20120831T050149: *: <== :joshmoore!~joshmoore@manz-590f36f5.pool.mediaWays.net JOIN #fiji-devel 20120831T134531: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu JOIN #fiji-devel 20120831T142700: *: <== :qwebirc13662!905c30e5@gateway/web/freenode/ip.144.92.48.229 JOIN #fiji-devel 20120831T142700: *: <== :qwebirc13662!905c30e5@gateway/web/freenode/ip.144.92.48.229 NICK :lstuyvenberg 20120831T142700: qwebirc13662# lstuyvenberg 20120831T164826: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :dscho: So I'm pretty sure I've grabbed something like fifty points in about ten minutes. Not quite sure how accurate they are, but. 20120831T164827: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: dscho: So I'm pretty sure I've grabbed something like fifty points in about ten minutes. Not quite sure how accurate they are, but. 20120831T164857: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Hey, you could visualize them in the 3D Viewer. 20120831T164857: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Hey, you could visualize them in the 3D Viewer. 20120831T164908: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Is there an easy way to do that? 20120831T164908: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Is there an easy way to do that? 20120831T164920: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :At the very least, I'd need to type all the points up again... 20120831T164920: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: At the very least, I'd need to type all the points up again... 20120831T164941: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Ah! Perhaps not. Copy works. 20120831T164941: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Ah! Perhaps not. Copy works. 20120831T164950: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Good. 20120831T164950: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Good. 20120831T165009: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If you open a Script Editor and select Language>Python, you should be able to do something like: 20120831T165009: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If you open a Script Editor and select Language>Python, you should be able to do something like: 20120831T165045: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :univ = Image3DUniverse(512, 512) 20120831T165045: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: univ = Image3DUniverse(512, 512) 20120831T165048: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :univ.addIcospheres(points, Color3f(1, 0, 0), 2, radius, 'Beads').setLocked(True) 20120831T165048: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: univ.addIcospheres(points, Color3f(1, 0, 0), 2, radius, 'Beads').setLocked(True) 20120831T165050: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :univ.show() 20120831T165050: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: univ.show() 20120831T165102: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(Obviously I pasted that from somewhere... it is the Fiji Paper...) 20120831T165102: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (Obviously I pasted that from somewhere... it is the Fiji Paper...) 20120831T165115: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Heh. What's the third argument to addIcospheres? 20120831T165115: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Heh. What's the third argument to addIcospheres? 20120831T165148: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :And should the dimensions of my Image3DUniverse include a third, and should they be large enough to contain my points or does that not matter? 20120831T165148: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: And should the dimensions of my Image3DUniverse include a third, and should they be large enough to contain my points or does that not matter? 20120831T165237: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :lstuyvenberg: http://fiji.sc/javadoc/ij3d/Image3DUniverse.html#addIcospheres%28java.util.List,%20javax.vecmath.Color3f,%20int,%20float,%20java.lang.String%29 20120831T165237: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: lstuyvenberg: http://fiji.sc/javadoc/ij3d/Image3DUniverse.html#addIcospheres%28java.util.List,%20javax.vecmath.Color3f,%20int,%20float,%20java.lang.String%29 20120831T165247: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Ah 20120831T165247: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Ah 20120831T165247: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :thanks. 20120831T165247: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: thanks. 20120831T165258: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :It's the subdivisions, i.e. the approximation to a sphere by polygonal shapes. 20120831T165258: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: It's the subdivisions, i.e. the approximation to a sphere by polygonal shapes. 20120831T165317: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :...Should this really be Python? o.o 20120831T165317: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: ...Should this really be Python? o.o 20120831T165324: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :IIRC it starts with a cube or something. 20120831T165324: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: IIRC it starts with a cube or something. 20120831T165341: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :It's the most expressive (read: programs are shortest) language we support at the moment. 20120831T165341: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: It's the most expressive (read: programs are shortest) language we support at the moment. 20120831T170410: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :It doesn't seem to know what an Image3DUniverse is... 20120831T170410: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: It doesn't seem to know what an Image3DUniverse is... 20120831T170421: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Ah 20120831T170421: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Ah 20120831T170423: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :forgot my imports. 20120831T170423: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: forgot my imports. 20120831T170632: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Hmm, I thought it knew ij3d.* already. 20120831T170632: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Hmm, I thought it knew ij3d.* already. 