20121203T080222: *: <== :joshmoore!~joshmoore@manz-590ee9d9.pool.mediaWays.net JOIN #fiji-devel 20121203T140423: *: <== :rubikcube_work!~quassel@134.76.218.252 JOIN #fiji-devel 20121203T145837: *: <== :joshmoore1!~joshmoore@89.14.233.217 JOIN #fiji-devel 20121203T150232: *: <== :joshmoore!~joshmoore@manz-590ee9d9.pool.mediaWays.net QUIT :Ping timeout: 265 seconds 20121203T154715: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 JOIN #fiji-devel 20121203T154722: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :hi 20121203T154722: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: hi 20121203T154814: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :can anyone help me? 20121203T154814: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: can anyone help me? 20121203T154840: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i have problems when i am trying to create a python script 20121203T154840: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i have problems when i am trying to create a python script 20121203T154958: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i am trying to call to this plugin: http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start 20121203T154958: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i am trying to call to this plugin: http://imagejdocu.tudor.lu/doku.php?id=plugin:segmentation:3d_spots_segmentation:start 20121203T155050: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu JOIN #fiji-devel 20121203T155306: *: <== :oosp!~oosp@cpc8-slam5-2-0-cust233.2-4.cable.virginmedia.com PRIVMSG #fiji-devel :qwebirc61303: what do you have so far in your python script? 20121203T155306: oosp!~oosp@cpc8-slam5-2-0-cust233.2-4.cable.virginmedia.com: qwebirc61303: what do you have so far in your python script? 20121203T155315: *: <== :oosp!~oosp@cpc8-slam5-2-0-cust233.2-4.cable.virginmedia.com PRIVMSG #fiji-devel :what problems are you having? 20121203T155315: oosp!~oosp@cpc8-slam5-2-0-cust233.2-4.cable.virginmedia.com: what problems are you having? 20121203T163634: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :hello oosp 20121203T163634: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: hello oosp 20121203T163649: *: <== :oosp!~oosp@cpc8-slam5-2-0-cust233.2-4.cable.virginmedia.com PRIVMSG #fiji-devel :hi 20121203T163649: oosp!~oosp@cpc8-slam5-2-0-cust233.2-4.cable.virginmedia.com: hi 20121203T163705: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :look, i tried to call to SeedSpots_Plus class 20121203T163705: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: look, i tried to call to SeedSpots_Plus class 20121203T163714: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :from mcib_plugins import SeedSpots_Plus 20121203T163714: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: from mcib_plugins import SeedSpots_Plus 20121203T163725: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :arg = "global_background=15 local_background=0 radius_0=2 radius_1=4 radius_2=6 weigth=0.50 radius_max=10 sd_value=1 local_threshold=[Local Mean] seg_spot=Classical watershed volume_min=1 volume_max=10000 seeds="+imp2.title+" spots="+im\ p.title SeedSpots_Plus.run(arg) 20121203T163725: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: arg = "global_background=15 local_background=0 radius_0=2 radius_1=4 radius_2=6 weigth=0.50 radius_max=10 sd_value=1 local_threshold=[Local Mean] seg_spot=Classical watershed volume_min=1 volume_max=10000 seeds="+imp2.title+" spots="+im\ p.title SeedSpots_Plus.run(arg) 20121203T163744: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :and i have this error: 20121203T163744: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: and i have this error: 20121203T163805: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :TypeError: run(): expected 2 args; got 1 20121203T163805: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: TypeError: run(): expected 2 args; got 1 20121203T163855: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i don't know why i have to put two arguments, the run function only has one argument... 20121203T163855: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i don't know why i have to put two arguments, the run function only has one argument... 20121203T164537: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: it is most likely a PlugInFilter. 20121203T164537: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: it is most likely a PlugInFilter. 20121203T164642: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If you want to use it in the slightly convoluted way by instantiating the plugin yourself, you will have to call setup(imp) first, check the return value, and then call run(arg, ip), where imp is the ImagePlus and ip is the ImageProcessor (the currently visible slice). 20121203T164642: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If you want to use it in the slightly convoluted way by instantiating the plugin yourself, you will have to call setup(imp) first, check the return value, and then call run(arg, ip), where imp is the ImagePlus and ip is the ImageProcessor (the currently visible slice). 20121203T164703: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I would agree that Java would prefer the approach to instantiate the plugin. 20121203T164703: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I would agree that Java would prefer the approach to instantiate the plugin. 20121203T164723: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But in ImageJ 1.x, it is easier to call things via IJ.run(imp, menuLabel, arg) 20121203T164723: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But in ImageJ 1.x, it is easier to call things via IJ.run(imp, menuLabel, arg) 20121203T164750: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :BTW that's also how the recorder shows it to you if you switch away from 'Macro' to, say, 'Javascript'. 20121203T164750: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: BTW that's also how the recorder shows it to you if you switch away from 'Macro' to, say, 'Javascript'. 20121203T164752: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i will try 20121203T164752: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i will try 20121203T164816: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: I will second dscho's suggestion of using "IJ.run(...)" if possible. 20121203T164816: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: qwebirc61303: I will second dscho's suggestion of using "IJ.run(...)" if possible. 20121203T164942: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : SeedSpots_Plus.setup(imp) AttributeError: type object 'mcib_plugins.SeedSpots_Plus' has no attribute 'setup' 20121203T164942: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: SeedSpots_Plus.setup(imp) AttributeError: type object 'mcib_plugins.SeedSpots_Plus' has no attribute 'setup' 20121203T165006: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i have tried with IJ.run 20121203T165006: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i have tried with IJ.run 20121203T165050: *: <== :joshmoore1!~joshmoore@89.14.233.217 QUIT :*.net *.split 20121203T165127: *: <== :joshmoore!~joshmoore@manz-590ee9d9.pool.mediaWays.net JOIN #fiji-devel 20121203T165224: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: have you looked at the source code of SeedSpots_Plus? 20121203T165224: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: have you looked at the source code of SeedSpots_Plus? 20121203T165231: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Have you tried to record a macro to run it? 20121203T165231: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Have you tried to record a macro to run it? 20121203T165231: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yes 20121203T165231: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yes 20121203T165242: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :with macro is so easy 20121203T165242: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: with macro is so easy 20121203T165245: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :What interface does it implement? 20121203T165245: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: What interface does it implement? 20121203T165258: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Should not be harder with Javascript/Java: use the recorder. 20121203T165258: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Should not be harder with Javascript/Java: use the recorder. 20121203T165312: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :my problem is that i need headless execution because i want to execute fiji in massive parallel 20121203T165312: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: my problem is that i need headless execution because i want to execute fiji in massive parallel 20121203T165345: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :the only way that i can execute in headless mode is using fiji and python 20121203T165345: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: the only way that i can execute in headless mode is using fiji and python 20121203T165356: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :using IJ.run i have this error: 20121203T165356: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: using IJ.run i have this error: 20121203T165357: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :3D spots segmentation java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:48) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37) at java.lang.reflect.Method.invoke(Method.java:600) 20121203T165357: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: 3D spots segmentation java.lang.reflect.InvocationTargetException at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:48) at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:37) at java.lang.reflect.Method.invoke(Method.java:600) 20121203T165604: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :That is incomplete... 20121203T165604: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: That is incomplete... 20121203T165625: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i know 20121203T165625: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i know 20121203T165629: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :more error: 20121203T165629: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: more error: 20121203T165630: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : at ij.Command.runPlugIn(Command.java:146) at ij.Command.runCommand(Command.java:95) at ij.Executer.run(Executer.java:64) at ij.IJ.run(IJ.java:251) at ij.IJ.run(IJ.java:300) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:48) at sun.reflect.DelegatingMethodAccessorImpl.invok 20121203T165630: *: ==> PRIVMSG #fiji-devel :Command.java:146 in Gitweb: http://tinyurl.com/crl64pu 20121203T165630: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: at ij.Command.runPlugIn(Command.java:146) at ij.Command.runCommand(Command.java:95) at ij.Executer.run(Executer.java:64) at ij.IJ.run(IJ.java:251) at ij.IJ.run(IJ.java:300) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:48) at sun.reflect.DelegatingMethodAccessorImpl.invok 20121203T165655: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Do you see the tell-tale "Caused by"? 20121203T165655: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Do you see the tell-tale "Caused by"? 20121203T165703: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :IJ.run(imp,"3D Spot Segmentation", arg) 20121203T165703: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: IJ.run(imp,"3D Spot Segmentation", arg) 20121203T165707: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :A TargetInvocationException always wraps another exception. 