View source for Depicting a cloud of observations on a tilt series

There are several ways of depicting a cloud of points on a set micrographs.

=dmarkers= 

<tt>dmarkers</tt> is the GUI that appears as exploration tool for tilt series when running alignment experiments. It can also be used independently of those workflows.

== Depict a static cloud of point ==
<tt>dmarkers </tt> offers the possibility of showing a static [[Clouds of points defined on a tilt series (format)| cloud of points | ]] defined on a tilt series. <br>
<code> gui = dmarkers(myStack, 'staticCloud',myCloud); </code>

=== Editing a depiction of a cloud of points ===
You can assign an internal name to a point cloud that you pass to dmarkers. <br>
<code> gui = dmarkers(myStack, 'staticCloud',myCloud,'name','someName'); </code>

Then, you will be able to locate the object that governs the depiction of the cloud. This graphical object  is stored in: <br>
<code>gui.opts.cloudDepictors.items.someName.hCloud </code>

You can change its properties manually. For instance, to get bigger markers:<br>
<code>gui.opts.cloudDepictors.items.someName.hCloud.MarkerSize = 12</code>

Note that if you invoked the addition of the static cloud without the flag <tt>cloudName</tt> you can still find the depictor under <tt>gui.opts.cloudDepictors.items</tt>, the name will be simply <tt>cloudDepictorXX</tt> where XX is an integer name.

== Show a set of markers that can be manually edited on screen == 
Depicting a set of markers on a tilt series, when those markers are organized as a <tt>.dms</tt> file.

<code> gui = dmarkers(myStack, 'staticCloud',myCloud); </code>

The <tt>gui</tt> object can be retained for further manipulations.

=== Changing the colors programmatically ===

The graphic objects that represent the points are governed by the <tt>depictor</tt> objects that are stored in the gui object that you recover into the left hand side. Inside this gui, the <tt>shapeSetManager</tt> <br>
<code>gui.shapeSetManager.depictors{1}.hPoints.MarkerFaceColor ='c';</code>

[[File:ChangeColorMarkersInDmarkers.png|thumb|center|400px| A marker set depicted  on <tt>dmarkers</tt> ]]

=dtmshow=

== With the GUI ==
In dtmshow, you can use the <tt>import</tt> option of the GUI to load a [[static cloud of points | ]]

== Programmatically ==
When invoking the code, you can use the flags <tt>cloud</tt> and <tt>colormapCloud</tt> to pass a cloud an its color</tt>



[[Category: Tricks]]