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h6. Overview
ScanImage requires an initialization |
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Overview
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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ScanImage
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.
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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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ScanImage 3.5 changes somewhat the way the INI file is loaded at startup. This is described in the section about Initialization (INI) File Handling. |
A subset of the INI file variables – termed the Rig Configuration variables – are demarcated at the beginning of the INI file. Rig Configuration variables are those which may require modification for a new ScanImage installation. These variables are rig-specific, and are not associated with either configuration (CFG) or user (USR) files. The values for these variables are not modified/modifiable during ScanImage program operation.
Rig Configuration Variable Reference
This section serves as a reference to the new and notable Rig Configuration variables in ScanImage 3.5.
Users should adjust the Rig Configuration values to match the hardware and experimental requirements for their rig, creating their own standard.ini file.
The standard_model.ini file contains comments which document the meaning of each of the variables.
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
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| title | New/Notable Variables in _standard_model.INI_ |
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triggerLineIndex: (Previously below Rig Configuration section) Allows specification of the static digital output line used as the 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, externalTriggerInputTerminal, externalTriggerTimeout: See the sections on Triggering Simplification and External Triggering for more details. outputBoardClockTerminal: See Clock Synchronization for more details. maxBufferedGrabTime: See Unlimited and Uninterrupted Acquisition for more details. scanOffsetX/Y: (Previously below Rig Configuration section) Specify offset voltages for mirror command signals, i.e. the center of the laser scan. These variables are unique among the Rig Configuration variables in that they can be altered during ScanImage operation. See Beam and Scan Alignment Tools for more details. parkAmplitudeX/Y: (Previously below Rig Configuration section) Specify voltages determining X/Y mirror positions when parked (i.e. when no acquisition is occurring).
Beam safety should be considered in setting these values.
When the beam is parked, the shutter is closed and the Pockels Cell set to minimum transmission. Shutter Variables - Variable shutterBoardIndex is new in ScanImage 3.5.
- Several variables (e.g. closed, epiShutterOpen, and epiShutterClosed) have been removed.
See Enhanced Shutter Configuration for more details. Motor (MP-285) Variables - Variables umPerStepX/Y/Z have been added, replacing calibrationX/Y/Z values in ScanImage 3.0.
- Variable posnResolution is also new in ScanImage 3.5.
See MP-285 Interface Improvements for more details. . A subset of _Rig Configuration_ variables are demarcated at the beginning of the INI file; these copmrise the variables that typically require modification for a new ScanImage installation. Rig Configuration variables are not associated with either CFG or USR files and are not modified during ScanImage program operation. Typically only one INI file is required per rig.
ScanImage r3.5 introduces some changes to the way INI files are handled. Please familiarized yourself with [Initialization (INI) File Handling|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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