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h6. Overview
ScanImage requires an initialization |
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Overview
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ScanImage requires an initialization (INI)
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file,
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usually
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named
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standard.ini
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,
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to
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be
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selected
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at
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startup.
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This
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file
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specifies
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&
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initializes
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all
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the
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state
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variables
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for
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the
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ScanImage
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configuration
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and
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determines
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which
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variables
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are
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associated
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with
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configuration
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(CFG)
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and
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user
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(USR)
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files.
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Typically
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there
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is
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only
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one
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INI
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file
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per
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ScanImage
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installation
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(a
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'rig').
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A
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subset
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of
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Rig
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Configuration
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variables
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are
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demarcated
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at
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the
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beginning
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of
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the
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INI
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file;
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these
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copmrise
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the
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variables
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that
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typically
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require
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modification
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for
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a
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new
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ScanImage
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installation.
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Rig
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Configuration
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variables
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are
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not
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associated
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with
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either
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CFG
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or
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USR
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files
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and
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are
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not
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modified
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during
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ScanImage
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program
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operation.
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Typically
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only
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one
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INI
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file
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is
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required
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per
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rig.
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ScanImage
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r3.5
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introduces
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some
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changes
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to
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the
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way
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INI
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files
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are
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handled.
...
Please
...
familiarized
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yourself
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with
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Initialization
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(INI)
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File
...
Handling.
In addition, the variables in the Rig Configuration section have been modified, as described in the following section.
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Rig Configuration Variable Reference
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The INI file contains a large number of variables. Only a small number of these typically require adjustment for a ScanImage installation to a new rig. These Rig Configuration variables are clearly grouped at the beginning of the standard_model.ini file. Users should adjust these values to match the hardware and experimental requirements for their rig, to create their own standard.ini file.
| Tip |
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The INI file parser is whitespace sensitive. The format <VARNAME>=<VARVALUE> must be strictly followed, i.e. no space to left or right of the equal sign |
The standard_model.ini file contains comments which document the meaning of each of the variables. As additional support, this section serves as a reference point for the new and notable Rig Configuration variables.
triggerLineIndex: (Previously below Rig Configuration section) Allows specification of the static digital output line used as shared trigger source for acquisition, mirror, and Pockels cell board(s). The use of Port 0 on the board specified by triggerBoardIndex is assumed.
triggerInputTerminal: See External Triggering and Trigger Simplification.
externalTriggerInputTerminal: See External Triggering and Trigger Simplification.
externalTriggerTimeout: See External Triggering and Trigger Simplification.
outputBoardClockTerminal: See Clock Synchronization for more details.
maxBufferedGrabTime: Specifies max duration, in seconds, of an acquisition (effectively limiting the max number of frames) to allow without using 'SaveDuringAcquisition' option. This value should typically not be altered. Longer acquisitions should employ the new Continuous Disk Logging feature.
maxFlybackRate: This value is reserved for r3.6.
scanOffsetX/Y: (Previously below Rig Configuration section) Specify offset voltages for mirror command signals. These variables are unique among the Rig Specific variables in that they can be altered during ScanImage operation. See Beam and Scan Alignment Tools for more information.
parkAmplitudeX/Y: (Previously below Rig Configuration section) Specify voltages for X/Y mirror when parked. 
Beam safety should be considered in setting these values.
maxAmplitudeX/Y: Specify max voltage allowed for X/Y amplitudes. This clamps the sum of the scan amplitude and the scan shift set in ScanImage, for each dimension.
Shutter Variables_
The separate values for 'open' and 'closed' have been removed. Variables open and epiShutterOpen are sufficient to specify 'polarity' of shutter interface.
shutterBoardIndex: See Shutter output line(s) can be on any board.
Motor Variables
The number of variables in the rig-specific motor section has been greatly reduced. Two variables, firmware and posnResolution, are new in r3.5. See MP-285 Interface Improvements for details.
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|Important Changes in ScanImage 3.5#Initialization (INI) File Handling].
