[chimera-dev] programming question: volume display

[Tom Goddard]

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
> =================================================
> =================================================
> From: Tom Goddard <goddard at sonic.net>
> Sent: Wednesday, April 5, 2017 2:13:06 PM
> To: Dougherty, Matthew T
> Cc: 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.
>> 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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