From dslice at morphometrics.org Wed Mar 6 06:16:45 2019 From: dslice at morphometrics.org (Dennis E. Slice) Date: Wed, 6 Mar 2019 06:16:45 -0500 Subject: [SC-MorphLab] Today, Wednesday 06, 2019 Message-ID: <8dcb873d-8e0c-ee7d-9190-dbc8ba7bd23d@fsu.edu> Please let me know (email) if anyone needs to meet with me before or after tea/seminar today so I will know if I need to come in early or plan to stay later. Of course, I can do either, but need to know especially if I need to come in before 3p - staying late is no problem. -ds -- Department of Scientific Computing, The Florida State University Department of Anthropology, University of Vienna, Austria Website: http://morphlab.sc.fsu.edu ---- If a response is important to you, keep trying -> I receive 50-100 msgs/day From dslice at morphometrics.org Wed Mar 6 06:25:55 2019 From: dslice at morphometrics.org (Dennis E. Slice) Date: Wed, 6 Mar 2019 06:25:55 -0500 Subject: [SC-MorphLab] Welcome Home, Andre... Message-ID: <5b24852c-cfa6-aed7-6297-8a463d2eec20@morphometrics.org> If you ever find yourself lacking in feces and urine around the house or getting too much sleep, you can address these issues with a new puppy. Attached are pictures of Andre (Andre the Giant (*)... Andre the Giant Schnauzer) who has been somewhat-to-very disruptive of my life since I left to retrieve him on Friday. Back home on Saturday. He and Sisi? appear to be getting along - no animosity, possibly even some degree of bonding and connection, lots of play. For now, Sisi has experience, speed, agility and endurance on Andre. Andre (9 weeks) has weight and possibly strength on Sisi, but is quite uncoordinated, even clumsy - he will start licking himself and just fall over, also no stamina - can only chase for a few yards. First vet visit yesterday for Andre: 18.5 lbs and two testicles (which took some poking about to determine, but apparently and important thing to find out). -ds (*) Andre the Giant: https://urldefense.proofpoint.com/v2/url?u=https-3A__en.wikipedia.org_wiki_Andr-25C3-25A9-5Fthe-5FGiant&d=DwIDaQ&c=HPMtquzZjKY31rtkyGRFnQ&r=YjpGtPaMcFHDzc5pw_JuNH5rzShZuguM3EvsFa7VmzQ&m=Duf_JpBVf0fR7ijlUSrlHF_8kqgjgcp6-26WOOJtkCE&s=uqdk4QrhgP3Mq_bNofHoagNTfzdLDFu14h-rlOuG1z8&e= -- If a response is important to you, keep trying -> I receive 50-100 msgs/day -------------- next part -------------- A non-text attachment was scrubbed... Name: P1030131 2.JPG Type: image/jpeg Size: 536965 bytes Desc: not available URL: -------------- next part -------------- A non-text attachment was scrubbed... Name: P1030138 2.JPG Type: image/jpeg Size: 1118655 bytes Desc: not available URL: From dslice at morphometrics.org Wed Mar 6 09:55:05 2019 From: dslice at morphometrics.org (Dennis E. Slice) Date: Wed, 6 Mar 2019 09:55:05 -0500 Subject: [SC-MorphLab] Today, Wednesday 06, 2019 In-Reply-To: <8dcb873d-8e0c-ee7d-9190-dbc8ba7bd23d@fsu.edu> References: <8dcb873d-8e0c-ee7d-9190-dbc8ba7bd23d@fsu.edu> Message-ID: Okay. In response to replies I will try to be in by 2p and prepared to stay after seminar as needed. -ds On 3/6/19 6:16 AM, Dennis E. Slice wrote: > Please let me know (email) if anyone needs to meet with me before or > after tea/seminar today so I will know if I need to come in early or > plan to stay later. Of course, I can do either, but need to know > especially if I need to come in before 3p - staying late is no > problem. -ds > -- Department of Scientific Computing, The Florida State University Department of Anthropology, University of Vienna, Austria Website: http://morphlab.sc.fsu.edu ---- If a response is important to you, keep trying -> I receive 50-100 msgs/day From dslice at morphometrics.org Wed Mar 6 13:12:01 2019 From: dslice at morphometrics.org (Dennis E. Slice) Date: Wed, 6 Mar 2019 13:12:01 -0500 Subject: [SC-MorphLab] Today, Wednesday 06, 2019 In-Reply-To: References: <8dcb873d-8e0c-ee7d-9190-dbc8ba7bd23d@fsu.edu> Message-ID: Leaving now: 1:11p -ds On 3/6/19 9:55 AM, Dennis E. Slice wrote: > Okay. In response to replies I will try to be in by 2p and prepared to > stay after seminar as needed. -ds > > On 3/6/19 6:16 AM, Dennis E. Slice wrote: >> Please let me know (email) if anyone needs to meet with me before or >> after tea/seminar today so I will know if I need to come in early or >> plan to stay later. Of course, I can do either, but need to know >> especially if I need to come in before 3p - staying late is no >> problem. -ds >> -- Department of Scientific Computing, The Florida State University Department of Anthropology, University of Vienna, Austria Website: http://morphlab.sc.fsu.edu ---- If a response is important to you, keep trying -> I receive 50-100 msgs/day From dabeamer973 at nashcc.edu Sat Mar 9 10:21:22 2019 From: dabeamer973 at nashcc.edu (David Beamer) Date: Sat, 9 Mar 2019 10:21:22 -0500 Subject: [SC-MorphLab] a few morpheus questions Message-ID: <08bf5437-3690-6b9b-4c7a-b96797c6e7f1@nashcc.edu> Hello I have recently begun to use Morpheus as part of a work flow to rapidly produce linear measurements from tps files. Students plot landmarks in tpsDig and the last two landmarks (#11 & #12) are points on a ruler 1 mm apart. To produce the measurements the tps file is imported into Morpheus and the following command is issued: SUPER BSC 11 12. My understanding is that as long as the distance between these points is 1 mm then issuing the following command: MEASUREMENT ADD DIST svl 1 2 should produce measurements in mm's. Can you verify that this is correct? My testing suggests that this is true but using the measure tool in tpsDig is very touchy and it is hard to get the exact same number reported in Morpheus. I feel pretty confident in the measurements but having verification that this method is sound would ease my mind! Following the manual I can make a new tps file from images in Morpheus but I am unclear if landmarks can be plotted in it as well. Is this possible? We run tpsDig in Wine but if we could do the same operation in Morpheus it would reduce the number of software packages in the work flow. The final issue may be related to the fact that all of our lab computers are running Linux (Ubuntu) and this is the report of java -version: java version "1.8.0_201" Java(TM) SE Runtime Environment (build 1.8.0_201-b09) Java HotSpot(TM) 64-Bit Server VM (build 25.201-b09, mixed mode). The third mouse button does indeed move the image up/down and left/right however the first and more importantly the second mouse buttons do not function. Is there another way to zoom the image in or out besides the second mouse button? thanks for your time David Beamer From dslice at morphometrics.org Wed Mar 20 21:15:04 2019 From: dslice at morphometrics.org (Dennis E. Slice) Date: Wed, 20 Mar 2019 21:15:04 -0400 Subject: [SC-MorphLab] Some success Message-ID: <61405a73-6cb7-dd0c-8989-bc31eb174c24@morphometrics.org> Attached is an image of morpheus showing newest feature. It has in places, I think, computation and summary system for PCA (and a management system for any number of other analyses, e.g., regression, relwarps, etc.). I think I can now focus entirely on the graphics - plotting and visualization. But much else to do during spring break. -ds -- If a response is important to you, keep trying -> I receive 50-100 msgs/day -------------- next part -------------- A non-text attachment was scrubbed... Name: Screen Shot 2019-03-20 at 9.11.34 PM.png Type: image/png Size: 361451 bytes Desc: not available URL: From dslice at morphometrics.org Wed Mar 20 21:35:24 2019 From: dslice at morphometrics.org (Dennis E. Slice) Date: Wed, 20 Mar 2019 21:35:24 -0400 Subject: [SC-MorphLab] Some success In-Reply-To: <61405a73-6cb7-dd0c-8989-bc31eb174c24@morphometrics.org> References: <61405a73-6cb7-dd0c-8989-bc31eb174c24@morphometrics.org> Message-ID: I might point out that the computations and display only took me today - for some reason, I had the computational code already embedded in Morpheus. What has taken me around the clock since last Thursday has been the analysis/window management system. -ds On 3/20/19 9:15 PM, Dennis E. Slice wrote: > Attached is an image of morpheus showing newest feature. It has in > places, I think, computation and summary system for PCA (and a > management system for any number of other analyses, e.g., regression, > relwarps, etc.). I think I can now focus entirely on the graphics - > plotting and visualization. But much else to do during spring break. -ds > > > _______________________________________________ > SC-MorphLab mailing list > SC-MorphLab at lists.fsu.edu > https://lists.fsu.edu/mailman/listinfo/sc-morphlab -- Department of Scientific Computing, The Florida State University Department of Anthropology, University of Vienna, Austria Website: http://morphlab.sc.fsu.edu ---- If a response is important to you, keep trying -> I