[chimera-dev] programming question: volume display

[Tom Goddard]

Hi Matt,

  If you want to erase inside the sphere displayed by the volume erase dialog, first get that dialog then call its erase method:

	from VolumeEraser.gui import volume_erase_dialog
	d = volume_eraser_dialog(create = True)
	d.erase_inside_sphere()

  Tom


	
> On Apr 7, 2017, at 5:37 PM, Dougherty, Matthew T  wrote:
> 
> 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
> =================================================
> =================================================
> From: Dougherty, Matthew T
> Sent: Friday, April 7, 2017 2:03:55 PM
> To: Tom Goddard
> Cc: chimera-dev at cgl.ucsf.edu <mailto: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
> =================================================
> =================================================
> From: Tom Goddard 
> Sent: Friday, April 7, 2017 12:58:14 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
>  
> 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 
>> 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 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 
>>> 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 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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