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#6799 closed enhancement (fixed)
RFE: Set scale factors from displayed contours
| Reported by: | Owned by: | Tom Goddard | |
|---|---|---|---|
| Priority: | moderate | Milestone: | |
| Component: | Volume Data | Version: | |
| Keywords: | Cc: | Elaine Meng | |
| Blocked By: | Blocking: | ||
| Notify when closed: | Platform: | all | |
| Project: | ChimeraX |
Description
From: Oliver Clarke via Chimera-users <chimera-users@…>
Subject: [Chimera-users] Set scale factors from displayed contours?
Date: May 6, 2022 at 1:23:22 PM PDT
Reply-To: Oliver Clarke <olibclarke@…>
Hi,
When combining maps using vop maximum (or volume maximum in chimerax), we often want to adjust the scale factors of the maps such that the overlapping bits of two aligned maps are visually on the same scale. It is possible to calculate the appropriate scale factors from the displayed thresholds, but this becomes a little time consuming when combining many maps.
Would it be possible to add a flag, something like "get scalefactor from display thresholds" that would take care of this automatically?
E.g. if the user has set map1 to a threshold of 1.0, and map2 to a threshold of 2.0, in order to make them visually equivalent in a combined map, map1 needs to be scaled by a factor of 2.
It would be great if this could be done automatically as a flag for the volume or vop command (as there is already a flag to provide per map scale factors).
On May 6, 2022, at 2:38 PM, Elaine Meng via Chimera-users <chimera-users@…> wrote:
Hi Oli,
Oh, I see, you already figured out the scale factors (essentially) by adjusting thresholds interactively. So the automation would simply be doing the math of taking the ratio of the thresholds and scaling the map(s) according to that, which sounds more feasible.
I can make a feature request ticket (probably ChimeraX), but can't make promises as I would not be the one to triage it.
Best,
Elaine
Done.
The volume command scaleFactors option now accepts "fromlevels" (e.g. volume max #1,2 scale fromlevels) and in that case uses scale factors that are 1/level for each volume where level is the maximum surface level shown. All volumes must have a surface and a nonzero maximum surface level. This option scales each map making the displayed surface level have value 1 before combining the maps.