin to import/export HDF5 files to or from Fiji/IJ? If not, is there an elegant way to load JNIs, since http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/hdf5.en.html this one uses them? 20100913T081247: rubikcube_work!~rubikcube@134.76.218.177: Good morning, I have two questions: Do you know if there's a standalone plugin to import/export HDF5 files to or from Fiji/IJ? If not, is there an elegant way to load JNIs, since http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/hdf5.en.html this one uses them? 20100913T085818: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de JOIN :#fiji-devel 20100913T085818: *: <== :ChanServ!ChanServ@services. MODE #fiji-devel +o dscho 20100913T091744: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :moin dscho, do you have a log here or may I repeat a question? 20100913T091744: rubikcube_work!~rubikcube@134.76.218.177: moin dscho, do you have a log here or may I repeat a question? 20100913T094832: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :rubikcube_work: Hi! 20100913T094832: dscho!~dscho@cbg-off-client.mpi-cbg.de: rubikcube_work: Hi! 20100913T094847: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :rubikcube_work: let me look at the log... 20100913T094847: dscho!~dscho@cbg-off-client.mpi-cbg.de: rubikcube_work: let me look at the log... 20100913T094917: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :ok 20100913T094917: rubikcube_work!~rubikcube@134.76.218.177: ok 20100913T094946: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :Okay, the question was about standalone HDF5 import/export. 20100913T094946: dscho!~dscho@cbg-off-client.mpi-cbg.de: Okay, the question was about standalone HDF5 import/export. 20100913T095002: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :I thought I saw something, but the better way would be to stick with bio-formats. 20100913T095002: dscho!~dscho@cbg-off-client.mpi-cbg.de: I thought I saw something, but the better way would be to stick with bio-formats. 20100913T095014: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :HDF5 is a _huge_ standard, and not trivial to support appropriately. 20100913T095014: dscho!~dscho@cbg-off-client.mpi-cbg.de: HDF5 is a _huge_ standard, and not trivial to support appropriately. 20100913T095045: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :if bio-formats work that's standolone enough for me :) 20100913T095045: rubikcube_work!~rubikcube@134.76.218.177: if bio-formats work that's standolone enough for me :) 20100913T095051: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :Heh. 20100913T095051: dscho!~dscho@cbg-off-client.mpi-cbg.de: Heh. 20100913T095055: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :I am not quite sure... 20100913T095055: dscho!~dscho@cbg-off-client.mpi-cbg.de: I am not quite sure... 20100913T095057: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :Let me look. 20100913T095057: dscho!~dscho@cbg-off-client.mpi-cbg.de: Let me look. 20100913T095135: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :hmm, it doesn't work with the test file I'm using 20100913T095135: rubikcube_work!~rubikcube@134.76.218.177: hmm, it doesn't work with the test file I'm using 20100913T095136: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :According to http://www.loci.wisc.edu/bio-formats/formats they do not support HDF5. 20100913T095136: dscho!~dscho@cbg-off-client.mpi-cbg.de: According to http://www.loci.wisc.edu/bio-formats/formats they do not support HDF5. 20100913T095157: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :standalone was referring to the trouble of using a JNI 20100913T095157: rubikcube_work!~rubikcube@134.76.218.177: standalone was referring to the trouble of using a JNI 20100913T095226: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :To use JNI is kind of not-so-intelligent, if you can avoid it. 20100913T095226: dscho!~dscho@cbg-off-client.mpi-cbg.de: To use JNI is kind of not-so-intelligent, if you can avoid it. 20100913T095242: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :yes, so I guess 20100913T095242: rubikcube_work!~rubikcube@134.76.218.177: yes, so I guess 20100913T095245: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :+ed 20100913T095245: rubikcube_work!~rubikcube@134.76.218.177: +ed 20100913T095259: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :The big problem then is that you have all kinds of hassles to 20100913T095259: dscho!~dscho@cbg-off-client.mpi-cbg.de: The big problem then is that you have all kinds of hassles to 20100913T095305: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :1) get the native libraries for your platform 20100913T095305: dscho!~dscho@cbg-off-client.mpi-cbg.de: 1) get the native libraries for your platform 20100913T095333: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :2) make sure that they can be loaded from Java (i.e. put them into the correct directories, or start Fiji with an option so Java knows where they are) 20100913T095333: dscho!