In addition, the variables in the Rig Configuration section have been modified. These changes are described in the following sections.
h6. Rig Configuration Variable Reference
The INI file contains a large number of variables. Only a small number of these typically require adjustment for a ScanImage installation to a new rig. These _Rig Configuration_ variables are clearly grouped at the beginning of the _standard\_model.ini_ file. Users should adjust these values to match the hardware and experimental requirements for their rig, to create their own _standard.ini_ file.
This section provides an overview of the new and notable variables in this section, serving as a reference
{tip}The INI file parser is whitespace sensitive. The format <VARNAME>=<VARVALUE> must be strictly followed, i.e. no space to left or right of the equal sign{tip}
ScanImage r3.5 has added a few and removed several variables from this frequently-modified section. \[{report-link:source=^standardINI_abridged.txt|key=attachment:download path|target="_blank"}View Frequently Modified Section of Standard.INI File{report-link}\]
New and notable INI file variables in this section are:
*triggerLineIndex*: (Previously below rig-specific section) Allows specification of the _static digital output line_ used as shared trigger source for acquisition, mirror, and Pockels cell board(s). The use of Port 0 on the board specified by _triggerBoardIndex_ is assumed.
*triggerInputTerminal*: Specifies the single _Programmable Function Interface (PFI) terminal_ which the acquisition, mirror, and Pockels Cell board(s) will all use as their default trigger input. This terminal on the one or more boards should be connected to the trigger source specified by _triggerBoardIndex_ and _triggerLineIndex_. This is part of trigger simplification feature in r3.5.
*externalTriggerInputTerminal*: Specifies the single _Programmable Function Interface (PFI) terminal_ which the acquisition, mirror, and Pockels Cell board(s) can all use as their optional external trigger input, as described in [External Triggering and Trigger Simplification].
*externalTriggerTimeout*: Specifies time to wait for external trigger input to arrive. See [External Triggering and Trigger Simplification].
*outputBoardClockTerminal*: Specify terminal, either PFI or RTSI(0-6), which will be used to synchronize the clocks of the acquisition/mirror board to the Pockels cell board (if present). Previously RTSI7 was assumed/required. See [Clock Synchronization|Important Changes in ScanImage 3.5#Clock Synchronization] for more details.
*maxBufferedGrabTime*: Specifies max duration, in seconds, of an acquisition (effectively limiting the max number of frames) to allow without using 'SaveDuringAcquisition' option. This value should typically not be altered. Longer acquisitions should employ the new [Continuous Disk Logging|Important New Features in ScanImage3.5#Continuous Disk Logging] feature.
*maxFlybackRate*: This value is reserved for r3.6.
*scanOffsetX/Y*: (Previously below rig-specific section) Specify offset voltages for mirror command signals. These variables are unique among the Rig Specific variables in that they can be altered during ScanImage operation. See [Beam and Scan Alignment Tools|Important New Features in ScanImage3.5#Beam and Scan Alignment Tools] for more information.
*parkAmplitudeX/Y*: (Previously below rig-specific section) Specify voltages for X/Y mirror when parked. (!) Beam safety should be considered in setting these values.
*maxAmplitudeX/Y*: Specify max voltage allowed for X/Y amplitudes. This clamps the sum of the scan amplitude and the scan shift set in ScanImage, for each dimension.
_Shutter_ Variables_
The separate values for 'open' and 'closed' have been removed. Variables _open_ and _epiShutterOpen_ are sufficient to specify 'polarity' of shutter interface.
*shutterBoardIndex*: See [Shutter output line(s) can be on any board|Other New Features and Changes in ScanImage 3.5#shutterAnyBoard].
_Motor Variables_
The number of variables in the rig-specific motor section has been greatly reduced. Two variables, _firmware_ and _posnResolution_, are new in r3.5. See [MP-285 Interface Improvements|Important New Features in ScanImage 3.5#MP-285 Interface Improvements] for details.
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