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 goddard@sonic.net Sent: Wednesday, April 5, 2017 2:13:06 PM To: Dougherty, Matthew T Cc: chimera-dev@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@bcm.edu mailto:matthewd@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@sonic.net mailto:goddard@sonic.net> Sent: Wednesday, April 5, 2017 11:41:35 AM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edu mailto:chimera-dev@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@bcm.edu mailto:matthewd@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 ================================================= ================================================= _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Ddev&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=yLoyNoWMgD5zwzJG94wrmIzOc4932AAOH-JyYzFd4lE&s=cGwvu-f8x6yixXfp3-QcfYHccDDif6Z9jWo8btcToNY&e=
thx
Matthew Dougherty National Center for Macromolecular Imaging Baylor College of Medicine ================================================= ================================================= ________________________________ From: Tom Goddard goddard@sonic.net Sent: Friday, April 7, 2017 12:58:14 PM To: Dougherty, Matthew T Cc: chimera-dev@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 <goddard@sonic.netmailto:goddard@sonic.net> Sent: Wednesday, April 5, 2017 2:13:06 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edumailto:chimera-dev@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@bcm.edumailto:matthewd@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@sonic.netmailto:goddard@sonic.net> Sent: Wednesday, April 5, 2017 11:41:35 AM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edumailto:chimera-dev@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@bcm.edumailto:matthewd@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 ================================================= ================================================= _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edumailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-devhttps://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Ddev&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=yLoyNoWMgD5zwzJG94wrmIzOc4932AAOH-JyYzFd4lE&s=cGwvu-f8x6yixXfp3-QcfYHccDDif6Z9jWo8btcToNY&e=
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@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 goddard@sonic.net Sent: Friday, April 7, 2017 12:58:14 PM To: Dougherty, Matthew T Cc: chimera-dev@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 <goddard@sonic.netmailto:goddard@sonic.net> Sent: Wednesday, April 5, 2017 2:13:06 PM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edumailto:chimera-dev@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@bcm.edumailto:matthewd@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@sonic.netmailto:goddard@sonic.net> Sent: Wednesday, April 5, 2017 11:41:35 AM To: Dougherty, Matthew T Cc: chimera-dev@cgl.ucsf.edumailto:chimera-dev@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@bcm.edumailto:matthewd@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 ================================================= ================================================= _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edumailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-devhttps://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Ddev&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=yLoyNoWMgD5zwzJG94wrmIzOc4932AAOH-JyYzFd4lE&s=cGwvu-f8x6yixXfp3-QcfYHccDDif6Z9jWo8btcToNY&e=
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@cgl.ucsf.edu mailto:chimera-dev@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@cgl.ucsf.edu mailto:chimera-dev@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@cgl.ucsf.edu mailto:chimera-dev@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@cgl.ucsf.edu mailto:chimera-dev@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 ================================================= ================================================= _______________________________________________ Chimera-dev mailing list Chimera-dev@cgl.ucsf.edu mailto:Chimera-dev@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-dev https://urldefense.proofpoint.com/v2/url?u=http-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimera-2Ddev&d=DwMFaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=lEMX2_AJ6Iksc5dFd0-VOg&m=yLoyNoWMgD5zwzJG94wrmIzOc4932AAOH-JyYzFd4lE&s=cGwvu-f8x6yixXfp3-QcfYHccDDif6Z9jWo8btcToNY&e=
participants (2)
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Dougherty, Matthew T -
Tom Goddard