20121203T165707: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: A TargetInvocationException always wraps another exception. 20121203T165722: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :Caused by: java.lang.NullPointerException at mcib_plugins.SeedSpots_Plus.run(SeedSpots_Plus.java:74) at ij.IJ.runUserPlugIn(IJ.java:185) 20121203T165722: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: Caused by: java.lang.NullPointerException at mcib_plugins.SeedSpots_Plus.run(SeedSpots_Plus.java:74) at ij.IJ.runUserPlugIn(IJ.java:185) 20121203T165738: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :So what is in line 74 in SeedSpots_Plus? 20121203T165738: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: So what is in line 74 in SeedSpots_Plus? 20121203T165750: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : for (int i = 0; i < nbima; i++) { names[i] = WindowManager.getImage(i + 1).getShortTitle(); } 20121203T165750: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: for (int i = 0; i < nbima; i++) { names[i] = WindowManager.getImage(i + 1).getShortTitle(); } 20121203T165809: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :the problem is the images 20121203T165809: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: the problem is the images 20121203T165813: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :My guess: getImage() returns null. 20121203T165813: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: My guess: getImage() returns null. 20121203T165837: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Most likely because you do not have a proper WindowManager in headless mode. 20121203T165837: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Most likely because you do not have a proper WindowManager in headless mode. 20121203T165854: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :There are only two ways to fix the problem: 20121203T165854: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: There are only two ways to fix the problem: 20121203T165914: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :1) fix the source code of SeedSpots_Plus to work headlessly 20121203T165914: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: 1) fix the source code of SeedSpots_Plus to work headlessly 20121203T165914: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :tell me please 20121203T165914: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: tell me please 20121203T165942: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :2) use the class purely via the Java API without going through the interface imposed by ImageJ 1.x. 20121203T165942: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: 2) use the class purely via the Java API without going through the interface imposed by ImageJ 1.x. 20121203T170009: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :As to 2), there might already be a method in that class that takes an ImagePlus directly and then a range of explicit parameters. 20121203T170009: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: As to 2), there might already be a method in that class that takes an ImagePlus directly and then a range of explicit parameters. 20121203T170017: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :can you explain me more about this second option? 20121203T170017: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: can you explain me more about this second option? 20121203T170019: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If not, you'd have to refactor the code. 20121203T170019: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If not, you'd have to refactor the code. 20121203T170115: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :let me see 20121203T170115: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: let me see 20121203T170149: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :ImagePlus segPlus = null; 20121203T170149: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ImagePlus segPlus = null; 20121203T170150: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :... 20121203T170150: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ... 20121203T170158: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :seedPlus = WindowManager.getImage(seed + 1); 20121203T170158: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: seedPlus = WindowManager.getImage(seed + 1); 20121203T170215: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :That is not exactly what I was looking for. 20121203T170215: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: That is not exactly what I was looking for. 20121203T170236: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The anatomy of an ImageJ 1.x plugin is: 1) setup, 2) GenericDialog, 3) process 20121203T170236: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The anatomy of an ImageJ 1.x plugin is: 1) setup, 2) GenericDialog, 3) process 20121203T170324: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yes 20121203T170324: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yes 20121203T170327: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i see 20121203T170327: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i see 20121203T170331: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :the GenericDialog is asking you for parameters (and is unfortunately also responsible for gathering them when run from macros, hence the problem in headless mode, a consequence of the lack of proper separation between user interface and processing). 20121203T170331: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: the GenericDialog is asking you for parameters (and is unfortunately also responsible for gathering them when run from macros, hence the problem in headless mode, a consequence of the lack of proper separation between user interface and processing). 20121203T170341: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : GenericDialog dia = new GenericDialog("Seeds spots"); 20121203T170341: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: GenericDialog dia = new GenericDialog("Seeds spots"); 20121203T170344: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Typically you will see three methods for the three different parts. 20121203T170344: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Typically you will see three methods for the three different parts. 20121203T170408: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i think is not the case 20121203T170408: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i think is not the case 20121203T170409: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Probably there are a couple of lines like "int radius = (int)dia.getNextNumber()" 20121203T170409: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Probably there are a couple of lines like "int radius = (int)dia.getNextNumber()" 20121203T170415: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :This is the last part of phase two. 20121203T170415: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: This is the last part of phase two. 20121203T170447: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If phase 2 and phase 3 are conflated in a single method, you will unfortunately have to refactor that before you can use it in a headless mode. 20121203T170447: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If phase 2 and phase 3 are conflated in a single method, you will unfortunately have to refactor that before you can use it in a headless mode. 20121203T170604: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :when i open a image in headless mode 20121203T170604: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: when i open a image in headless mode 20121203T170619: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :how can i access to this image in java??? 20121203T170619: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: how can i access to this image in java??? 20121203T170637: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i see that in interactive mode, is using windowManager 20121203T170637: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i see that in interactive mode, is using windowManager 20121203T170727: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You can access it by the reference returned by IJ.openImage(). 20121203T170727: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You can access it by the reference returned by IJ.openImage(). 20121203T170748: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :However, it looks as if the particular plugin you try to use wants to use a *second* image, too. 20121203T170748: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: However, it looks as if the particular plugin you try to use wants to use a *second* image, too. 20121203T170801: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :To get at that, it apparently builds a list of open images. 20121203T170801: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: To get at that, it apparently builds a list of open images. 20121203T170805: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :That fails in headless mode. 20121203T170805: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: That fails in headless mode. 20121203T170940: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :and can i create a method inside SeedSpots, passing the two images as arguments 20121203T170940: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: and can i create a method inside SeedSpots, passing the two images as arguments 20121203T171016: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :save internally in the class as privated variables 20121203T171016: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: save internally in the class as privated variables 20121203T171035: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :and modify run method in order to use this private variables?? 20121203T171035: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: and modify run method in order to use this private variables?? 20121203T171048: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :of course in headless mode... 20121203T171048: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: of course in headless mode... 20121203T171117: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :That is what I tried to suggest when I used the word "refactor". 20121203T171117: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: That is what I tried to suggest when I used the word "refactor". 20121203T171143: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Refactoring describes the process of modifying code without modifying functionality, for the sake of better maintenance/usage. 20121203T171143: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Refactoring describes the process of modifying code without modifying functionality, for the sake of better maintenance/usage. 20121203T171226: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :For example, when you want to split a method into two (in this particular case because two phases were conflated and you need to call only the latter from your Python script), that is called "refactoring a method into two" or "refactoring out the process phase". 20121203T171226: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: For example, when you want to split a method into two (in this particular case because two phases were conflated and you need to call only the latter from your Python script), that is called "refactoring a method into two" or "refactoring out the process phase". 