# Issues with display of optimism **URL:** \ **Category:** Uncategorized\ **Created:** [December 13, 2022, 11:57am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100 "2022-12-13T11:57:08Z")\ **Posts on this page:** 20\ **Page:** 1
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [December 13, 2022, 11:57am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/1 "2022-12-13T11:57:08Z")
Hello, I am trying to analysis the left atrial shapes, but the outcome of optimism is awkward. How to deal with it? Thank you! ![test](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/8f2f2383c73a7b21829d0c27f55cd746598393cb.jpeg) ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [December 13, 2022, 11:57am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/2 "2022-12-13T11:57:52Z")
The picture shows the mean shape of my data. ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [December 14, 2022, 12:36am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/3 "2022-12-14T00:36:08Z")
If you turn the isosurface off and move the PCA mode slider back and forth, are the particles going crazy, or do they look as you might expect? I’m trying to figure out if it’s a surface reconstruction problem, or if the optimization has gone wrong. ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [December 14, 2022, 2:29pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/4 "2022-12-14T14:29:44Z")
Hi, Thank you for the response. When I move the PCA mode slider, the particles are reasonable as expected. So it might be a surface reconstruction problem. I tried three reconstruction options in the software, the results are all weird. [ xby [xbyzju@126.com](mailto:xbyzju@126.com) ]([头像签名](https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=xby&uid=xbyzju%40126.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%22xbyzju%40126.com%22%5D)) ---- Replied Message ---- > From | [Alan Morris via ShapeWorks](mailto:notifications@shapeworks.discoursemail.com)[notifications@shapeworks.discoursemail.com](mailto:notifications@shapeworks.discoursemail.com) | > > - | - | > Date | 12/14/2022 08:46 | > To | [xbyzju@126.com](mailto:xbyzju@126.com) | > Subject | [ShapeWorks] Issues with display of optimism | > ![](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/cd5bd4b71fbe76e51aa3eb293d04a7cdd25acb62.png "amorris") | [amorris](https://shapeworks.discourse.group/u/amorris) > December 14 | > > - | - | If you turn the isosurface off and move the PCA mode slider back and forth, are the particles going crazy, or do they look as you might expect? I’m trying to figure out if it’s a surface reconstruction problem, or if the optimization has gone wrong. ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [December 20, 2022, 6:51am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/5 "2022-12-20T06:51:21Z")
Are these the left atrium shapes from the shapeworks use case? Or are they from elsewhere? ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [December 20, 2022, 7:09am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/6 "2022-12-20T07:09:43Z")
They are our own data from left atrial CT Angiography. ---- Replied Message ---- > From | [Alan Morris via ShapeWorks](mailto:notifications@shapeworks.discoursemail.com)[notifications@shapeworks.discoursemail.com](mailto:notifications@shapeworks.discoursemail.com) | > > - | - | > Date | 12/20/2022 15:01 | > To | [xbyzju@126.com](mailto:xbyzju@126.com)[xbyzju@126.com](mailto:xbyzju@126.com) | > Cc | | > Subject | [ShapeWorks] Issues with display of optimism | > ![](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/cd5bd4b71fbe76e51aa3eb293d04a7cdd25acb62.png "amorris") | [amorris](https://shapeworks.discourse.group/u/amorris) > December 20 | > > - | - | Are these the left atrium shapes from the shapeworks use case? Or are they from elsewhere? ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [December 21, 2022, 3:18pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/7 "2022-12-21T15:18:31Z")
Can you try (after the optimization) to reduce the number of shapes to just a few (e.g. two) and see if the problem persists. I am wondering if it is a particular shape. To do this, open the xlsx file and cut all but the first two subject lines, then re-load in Studio. ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [December 21, 2022, 3:19pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/8 "2022-12-21T15:19:24Z")
Also, is this the latest ShapeWorks Studio? 6.3.2? ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [December 23, 2022, 1:41pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/9 "2022-12-23T13:41:39Z")