20120831T170642: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But no... 20120831T170642: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But no... 20120831T170651: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You have to: 20120831T170651: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You have to: 20120831T170653: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :from ij3d import Image3DUniverse 20120831T170653: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: from ij3d import Image3DUniverse 20120831T170655: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :from javax.vecmath import Color3f 20120831T170655: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: from javax.vecmath import Color3f 20120831T170708: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :And Point3f. 20120831T170708: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: And Point3f. 20120831T170723: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Whoa 20120831T170723: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Whoa 20120831T170724: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :way off. 20120831T170724: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: way off. 20120831T170729: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Heh. 20120831T170729: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Heh. 20120831T170738: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :It looks somewhat circular at first, then suddenly flies off in a weird direction. 20120831T170738: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: It looks somewhat circular at first, then suddenly flies off in a weird direction. 20120831T170752: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Probably found a different bead? 20120831T170752: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Probably found a different bead? 20120831T170806: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Entirely possible. But it almost looks like the curvature changed. :| 20120831T170806: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Entirely possible. But it almost looks like the curvature changed. :| 20120831T170832: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Always keep in mind that the syringe setup we have might just be too unstable. 20120831T170832: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Always keep in mind that the syringe setup we have might just be too unstable. 20120831T170852: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I refuse to believe it! The thought makes me too sad. 20120831T170852: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I refuse to believe it! The thought makes me too sad. 20120831T170902: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :If that's what we find out doing the rotational axis calibration, we have to increase the priority of that ticket. 20120831T170902: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: If that's what we find out doing the rotational axis calibration, we have to increase the priority of that ticket. 20120831T170911: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(The ticket to think about a better sample holder) 20120831T170911: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (The ticket to think about a better sample holder) 20120831T170915: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Yeah. 20120831T170915: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Yeah. 20120831T171337: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :http://openspim.org/bugs/file_download.php?file_id=18&type=bug 20120831T171337: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: http://openspim.org/bugs/file_download.php?file_id=18&type=bug 20120831T171348: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :dscho: After throwing out the unruly points. 20120831T171348: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: dscho: After throwing out the unruly points. 20120831T171452: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Are you sure that the right half of the points are not just a little closer? 20120831T171452: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Are you sure that the right half of the points are not just a little closer? 20120831T171513: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Quite. I was wanting to throw those out too. Here's the fun part: Those three points on the edge? They're not the last three points in the list. 20120831T171513: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Quite. I was wanting to throw those out too. Here's the fun part: Those three points on the edge? They're not the last three points in the list. 20120831T171539: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I'm not entirely sure where they came from. 20120831T171539: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I'm not entirely sure where they came from. 20120831T171549: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Whoa... ;-) 20120831T171549: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Whoa... ;-) 20120831T171611: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :But even then, they're not *that* far off. :| 20120831T171611: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: But even then, they're not *that* far off. :| 20120831T171618: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :lstuyvenberg: are these points corrected for the (x,z) adjustment? 20120831T171618: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: lstuyvenberg: are these points corrected for the (x,z) adjustment? 20120831T171630: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :? 20120831T171630: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: ? 20120831T171659: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Well, you move the x and z motors during calibration. The coordinates you got, are they compensation for said motion? 20120831T171659: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Well, you move the x and z motors during calibration. The coordinates you got, are they compensation for said motion? 20120831T171711: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I know this sounds stupid, but that's a mistake I'd be likely to make. 20120831T171711: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I know this sounds stupid, but that's a mistake I'd be likely to make. 20120831T171753: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Of course. I take the current position of the motors, and add (upper-left corner of roi + center of gaussian fit relative to cropped-by-roi)*'um' per pixel. 20120831T171753: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Of course. I take the current position of the motors, and add (upper-left corner of roi + center of gaussian fit relative to cropped-by-roi)*'um' per pixel. 20120831T171807: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Rather... 20120831T171807: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Rather... 20120831T171825: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :That second part is made relative to the center of the screen (using the original imageprocessor's getwidth/height). 