Re: [Chimera-users] Stereo Red Cyan
Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book. -- Greg On 9/21/2020 11:43 PM, Michael Elbaum wrote:
Red-cyan, sorry. No, I didn't look for stereo at all, just to reproduce the condition posted that one channel appears in red and the other in gray. Is that normal? Michael ------------------------------------------------------------------------ *From:* Greg Couch <gregc@cgl.ucsf.edu> *Sent:* Tuesday, September 22, 2020 4:57:50 AM *To:* Michael Elbaum <michael.elbaum@weizmann.ac.il> *Subject:* Re: [Chimera-users] Stereo Red Cyan
Are you wearing red-cyan glasses to see the stereo? It doesn't work without them.
-- Greg
On 9/21/2020 1:08 PM, Michael Elbaum wrote:
I'm confirming the problem with a different dataset (optical deconvolution in tif format). Red-green shows red and gray, green-magenta shows green and gray. This is with version 1.14 on linux.
regards, Michael
------------------------------------------------------------------------ *From:* Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Angus McDonald <amcdonald@boisestate.edu> *Sent:* Monday, September 21, 2020 9:46:24 PM *To:* chimera-users@cgl.ucsf.edu BB *Subject:* [Chimera-users] Stereo Red Cyan I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious?
Thanks for your time.
-- Angus McDonald amcdonald@boisestate.edu <mailto:amcdonald@boisestate.edu>
_______________________________________________ Chimera-users mailing list:Chimera-users@cgl.ucsf.edu Manage subscription:https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Hello Angus and Michael, It may be a function of the map display style. If I open a map from EMDB, e.g. commands: open emdbID:1024 stereo anaglyph I can clearly see the 3D effect when wearing red-cyan glasses (and red and cyan fringes with the glasses taken off) if I am showing surface or mesh isosurfaces for the map, but not if showing the diffuse cloud of the "solid" style. I attach an image of the map in surface style. I don't know if you can expect to see a 3D effect with the transparent "solid" style even with anaglyph stereo working correctly. I couldn't perceive it with that style. Tested Chimera 1.14 on Mac, and I believe that the map from EMDB is 32-bit floating point like your data. I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2020, at 10:03 AM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book.
-- Greg
On 9/21/2020 11:43 PM, Michael Elbaum wrote:
Red-cyan, sorry. No, I didn't look for stereo at all, just to reproduce the condition posted that one channel appears in red and the other in gray. Is that normal? Michael From: Greg Couch <gregc@cgl.ucsf.edu> Sent: Tuesday, September 22, 2020 4:57:50 AM To: Michael Elbaum <michael.elbaum@weizmann.ac.il> Subject: Re: [Chimera-users] Stereo Red Cyan
Are you wearing red-cyan glasses to see the stereo? It doesn't work without them.
-- Greg
On 9/21/2020 1:08 PM, Michael Elbaum wrote:
I'm confirming the problem with a different dataset (optical deconvolution in tif format). Red-green shows red and gray, green-magenta shows green and gray. This is with version 1.14 on linux. regards, Michael
From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Angus McDonald <amcdonald@boisestate.edu> Sent: Monday, September 21, 2020 9:46:24 PM To: chimera-users@cgl.ucsf.edu BB Subject: [Chimera-users] Stereo Red Cyan
I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious?
Thanks for your time. -- Angus McDonald amcdonald@boisestate.edu
I did look at the Red-Cyan stereo images with Red-Cyan glasses and did not see stereo. I will try Elaine's suggestion On Tue, Sep 22, 2020 at 6:09 PM Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Angus and Michael, It may be a function of the map display style. If I open a map from EMDB, e.g. commands:
open emdbID:1024 stereo anaglyph
I can clearly see the 3D effect when wearing red-cyan glasses (and red and cyan fringes with the glasses taken off) if I am showing surface or mesh isosurfaces for the map, but not if showing the diffuse cloud of the "solid" style. I attach an image of the map in surface style.
I don't know if you can expect to see a 3D effect with the transparent "solid" style even with anaglyph stereo working correctly. I couldn't perceive it with that style.
