JAHC Hole Finder (Template Hole Finder)¶

The JAHC Hole Finder class is a variation of Hole Finder class. The purpose and operation
is similar in the two node classes. The differences are 1: JAHC Hole Finder does not use edge
image for correlation but the original, and 2: JAHC Hole Finder uses a scaled template image
rather than a simple geometric ring for the correlation step. Like the Hole Finder, the values
in this node vary so much from grid to grid (and from square to square) that the best way to
find these parameters is by going through a step-by-step trial and error process. To proceed
from one step of the hole targeting process to another, simply proceed from top to bottom
through the display selection buttons in the image control panel. The display settings
associated with each display selection are the locations where the JAHC Hole Finder parameters
can be adjusted. To see the final acquisition and focus targets, enable only the Original,
acquisition, and focus display selections.

Required bindings for recieving images and publishing targets:

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

<highlights>
<simplelist type="vert">
<member> JAHC Hole Finder- (ImageProcessDoneEvent) -> previous Acquisition</member>
<member> next Acquisition - (TargetListDoneEvent) -> JAHC 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• Queue up targets = When enabled, submit targets do not publish them immediately
  but to put them in a target list queue.

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

• Skip automated hole finder= When enabled, the automatic Hole Finder algorithm
  will be skipped altogether.

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 JAHC Hole Finder step Display must be enabled
before using the Test feature in that step's Display Settings.

Original¶

Display¶

To view the original input image without any image processing done to it, enable
this button. Enabling this button will disable/override the Edge, Template, and
Threshold Displays.

Display Settings¶

• Original Image: File Entry = Enter the path and name of an MRC image that the
  JAHC Hole Finder can be tested on. This feature allows JAHC Hole Finder to be
  tested without having run a full Leginon MSI application.

Template¶

The purpose of the Template step is to cross correlate a template of the properly
sized template holes against the original image.

Display¶

To view the Template image, enable this button. Enabling this button will
disable/override the Original, Edge, and Threshold Displays.

Display Settings¶

• Use "phase | cross" correlation = to do this calculation.

• Template Filename = Enter the path and name of a template MRC image.

• Original Template Diameter = Enter the value in pixel.

• Final Template Diameter = A scaled diameter in pixel. It should be chosen
  give the sharpest correlation peak upon testing.

• Test = Press this button to test/apply the parameters that have been adjusted
  in this step.

Threshold¶

The purpose of the Threshold step is to apply a threshold to the previous Template
image. It is in unit of number of standard deviation above the mean. The Threshold image
should have dots that represent the center of all the found holes.

Display¶

To view the Threshold image, enable this button. Enabling this button will
disable/override the Original, Edge, and Template Displays.

Display Settings¶

• Threshold = Enter the Threshold value of a dot that represents the center of
  a hole (either as absolute value or relative to the value with the stdv shown for
  the correlation image).

• Test = Press this button to test/apply the Threshold to the template
  correlation image. Only the dots hat represent the center of the holes should
  appear. It is highly likely that dots not representing the center of a hole will
  also appear.

Blobs¶

The purpose of the Blobs step is to begin to narrow down the "hole center dots" that
have been found. This step serves as additional criteria for finding good holes.

Display¶

To view Blobs, either the Original, Edge, Template, or Threshold Displays must be
enabled. The Blobs that pass this step will be shown with a turquoise crosshair.

Display Settings¶

• Border = The pixel value distance from the edge of the image where all
  potential hole targets will be erased.

• Max. blobs = The maximum number of hole targets or blobs at this point that
  are allowed. If the number of blobs exceeds this number, the extra blobs will be
  eliminated.

• Max. blob size = The maximum size of a blob that is allowed to pass. This is
  roughly the square of an average blob diameter. Use the ruler tool on the
  Threshold image to determine the average diameter of a blob.

• Test = Press this button to test/apply the Blobs criteria to the Threshold
  image.

Lattice¶

The purpose of the Lattice step is to determine whether the blobs or "hole center
dots" fit in a lattice that describes how the hole layout.

Display¶

To view Lattice, either the Original, Template, or Threshold Displays must be
enabled. The Lattice blobs that pass this step will be shown with a pink
crosshair.