20120831T171825: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: That second part is made relative to the center of the screen (using the original imageprocessor's getwidth/height). 20120831T171922: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :(I copy/pasted the code from the manual calibrator.) 20120831T171922: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: (I copy/pasted the code from the manual calibrator.) 20120831T171958: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Right. 20120831T171958: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Right. 20120831T172132: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :lstuyvenberg: I fear we'll only get a clearer picture after doing a couple of these... 20120831T172132: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: lstuyvenberg: I fear we'll only get a clearer picture after doing a couple of these... 20120831T172143: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I'll keep working, then. :) 20120831T172143: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I'll keep working, then. :) 20120831T172152: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :It's really easy to do! I'm kinda surprised. 20120831T172152: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: It's really easy to do! I'm kinda surprised. 20120831T172208: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :And maybe you want to take coordinates after centering the beads in the live window? 20120831T172208: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: And maybe you want to take coordinates after centering the beads in the live window? 20120831T172212: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Heh. 20120831T172212: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Heh. 20120831T172232: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Well, Fiji was really meant as a fast-prototyping platform for scientists, and it really pays off now. 20120831T172232: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Well, Fiji was really meant as a fast-prototyping platform for scientists, and it really pays off now. 20120831T172244: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :The problem is that I can't center the bead until I have the coordinates. Chicken and egg. 20120831T172244: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: The problem is that I can't center the bead until I have the coordinates. Chicken and egg. 20120831T172318: *: <== :joshmoore!~joshmoore@manz-590f36f5.pool.mediaWays.net QUIT :Ping timeout: 246 seconds 20120831T172421: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :At present, the only time the bead is particularly far from the center of the screen is the first point. 20120831T172421: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: At present, the only time the bead is particularly far from the center of the screen is the first point. 20120831T172430: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :The rest, it's rotated 1 tick off-center. 20120831T172430: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: The rest, it's rotated 1 tick off-center. 20120831T172528: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :What I meant is: you should be able to adjust the motor positions after each rotation (and at the very beginning) such that the beads are dead-center. 20120831T172528: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: What I meant is: you should be able to adjust the motor positions after each rotation (and at the very beginning) such that the beads are dead-center. 20120831T172550: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Then you only need to visualize the motor positions interpreted as (x,y,z) coordinates. 20120831T172550: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Then you only need to visualize the motor positions interpreted as (x,y,z) coordinates. 20120831T172601: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But wait! 20120831T172601: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But wait! 20120831T172607: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Except that would be motor-resolution. Which is worse than pixel-resolution. 20120831T172607: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Except that would be motor-resolution. Which is worse than pixel-resolution. 20120831T172644: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Sure. 20120831T172644: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Sure. 20120831T172704: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I am now thinking that maybe it is a thinko to expect those coordinates to describe a perfect circle. 20120831T172704: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I am now thinking that maybe it is a thinko to expect those coordinates to describe a perfect circle. 20120831T172715: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :A 'thinko'? 20120831T172715: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: A 'thinko'? 20120831T172720: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :After all, we are describing the compensation against the rotation. 20120831T172720: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: After all, we are describing the compensation against the rotation. 20120831T172728: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Yes, a false assumption. 20120831T172728: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Yes, a false assumption. 20120831T172932: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Okay, I'm not sure where that's headed. Why might those coordinates -- the result of a single point rotating around an arbitrary axis -- not form a circle? 20120831T172932: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Okay, I'm not sure where that's headed. Why might those coordinates -- the result of a single point rotating around an arbitrary axis -- not form a circle? 20120831T173000: *: <== :joshmoore!~joshmoore@manz-590f36f5.pool.mediaWays.net JOIN #fiji-devel 20120831T173528: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :lstuyvenberg: the result should form a circle, *in the appropriate coordinate system* 20120831T173528: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: lstuyvenberg: the result should form a circle, *in the appropriate coordinate system* 20120831T173600: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :And is the appropriate coordinate system not a simple one...? 20120831T173600: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: And is the appropriate coordinate system not a simple one...? 20120831T173613: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :So what I try to wrap my head around is: is the x,y,z motor coordinate system the correct one? 20120831T173613: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: So what I try to wrap my head around is: is the x,y,z motor coordinate system the correct one? 20120831T173652: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But you're right, it should be. after all, the twister is the last motor in the stage, right? 