Tested Chimera 1.14 on Mac, and I believe that the map from EMDB is 32-bit floating point like your data.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Sep 22, 2020, at 10:03 AM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book.
-- Greg
On 9/21/2020 11:43 PM, Michael Elbaum wrote:
Red-cyan, sorry. No, I didn't look for stereo at all, just to reproduce the condition posted that one channel appears in red and the other in gray. Is that normal? Michael From: Greg Couch <gregc@cgl.ucsf.edu> Sent: Tuesday, September 22, 2020 4:57:50 AM To: Michael Elbaum <michael.elbaum@weizmann.ac.il> Subject: Re: [Chimera-users] Stereo Red Cyan
Are you wearing red-cyan glasses to see the stereo? It doesn't work without them.
-- Greg
On 9/21/2020 1:08 PM, Michael Elbaum wrote:
I'm confirming the problem with a different dataset (optical deconvolution in tif format). Red-green shows red and gray, green-magenta shows green and gray. This is with version 1.14 on linux. regards, Michael
From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Angus McDonald <amcdonald@boisestate.edu> Sent: Monday, September 21, 2020 9:46:24 PM To: chimera-users@cgl.ucsf.edu BB Subject: [Chimera-users] Stereo Red Cyan
I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious?
Thanks for your time. -- Angus McDonald amcdonald@boisestate.edu
-- Angus McDonald amcdonald@boisestate.edu
Hi Michael, Angus, Elaine, The solid style volume rendering does only show red and gray with no cyan and that is a bug. I also see that surface style works correctly if the surface is opaque, but if the surface is even the slighting bit transparent (0.99 opaque) then cyan disappears. The solid style is also a form of transparent rendering. I believe that all transparent models will fail to show the cyan and so anaglyph stereo will not work with transparency. This bug is likely related to the fact that Chimera cannot correctly combine two transparent models. We currently only fix critical bugs in Chimera since all development effort and funding is for the next generation ChimeraX (which does not yet have anaglyph stereo). I've made a ticket for this Chimera bug https://plato.cgl.ucsf.edu/trac/chimera/ticket/17771 <https://plato.cgl.ucsf.edu/trac/chimera/ticket/17771> but we do not have the resources to fix it. Tom
On Sep 22, 2020, at 5:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Angus and Michael, It may be a function of the map display style. If I open a map from EMDB, e.g. commands:
open emdbID:1024 stereo anaglyph
I can clearly see the 3D effect when wearing red-cyan glasses (and red and cyan fringes with the glasses taken off) if I am showing surface or mesh isosurfaces for the map, but not if showing the diffuse cloud of the "solid" style. I attach an image of the map in surface style.
I don't know if you can expect to see a 3D effect with the transparent "solid" style even with anaglyph stereo working correctly. I couldn't perceive it with that style.
Tested Chimera 1.14 on Mac, and I believe that the map from EMDB is 32-bit floating point like your data.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<anaglyph.png>
On Sep 22, 2020, at 10:03 AM, Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> wrote:
Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book.
-- Greg
On 9/21/2020 11:43 PM, Michael Elbaum wrote:
Red-cyan, sorry. No, I didn't look for stereo at all, just to reproduce the condition posted that one channel appears in red and the other in gray. Is that normal? Michael From: Greg Couch <gregc@cgl.ucsf.edu <mailto:gregc@cgl.ucsf.edu>> Sent: Tuesday, September 22, 2020 4:57:50 AM To: Michael Elbaum <michael.elbaum@weizmann.ac.il <mailto:michael.elbaum@weizmann.ac.il>> Subject: Re: [Chimera-users] Stereo Red Cyan
Are you wearing red-cyan glasses to see the stereo? It doesn't work without them.
-- Greg
On 9/21/2020 1:08 PM, Michael Elbaum wrote:
I'm confirming the problem with a different dataset (optical deconvolution in tif format). Red-green shows red and gray, green-magenta shows green and gray. This is with version 1.14 on linux. regards, Michael
From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu <mailto:chimera-users-bounces@cgl.ucsf.edu>> on behalf of Angus McDonald <amcdonald@boisestate.edu <mailto:amcdonald@boisestate.edu>> Sent: Monday, September 21, 2020 9:46:24 PM To: chimera-users@cgl.ucsf.edu <mailto:chimera-users@cgl.ucsf.edu> BB Subject: [Chimera-users] Stereo Red Cyan
I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious?
