Cycle Controls (r3.8)

Cycle Mode Overview

Cycle mode allows control and timing of acquisition sequences. Cycle acquisitions are started when 1) is enabled on the Cycle Controls panel and 2) a LOOP acquisition is started.

Cycle acquisitions consist of Iterations each of which is a Loop of 1 or more acquisitions (Loop Repeats) – i.e. a Cycle is effectively a meta-loop, or loop of loops.

At the start of each Cycle Iteration, one or more of the following actions can be specified:

• Wait a specified Iteration Delay before starting Iteration acquisition
• Load a specified Configuration (CFG) file, updating configuration parameters to use for that iteration's acquisition(s)
• Step motor by specified increment, or move motor to coordinates associated with specified ROI ID or Position ID
• Update ROI Scan Parameters to those associated with specified ROI ID
• Override Configuration parameters (e.g. # Repeats, # Frames, # Slices, etc) with Iteration-specific values

Left Side Controls

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  : Enables Cycle mode – subsequently started LOOP acquisitions will follow the Cycle parameters configured in this panel.

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  : Name of Cycle file (.CYC), if any, that has last been loaded or saved
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  : Load a Cycle file (.CYC), updating current Cycle parameters.
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  : Save current Cycle parameters to a Cycle file (.CYC). Dialog is launched to select the folder/file to save to.

The current Cycle parameters are exactly those displayed in the

table
See Cycle (CYC) File Format section below

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  : On right, sets the number of Cycles to complete before automatically terminating the LOOP acquisition. On left, displays the number of Cycles which have been completed so far. In case of
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  disabled, value at left can be edited to specify which Cycle count value to start with for next started LOOP acquisition.
  • For value > 1, Cycle wraps around to Iteration 1 following the final Iteration N.
  • For value Inf, Cycle wraps around indefinitely and never completes until user hits
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    on the Main Controls panel.

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  : On right, shows the number of Iterations to be executed per-Cycle, i.e. the number defined in the
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  table. On left, displays the number of Iterations which have been completed for the current Cycle count value so far. In case of
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  disabled, value at left can be edited to specify which Iteration to start with for next started LOOP acquisition.

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  : If enabled, the motor position is recorded at start of each Cycle-enabled LOOP acquisition. Upon completion or abort of the acquisition, the motor is moved to restore the starting position.

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  : If enabled, the prevailing Configuration is cached at start of each Cycle-enabled LOOP acquisition – the active settings, not just the settings in the last-loaded Configuration file. Upon completion or abort of the acquisition, the cached Configuration settings are restored.

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  : If enabled, the
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  and
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  values are reset to 0 and 1, respectively, upon completion or abort of each Cycle-enabled LOOP acquisition. If disabled,

Disabling

allows user to handle cases where an ongoing Cycle may need to be aborted/restarted, e.g. for motion or other interruption, perhaps redoing particular iteration(s).

If

is disabled, the following controls are available:

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  : Manually reset the
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  and
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  values to 0 and 1, respectively.

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  : Specifies the number of Cycle iterations to execute before automatically terminating for each started LOOP acquisition. Value of Inf implies to execute all iterations until specified number of Cycles (see
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  ) have completed, if ever.

Setting

to finite value allows one to use

as a 'to-do' list of acquisitions to obtain, one or more at a time.

Right Side Controls

: Table specifying number of Cycle Iterations and the actions to implement for each one. Each column is a possible per-Iteration action:

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  : Specify a Configuration (CFG) file to load for that Iteration
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  : Time, in seconds, to wait before start of this Iteration (the first Repeat, if # Repeats > 1 for that Iteration
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  : Specify, together with
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  , to take a motor step, or to move motor to specified Position ID, or to update ROI Scan Parameters and execute possible motor move according to specified ROI ID
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  : For specified type of
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  :
  • Motor Step: Specify a 1x3, or 1x4, vector indicating increment of motor position, in microns, e.g. [0 0 1] for a 1um step in the Z dimension
  • Posn #: Specify one of the position IDs identified in the Position Controls
  • ROI #: Specify one of the ROI IDs identified in the ROI Controls

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  /
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  /etc: Specify Iteration-override value to use for acquisition (including multiple Repeats if applicable) for particular Iteration. Overrides value loaded as part of specified Iteration [Configuration (CFG) file] (
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  ), if any.

KEY POINTS:
Leaving a column blank implies that particular action is not taken for that particular Iteration.
For an Iteration with no Configuration (CFG) file loaded and no Iteration-override specified for a particular parameter, the prevailing parameter value at the start of the LOOP acquisition is used. In other words, subsequent Iterations 'forget' overrides and loaded Configurations at previous Iterations.

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Table Edit Tools

: Add an Iteration to Cycle, i.e. add row at end of table

: Remove Iteration associated with currently selected row

: Launch dialog to select Configuration (CFG) file to load for Iteration in currently selected row

: Clears the contents of the selected cells in the table
Hitting <Delete> key has equivalent behavior

: If enabled, an edit in particular column for particular Iteration will be applied (copied) to all Iterations (rows) in table

: Clears data in all rows of

Cycle (CYC) File Format

The Cycle (CYC) file format is text, i.e. human-readable and human-editable. Advanced users may find it necessary/useful to generate CYC files programatically .

The first 5 lines capture the left-hand-side of the Cycle Controls panel:

cycleName <string val>
cycleLength <numeric val>
numCycleRepeats <numeric val>
returnHomeAtCycleEnd <0 or 1>
restoreOriginalConfig <0 or 1>

Subsequently there is one line per Cycle iteration, following general format

<iteration #> <columnName1> <columnVal1> <columnName2> <columnVal2> ....

i.e., one name/value pair, e.g. 'repeatPeriod 3', for each non-empty column for each iteration. Note that column names are specified with lower-case names using camel casing.

Users interested in programmatically generating CYC files should enter similar entries directly into Cycle Controls table and save to a demonstration CYC file to better understand the file format that should be followed.