I tried to reduce the number of shapes to 4 and the results are as follows: Surface reconstruction method: Legacy: ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/ad4cfbeae84a5559ed2c00cbebda41ca77e7941a.jpeg) Mesh Warping based: ![截屏2022-12-23 下午9.35.32](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/adcf1f7e7913a428bd29a91c15c3205464f346d3.jpeg) Distance Transform Based( default parameters) ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/ad4cfbeae84a5559ed2c00cbebda41ca77e7941a.jpeg) The version of ShapeWorks Studio is 6.3.0 ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [December 29, 2022, 5:31pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/10 "2022-12-29T17:31:18Z")
Is there a chance you could make a zip of the 4 patient project and point me to it? You can email me at amorris@sci.utah.edu ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [January 1, 2023, 9:59am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/11 "2023-01-01T09:59:03Z")
OK, I have sent the shapes to you. Happy new year! 😃 ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [January 3, 2023, 6:28pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/12 "2023-01-03T18:28:55Z")
Can you try this project (no need to re-optimize) with the 6.3.1 or 6.3.2 release? I ran the shapes you sent and see a similar problem with the 6.3.0 release, but loading the project in 6.3.1/6.3.2 and the mesh warping is fixed. I don’t see anything on our release notes for 6.3.1 about the mesh warping, but we must have fixed some bugs in that time. ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [January 15, 2023, 1:54pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/13 "2023-01-15T13:54:17Z")
Hi, I tried this project with the 6.3.2 release. But there is the similar problem with mesh reconstruction. ![test](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/7ac2f7aa510d2ddaabfb138b71f0280e2c87f4f0.jpeg) ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [January 24, 2023, 3:24pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/14 "2023-01-24T15:24:39Z")
In this case, the particles look a bit mixed up to me. If you run through the first few PCA modes, do you see particles crossing paths? Can you try a lower number of particles, such as 64 or 128 and see what that looks like to confirm whether it is a mesh reconstruction problem or a problem with the model itself? ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [February 4, 2023, 4:39pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/15 "2023-02-04T16:39:29Z")
Hi, Amorris I tried 512 particles with more shapes (40 cases), the results were good as follows. ![test](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/06e52b168303dcf4d3512aff6d56b4b0baab162a.jpeg) However, when i tried to analysis the full data (220 cases), it reported mistakes like this. ![image](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/6873c48e0c850ecd4147a2942f4f6c2714acc46c.jpeg) ![error2](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/0d8dd78e5799e06e7ebc440b289a90e1dc2fc543.jpeg) I sent a log file to shapeworks-dev-support@sci.utah.edu. Thank you! ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [February 6, 2023, 7:00pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/16 "2023-02-06T19:00:42Z")
I haven’t seen the log come through on shapeworks-dev-support yet. Could you try sending it to me directly at amorris@sci.utah.edu? ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [February 8, 2023, 2:27pm UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/17 "2023-02-08T14:27:00Z")
> [@amorris](#): > > amorris@sci.utah.edu I have sent it to you. Thank you! ---
**Author:** ![amorris](https://avatars.discourse-cdn.com/v4/letter/a/73ab20/32.png) [@amorris](https://shapeworks.discourse.group/u/amorris)\ **Post date:** [February 11, 2023, 5:20am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/18 "2023-02-11T05:20:08Z")
Thanks! I’ve fixed the crash if you want to try the development build of ShapeWorks: > **[Releases · SCIInstitute/ShapeWorks](https://github.com/SCIInstitute/ShapeWorks/releases)** > > ShapeWorks. Contribute to SCIInstitute/ShapeWorks development by creating an account on GitHub. I am not sure about the mesh warp problem, but I added additional diagnostic messages that may help us track it down if you try this version and we check the logs. ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [February 17, 2023, 6:22am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/19 "2023-02-17T06:22:07Z")
