View source for Walkthrough on creation of 3d scenes

This walkthrough shows how to create graphic depictions of tomogram contents. Those include:

* Slices of tomograms.
* Proteins located in the tomogram, with the orientations provided during the alignment.
* Geometrical objects (as membranes represented by triangulations).

 [[ File:Fhv3dAntialiasing.png |thumb|center| 600px| Goal of the tutorial. An antialiasing filter has been used.]]

== The data set ==

This walkthrough works with the data set from the [[advanced starters guide]].  The goal is to depict:
* One slice of the tomogram in 3D.
<br />This requires a tomogram file.
* The viruses placed an oriented along the directions found during a previous computed average.
<br /> This requires a ''template'' represe.
* A sketch of the membrane 
 <br /> This requires a ''model'' object.  

=== From the ''Dynamo'' web ===

The tomogram can get fetched through:

 <tt>wget  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec </tt>

in a linux shell, or through: 

<tt>curl -O  https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/crop.rec </tt>
under MacOS.

The table, template and membrane model can be fetched similarly with names  
 <nowiki>https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/alignmentLocalRefinement.tbl
https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/averagedLocalRefinement.em
https://wiki.dynamo.biozentrum.unibas.ch/w/doc/data/fhv/membraneModel.omd</nowiki>

=== From your previos work ===

Assuming you have done the  [[advanced starters guide| tutorial on the FHV]] data set, you can use the elements that you have already computed. Just extract them from the best project that you completed. Do not use a subboxing project: we want to get a template for the full crown. Examples below are given assuming that your best project was named <tt>localized</tt>, substitute if not.

==== Table ====

Recover the last computed refined table in the data base of your project

<tt>ddb localized:rt -r t</tt>

and write it to a file

<tt>dwrite(t,'alignmentLocalRefinement.tbl')

==== Template ====

Fetch the last computed average 

<tt>ddb localizedFullAngle:rt -r a</tt>

and write it into disk

<tt> dwrite(t,'averagedLocalRefinement.tbl'); </tt>

==== Membrane model ====
If you [[created manually a membrane model]], it should be inside your catalogue with the name <tt>mySurface</tt> (or any other you put). You can check inside the catalogue <tt>fhv</tt>

 <tt>dcmodels fhv -nc mySurf</tt>

Here <tt>-nc mySurf</tt> will look for models with the string "mySurf" in the name. You should get a reply as:

<nowiki>Volume 1. Matching models: 1 (total: 1)
/Users/casdanie/dynamo/examples/fhvParis/fhv/tomograms/volume_1/models/mySurface.omd</nowiki>

So you can read the model into a new variable (arbitrarily called <tt>m</tt>)

<tt>m = drread('Users/casdanie/dynamo/examples/fhvParis/fhv/tomograms/volume_1/models/mySurface.omd');</tt>

and write it to disk

<tt>dwrite(m,'membraneModel.omd');</tt>

== Depicting a slice of a tomogram ==

=== The slice object ===

<tt>s = dpktomo.volume.slices.Slice(); </tt>

Here <tt>s</tt> is just an object that will read data from a tomogram file to be defined, along with geometrical parameters as <tt>center</tt>, <tt>eulers</tt> (orientation), <tt>l</tt>, (sidelength)...

 <nowiki>s.source = 'crop.rec';
s.center = 'center';
s.l = [1000,1000];
s.eulers =  'z';
s.fetchData();</nowiki>

=== The slice depictor object ===

We first create a figure with and empty axis </tt>
<tt>f = figure; haxis = gca();hold on;</tt>

 [[  File:Fhv3dEmptyAxis.png |thumb|center| 400px| Empty matlab figure with an empty axis.]]

Here, <tt>f</tt> are ''handles'' that will be used later to direct the graphical output to our figure. 
 
Now, we initialize a depiction object associated with the slice <tt>s</tt>
<tt>sz = dpktomo.volume.slices.SliceGraphic(s);</tt>
Note that no graphical output has been created yet. We first inform the object <tt>sz</tt> in which axis it is to be created. 

<tt>sz.axis.h = haxis;</tt>

and then create the slice in the available axis.

<tt>sz.create();</tt>

If the figure is below other windows in your system you can rise it through

<tt>shg; </tt>

or 

<tt>figure(f);</tt>

We can change the angle of view with the rotation icon or programmatically:
<tt>view([-38,60]);</tt>

 [[  File:Fhv3dSlice.png |thumb|center| 400px| View of the slice with the viewing perspective ([-38,60]).]]