20121203T171247: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :ok, i will try! 20121203T171247: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ok, i will try! 20121203T171301: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :thanks for all @dscho 20121203T171301: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: thanks for all @dscho 20121203T171305: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :And BTW parameters cannot be "private" ;-) 20121203T171305: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: And BTW parameters cannot be "private" ;-) 20121203T171316: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :They are parameters, so they are local to the method anyway. 20121203T171316: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: They are parameters, so they are local to the method anyway. 20121203T171319: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :well, thanks everybody! 20121203T171319: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: well, thanks everybody! 20121203T171324: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Good luck! 20121203T171324: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Good luck! 20121203T171334: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :And make sure to make your modified version available ;-) 20121203T171334: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: And make sure to make your modified version available ;-) 20121203T171337: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yeah, correct 20121203T171337: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yeah, correct 20121203T171339: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :;) 20121203T171339: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ;) 20121203T171342: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :thanks! 20121203T171342: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: thanks! 20121203T171354: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(That's how you "pay" me back for my help...) 20121203T171354: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (That's how you "pay" me back for my help...) 20121203T171356: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :where??? 20121203T171356: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: where??? 20121203T171414: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ImageJ mailing list would make sense: imagej@list.nih.gov 20121203T171414: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ImageJ mailing list would make sense: imagej@list.nih.gov 20121203T171427: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Or the Fiji mailing list: fiji-devel@googlegroups.com 20121203T171427: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Or the Fiji mailing list: fiji-devel@googlegroups.com 20121203T171438: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Or directly on the ImageJ Documentation Wiki. 20121203T171438: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Or directly on the ImageJ Documentation Wiki. 20121203T171438: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i can put in my webpage...but is not a official plugin of Fiji... 20121203T171438: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i can put in my webpage...but is not a official plugin of Fiji... 20121203T171459: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :ok 20121203T171459: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ok 20121203T171506: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Well, you got help in the Fiji channel, so you might as well contribute the code back to Fiji ;-) 20121203T171506: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Well, you got help in the Fiji channel, so you might as well contribute the code back to Fiji ;-) 20121203T171529: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :of course 20121203T171529: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: of course 20121203T171555: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :something interesting: all this is to execute massive image processing using CeSViMa 20121203T171555: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: something interesting: all this is to execute massive image processing using CeSViMa 20121203T171608: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :http://www.cesvima.upm.es/index 20121203T171608: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: http://www.cesvima.upm.es/index 20121203T171638: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i had to compile all fiji in powerpc-64 20121203T171638: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i had to compile all fiji in powerpc-64 20121203T171644: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :very very complex!! 20121203T171644: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: very very complex!! 20121203T171726: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :see you soon! 20121203T171726: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: see you soon! 20121203T172346: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Ouch. 20121203T172346: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Ouch. 20121203T172405: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :PPC64... there is not even a Java 6 available for it. 20121203T172405: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: PPC64... there is not even a Java 6 available for it. 20121203T172423: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Unless this is Linux and you use OpenJDK, that is... 20121203T172423: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Unless this is Linux and you use OpenJDK, that is... 20121203T173036: *: <== :rubikcube_work!~quassel@134.76.218.252 QUIT :Remote host closed the connection 20121203T173623: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :dscho: Does Fiji-Maven deploy artifact builds for submodules to the ImageJ Maven repository? 20121203T173623: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: dscho: Does Fiji-Maven deploy artifact builds for submodules to the ImageJ Maven repository? 20121203T173723: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I tracked down why Larry had so much trouble with his dependencies 20121203T173723: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I tracked down why Larry had so much trouble with his dependencies 20121203T173732: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :mpicbg:mpicbg:0.6.0-SNAPSHOT is not being deployed. 20121203T173732: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: mpicbg:mpicbg:0.6.0-SNAPSHOT is not being deployed. 20121203T173743: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :So I'm curious: do the Fiji Jenkins jobs deploy mpicbg, ever? 20121203T173743: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: So I'm curious: do the Fiji Jenkins jobs deploy mpicbg, ever? 20121203T173750: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I assume yes... 20121203T173750: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I assume yes... 20121203T173804: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :So then the reason 0.6.0-SNAPSHOT isn't there is because fiji.git's submodule pointer to mpicbg is too old. 20121203T173804: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: So then the reason 0.6.0-SNAPSHOT isn't there is because fiji.git's submodule pointer to mpicbg is too old. 20121203T173925: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Ideally we would set up a separate Jenkins job for mpicbg (and one for TrakEM2 once it is Mavenized) so that the Fiji jobs don't have to work so hard (i.e., get rid of the submodules). 20121203T173925: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Ideally we would set up a separate Jenkins job for mpicbg (and one for TrakEM2 once it is Mavenized) so that the Fiji jobs don't have to work so hard (i.e., get rid of the submodules). 20121203T174535: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: Fiji-Maven does not deploy any submodules, that would conflict with ImgLib. 20121203T174535: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: Fiji-Maven does not deploy any submodules, that would conflict with ImgLib. 20121203T174611: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If we want to deploy mpicbg_ and mpicbg, we have to make new, separate jobs for that. 20121203T174611: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If we want to deploy mpicbg_ and mpicbg, we have to make new, separate jobs for that. 20121203T174640: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I am all in favor of doing that, it is all held up (for a quite long time now, PAvel asked me to help them in July and I did it in August) by TrakEM2. 20121203T174640: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I am all in favor of doing that, it is all held up (for a quite long time now, PAvel asked me to help them in July and I did it in August) by TrakEM2. 20121203T174859: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :As to Larry's problem, I assumed that he would have the correct mpicbg version checked out. 20121203T174859: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: As to Larry's problem, I assumed that he would have the correct mpicbg version checked out. 20121203T174927: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :In that case, MiniMaven builds it from there (but does not install it into $HOME/.m2/repository/... I did not want to risk complications with that) 20121203T174927: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: In that case, MiniMaven builds it from there (but does not install it into $HOME/.m2/repository/... I did not want to risk complications with that) 20121203T175212: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I will create an mpicbg Jenkins job now. 20121203T175212: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I will create an mpicbg Jenkins job now. 20121203T175219: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Do you have time? 20121203T175219: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Do you have time? 20121203T175225: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Should be quick to do. 20121203T175225: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Should be quick to do. 20121203T175225: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Otherwise: I was on my way to do that. 20121203T175225: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Otherwise: I was on my way to do that. 20121203T175227: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Do you want me to wait to remove the mpicbg submodule from fiji.git? 20121203T175227: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Do you want me to wait to remove the mpicbg submodule from fiji.git? 20121203T175232: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Oh, if you are already about to do it, then go for it. 20121203T175232: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Oh, if you are already about to do it, then go for it. 20121203T175239: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Nope, I think it makes absolute sense to remove it. 20121203T175239: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Nope, I think it makes absolute sense to remove it. 20121203T175242: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Use github.com/axtimwalde/mpicbg.git, right? 20121203T175242: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Use github.com/axtimwalde/mpicbg.git, right? 20121203T175243: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I'm on it. 20121203T175243: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I'm on it. 20121203T175246: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Thanks! 