Thanks for your time. -- Angus McDonald amcdonald@boisestate.edu
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
Red Cyan stereo is working with transparent solid in the 09/23/2020 build. Thank you all. -angus On Tue, Sep 22, 2020 at 7:02 PM Tom Goddard <goddard@sonic.net> wrote:
Hi Michael, Angus, Elaine,
The solid style volume rendering does only show red and gray with no cyan and that is a bug. I also see that surface style works correctly if the surface is opaque, but if the surface is even the slighting bit transparent (0.99 opaque) then cyan disappears. The solid style is also a form of transparent rendering. I believe that all transparent models will fail to show the cyan and so anaglyph stereo will not work with transparency. This bug is likely related to the fact that Chimera cannot correctly combine two transparent models.
We currently only fix critical bugs in Chimera since all development effort and funding is for the next generation ChimeraX (which does not yet have anaglyph stereo). I've made a ticket for this Chimera bug
https://plato.cgl.ucsf.edu/trac/chimera/ticket/17771
but we do not have the resources to fix it.
Tom
On Sep 22, 2020, at 5:09 PM, Elaine Meng <meng@cgl.ucsf.edu> wrote:
Hello Angus and Michael, It may be a function of the map display style. If I open a map from EMDB, e.g. commands:
open emdbID:1024 stereo anaglyph
I can clearly see the 3D effect when wearing red-cyan glasses (and red and cyan fringes with the glasses taken off) if I am showing surface or mesh isosurfaces for the map, but not if showing the diffuse cloud of the "solid" style. I attach an image of the map in surface style.
I don't know if you can expect to see a 3D effect with the transparent "solid" style even with anaglyph stereo working correctly. I couldn't perceive it with that style.
Tested Chimera 1.14 on Mac, and I believe that the map from EMDB is 32-bit floating point like your data.
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
<anaglyph.png>
On Sep 22, 2020, at 10:03 AM, Greg Couch <gregc@cgl.ucsf.edu> wrote:
Yes, the red and gray is normal, but you're seeing the combined channels. You need the glasses to separate the channels. Try viewing the image with the glasses that come with a 3D comic book.
-- Greg
On 9/21/2020 11:43 PM, Michael Elbaum wrote:
Red-cyan, sorry. No, I didn't look for stereo at all, just to reproduce the condition posted that one channel appears in red and the other in gray. Is that normal? Michael From: Greg Couch <gregc@cgl.ucsf.edu> Sent: Tuesday, September 22, 2020 4:57:50 AM To: Michael Elbaum <michael.elbaum@weizmann.ac.il> Subject: Re: [Chimera-users] Stereo Red Cyan
Are you wearing red-cyan glasses to see the stereo? It doesn't work without them.
-- Greg
On 9/21/2020 1:08 PM, Michael Elbaum wrote:
I'm confirming the problem with a different dataset (optical deconvolution in tif format). Red-green shows red and gray, green-magenta shows green and gray. This is with version 1.14 on linux. regards, Michael
From: Chimera-users <chimera-users-bounces@cgl.ucsf.edu> on behalf of Angus McDonald <amcdonald@boisestate.edu> Sent: Monday, September 21, 2020 9:46:24 PM To: chimera-users@cgl.ucsf.edu BB Subject: [Chimera-users] Stereo Red Cyan
I am looking at some cryo em data. When I try to view a a 3D stack of em dat with the Red-Cyan stereo setting I seem to only get Red and grayscale. The data is in 32-bit floating point and is in MRC2014 header format. I cannot figure out what I am doing wrong. Is anything obvious?
Thanks for your time. -- Angus McDonald amcdonald@boisestate.edu
_______________________________________________ Chimera-users mailing list: Chimera-users@cgl.ucsf.edu Manage subscription: https://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
-- Angus McDonald amcdonald@boisestate.edu
participants (4)
-
Angus McDonald -
Elaine Meng -
Greg Couch -
Tom Goddard