20120831T173652: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But you're right, it should be. after all, the twister is the last motor in the stage, right? 20120831T173658: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Yes. 20120831T173658: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Yes. 20120831T173722: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Oh, one thing we might need to take into account: the x,y,z motors are actually ordered x, z, y, correct? 20120831T173722: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Oh, one thing we might need to take into account: the x,y,z motors are actually ordered x, z, y, correct? 20120831T173733: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :And they might not be half as accurate as we'd like them to be. 20120831T173733: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: And they might not be half as accurate as we'd like them to be. 20120831T173740: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Correct on both counts. 20120831T173740: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Correct on both counts. 20120831T173746: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Especially considering how "perpendicular" they are. 20120831T173746: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Especially considering how "perpendicular" they are. 20120831T173752: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Though honestly, it's the twister that concerns me. 20120831T173752: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Though honestly, it's the twister that concerns me. 20120831T173909: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Okay, here is a thought we might be able to determine whether the sample holder is actually the issue: Could you implement a horrible jitter, by moving the (x,z) motors pseudo-randomly for a while and then trying to re-center the bead? 20120831T173909: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Okay, here is a thought we might be able to determine whether the sample holder is actually the issue: Could you implement a horrible jitter, by moving the (x,z) motors pseudo-randomly for a while and then trying to re-center the bead? 20120831T173920: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Do that a couple of times. Maybe even the y motor. 20120831T173920: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Do that a couple of times. Maybe even the y motor. 20120831T173931: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :And then we should see how far off-center the bead is. 20120831T173931: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: And then we should see how far off-center the bead is. 20120831T174001: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :This will give us the first indication of the stability of the setup, especially with regards to the sample holder (although it could be motor inaccuracy as well). 20120831T174001: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: This will give us the first indication of the stability of the setup, especially with regards to the sample holder (although it could be motor inaccuracy as well). 20120831T174012: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Note: this method should leave the twister alone. 20120831T174012: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Note: this method should leave the twister alone. 20120831T174058: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(In testing in general it is a good idea to exclude certain things from testing so you can be certain that you test only the other components) 20120831T174058: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (In testing in general it is a good idea to exclude certain things from testing so you can be certain that you test only the other components) 20120831T174326: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :...Huh. That's a bizarre one -- I think I caught a different bead half-way through again. It looks like the start of a nice rotation, then suddenly like it flattened against a wall. 20120831T174326: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: ...Huh. That's a bizarre one -- I think I caught a different bead half-way through again. It looks like the start of a nice rotation, then suddenly like it flattened against a wall. 20120831T174343: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Anyway 20120831T174343: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Anyway 20120831T174348: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :trying random movements then recovering the bead. 20120831T174348: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: trying random movements then recovering the bead. 20120831T174444: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Aaand jammed up the RunTo for X. 20120831T174444: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Aaand jammed up the RunTo for X. 20120831T174715: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Hehe... is that a dead-lock? 20120831T174715: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Hehe... is that a dead-lock? 20120831T174728: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Or is it the thing that it tries to reach a goal that is never reached? 20120831T174728: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Or is it the thing that it tries to reach a goal that is never reached? 20120831T174840: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :? 20120831T174840: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: ? 20120831T174929: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Well, the bead is decidedly absent. I'll try a few more of the positions I have saved. 20120831T174929: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Well, the bead is decidedly absent. I'll try a few more of the positions I have saved. 20120831T175108: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Got a bead that's *pretty* close to the specified position. 20120831T175108: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Got a bead that's *pretty* close to the specified position. 20120831T175123: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :...Oh. 20120831T175123: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: ...Oh. 20120831T175124: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Right. 20120831T175124: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Right. 20120831T175134: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I was checking the wrong points. 