20121203T175246: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Thanks! 20121203T175315: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I just want us to be able to reply to Larry and say "sorry you had to do that (provided scopes)" and "it is no longer necessary now" etc. 20121203T175315: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I just want us to be able to reply to Larry and say "sorry you had to do that (provided scopes)" and "it is no longer necessary now" etc. 20121203T175723: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: http://jenkins.imagej.net/job/Saalfeld-MPICBG-Maven/ 20121203T175723: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: http://jenkins.imagej.net/job/Saalfeld-MPICBG-Maven/ 20121203T175753: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Sure, you can write Larry. 20121203T175753: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Sure, you can write Larry. 20121203T175811: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :As to the official repository: I used git://fiji.sc/mpicbg.git instead for now. 20121203T175811: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: As to the official repository: I used git://fiji.sc/mpicbg.git instead for now. 20121203T175853: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You could ask Stephan in the mail whether he wants the GitHub repository instead, but my impression was that it'll be obsolete soon, when ImgLib2 does what he needs, better. 20121203T175853: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You could ask Stephan in the mail whether he wants the GitHub repository instead, but my impression was that it'll be obsolete soon, when ImgLib2 does what he needs, better. 20121203T175924: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :If we use the GitHub one and Stephan enables the notification, we won't need 5 minute polling. 20121203T175924: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: If we use the GitHub one and Stephan enables the notification, we won't need 5 minute polling. 20121203T175927: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I'll ask him. 20121203T175927: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I'll ask him. 20121203T175940: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I doubt he will be getting rid of that code any time soon. He put too much work into Mavenizing it for it to be nearly-obsolete. 20121203T175940: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I doubt he will be getting rid of that code any time soon. He put too much work into Mavenizing it for it to be nearly-obsolete. 20121203T180028: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :If it sticks around for a long time, I will ask him about renaming it too, since "mpicbg" does not convey anything about its function, nor would a groupId of "mpicbg" be accepted into Maven central. 20121203T180028: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: If it sticks around for a long time, I will ask him about renaming it too, since "mpicbg" does not convey anything about its function, nor would a groupId of "mpicbg" be accepted into Maven central. 20121203T180049: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :(But that can wait of course.) 20121203T180049: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: (But that can wait of course.) 20121203T180405: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :dscho: Thanks for creating that mpicbg job. Looks good, 0.6.0-SNAPSHOT is now deployed. 20121203T180405: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: dscho: Thanks for creating that mpicbg job. Looks good, 0.6.0-SNAPSHOT is now deployed. 20121203T180409: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :One question though... 20121203T180409: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: One question though... 20121203T180426: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I notice that the last deploy timestamp for 2.0.0-SNAPSHOT is Mon Dec 3 (today)! Which job could be responsible for that...? 20121203T180426: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I notice that the last deploy timestamp for 2.0.0-SNAPSHOT is Mon Dec 3 (today)! Which job could be responsible for that...? 20121203T180452: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Time is 00:10:33 so perhaps a daily build? 20121203T180452: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Time is 00:10:33 so perhaps a daily build? 20121203T180922: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Hmm. 20121203T180922: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Hmm. 20121203T180942: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Maybe it *is* Fiji-Maven? 20121203T180942: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Maybe it *is* Fiji-Maven? 20121203T181012: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Nope, that did not run 00:10:33. 20121203T181012: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Nope, that did not run 00:10:33. 20121203T181047: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I also checked, and bin/incremental-deploy.sh does not try to deploy submodules. 20121203T181047: *: ==> PRIVMSG #fiji-devel :bin/incremental-deploy.sh in Gitweb: http://tinyurl.com/cv9xqrk 20121203T181047: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I also checked, and bin/incremental-deploy.sh does not try to deploy submodules. 20121203T181052: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :("git ls-files \*pom.xml") 20121203T181052: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: ("git ls-files \*pom.xml") 20121203T181130: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I want to remove the 2.0.0-SNAPSHOT because it is very confusing (since Stephan rolled the version backward). 20121203T181130: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I want to remove the 2.0.0-SNAPSHOT because it is very confusing (since Stephan rolled the version backward). 20121203T181131: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I'll grep in Jenkins' logs. 20121203T181131: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I'll grep in Jenkins' logs. 20121203T181134: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Thanks. 20121203T181134: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Thanks. 20121203T181143: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I know, it is confusing and misleading. 20121203T181143: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I know, it is confusing and misleading. 20121203T181154: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :And it will break builds to remove it when we try to bisect. 20121203T181154: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: And it will break builds to remove it when we try to bisect. 20121203T181200: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But I kinda gave up on that idea. 20121203T181200: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But I kinda gave up on that idea. 20121203T181212: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :It would require too much discipline of the Fiji team. 20121203T181212: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: It would require too much discipline of the Fiji team. 20121203T181218: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :SeedSpots_Plus.java:184: cannot find symbol symbol : method warp(ij.ImagePlus) location: class mcib3d.image3d.ImageHandler spot3DImage = ImageHandler.warp(spotPlus); ^ SeedSpots_Plus.java:189: cannot find symbol symbol : method warp(ij.ImagePlus) location: class mcib3d.image3d.ImageHandler seed3DImage = ImageHandler.warp(seedPlus); 20121203T181218: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: SeedSpots_Plus.java:184: cannot find symbol symbol : method warp(ij.ImagePlus) location: class mcib3d.image3d.ImageHandler spot3DImage = ImageHandler.warp(spotPlus); ^ SeedSpots_Plus.java:189: cannot find symbol symbol : method warp(ij.ImagePlus) location: class mcib3d.image3d.ImageHandler seed3DImage = ImageHandler.warp(seedPlus); 20121203T181233: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i have these errors... :( 20121203T181233: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i have these errors... :( 20121203T181252: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: when... compiling the plugin? ... running the Python script? 20121203T181252: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: when... compiling the plugin? ... running the Python script? 20121203T181302: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :same error 20121203T181302: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: same error 20121203T181313: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :compiling the plugin 20121203T181313: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: compiling the plugin 20121203T181340: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :using javac or using compile & run the plugin option of Fiji 20121203T181340: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: using javac or using compile & run the plugin option of Fiji 20121203T181349: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel ::( 20121203T181349: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: :( 20121203T181407: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i don't understand, this is not my code 20121203T181407: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i don't understand, this is not my code 20121203T181409: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Where does that ImageHandler class live? 20121203T181409: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Where does that ImageHandler class live? 20121203T181423: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(BTW it is not my code, either ;-) 20121203T181423: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (BTW it is not my code, either ;-) 20121203T181432: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :is from mcib3d-core 20121203T181432: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: is from mcib3d-core 20121203T181450: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :mcib3d-core2.3.jar 20121203T181450: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: mcib3d-core2.3.jar 20121203T181525: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :if this code is correct the compilation must be correct... 20121203T181525: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: if this code is correct the compilation must be correct... 20121203T181541: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: did you call javac with *all* the .java files from that .jar? 20121203T181541: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: did you call javac with *all* the .java files from that .jar? 20121203T181552: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yes 20121203T181552: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yes 20121203T181605: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Is there an ImageHandler.java, too? 20121203T181605: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Is there an ImageHandler.java, too? 20121203T181653: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :no, it is only in the mcib3d-core2.3.jar file 20121203T181653: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: no, it is only in the mcib3d-core2.3.jar file 20121203T181757: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Okay, so just to make things clear for me: you did, or you did not, pass all the .java files from that .jar as parameters to javac? 