[chimera-dev] programming question: volume display

[Dougherty, Matthew T]

here is a related question, let me know if I should open a new thread.


The VolumeEraser code does this for erasing:  self.erase_inside_sphere()


writing python code, how can I activate that code in my modules?

assuming I have issued a 'start Volume Eraser' command to get the gui up.



Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
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From: Dougherty, Matthew T
Sent: Friday, April 7, 2017 2:03:55 PM
To: Tom Goddard
Cc: chimera-dev at cgl.ucsf.edu
Subject: Re: [chimera-dev] programming question: volume display


thx


Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
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From: Tom Goddard <goddard at sonic.net>
Sent: Friday, April 7, 2017 12:58:14 PM
To: Dougherty, Matthew T
Cc: chimera-dev at cgl.ucsf.edu
Subject: Re: [chimera-dev] programming question: volume display

Hi Matt,

  To get the current region and step for a volume

ijk_min, ijk_max, ijk_step = v.region

To avoid having the step adjust automatically in the new_region() call use

new_region(..., adjust_step = False)

Chimera adusts the step to show no more than some specified number of grid points (e.g. 2 million) and this parameter is

v.rendering_options.voxel_limit = 1    # In millions of voxels
v.rendering_options.limit_voxel_count = True  # Whether to auto-adjust step

These options are also present in the Volume Viewer dialog, menu Features / Data Display Options.

Tom

On Apr 7, 2017, at 10:52 AM, Dougherty, Matthew T wrote:

Got it, thx.  Was wondering if there was an alternate API.



having a problem with ijk_step using this:

   v.new_region(ijk_min=(i_min, j_min, k_min), ijk_max=(i_max, j_max, k_max), ijk_step=(1,1,1))

The min and max act correctly, but it jumps into other step sizes when I vary min & max.
would think the step size would be

when the relative min/max is small (i.e., volume is small) the gui step size is one.
as the volume increases, the step size increases.
if I maximize the volume and manually set the gui step size to one, then the python call works as expected.

Any ideas?

also, if I wanted to get the min/max values for the region, how do I get that.

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
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________________________________
From: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Sent: Wednesday, April 5, 2017 2:13:06 PM
To: Dougherty, Matthew T
Cc: chimera-dev at cgl.ucsf.edu<mailto:chimera-dev at cgl.ucsf.edu>
Subject: Re: [chimera-dev] programming question: volume display

Yes.  In fact all that is done with the new_region() routine.  (set step with the ijk_step argument, eg. ijk_step = (2,2,2).  Set plane number by setting ijk_min, ijk_max to show one plane).

Tom


On Apr 5, 2017, at 12:00 PM, Dougherty, Matthew T <matthewd at bcm.edu<mailto:matthewd at bcm.edu>> wrote:

thx

is volume.py where I would find how to change step size, plane number & depth?

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
=================================================
=================================================
________________________________
From: Tom Goddard <goddard at sonic.net<mailto:goddard at sonic.net>>
Sent: Wednesday, April 5, 2017 11:41:35 AM
To: Dougherty, Matthew T
Cc: chimera-dev at cgl.ucsf.edu<mailto:chimera-dev at cgl.ucsf.edu>
Subject: Re: [chimera-dev] programming question: volume display

***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.
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To change the region bounds of a volume v in Python:

v.new_region((0,0,0), (50,60,70))

Here’s the Python declaration in chimera/share/VolumeViewer/volume.py where the Volume class is defined.

  def new_region(self, ijk_min = None, ijk_max = None, ijk_step = None,
                 show = True, adjust_step = True, save_in_region_queue = True):

Tom


On Apr 4, 2017, at 3:58 PM, Dougherty, Matthew T <matthewd at bcm.edu<mailto:matthewd at bcm.edu>> wrote:

I am trying to modify the region bounds of the volume viewer using python.
What module should I be looking at to determine the api calls?

thanks,

Matthew Dougherty
National Center for Macromolecular Imaging
Baylor College of Medicine
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