20120831T175134: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I was checking the wrong points. 20120831T175142: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Namely, those of rotations past. 20120831T175142: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Namely, those of rotations past. 20120831T175520: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :;-) 20120831T175520: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ;-) 20120831T181339: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Huh. That one worked okay. Took a 45-degree slice of the circle. 20120831T181339: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Huh. That one worked okay. Took a 45-degree slice of the circle. 20120831T183412: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Nice! 20120831T183412: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Nice! 20120831T183439: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :IIRC the FitHypersphere code does not have any in-built quality measure, right? 20120831T183439: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: IIRC the FitHypersphere code does not have any in-built quality measure, right? 20120831T183536: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Should not be too hard to get the standard deviation of the distance to the center of the sphere... 20120831T183536: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Should not be too hard to get the standard deviation of the distance to the center of the sphere... 20120831T184206: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :dscho: Correct; it only provides center and radius. 20120831T184206: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: dscho: Correct; it only provides center and radius. 20120831T184239: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :That quality measure'd give us a good idea how accurate our estimate could possibly be... 20120831T184239: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: That quality measure'd give us a good idea how accurate our estimate could possibly be... 20120831T184304: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :So far we only use a 2d fit, correct? We might want to have a 3d fit. 20120831T184304: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: So far we only use a 2d fit, correct? We might want to have a 3d fit. 20120831T184408: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I'm actually doing a 3D (spherical) fit at the moment. It should really be cylindrical, but oh well. 20120831T184408: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I'm actually doing a 3D (spherical) fit at the moment. It should really be cylindrical, but oh well. 20120831T184428: *: <== :qwebirc20695!905c30f3@gateway/web/freenode/ip.144.92.48.243 JOIN #fiji-devel 20120831T184431: *: <== :qwebirc20695!905c30f3@gateway/web/freenode/ip.144.92.48.243 NICK :imagejdev-irc 20120831T184431: qwebirc20695# imagejdev-irc 20120831T184458: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I meant the bead segmentation... 20120831T184458: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I meant the bead segmentation... 20120831T184534: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :? 20120831T184534: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: ? 20120831T184544: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :The Gaussian fit... 20120831T184544: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: The Gaussian fit... 20120831T184603: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Oh. It's several-slice 2D fit using intensity/bg ratio-weighted averaging. 20120831T184603: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Oh. It's several-slice 2D fit using intensity/bg ratio-weighted averaging. 20120831T184705: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :And you take the most intense slice, correct? 20120831T184705: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: And you take the most intense slice, correct? 20120831T184751: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :For z? Not at present; it also is on the weighted average. 20120831T184751: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: For z? Not at present; it also is on the weighted average. 20120831T184832: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :(The intensity should decay the same in both directions, no?) 20120831T184832: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: (The intensity should decay the same in both directions, no?) 20120831T184922: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :It should indeed. 20120831T184922: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: It should indeed. 20120831T185833: *: <== :imagejdev-irc!905c30f3@gateway/web/freenode/ip.144.92.48.243 PART #fiji-devel 20120831T192345: *: <== :joshmoore!~joshmoore@manz-590f36f5.pool.mediaWays.net QUIT :Quit: Leaving. 20120831T193030: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Well. That's not encouraging at all. 20120831T193030: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Well. That's not encouraging at all. 20120831T193048: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Hmm... 20120831T193048: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Hmm... 20120831T193059: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I'll attach it to the issue. 20120831T193059: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I'll attach it to the issue. 20120831T193101: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You get inconsistent results? 20120831T193101: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You get inconsistent results? 20120831T193104: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :k 20120831T193104: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: k 20120831T193200: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :http://openspim.org/bugs/file_download.php?file_id=19&type=bug 20120831T193200: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: http://openspim.org/bugs/file_download.php?file_id=19&type=bug 20120831T193219: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :(That's at an angle, in case it's not clear.) 20120831T193219: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: (That's at an angle, in case it's not clear.) 20120831T193253: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I'm wondering if twice I picked up the wrong bead, then found the right one again at the end. XD 20120831T193253: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I'm wondering if twice I picked up the wrong bead, then found the right one again at the end. XD 20120831T193659: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Looks a little bit like http://en.wikipedia.org/wiki/Deferent_and_epicycle to me. 20120831T193659: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Looks a little bit like http://en.wikipedia.org/wiki/Deferent_and_epicycle to me. 20120831T193812: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :I really wonder whether we're not falling prey to wrong assumptions. 