Matlab Target Finder¶

The Matlabe Target Finder node behaves like other target finding nodes in that it takes
images as input and outputs a list of targets. In this case, Leginon sends the image to an
externally running Matlab process, which then sends the list of targets back to
Leginon.

In order to use the Matlab Target Finder, you must:

<highlights>
<simplelist type="vert">
<member> have matlab installed on the machine where the node will run</member>
<member> have the pymat python module installed (pymat.sourceforge.net)</member>
<member> include the path of libeng.so in the environment variable LD_LIBRARY_PATH. This
library is dynamically linked by pymat in order to connect with matlab.</member>
</simplelist>
</highlights>

In addition to the usual target finder settings, this node needs to be configured with the
matlab function (.m file) that should be executed on the image. The function should take the
image as input in the form of a two dimensional array. The output should be two arrays, one
for focus targets and one for acquisition targets. Each is an array of x,y pairs. Here is a
simple example where the function generates a constant set of targets for any input image:

% example Matlab module for target finding
function [acquisition, focus] = example(image)
acquisition = [168, 234; 203, 54; 450, 390]
focus = [324, 42; 36, 248; 151, 94]

This generates three acquisition targets and three focus targets. Leginon will display
the targets on the image and optionally allow the user to edit the targets before submitting
them.

Required bindings for recieving images and publishing targets:

<highlights>
<simplelist type="vert">
<member> previous Acquisition - (AcquisitionImagePublishEvent) -> Hole Finder</member>
<member> Hole Finder - (ImageTargetListPublishEvent) -> next Acquisition</member>
<member> Hole Finder - (QueuePublishEvent) -> next Acquisition</member>
</simplelist>
</highlights>
Required bindings for proper waiting among nodes:

<highlights>
<simplelist type="vert">
<member> Hole Finder- (ImageProcessDoneEvent) -> previous Acquisition</member>
<member> next Acquisition - (TargetListDoneEvent) -> Hole Finder</member>
</simplelist>
</highlights>

Settings¶

• Allow for user verification of picked holes = When enabled, this feature will
  pause and wait for the user to verify whether the correct exposure and focus targets
  have been selected after the Hole Finder finished processing the input image.

• Queue up targets = When enabled, submitting targets do not publish them
  immediately but to put them in a target list queue.

• Declare drift when queue submitted= When enabled, the node forces target shift
  correction when the queue is submitted. Useful when accurate targeting is
  needed.

• Matlab Module File = the entry defines the Matlab script file used in the target
  finder.

Image Control Panel¶

NOTE: To see the effects of Testing the settings for a particular Hole Finder step in
the Image Control Panel, the corresponding Hole Finder step Display must be enabled before
using the Test feature in that step's Display Settings.

Image¶

Display¶

To view the original input image, enable this button.

Display Settings¶

• Test Image: File Entry = Enter the path and name of a MRC image that the
  Matlab Target Finder can be tested on.

acquisition¶

In Matlab target finder, the purpose of the acquisition setting is only for display
and user selection.

Display¶

To view acquisition, the Image Display must be enabled. The acquisition targets
that the finder chooses will be shown with a green crosshair.

focus¶

In Matlab target finder, the purpose of the focus setting is only for display and
user selection.

Display¶

To view focus, , the Image Display must be enabled. The focus targets that the
finder chooses will be shown with a blue crosshair.

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