Daniel Castaño at 10:17, 27 June 2018

2018-06-27T10:17:32Z

Daniel Castaño: Created page with "`dtmshow` is the simplest tomogram browser in ''Dynamo'' == Invoking `dtmshow` == === Tomogram preload=== Depending on the size of your tomogram, this option..."

2018-06-27T10:15:17Z

Created page with "<tt>dtmshow</tt> is the simplest tomogram browser in ''Dynamo'' == Invoking <tt>dtmshow</tt> == === Tomogram preload=== Depending on the size of your tomogram, this option..."

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<tt>dtmshow</tt> is the simplest tomogram browser in ''Dynamo''

== Invoking <tt>dtmshow</tt> ==

=== Tomogram preload===

Depending on the size of your tomogram, this option might take a long time or even block your system's memory.

<tt>dtmshow myFile.mrc</tt>

<tt>dtmshow(<variable name>)</tt>

<tt>dtmshow(<file name>)</tt>

=== On the fly access ===

This option is only available when the ''z'' viewing is active.

<tt>dtmshow -otf myFile.mrc</tt>

== Basic controls ==

=== Depicted height ===

Once a direction ''x'',''y'' or ''z'' is selected you can move the depicted height by:
* dragging the slider on the top
* scrolling the mouse
* up and down arrow keys

=== Zoom ===

Zooming can be performed by keeping [control] pressed + mouse wheel. This will zoom in and out on the current position of the cursor.
Alternatively you can use the magnifying glass icon in the toolbar.

=== Drag ===

Dragging of the viewed scene after zooming can be performed by keeping [shift] pressed + mouse wheel.
Alternatively you can use the hand glass icon in the toolbar.

=== Slice orientation===
There are two options which are '''not''' equivalent

* Use the pushbuttons in the top bar to just show the central slice in the wished orientation
* Press the keys 'x','y','z' to force the wished orientation AND set the height in the new orientation to the position of the cursor in the moment you clicked on it.

== Depicted slice ==

You have options for binning, bandpassing or projeting several physical slices on the depicted scene (called ''thickness'' in the GUI). When they are active, the respective operations will be carried on the requested slice each time you produce a new one.

The dimensions of the depicted scene will always correspond to the unbinned slice: if your tomo has xy dimensions of 2000x2000 pixels, a binned x2 slice will have physically 500x500 pixels. Still the range of the axes in <tt>dtmshow</tt> will be from 0 to 2000.

== Prebinned stacks ==

When browsing on tomograms with a sidelength larger than, say, 2000 pixels (depending on your system) the slice transition can be rather slow. A technique to comfortably browse on your tomogram consists in launching a ''prebinning'' request. When you do so, after chosing a binning level, ''Dynamo'' will create internally a binned version of the tomo currently depicted. The tomogram may lay in memory or be available for on-the-fly access; in both cases the prebinned version will be in memory just during the existence of the <tt>dtmshow</tt> GUI.

When you use the <tt>bin</tt> option in the GUI (i.e., if the radiobutton is connected), if the current bin factor corresponds to a bin factor that has been previously used to generate an internal prebinned stack, then the slice will be directly extracted from it.

== Simultaneous browsers ==

Sometimes it is convenient to have two ''linked'' <tt>dtmshow</tt> browsers, each one showing the same area in different tomograms. For instance, this might be interesting when comparing SIRT and WBP reconstructions.

This is triggered by passing two tomograms to the input:

<tt>dtmshow({vol1,vol2});</tt>

@@ Line 7: / Line 7: @@
 Depending on the size of your tomogram, this option might take a long time or even block your system's memory.
-  <tt>dtmshow myFile.mrc</tt>
+  <pre>dtmshow myFile.mrc
- <tt>dtmshow(<variable name>)</tt>
+=== On the fly access ===
- <tt>dtmshow(<file name>)</tt>
+This option is only available when the ''z'' viewing is active.
-=== On the fly access ===
+=== Left hand side ===
-This option is only available when the ''z'' viewing is active.
+<tt>dtmshow</tt> accepts a left hand side, i.e., a handle that you can use to interact with the GUI programmatically. You need to use the () notation for this:
-  <tt>dtmshow -otf myFile.mrc</tt>
+  <tt>gui = dtmshow(<file name>)</tt>
 == Basic controls ==
@@ Line 43: / Line 46: @@
 * Use the pushbuttons in the top bar to just show the central slice in the wished orientation
-* Press the keys 'x','y','z' to force the wished orientation AND set the height in the new orientation to the position of the cursor in the moment you clicked on it.
+* Press the keys ''x'',''y'',''z'' to force the wished orientation AND set the height in the new orientation to the position of the cursor in the moment you clicked on it.
 == Depicted slice ==
@@ Line 56: / Line 59: @@
 When you use the <tt>bin</tt> option in the GUI (i.e., if the radiobutton is connected), if the current  bin factor   corresponds to a bin factor that has been previously used to generate an internal prebinned stack, then the slice will be directly extracted from it.
 == Simultaneous browsers ==

Dtmshow - Revision history

Daniel Castaño at 10:17, 27 June 2018

Daniel Castaño: Created page with "dtmshow is the simplest tomogram browser in ''Dynamo'' == Invoking dtmshow == === Tomogram preload=== Depending on the size of your tomogram, this option..."

Daniel Castaño: Created page with "`dtmshow` is the simplest tomogram browser in ''Dynamo'' == Invoking `dtmshow` == === Tomogram preload=== Depending on the size of your tomogram, this option..."