20121203T181757: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Okay, so just to make things clear for me: you did, or you did not, pass all the .java files from that .jar as parameters to javac? 20121203T181758: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :and i include this jar as classpath 20121203T181758: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: and i include this jar as classpath 20121203T181853: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i put as classpath this jar, ij jar and others classes necessary for this clases 20121203T181853: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i put as classpath this jar, ij jar and others classes necessary for this clases 20121203T181900: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i put as classpath this jar, ij jar and others classes necessary for this class 20121203T181900: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i put as classpath this jar, ij jar and others classes necessary for this class 20121203T181936: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Then I suspect that the ImageHandler class in that .jar is not of the version required to compile the .java file you want to compile. 20121203T181936: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Then I suspect that the ImageHandler class in that .jar is not of the version required to compile the .java file you want to compile. 20121203T181955: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Have you tried to compile the .java sources from scratch, without any modifications? 20121203T181955: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Have you tried to compile the .java sources from scratch, without any modifications? 20121203T182001: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :javac -cp ../mcib3d-core2.3.jar:../quickhull3d.jar:../../fiji/jars/ij-1.47a.jar:*.class SeedSpots_Plus.java 20121203T182001: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: javac -cp ../mcib3d-core2.3.jar:../quickhull3d.jar:../../fiji/jars/ij-1.47a.jar:*.class SeedSpots_Plus.java 20121203T182009: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If that does not work, there is little hope to get it to compile without the help of the original author. 20121203T182009: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If that does not work, there is little hope to get it to compile without the help of the original author. 20121203T182024: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yes, i have downloaded the sources, and tried to compile (without changes) 20121203T182024: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yes, i have downloaded the sources, and tried to compile (without changes) 20121203T182101: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i want to cry... :( 20121203T182101: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i want to cry... :( 20121203T182132: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :From the page: GPL distribution (see licence ). Sources for plugins are available freely. Sources for core are available on request. 20121203T182132: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: From the page: GPL distribution (see licence ). Sources for plugins are available freely. Sources for core are available on request. 20121203T182134: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Pity. 20121203T182134: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Pity. 20121203T182233: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You could try one last thing before mailing Thomas Boudier (and don't forget to Cc: the ImageJ mailing list so that he does not have to repeat the same answers over and over again, privately) would be to try to adapt the .java source you have to the version of ImageHandler you have. 20121203T182233: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You could try one last thing before mailing Thomas Boudier (and don't forget to Cc: the ImageJ mailing list so that he does not have to repeat the same answers over and over again, privately) would be to try to adapt the .java source you have to the version of ImageHandler you have. 20121203T182243: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :ok, thanks anyway! 20121203T182243: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ok, thanks anyway! 20121203T182304: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :other question 20121203T182304: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: other question 20121203T182307: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If you call javap -classpath mcib3d-core2.3.jar .ImageHandler, do you see any reference to a warp() method? 20121203T182307: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If you call javap -classpath mcib3d-core2.3.jar .ImageHandler, do you see any reference to a warp() method? 20121203T182323: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :ImageJ mailing list ?? 20121203T182323: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ImageJ mailing list ?? 20121203T182339: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :imagej@list.nih.gov. 20121203T182339: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: imagej@list.nih.gov. 20121203T182347: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The best place to ask ImageJ questions. 20121203T182347: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The best place to ask ImageJ questions. 20121203T182422: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :http://imagej.net/list.html 20121203T182422: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: http://imagej.net/list.html 20121203T182450: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : a51079680@login22:~/tmp/mcib3d-suite> javap -classpath mcib3d-core2.3.jar mcib3d.image3d.ImageHandler | grep wrap public static mcib3d.image3d.ImageHandler wrap(ij.ImagePlus); public static mcib3d.image3d.ImageHandler wrap(ij.ImageStack); a51079680@login22:~/tmp/mcib3d-suite> 20121203T182450: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: a51079680@login22:~/tmp/mcib3d-suite> javap -classpath mcib3d-core2.3.jar mcib3d.image3d.ImageHandler | grep wrap public static mcib3d.image3d.ImageHandler wrap(ij.ImagePlus); public static mcib3d.image3d.ImageHandler wrap(ij.ImageStack); a51079680@login22:~/tmp/mcib3d-suite> 20121203T182505: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :it exists!! :( 20121203T182505: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: it exists!! :( 20121203T182505: *: <== :joshmoore1!~joshmoore@manz-590ee9d9.pool.mediaWays.net JOIN #fiji-devel 20121203T182519: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But it takes a stack, not an ImagePlus. 20121203T182519: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But it takes a stack, not an ImagePlus. 20121203T182530: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Happily, you can get the stack by calling imp.getStack() 20121203T182530: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Happily, you can get the stack by calling imp.getStack() 20121203T182543: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If you modify the respective code in the plugin .java file, it should compile. 20121203T182543: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If you modify the respective code in the plugin .java file, it should compile. 20121203T182608: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :both 20121203T182608: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: both 20121203T182623: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : public static mcib3d.image3d.ImageHandler wrap(ij.ImagePlus); 20121203T182623: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: public static mcib3d.image3d.ImageHandler wrap(ij.ImagePlus); 20121203T182628: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : public static mcib3d.image3d.ImageHandler wrap(ij.ImageStack); 20121203T182628: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: public static mcib3d.image3d.ImageHandler wrap(ij.ImageStack); 20121203T182733: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :it has no sense 20121203T182733: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: it has no sense 20121203T182831: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :It suggests that there might be an import problem: if another ImageHandler class is imported first (e.g. quickhull3d.jar could contain one, too), then the wrong class is asked. 20121203T182831: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: It suggests that there might be an import problem: if another ImageHandler class is imported first (e.g. quickhull3d.jar could contain one, too), then the wrong class is asked. 20121203T182854: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Actually. 20121203T182854: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Actually. 20121203T182859: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :understood 20121203T182859: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: understood 20121203T182902: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The .java class looks for warp(). 20121203T182902: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The .java class looks for warp(). 20121203T182904: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Not for wrap(). 20121203T182904: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Not for wrap(). 20121203T182908: *: <== :joshmoore!~joshmoore@manz-590ee9d9.pool.mediaWays.net QUIT :Ping timeout: 260 seconds 20121203T182915: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I just realized that you looked for wrap() in the javap. 20121203T182915: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I just realized that you looked for wrap() in the javap. 20121203T182931: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Stuipd graammr 20121203T182931: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Stuipd graammr 20121203T182943: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :dscho: I have a commit ready that removes the mpicbg submodule. Might it break the Fiji Jenkins jobs if I push? Or is it OK? 20121203T182943: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: dscho: I have a commit ready that removes the mpicbg submodule. Might it break the Fiji Jenkins jobs if I push? Or is it OK? 20121203T182944: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :oooooooooooooooooooooooouuuuuuuuuuuuuuuuuuuuuuuuuuchhhhhhhhhhhhhhhhh 20121203T182944: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: oooooooooooooooooooooooouuuuuuuuuuuuuuuuuuuuuuuuuuchhhhhhhhhhhhhhhhh 20121203T182951: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :shiiiiiiiiit 20121203T182951: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: shiiiiiiiiit 20121203T182953: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :XDD 20121203T182953: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: XDD 20121203T183027: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i will try 20121203T183027: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i will try 20121203T183046: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yeah it compiles!!!! 20121203T183046: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yeah it compiles!!!! 