Display Settings¶

• Lattice Fitting Spacing = The distance from the center of two holes in the
  horizontal/vertical lattice directions (not the diagonal lattice
  directions).

• Lattice Fitting Tolerance = The tolerance allowed for holes that may not
  exactly lie in the described lattice.

• Hole Statistics Radius = The radius in pixels of the holes (that pass the
  lattice criteria) that will be used to determine each hole's statistics.

• Hole Statistics Zero Thickness = The intensity value of an empty hole, i.e.
  zero thickness intensity.

• Test = Press this button to test/apply the Lattice criteria to the result of
  the Blobs criteria.

acquisition¶

The purpose of the acquisition step is to select holes of the proper ice thickness
and arrange the desired acquisition target layout. The "focus" and "acquisition" JAHC Hole
Finder steps Display Settings appear in the same window. For the purpose of this
documentation to facilitate the separation of steps in the user interface, acquisition and
focus will be addressed separately. Therefore, only the parameters pertaining to
acquisition targets will discussed in this section. The parameters not covered in this
section are part of the focus section.

Display¶

To view acquisition, either the Original, Edge, Template, or Threshold Displays
must be enabled. The acquisition targets that pass this step will be shown with a green
crosshair.

Display Settings¶

Ice Thickness Threshold:

• Min. mean = Enter the minimum hole ice thickness value allowed.

• Max. mean = Enter the maximum hole ice thickness value allowed.

• Max. stdev = Enter the maximum hole standard deviation value allowed.

Target Template:

• Use target template = When enabled, template targets will be used to compose
  a target list. When not enabled, the center of the hole is the default
  target.

• Acquisition Target Template (Add|Edit|Delete) = Add|Edit|Delete acquisition
  targets that define the locations of each acquisition target. The acquisition
  target coordinates (x,y) are measured relative to the center of a hole. Use the
  ruler tool to determine this distance.

• Test = Press this button to test/apply the ice thickness criteria and
  potentially create an acquisition target template.

focus¶

The purpose of the focus step is to focus targets near selected holes. The "focus"
and "acquisition" Hole Finder steps Display Settings appear in the same window. For the
purpose of this documentation to facilitate the separation of steps in the user interface,
acquisition and focus will be addressed separately. Therefore, only the parameters
pertaining to focus targets will discussed in this section. The parameters not covered in
this section are part of the acquisition section.

Display¶

To view focus, either the Original, Edge, Template, or Threshold Displays must be
enabled. The focus targets that pass this step will be shown with a blue
crosshair.

Display Settings¶

Ice Thickness Threshold:

• Focus hole selection = Any Hole | Off | Good Hole; Select the type of Z Focus
  target selection. This hole will be used by Z Focus to correct stage z height when
  first moving to the new square.

- Good Hole will select one of the good holes that passed the ice thickness
test.

- Any Hole will select any of the holes that passed (up until before the ice
thickness test).

- Off will turn Z Focus correction off.

Target Template:

• Use target template = When enabled, template targets will be used to compose
  a target list. When not enabled, the center of the hole is the default
  target.

• Focus Target Template (Add|Edit|Delete) = Add|Edit|Delete focus targets that
  define the locations of each focus target. The focus target coordinates (x,y) are
  measured relative to the center of a hole. Use the ruler tool to determine this
  distance.

• Focus template thickness = Enter values that are used to determine whether
  the area where the focusing has ice that is too thick. If the ice is to thick and
  does not pass this ice thickness criteria, then that focus target will not be
  used. Only the first focus target that passes is used. More than one focus target
  can pass the focus template thickness criteria.

- Use focus template thickness = When enabled, focus template targets will be
checked against these ice thickness criteria.

- Stats. radius = the radius surrounding the focus target that is included in
the statistics measurement

- Min. mean thickness = Enter the minimum ice thickness value allowed.

- Max. mean thickness = Enter the maximum ice thickness value allowed.

- Max. std. thickness = Enter the maximum standard deviation value
allowed.

• Test = Press this button to test/apply the ice thicness focus criteria and
  create a focus target template.

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