20120831T193812: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: I really wonder whether we're not falling prey to wrong assumptions. 20120831T193911: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Because basically our assumption is that the axis of rotation and the translational coordinate system always have the same relationship to each other. 20120831T193911: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Because basically our assumption is that the axis of rotation and the translational coordinate system always have the same relationship to each other. 20120831T193926: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :The turns just seem too abrupt. Jagged. Specifically the second turn from the right. 20120831T193926: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: The turns just seem too abrupt. Jagged. Specifically the second turn from the right. 20120831T193941: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Okay, but how could they *not*? 20120831T193941: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Okay, but how could they *not*? 20120831T193957: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Have a look at this: http://en.wikipedia.org/wiki/Epicycloid 20120831T193957: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Have a look at this: http://en.wikipedia.org/wiki/Epicycloid 20120831T194044: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Let's base our considerations on the coordinate system defined by the rotational axis and the bead. 20120831T194044: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Let's base our considerations on the coordinate system defined by the rotational axis and the bead. 20120831T194045: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I see that. But you get either sharp points or curves, not straight lines and ninety-degree turns. 20120831T194045: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I see that. But you get either sharp points or curves, not straight lines and ninety-degree turns. 20120831T194054: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Okay. 20120831T194054: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Okay. 20120831T194103: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Let's assume that the bead is defining y = 0, and the axis defines x = 0, z = 0. 20120831T194103: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Let's assume that the bead is defining y = 0, and the axis defines x = 0, z = 0. 20120831T194112: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Okay. 20120831T194112: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Okay. 20120831T194136: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :When we rotate that, all of a sudden the x, z translational motors do something pretty different than before the rotation. 20120831T194136: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: When we rotate that, all of a sudden the x, z translational motors do something pretty different than before the rotation. 20120831T194213: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :They do? 20120831T194213: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: They do? 20120831T194232: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Yep, they no longer translate along the same vectors in said coordinate system. 20120831T194232: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Yep, they no longer translate along the same vectors in said coordinate system. 20120831T194243: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But along rotated vectors. 20120831T194243: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But along rotated vectors. 20120831T194324: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Ah; you left out that the bead's relationship to the axis should also define a direction (the X axis, suppose). 20120831T194324: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Ah; you left out that the bead's relationship to the axis should also define a direction (the X axis, suppose). 20120831T194357: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Well, that's what I meant by "defined by the rotational axis and the bead"... ;-) 20120831T194357: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Well, that's what I meant by "defined by the rotational axis and the bead"... ;-) 20120831T194440: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :I took that to be a general statement, not a specific one. :P Your explicitly-stated assumptions contain nothing about the direction of the axes. 20120831T194440: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: I took that to be a general statement, not a specific one. :P Your explicitly-stated assumptions contain nothing about the direction of the axes. 20120831T194454: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Yeah, I avoided that. 20120831T194454: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Yeah, I avoided that. 20120831T194500: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Anyway. 20120831T194500: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Anyway. 20120831T194513: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Okay, so yes, the motors now move along rotated vectors. 20120831T194513: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Okay, so yes, the motors now move along rotated vectors. 20120831T194515: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :But we can define the x axis by the bead and the axis. 20120831T194515: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: But we can define the x axis by the bead and the axis. 20120831T194551: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :It's just the perpendicular between the two. 20120831T194551: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: It's just the perpendicular between the two. 20120831T194618: *: <== :GitHub115!~GitHub115@sh2.rs.github.com NOTICE #fiji-devel :[fiji] none pushed 1 new commit to imglib2-spim: http://git.io/WTIo_g 20120831T194619: *: <== :GitHub115!~GitHub115@sh2.rs.github.com NOTICE #fiji-devel :[fiji/imglib2-spim] Merge remote-tracking branch 'origin/master' into imglib2-spim - Tobias Pietzsch 20120831T194654: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :(This only fails when the bead is *on* the axis, which we may need to handle as a special-case) 20120831T194654: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: (This only fails when the bead is *on* the axis, which we may need to handle as a special-case) 20120831T195150: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :If the bead is on the axis, our system is degenerate, but it's a moot point -- the bead's position gives us the location of the axis. 20120831T195150: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: If the bead is on the axis, our system is degenerate, but it's a moot point -- the bead's position gives us the location of the axis. 20120831T195207: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Exactly. 