20121203T183047: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel ::) 20121203T183047: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: :) 20121203T183408: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: you can push that. It won't break the Fiji Jenkins jobs; it just means that we really shun the bisectability of fiji.git. 20121203T183408: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: you can push that. It won't break the Fiji Jenkins jobs; it just means that we really shun the bisectability of fiji.git. 20121203T183418: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(Basically we'd arrive at the same state at imagej.git right now) 20121203T183418: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (Basically we'd arrive at the same state at imagej.git right now) 20121203T183420: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I'm sorry about that. :-( 20121203T183420: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I'm sorry about that. :-( 20121203T183437: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :That is the one nice thing about submodules: the pointers ensure bisectability. 20121203T183437: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: That is the one nice thing about submodules: the pointers ensure bisectability. 20121203T183444: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :So far, we committed ("soft-commit") the submodules whenever an API change or bug fix was required. 20121203T183444: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: So far, we committed ("soft-commit") the submodules whenever an API change or bug fix was required. 20121203T183458: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :So maybe for now update the submodule pointer instead? 20121203T183458: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: So maybe for now update the submodule pointer instead? 20121203T183502: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Right. So the change in our process would now be to do a new release of the artifact instead when that happens. 20121203T183502: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Right. So the change in our process would now be to do a new release of the artifact instead when that happens. 20121203T183506: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :As we discussed before. 20121203T183506: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: As we discussed before. 20121203T183519: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :But I understand there are some logistical issues with doing things that way. 20121203T183519: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: But I understand there are some logistical issues with doing things that way. 20121203T183550: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :All right, I will update the submodule pointer instead. 20121203T183550: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: All right, I will update the submodule pointer instead. 20121203T183554: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Well, mpicbg is Stephan's baby. I don't even want to suggest a way to go forward because he might have other ideas. 20121203T183554: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Well, mpicbg is Stephan's baby. I don't even want to suggest a way to go forward because he might have other ideas. 20121203T183646: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Well, we can't do a release of anything that depends on mpicbg or mpicbg_ until they are locked down to a release. 20121203T183646: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Well, we can't do a release of anything that depends on mpicbg or mpicbg_ until they are locked down to a release. 20121203T183655: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :The build is simply not repeatable otherwise. 20121203T183655: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: The build is simply not repeatable otherwise. 20121203T183724: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :ok, in SeedSpots_Plus i invent a method 20121203T183724: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ok, in SeedSpots_Plus i invent a method 20121203T183742: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :which i pass the two images SeedSpots_Plus.getImages(imp2,imp); 20121203T183742: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: which i pass the two images SeedSpots_Plus.getImages(imp2,imp); 20121203T183811: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :when i execute via python scripting 20121203T183811: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: when i execute via python scripting 20121203T183811: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: Actually, in fiji.git we basically had nothing but snapshot versions so far, with the only thing that we had submodule pointers and tagged all that to make a "release" version. 20121203T183811: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: Actually, in fiji.git we basically had nothing but snapshot versions so far, with the only thing that we had submodule pointers and tagged all that to make a "release" version. 20121203T183815: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i have the same error 20121203T183815: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i have the same error 20121203T183825: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : SeedSpots_Plus.getImages(imp2,imp); TypeError: getImages(): expected 3 args; got 2 20121203T183825: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: SeedSpots_Plus.getImages(imp2,imp); TypeError: getImages(): expected 3 args; got 2 20121203T183848: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: is it possible that you added a third parameter to getImages()? 20121203T183848: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: is it possible that you added a third parameter to getImages()? 20121203T184032: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: after you push the update of the submodule pointer, I will cherry-pick the last commit of mpicbg-trakem2-maven. 20121203T184032: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: after you push the update of the submodule pointer, I will cherry-pick the last commit of mpicbg-trakem2-maven. 20121203T184058: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: I assumed that the TrakEM2 situation would be resolved instantaneously after resolving the mpicbg situation. I was wrong. 20121203T184058: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: I assumed that the TrakEM2 situation would be resolved instantaneously after resolving the mpicbg situation. I was wrong. 20121203T184123: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: or you made that a non-static method. 20121203T184123: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: or you made that a non-static method. 20121203T184144: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: in that case, you have to instantiate the class and call instance.getImages(imp2, imp) instead. 20121203T184144: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: in that case, you have to instantiate the class and call instance.getImages(imp2, imp) instead. 20121203T184229: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :in Python also? 20121203T184229: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: in Python also? 20121203T184242: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :is a non-static method 20121203T184242: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: is a non-static method 20121203T184250: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Hmm, I seem to have hosed my mpicbg submodule by restoring it. 20121203T184250: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Hmm, I seem to have hosed my mpicbg submodule by restoring it. 20121203T184304: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :$ git submodule init modules/mpicbg 20121203T184304: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: $ git submodule init modules/mpicbg 20121203T184304: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Submodule 'mpicbg' () registered for path 'modules/mpicbg' 20121203T184304: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Submodule 'mpicbg' () registered for path 'modules/mpicbg' 20121203T184304: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :$ git submodule update 20121203T184304: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: $ git submodule update 20121203T184304: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :fatal: Not a git repository: ../.git/modules/modules/mpicbg 20121203T184304: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: fatal: Not a git repository: ../.git/modules/modules/mpicbg 20121203T184304: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Unable to find current revision in submodule path 'modules/mpicbg' 20121203T184304: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Unable to find current revision in submodule path 'modules/mpicbg' 20121203T184307: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: since it is a non-static method, it needs an instance, correct? You did not pass that. 20121203T184307: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: since it is a non-static method, it needs an instance, correct? You did not pass that. 20121203T184335: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: you called SeedSpots_Plus.getImages(imp2, imp) instead, which is how you would call static methods which do *not* require an instance. 20121203T184335: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: you called SeedSpots_Plus.getImages(imp2, imp) instead, which is how you would call static methods which do *not* require an instance. 20121203T184429: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: heh, you probably have a .git *file* in modules/mpicbg/ 20121203T184429: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: heh, you probably have a .git *file* in modules/mpicbg/ 20121203T184439: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :That did not quite restore it ;-) 20121203T184439: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: That did not quite restore it ;-) 20121203T184522: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I do not know whose genius idea it was to put the submodules' repositories into the superproject's .git/ directory (I have a hunch, though), but I am not a fan. 20121203T184522: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I do not know whose genius idea it was to put the submodules' repositories into the superproject's .git/ directory (I have a hunch, though), but I am not a fan. 20121203T184537: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I have mixed feelings about it. But overall I think it makes things harder. 20121203T184537: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I have mixed feelings about it. But overall I think it makes things harder. 20121203T184544: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :Firstly, the path in the .git file was wrong. 20121203T184544: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: Firstly, the path in the .git file was wrong. 20121203T184553: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: to make it more explicit: you might want to call SeedSpots_Plus().getImages(imp2, imp) instead. 20121203T184553: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: to make it more explicit: you might want to call SeedSpots_Plus().getImages(imp2, imp) instead. 20121203T184554: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :But now .git/modules/modules/mpicbg is missing. 20121203T184554: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: But now .git/modules/modules/mpicbg is missing. 20121203T184603: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :I should be able to work around it; ignore me! 20121203T184603: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: I should be able to work around it; ignore me! 20121203T184643: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: but note that I am not a psychic, I have no idea whether that is correct, and I want to suggest to understand the difference first before trying it, otherwise things could go horribly wrong. 