~dscho@cbg-off-client.mpi-cbg.de: 2) make sure that they can be loaded from Java (i.e. put them into the correct directories, or start Fiji with an option so Java knows where they are) 20100913T095449: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :This is the best reference I found that states that Bio-Formats has beginnings of HDF support: http://imagej.588099.n2.nabble.com/pure-java-HDF-reader-td3908479.html 20100913T095449: dscho!~dscho@cbg-off-client.mpi-cbg.de: This is the best reference I found that states that Bio-Formats has beginnings of HDF support: http://imagej.588099.n2.nabble.com/pure-java-HDF-reader-td3908479.html 20100913T095710: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :I think I've come across that thread a few days ago :) 20100913T095710: rubikcube_work!~rubikcube@134.76.218.177: I think I've come across that thread a few days ago :) 20100913T095956: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :but thanks anyways 20100913T095956: rubikcube_work!~rubikcube@134.76.218.177: but thanks anyways 20100913T100147: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :rubikcube_work: could you upload the sample image with Fiji's Help>Upload Sample Image please? 20100913T100147: dscho!~dscho@cbg-off-client.mpi-cbg.de: rubikcube_work: could you upload the sample image with Fiji's Help>Upload Sample Image please? 20100913T100236: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :sure 20100913T100236: rubikcube_work!~rubikcube@134.76.218.177: sure 20100913T100257: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :it's called test.h5 20100913T100257: rubikcube_work!~rubikcube@134.76.218.177: it's called test.h5 20100913T100435: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :Thanks. 20100913T100435: dscho!~dscho@cbg-off-client.mpi-cbg.de: Thanks. 20100913T100442: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :Have you tried http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/netcdf.en.html for reading? 20100913T100442: dscho!~dscho@cbg-off-client.mpi-cbg.de: Have you tried http://lmb.informatik.uni-freiburg.de/lmbsoft/imagej_plugins/netcdf.en.html for reading? 20100913T101126: *: <== :oosp_!~mark@ini-firewall.uzh.ch JOIN :#fiji-devel 20100913T101249: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :thank you! This seems to work for reading at least :) 20100913T101249: rubikcube_work!~rubikcube@134.76.218.177: thank you! This seems to work for reading at least :) 20100913T101300: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :rubikcube_work: okay! 20100913T101300: dscho!~dscho@cbg-off-client.mpi-cbg.de: rubikcube_work: okay! 20100913T101325: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :in case you ever nee to create sample files yourself, Matlab (and probably Octave as well) know hdf5 20100913T101325: rubikcube_work!~rubikcube@134.76.218.177: in case you ever nee to create sample files yourself, Matlab (and probably Octave as well) know hdf5 20100913T101345: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :There seems to be a project called "Nujan" to do that with Java, too... ;-) 20100913T101345: dscho!~dscho@cbg-off-client.mpi-cbg.de: There seems to be a project called "Nujan" to do that with Java, too... ;-) 20100913T102232: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :sounds interesting :) 20100913T102232: rubikcube_work!~rubikcube@134.76.218.177: sounds interesting :) 20100913T102308: *: <== :rubikcube_work!~rubikcube@134.76.218.177 PRIVMSG #fiji-devel :and at least for writing, I currently won't bump into the 2GB limit 20100913T102308: rubikcube_work!~rubikcube@134.76.218.177: and at least for writing, I currently won't bump into the 2GB limit 20100913T102357: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel ::-) 20100913T102357: dscho!~dscho@cbg-off-client.mpi-cbg.de: :-) 20100913T151605: *: <== :rubikcube_work!~rubikcube@134.76.218.177 QUIT :Quit: rubikcube_work 20100913T151842: *: <== :duncanm!~duncan@a-chinaman.com JOIN :#fiji-devel 20100913T151846: *: <== :duncanm!~duncan@a-chinaman.com PRIVMSG #fiji-devel :hola 20100913T151846: duncanm!~duncan@a-chinaman.com: hola 20100913T152304: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :Hi duncanm 20100913T152304: dscho!~dscho@cbg-off-client.mpi-cbg.de: Hi duncanm 20100913T153620: *: <== :oosp_!~mark@ini-firewall.uzh.ch QUIT :Quit: Leaving 20100913T160716: *: <== :oosp!~mark@ini-firewall.uzh.ch QUIT :Quit: Leaving 20100913T160825: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de PRIVMSG #fiji-devel :Bubye... 20100913T160825: dscho!~dscho@cbg-off-client.mpi-cbg.de: Bubye... 20100913T160828: *: <== :dscho!~dscho@cbg-off-client.mpi-cbg.de QUIT :Remote host closed the connection