20120831T195207: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Exactly. 20120831T195816: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Let's try to think of the transformation which -- given an x, y, z position of the translators and a theta of the twister -- turns axis/bead coordinates into coordinates defined by the x,y,z motors... 20120831T195816: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Let's try to think of the transformation which -- given an x, y, z position of the translators and a theta of the twister -- turns axis/bead coordinates into coordinates defined by the x,y,z motors... 20120831T195917: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :For the moment, let's assume perfectly perpendicular x, y, z translators, and that y is parallel to the rotational axis. 20120831T195917: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: For the moment, let's assume perfectly perpendicular x, y, z translators, and that y is parallel to the rotational axis. 20120831T200009: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Then the problem is only to transform from (u, v) coordinates (where the bead would be (d, 0) with d being the distance to the rotational axis) to (x, z) coordinates. 20120831T200009: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Then the problem is only to transform from (u, v) coordinates (where the bead would be (d, 0) with d being the distance to the rotational axis) to (x, z) coordinates. 20120831T204702: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 QUIT :K-Lined 20120831T205307: *: <== :qwebirc92101!905c30e5@gateway/web/freenode/ip.144.92.48.229 JOIN #fiji-devel 20120831T205313: *: <== :qwebirc92101!905c30e5@gateway/web/freenode/ip.144.92.48.229 NICK :lstuyvenberg 20120831T205313: qwebirc92101# lstuyvenberg 20120831T205411: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Huh 20120831T205411: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Huh 20120831T205413: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :and now I'm here. 20120831T205413: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: and now I'm here. 20120831T205424: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Oh right -- you logged me in. 20120831T205424: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Oh right -- you logged me in. 20120831T205516: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :dscho: It seems the acquisition will be done with time to spare, though I doubt very much this computer will be able to view it the way we want to. 20120831T205516: lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: dscho: It seems the acquisition will be done with time to spare, though I doubt very much this computer will be able to view it the way we want to. 20120831T205533: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Heh... 20120831T205533: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Heh... 20120831T205602: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :You can scp it to my machine. 20120831T205602: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: You can scp it to my machine. 20120831T205608: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Should be in .ssh/config as bigmac 20120831T205608: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Should be in .ssh/config as bigmac 20120831T210028: *: <== :qwebirc21631!905c30e5@gateway/web/freenode/ip.144.92.48.229 JOIN #fiji-devel 20120831T210028: *: <== :qwebirc21631!905c30e5@gateway/web/freenode/ip.144.92.48.229 NICK :stuyvenberg 20120831T210028: qwebirc21631# stuyvenberg 20120831T210035: *: <== :stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :*sigh* 20120831T210035: stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: *sigh* 20120831T210046: *: <== :stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :In other news, acquisition is already half-way done. I can see how Pete used up his hard drive. 20120831T210046: stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: In other news, acquisition is already half-way done. I can see how Pete used up his hard drive. 20120831T210335: *: <== :ctrueden!~ctrueden@dyn-144-92-48-222.microscopy.wisc.edu QUIT :Quit: Leaving. 20120831T210508: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :;-) 20120831T210508: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: ;-) 20120831T210541: *: <== :stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :We are, however, going to have some lighting changes among images. *sigh* Hopefully this last set will endure no interruptions... 20120831T210541: stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: We are, however, going to have some lighting changes among images. *sigh* Hopefully this last set will endure no interruptions... 20120831T212603: *: <== :stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :dscho: Done. 2.5k images, 6.64 GB. 20120831T212603: stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: dscho: Done. 2.5k images, 6.64 GB. 20120831T212659: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Nice! 20120831T212659: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Nice! 20120831T212706: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Did you scp them already? 20120831T212706: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Did you scp them already? 20120831T212733: *: <== :stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Alas no; where do you want them? 20120831T212733: stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Alas no; where do you want them? 20120831T212921: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :Your home would be good, on bigmac. 20120831T212921: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: Your home would be good, on bigmac. 20120831T213055: *: <== :stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 PRIVMSG #fiji-devel :Started. I'm going to clean up and commit some changes. 20120831T213055: stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229: Started. I'm going to clean up and commit some changes. 20120831T213422: *: <== :dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu PRIVMSG #fiji-devel :k 20120831T213422: dscho!~gene099@dyn-144-92-48-243.microscopy.wisc.edu: k 20120831T213632: *: <== :stuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 QUIT :Quit: Out 20120831T213912: *: <== :lstuyvenberg!905c30e5@gateway/web/freenode/ip.144.92.48.229 QUIT :Ping timeout: 245 seconds