20121203T184643: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: but note that I am not a psychic, I have no idea whether that is correct, and I want to suggest to understand the difference first before trying it, otherwise things could go horribly wrong. 20121203T184722: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: When you first checked out that submodule, genius Git created the Git *repository* in /.git/modules/modules/mpicbg. 20121203T184722: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: When you first checked out that submodule, genius Git created the Git *repository* in /.git/modules/modules/mpicbg. 20121203T184738: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: when you backed up modules/mpicbg, that directory was not backed up, of course. 20121203T184738: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: when you backed up modules/mpicbg, that directory was not backed up, of course. 20121203T184744: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But the .git *file* which pointed there. 20121203T184744: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But the .git *file* which pointed there. 20121203T184749: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I got bitten by the same bug. 20121203T184749: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I got bitten by the same bug. 20121203T184809: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The idea is probably to make it easier to share the object pools in case things got moved around. 20121203T184809: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The idea is probably to make it easier to share the object pools in case things got moved around. 20121203T184812: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :in Python, instantiate a java class is : spot = SeedSpots_Plus(); ??? 20121203T184812: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: in Python, instantiate a java class is : spot = SeedSpots_Plus(); ??? 20121203T184812: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :A good idea. 20121203T184812: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: A good idea. 20121203T184836: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: In practice, however, it broke so many submodule setups (which were not exactly in dear need of being broken even more) 20121203T184836: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: In practice, however, it broke so many submodule setups (which were not exactly in dear need of being broken even more) 20121203T184841: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: yes. 20121203T184841: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: yes. 20121203T184849: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :java.lang.RuntimeException: java.lang.RuntimeException: Cannot instantiate headless dialog except in macro mode 20121203T184849: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: java.lang.RuntimeException: java.lang.RuntimeException: Cannot instantiate headless dialog except in macro mode 20121203T184850: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu PRIVMSG #fiji-devel :dscho: Thanks, I got it working. 20121203T184850: ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu: dscho: Thanks, I got it working. 20121203T184902: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel : spot.run(arg) at fiji.Headless$GenericDialog.(Headless.java:261) at ij.gui.GenericDialog.(GenericDialog.java:93) at ij.gui.GenericDialog.(GenericDialog.java:87) at mcib_plugins.SeedSpots_Plus.run(SeedSpots_Plus.java:123) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 20121203T184902: *: ==> PRIVMSG #fiji-devel :Headless.java:261 in Gitweb: http://tinyurl.com/chhz9e6 20121203T184902: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: spot.run(arg) at fiji.Headless$GenericDialog.(Headless.java:261) at ij.gui.GenericDialog.(GenericDialog.java:93) at ij.gui.GenericDialog.(GenericDialog.java:87) at mcib_plugins.SeedSpots_Plus.run(SeedSpots_Plus.java:123) at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java: 20121203T184903: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: instantiating a class in general. 20121203T184903: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: instantiating a class in general. 20121203T184928: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: I thought you had the processing part factored out of run() and did not call that anymore? 20121203T184928: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: I thought you had the processing part factored out of run() and did not call that anymore? 20121203T184936: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :ctrueden: great! 20121203T184936: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ctrueden: great! 20121203T185001: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yeah but, how can i pass the two images to the static run??? 20121203T185001: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yeah but, how can i pass the two images to the static run??? 20121203T185009: *: <== :GitHub182!~GitHub182@sh3.rs.github.com NOTICE #fiji-devel :[fiji] ctrueden pushed 1 new commit to master: http://git.io/CPhPUg 20121203T185009: *: <== :GitHub182!~GitHub182@sh3.rs.github.com NOTICE #fiji-devel :fiji/master 9a52b3d Curtis Rueden: Update mpicbg submodule pointer to latest version... 20121203T185014: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :using a non-static method? 20121203T185014: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: using a non-static method? 20121203T185054: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i explain it again 20121203T185054: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i explain it again 20121203T185104: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :getImages is a non-static method 20121203T185104: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: getImages is a non-static method 20121203T185114: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Right. 20121203T185114: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Right. 20121203T185134: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :that takes the two arguments (images) and put into private variables of the class 20121203T185134: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: that takes the two arguments (images) and put into private variables of the class 20121203T185139: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :run() is not static, BTW. 20121203T185139: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: run() is not static, BTW. 20121203T185205: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :true 20121203T185205: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: true 20121203T185211: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :so 20121203T185211: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: so 20121203T185219: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :spot = SeedSpots_Plus(); spot.getImages(imp2,imp); 20121203T185219: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: spot = SeedSpots_Plus(); spot.getImages(imp2,imp); 20121203T185235: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :spot instance has the two variables with variables 20121203T185235: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: spot instance has the two variables with variables 20121203T185237: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The idea I tried to relate is to end the run() method after getting all the parameters from the GenericDialog. 20121203T185237: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The idea I tried to relate is to end the run() method after getting all the parameters from the GenericDialog. 20121203T185259: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Then insert a single call to the method that would contain the rest of the former run() method. 20121203T185259: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Then insert a single call to the method that would contain the rest of the former run() method. 20121203T185323: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :This method would now take all those variables as parameters and could be called *without* calling run(). 20121203T185323: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: This method would now take all those variables as parameters and could be called *without* calling run(). 20121203T185329: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Let me find an example. 20121203T185329: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Let me find an example. 20121203T185346: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :http://fiji.sc/Process_Pixels.java 20121203T185346: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: http://fiji.sc/Process_Pixels.java 20121203T185413: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You see the run() method actually calls a showDialog() method and then a process() method. 20121203T185413: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You see the run() method actually calls a showDialog() method and then a process() method. 20121203T185438: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yes 20121203T185438: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yes 20121203T185517: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :It is actually not quite correct since you do not have a way to set the parameters "value" and "name" other than by calling showDialog(), so you'd need getters and setters. 20121203T185517: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: It is actually not quite correct since you do not have a way to set the parameters "value" and "name" other than by calling showDialog(), so you'd need getters and setters. 20121203T185532: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The point, however, is that the real processing is done in the process() method. 20121203T185532: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The point, however, is that the real processing is done in the process() method. 20121203T185544: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :This method can be called *without* constructing a GenericDialog, ever. 20121203T185544: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: This method can be called *without* constructing a GenericDialog, ever. 20121203T185602: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :See? That's the refactoring result I had in mind: separating the user interface from the processing. 20121203T185602: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: See? That's the refactoring result I had in mind: separating the user interface from the processing. 20121203T185628: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :now i am lost 20121203T185628: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: now i am lost 20121203T185633: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(In industry, this is called a "best practice". You separate even the classes implementing the business logic from the classes interacting with the user) 20121203T185633: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (In industry, this is called a "best practice". You separate even the classes implementing the business logic from the classes interacting with the user) 20121203T185649: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Let's start agin. 20121203T185649: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Let's start agin. 20121203T185653: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :again, even. 20121203T185653: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: again, even. 20121203T185657: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :my problem 20121203T185657: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: my problem 20121203T185702: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :In SeedSpots_Plus, you have a run() method, correct? 