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<p>here is a related question, let me know if I should open a new thread. </p>
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<p>The VolumeEraser code does this for erasing: self.erase_inside_sphere()</p>
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<p>writing python code, how can I activate that code in my modules?</p>
<p>assuming I have issued a 'start Volume Eraser' command to get the gui up.</p>
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<div class="PlainText">Matthew Dougherty<br>
National Center for Macromolecular Imaging<br>
Baylor College of Medicine<br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Dougherty, Matthew T<br>
<b>Sent:</b> Friday, April 7, 2017 2:03:55 PM<br>
<b>To:</b> Tom Goddard<br>
<b>Cc:</b> chimera-dev@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [chimera-dev] programming question: volume display</font>
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<p>thx</p>
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<div class="PlainText">Matthew Dougherty<br>
National Center for Macromolecular Imaging<br>
Baylor College of Medicine<br>
<span style="font-size:13.0pt; font-family:Calibri">=================================================</span><br>
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<div id="divRplyFwdMsg" dir="ltr"><font face="Calibri, sans-serif" style="font-size:11pt" color="#000000"><b>From:</b> Tom Goddard <goddard@sonic.net><br>
<b>Sent:</b> Friday, April 7, 2017 12:58:14 PM<br>
<b>To:</b> Dougherty, Matthew T<br>
<b>Cc:</b> chimera-dev@cgl.ucsf.edu<br>
<b>Subject:</b> Re: [chimera-dev] programming question: volume display</font>
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<div>Hi Matt,
<div class=""><br class="">
</div>
<div class=""> To get the current region and step for a volume</div>
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</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>ijk_min, ijk_max, ijk_step = v.region</div>
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<div class="">To avoid having the step adjust automatically in the new_region() call use</div>
<div class=""><br class="">
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>new_region(..., adjust_step = False)</div>
<div class=""><br class="">
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<div class="">Chimera adusts the step to show no more than some specified number of grid points (e.g. 2 million) and this parameter is</div>
<div class=""><br class="">
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>v.rendering_options.voxel_limit = 1 # In millions of voxels</div>
<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>v.rendering_options.limit_voxel_count = True # Whether to auto-adjust step</div>
<div class=""><br class="">
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<div class="">These options are also present in the Volume Viewer dialog, menu Features / Data Display Options.</div>
<div class=""><br class="">
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<div class=""><span class="Apple-tab-span" style="white-space:pre"></span>Tom</div>
<div class=""><br class="">
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<blockquote type="cite" class="">
<div class="">On Apr 7, 2017, at 10:52 AM, Dougherty, Matthew T wrote:</div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Got it, thx. Was wondering if there was an alternate API. </div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">having a problem with ijk_step using this:</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""> v.new_region(ijk_min=(i_min, j_min, k_min), ijk_max=(i_max, j_max, k_max), ijk_step=(1,1,1))<br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">The min and max act correctly, but it<span style="font-size: 12pt;" class=""> jumps into other step sizes when I vary min & max. </span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><span style="font-size: 12pt;" class="">would think the step size would be </span></div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">when the relative min/max is small (i.e., volume is small) the gui step size is one.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">as the volume increases, the step size increases.</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class="">if I maximize the volume and manually set the gui step size to one, then the python call works as expected. </div>
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">Any ideas?</div>
<div style="margin-top: 0px; margin-bottom: 0px;" class=""><br class="">
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<div style="margin-top: 0px; margin-bottom: 0px;" class="">also, if I wanted to get the min/max values for the region, how do I get that.</div>
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<div class="BodyFragment"><font size="2" class="">
<div class="PlainText">Matthew Dougherty<br class="">
National Center for Macromolecular Imaging<br class="">
Baylor College of Medicine<br class="">
<span style="font-size: 13pt; font-family: Calibri;" class="">=================================================</span><br class="">
</div>
<div class="PlainText"><span style="font-size: 13pt; font-family: Calibri;" class="">=================================================</span><span style="font-size: 13pt; font-family: Calibri;" class=""><br class="">
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<div id="divRplyFwdMsg" dir="ltr" class=""><font face="Calibri, sans-serif" style="font-size: 11pt;" class=""><b class="">From:</b><span class="Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, April 5, 2017 2:13:06 PM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Dougherty, Matthew T<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-dev@cgl.ucsf.edu" class="">chimera-dev@cgl.ucsf.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimera-dev] programming question: volume display</font>
<div class=""> </div>
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<div class="">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).
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>Tom</div>
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<blockquote type="cite" class="">
<div class="">On Apr 5, 2017, at 12:00 PM, Dougherty, Matthew T <<a href="mailto:matthewd@bcm.edu" class="">matthewd@bcm.edu</a>> wrote:</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">thx</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">is volume.py where I would find how to change step size, plane number & depth?</div>
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<div class="BodyFragment"><font size="2" class="">
<div class="PlainText">Matthew Dougherty<br class="">
National Center for Macromolecular Imaging<br class="">
Baylor College of Medicine<br class="">
<span class="" style="font-size: 13pt; font-family: Calibri;">=================================================</span><br class="">
</div>
<div class="PlainText"><span class="" style="font-size: 13pt; font-family: Calibri;">=================================================</span><span class="" style="font-size: 13pt; font-family: Calibri;"><br class="">
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<font face="Calibri, sans-serif" class="" style="font-size: 11pt;"><b class="">From:</b><span class="Apple-converted-space"> </span>Tom Goddard <<a href="mailto:goddard@sonic.net" class="">goddard@sonic.net</a>><br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Wednesday, April 5, 2017 11:41:35 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Dougherty, Matthew T<br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a href="mailto:chimera-dev@cgl.ucsf.edu" class="">chimera-dev@cgl.ucsf.edu</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [chimera-dev] programming question: volume display</font>
<div class=""> </div>
</div>
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<font size="2" class=""><b class="">***CAUTION:*** This email is not from a BCM Source. Only click links or open attachments you know are safe.</b></font>
<hr class="">
To change the region bounds of a volume v in Python:
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>v.new_region((0,0,0), (50,60,70))</div>
<div class=""><br class="">
</div>
<div class="">Here’s the Python declaration in chimera/share/VolumeViewer/volume.py where the Volume class is defined.<br class="">
<div class=""><br class="">
</div>
<div class="">
<div class=""> def new_region(self, ijk_min = None, ijk_max = None, ijk_step = None,</div>
<div class=""> show = True, adjust_step = True, save_in_region_queue = True):</div>
<div class=""><br class="">
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<div class=""><span class="Apple-tab-span" style="white-space: pre;"></span>Tom</div>
<div class=""><br class="">
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<div class=""><br class="">
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<div class="">
<blockquote type="cite" class="">
<div class="">On Apr 4, 2017, at 3:58 PM, Dougherty, Matthew T <<a href="mailto:matthewd@bcm.edu" class="">matthewd@bcm.edu</a>> wrote:</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">I am trying to modify the region bounds of the volume viewer using python.</div>
<div class="" style="margin-top: 0px; margin-bottom: 0px;">What module should I be looking at to determine the api calls?</div>
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<div class="" style="margin-top: 0px; margin-bottom: 0px;">thanks, </div>
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<div class="PlainText">Matthew Dougherty<br class="">
National Center for Macromolecular Imaging<br class="">
Baylor College of Medicine<br class="">
<span class="" style="font-size: 13pt; font-family: Calibri;">=================================================</span><br class="">
</div>
<div class="PlainText"><span class="" style="font-size: 13pt; font-family: Calibri;">=================================================</span><span class="" style="font-size: 13pt; font-family: Calibri;"><br class="">
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