Example of use of dcoordinates - Revision history

Daniel Castaño at 18:44, 12 February 2019

2019-02-12T18:44:20Z

Daniel Castaño at 18:40, 12 February 2019

2019-02-12T18:40:49Z

Daniel Castaño at 18:37, 12 February 2019

2019-02-12T18:37:47Z

Daniel Castaño at 18:22, 12 February 2019

2019-02-12T18:22:07Z

Daniel Castaño at 18:19, 12 February 2019

2019-02-12T18:19:53Z

Daniel Castaño: Created page with "

vol  = dsphere(30,256); v = dmodels.vesicle(); v.center = 128.5*[1,1,1]; v.separation = 20; v.radius = 40; v.updateCrop; t = v.grepTable(); myTemplate = dcylinder([4,12],..."

2019-02-12T18:09:11Z

Created page with "<pre>vol = dsphere(30,256); v = dmodels.vesicle(); v.center = 128.5*[1,1,1]; v.separation = 20; v.radius = 40; v.updateCrop; t = v.grepTable(); myTemplate = dcylinder([4,12],..."

New page

<pre>vol = dsphere(30,256);
v = dmodels.vesicle();
v.center = 128.5*[1,1,1];
v.separation = 20;
v.radius = 40;
v.updateCrop;
t = v.grepTable();
myTemplate = dcylinder([4,12],24);
mask = myTemplate;
for i=1:size(t,1);
rotTemplate = dynamo_rot(myTemplate,t(i,7:9));
rotMask = dynamo_rot(mask,t(i,7:9));
vol = dpkvol.embed(rotTemplate,vol,t(i,24:26),rotMask);
end </pre>

We can quickly check how our " virus" looks like:
<pre>disoview(vol); </pre>
Remember that <tt>disoview</tt> is a very basic renderer of isosurfaces.

vols = dcoordinates(vol,'cart2sph');

<pre>
figure;
dshow(squeeze(sum(vols(30:32,:,:),1))); </pre>

<pre>figure;
dshow(squeeze(sum(vols(35:40,:,:),1)));</pre>

@@ Line 1: / Line 1: @@
-This is a toy example to illustrate the conversion of volumes into spherical coordinates through the command <tt>dcoordinates</tt>.
+This is a toy example to illustrate the conversion of volumes into spherical coordinates through the command <tt>dcoordinates</tt>.  This function has not been optimized (is purely written in Matlab, without a C++ core), and will probably stuck your computer for volumes with a size above 256 pixels of sidelength.
-We  will create a small virus model by attaching a regular distribution of ''spikes'' (cylinders) to a virus (a sphere)
+We  will create a small virus model by attaching a regular distribution of ''spikes'' (cylinders) to a virus (a sphere with a radius of 30 pixels):
 <pre>vol  = dsphere(30,256);

@@ Line 22: / Line 22: @@
 Remember that <tt>disoview</tt> is a very basic renderer of isosurfaces. We use it as a fallback when Chimera is not performing in the system.
-[[File:ExampleTomoslice.png|center|right|400px| <tt>disoview</tt> ]]
+[[File:MercatorIsosurface.png|center|right|400px| <tt>disoview</tt> ]]
-Alternatively we can visualize the grey map
+Alternatively we can visualize the grey map:
-[[File:ExampleTomoslice.png|center|right|400px| <tt>dview</tt> ]]
+[[File:MercatorDview.png|center|right|400px| <tt>dview</tt> ]]
 Now we can perform the coordinate conversion:
@@ Line 39: / Line 39: @@
 dshow(squeeze(sum(vols(28:32,:,:),1))); </pre>
-[[File:ExampleTomoslice.png|centering|center|400px| <tt>dshow</tt> of surface of virus ]]
+[[File:MercatorRadiusClose.png|centering|center|400px| <tt>dshow</tt> of surface of virus ]]
 Here,
@@ Line 50: / Line 50: @@
 dshow(squeeze(sum(vols(35:40,:,:),1)));</pre>
-[[File:ExampleTomoslice.png|center|right|400px| <tt>dshow</tt> of spikes far away from radius of virus ]]
+[[File:MercatorRadiusFar.png|center|right|400px| <tt>dshow</tt> of spikes far away from radius of virus ]]

@@ Line 21: / Line 21: @@
   <pre>disoview(vol); </pre>
 Remember that <tt>disoview</tt> is a very basic renderer of isosurfaces. We use it as a fallback when Chimera is not performing in the system.
 Now we can perform the coordinate conversion:
   <tt>vols = dcoordinates(vol,'cart2sph');</tt>
 After this transform, the radial direction is stored along the first dimension of <tt>vols</tt>. Second and third dimension correspond to the spherical angles.
@@ Line 31: / Line 38: @@
 figure;
 dshow(squeeze(sum(vols(28:32,:,:),1))); </pre>
 Here,
@@ Line 40: / Line 49: @@
 <pre>figure;
 dshow(squeeze(sum(vols(35:40,:,:),1)));</pre>

@@ Line 1: / Line 1: @@
 This is a toy example to illustrate the conversion of volumes into spherical coordinates through the command <tt>dcoordinates</tt>.
 <pre>vol  = dsphere(30,256);
@@ Line 25: / Line 27: @@
 After this transform, the radial direction is stored along the first dimension of <tt>vols</tt>. Second and third dimension correspond to the spherical angles.
-We can now check the surface of the virus at the radial distance 30, adding  layers 28 to 32.
+We can now check the surface of the virus at the radial distance 30 (the "surface" of the virus in this example), adding  layers 28 to 32.
 <pre>
 figure;
@@ Line 35: / Line 37: @@
 *  the <tt>squeeze</tt> command is just Matlab formating: it converts the (nominal) volume created by <tt>sum</tt> (with dimensions 1 x 256 x512) into an image 256 x 512 that can then be fed into <tt>show</tt>;
 <pre>figure;
 dshow(squeeze(sum(vols(35:40,:,:),1)));</pre>