Dear Alan Morris: I tried the new version and the crash did not happen. However, the mean mesh constructed is still a little wired. The attachment is the mean mesh. In addition, I have a question: if the mesh reconstructed was not perfect, are the results of PCA component score still correct? If I want to classify the outcomes with shape statistic model, I shall compare the PCA component score exported by Shapeworks, right? Thank you very much! [ ![](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/1eb7f0e5fc0b98923286e20719f039fe30e88414.png) xby [xbyzju@126.com](mailto:xbyzju@126.com) ]([https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=xby&uid=xbyzju%40126.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=["xbyzju%40126.com"]](https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=xby&uid=xbyzju%40126.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%22xbyzju%40126.com%22%5D)) ---- Replied Message ---- > From | [Alan Morris via ShapeWorks](mailto:notifications@shapeworks.discoursemail.com)[notifications@shapeworks.discoursemail.com](mailto:notifications@shapeworks.discoursemail.com) | > > - | - | > Date | 02/11/2023 13:30 | > To | [xbyzju@126.com](mailto:xbyzju@126.com) | > Subject | [ShapeWorks] Issues with display of optimism | > ![](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/705c6a87b94836dd958e75ccc052e806bcd6eafb.png "amorris") | [amorris](https://shapeworks.discourse.group/u/amorris) > February 11 | > > - | - | Thanks! I’ve fixed the crash if you want to try the development build of ShapeWorks: [GitHub](https://github.com/SCIInstitute/ShapeWorks/releases) ### [Releases · SCIInstitute/ShapeWorks](https://github.com/SCIInstitute/ShapeWorks/releases) ShapeWorks. Contribute to SCIInstitute/ShapeWorks development by creating an account on GitHub. I am not sure about the mesh warp problem, but I added additional diagnostic messages that may help us track it down if you try this version and we check the logs. (Attachment MeshWarp.vtk is missing) ---
**Author:** ![xbyzju](https://avatars.discourse-cdn.com/v4/letter/x/a5b964/32.png) [@xbyzju](https://shapeworks.discourse.group/u/xbyzju)\ **Post date:** [February 17, 2023, 6:25am UTC](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100/20 "2023-02-17T06:25:35Z")
Dear Alan Morris: I tried the new version and the crash did not happen. However, the mean mesh constructed is still a little wired. The attachment is the mean mesh. In addition, I have a question: if the mesh reconstructed was not perfect, are the results of PCA component score still correct? If I want to classify the outcomes with shape statistic model, I shall compare the PCA component score exported by Shapeworks, right? Thank you very much! [ ![](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/1eb7f0e5fc0b98923286e20719f039fe30e88414.png) xby [xbyzju@126.com](mailto:xbyzju@126.com) ]([https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=xby&uid=xbyzju%40126.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=["xbyzju%40126.com"]](https://maas.mail.163.com/dashi-web-extend/html/proSignature.html?ftlId=1&name=xby&uid=xbyzju%40126.com&iconUrl=https%3A%2F%2Fmail-online.nosdn.127.net%2Fqiyelogo%2FdefaultAvatar.png&items=%5B%22xbyzju%40126.com%22%5D)) ---- Replied Message ---- > From | [Alan Morris via ShapeWorks](mailto:notifications@shapeworks.discoursemail.com)[notifications@shapeworks.discoursemail.com](mailto:notifications@shapeworks.discoursemail.com) | > > - | - | > Date | 02/11/2023 13:30 | > To | [xbyzju@126.com](mailto:xbyzju@126.com) | > Subject | [ShapeWorks] Issues with display of optimism | > ![](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/705c6a87b94836dd958e75ccc052e806bcd6eafb.png "amorris") | [amorris](https://shapeworks.discourse.group/u/amorris) > February 11 | > > - | - | Thanks! I’ve fixed the crash if you want to try the development build of ShapeWorks: [GitHub](https://github.com/SCIInstitute/ShapeWorks/releases) ### [Releases · SCIInstitute/ShapeWorks](https://github.com/SCIInstitute/ShapeWorks/releases) ShapeWorks. Contribute to SCIInstitute/ShapeWorks development by creating an account on GitHub. I am not sure about the mesh warp problem, but I added additional diagnostic messages that may help us track it down if you try this version and we check the logs. ![mesh.jpeg](https://global.discourse-cdn.com/free1/uploads/shapeworks/original/1X/a94ede4cc2df3e76d2c7e8973cb5a02ffae63853.jpeg) [Next page](https://shapeworks.discourse.group/t/issues-with-display-of-optimism/100.md?page=2)