receive 50-100 msgs/day -------------- next part -------------- An HTML attachment was scrubbed... URL: From dslice at morphometrics.org Thu Mar 28 13:36:31 2019 From: dslice at morphometrics.org (Dennis E. Slice) Date: Thu, 28 Mar 2019 13:36:31 -0400 Subject: [SC-MorphLab] a few morpheus questions In-Reply-To: <08bf5437-3690-6b9b-4c7a-b96797c6e7f1@nashcc.edu> References: <08bf5437-3690-6b9b-4c7a-b96797c6e7f1@nashcc.edu> Message-ID: <97e88d5e-9a93-a9dd-93f6-27a049c598fe@fsu.edu> Catching up a bit on email. Sorry for the delay. On 3/9/19 10:21 AM, David Beamer wrote: > Hello > > I have recently begun to use Morpheus as part of a work flow to > rapidly produce linear measurements from tps files. Students plot > landmarks in tpsDig and the last two landmarks (#11 & #12) are points > on a ruler 1 mm apart. In tps the distance between scale-setting points is irrelevant. I don't know what you are digitizing, but 1mm sounds pretty small. For many things, I try to have 10cm (100mm) or so. At any rate, the scale should be comparable to the size of what you are scaling. Otherwise, scale errors can be magnified. > > To produce the measurements the tps file is imported into Morpheus and > the following command is issued: SUPER BSC 11 12. My understanding is > that as long as the distance between these points is Unnecessary. Distance between points are independent of any or no superimposition. > 1 mm then issuing the following command: MEASUREMENT ADD DIST svl 1 2 > should produce measurements in mm's. Can you verify that this is > correct? My testing suggests that this is true but If you set the scale for mm (and the scale can be 1, 100, or 53 or whatever), then resulting measurements from Morpheus will be in mm. > using the measure tool in tpsDig is very touchy and it is hard to get > the exact same number reported in Morpheus. I feel pretty confident in > the measurements but having verification that this method is sound > would ease my mind! > > Following the manual I can make a new tps file from images in Morpheus > but I am unclear if landmarks can be plotted in it as well. Is this > possible? We run tpsDig in Wine but if we could do the same operation > in Morpheus it would reduce the number of software packages in the > work flow. Not sure if I understand the question, but once imported, Morpheus should plot the individual image and landmarks. It does not, at this point, plot the measurements. I just have neglected adding that due to my equivocation on what color to use for measurements and how to who areas. > > The final issue may be related to the fact that all of our lab > computers are running Linux (Ubuntu) and this is the report of java > -version: > > java version "1.8.0_201" > Java(TM) SE Runtime Environment (build 1.8.0_201-b09) > Java HotSpot(TM) 64-Bit Server VM (build 25.201-b09, mixed mode). > > The third mouse button does indeed move the image up/down and > left/right however the first and more importantly the second mouse > buttons do not function. Is there another way to zoom the image in or > out besides the second mouse button? Mouse button support on different systems is by guesswork - I develop on a Mac with a funky apple mouse. Anyway, all functions should be available through key+M1. On my Mac, Command+M1 = translation; Alt/Option + M1 is scaling with the mouse moving towards/away from you, and Control+M1 is just rotation, which is just the M1 function. There should be similar key combos available on your system. Try Alt+ and Ctrl+ and see if that gets what you want, then try some other key combos that might suggest themselves - not sure what you have on your kbd. Let me know of any continued questions/problems. Oh, I am interested in your running on a Linux system. I am having trouble running Ubuntu under VirtualBox with various (oracle, openjdk) versions. What are your... OS (with version) Java version: are you running the latest Oracle or Openjdk or do you know? Best, ds > > thanks for your time > > David Beamer > > > _______________________________________________ > SC-MorphLab mailing list > SC-MorphLab at lists.fsu.edu > https://lists.fsu.edu/mailman/listinfo/sc-morphlab -- Department of Scientific Computing, The Florida State University Department of Anthropology, University of Vienna, Austria Website: http://morphlab.sc.fsu.edu ---- If a response is important to you, keep trying -> I receive 50-100 msgs/day