20121203T185702: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: In SeedSpots_Plus, you have a run() method, correct? 20121203T185709: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yeah 20121203T185709: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yeah 20121203T185724: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :run needs two images 20121203T185724: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: run needs two images 20121203T185726: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :This method does *two* things: it interacts with the user, enquiring for the parameters required for processing, and then processes. 20121203T185726: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: This method does *two* things: it interacts with the user, enquiring for the parameters required for processing, and then processes. 20121203T185743: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :you only want the latter part, though. 20121203T185743: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: you only want the latter part, though. 20121203T185755: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :ok 20121203T185755: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ok 20121203T185755: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :So what you can do is split off the latter part into its own method. 20121203T185755: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: So what you can do is split off the latter part into its own method. 20121203T185814: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I would call it "process()", but of course you are free to call it whatever you like. 20121203T185814: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I would call it "process()", but of course you are free to call it whatever you like. 20121203T185821: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yes but how can i pass the two images??? 20121203T185821: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yes but how can i pass the two images??? 20121203T185841: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :"process()" would have the advantage that other people, and you in two months, would still remember what this method is about. 20121203T185841: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: "process()" would have the advantage that other people, and you in two months, would still remember what this method is about. 20121203T185855: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :By adding them as parameters, as you did with the getImages() method. 20121203T185855: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: By adding them as parameters, as you did with the getImages() method. 20121203T185924: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :so, run calls process 20121203T185924: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: so, run calls process 20121203T185925: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The signature for the process() method would read: "public void process(ImagePlus imp, ImagePlus spots)" 20121203T185925: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The signature for the process() method would read: "public void process(ImagePlus imp, ImagePlus spots)" 20121203T185933: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :That is what I suggested, yes. 20121203T185933: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: That is what I suggested, yes. 20121203T185937: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :and process has two arguments 20121203T185937: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: and process has two arguments 20121203T185944: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Right. 20121203T185944: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Right. 20121203T190010: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :mmm something stupid 20121203T190010: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: mmm something stupid 20121203T190024: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :from python i have two variables as images 20121203T190024: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: from python i have two variables as images 20121203T190027: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :imp and imp2 20121203T190027: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: imp and imp2 20121203T190040: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Right. 20121203T190040: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Right. 20121203T190057: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You pass them via "plugin.process(imp, imp2)" 20121203T190057: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You pass them via "plugin.process(imp, imp2)" 20121203T190106: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :how can i send to run and to process? 20121203T190106: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: how can i send to run and to process? 20121203T190112: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(Except that I would use the variable name "spots", again for clarity) 20121203T190112: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (Except that I would use the variable name "spots", again for clarity) 20121203T190122: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Why do you want to call run()? 20121203T190122: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Why do you want to call run()? 20121203T190156: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :if you call run(), the generic dialog is instantiated, blowing up your headless mode. 20121203T190156: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: if you call run(), the generic dialog is instantiated, blowing up your headless mode. 20121203T190212: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :SeedSpots_Plus.process(imp,imp2) 20121203T190212: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: SeedSpots_Plus.process(imp,imp2) 20121203T190217: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The idea of the refactoring is to make it possible to call process() *without* calling run(). 20121203T190217: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The idea of the refactoring is to make it possible to call process() *without* calling run(). 20121203T190230: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If you can make process() static. 20121203T190230: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If you can make process() static. 20121203T190237: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :if you can, great, go for it. 20121203T190237: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: if you can, great, go for it. 20121203T190240: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :and process makes the last part of run 20121203T190240: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: and process makes the last part of run 20121203T190243: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :correct? 20121203T190243: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: correct? 20121203T190302: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :but if that method requires an instance variable, you need to call SeedSpots_Plus().process(imp, imp2). 20121203T190302: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: but if that method requires an instance variable, you need to call SeedSpots_Plus().process(imp, imp2). 20121203T190322: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Yes, process() is *called* at the end of run(). 20121203T190322: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Yes, process() is *called* at the end of run(). 20121203T190326: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :ok 20121203T190326: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: ok 20121203T190343: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :To make it elegant, run() would be refactored even further, to call a method called showDialog(). 20121203T190343: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: To make it elegant, run() would be refactored even further, to call a method called showDialog(). 20121203T190346: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :understood 20121203T190346: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: understood 20121203T190356: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :and seriously, I strongly suggest to improve the naming. 20121203T190356: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: and seriously, I strongly suggest to improve the naming. 20121203T190407: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :yeah yeah 20121203T190407: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: yeah yeah 20121203T190427: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :i will try it 20121203T190427: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: i will try it 20121203T190428: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :thanks 20121203T190428: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: thanks 20121203T190506: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You're welcome1 20121203T190506: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You're welcome1 20121203T190518: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :s/1/!/ (my left Shift key does not like me today) 20121203T190518: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: s/1/!/ (my left Shift key does not like me today) 20121203T191457: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :@dscho it runs!!!! 20121203T191457: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: @dscho it runs!!!! 20121203T191501: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :thanks a lot!!! 20121203T191501: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: thanks a lot!!! 20121203T192034: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :the last stupid question 20121203T192034: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: the last stupid question 20121203T192102: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :segPlus.show(); 20121203T192102: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: segPlus.show(); 20121203T192113: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :this has no sense in headless mode, correct??? 20121203T192113: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: this has no sense in headless mode, correct??? 20121203T192224: *: <== :qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116 PRIVMSG #fiji-devel :and, how can i save the final result segmentation image (after process method) in python?? 20121203T192224: qwebirc61303!8a048374@gateway/web/freenode/ip.138.4.131.116: and, how can i save the final result segmentation image (after process method) in python?? 20121203T193138: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: you return segPlus in process() and call the .show() on it in run(). 20121203T193138: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: you return segPlus in process() and call the .show() on it in run(). 20121203T202059: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :qwebirc61303: did that solve your problem? 20121203T202059: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: qwebirc61303: did that solve your problem? 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