tomoScanApp EPICS application¶

tomoscan includes a complete example EPICS application, including:

A database file and corresponding autosave request file that contain the PVs required by the tomoscan.py base class.
A database file and corresponding autosave request file that contain the PVs required by the tomoscan_pso.py intermediate base class.
Database files and corresponding autosave request files that contain PVs used by the beamline-specific derived classes.
OPI screens for medm, edm, caQtDM, CSS/Boy, and CSS/Phoebus
An example IOC application that can be used to run the above databases. The databases are loaded in the IOC with the example substitutions file, tomoScan.substitutions.

Base class files¶

The following tables list all of the records in the tomoScan.template file. These records are used by the tomoscan base class and so are required.

tomoScan.template¶

This is the database file that contains only the PVs required by the tomoscan.py base class tomoScan.template.

Camera and File Plugin PV Prefixes¶

Record name	Record type	Description
$(P)$(R)CameraPVPrefix	stringout	Contains the prefix for the camera, e.g. 13BMDPG1:
$(P)$(R)FilePluginPVPrefix	stringout	Contains the prefix for the file plugin, e.g. 13BMDPG1:HDF1: or 13BMDPG1:netCDF1:

Shutter control¶

Record name	Record type	Description
$(P)$(R)CloseShutterPVName	stringout	Contains the name of the PV to close the shutter
$(P)$(R)CloseShutterValue	stringout	Contains the value to write to close the shutter
$(P)$(R)OpenShutterPVName	stringout	Contains the name of the PV to open the shutter
$(P)$(R)OpenShutterValue	stringout	Contains the value to write to open the shutter

Rotation, sample X and Y translation motors¶

Record name	Record type	Description
$(P)$(R)RotationPVName	stringout	Contains the name of the rotation motor PV, e.g. 13BMD:m38
$(P)$(R)SampleXPVName	stringout	Contains the name of the sample X translation PV, e.g. 13BMD:m85
$(P)$(R)SampleYPVName	stringout	Contains the name of the sample Y translation PV, e.g. 13BMD:m90

Data collection control¶

Record name	Record type	Description
$(P)$(R)RotationStart	ao	The starting rotation angle
$(P)$(R)RotationStep	ao	The rotation step size
$(P)$(R)RotationStop	calc	The final projection angle. Computed as RotationStart + RotationStep*NumAngles. Provided as a convenience to check that the scan is correctly defined.
$(P)$(R)NumAngles	ao	The number of angles (projections) to collect
$(P)$(R)ReturnRotation	bo	Flag controlling whether to return rotation to RotationStart at the end of collection. Choices are ‘No’ and ‘Yes’. When ‘Yes’ the ScanStatus will report complete before the rotation axis returns to the start.

Dark field control¶

Record name	Record type	Description
$(P)$(R)NumDarkFields	longout	Number of dark fields to collect
$(P)$(R)DarkFieldMode	mbbo	When to collect dark fields. Choices are ‘Start’, ‘End’, ‘Both’, ‘None’.
$(P)$(R)DarkFieldValue	ao	A constant dark field value for every pixel, typically used when DarkFieldMode=None.

Flat field control¶

Record name	Record type	Description
$(P)$(R)NumFlatFields	longout	Number of flat fields to collect
$(P)$(R)FlatFieldMode	mbbo	When to collect flat fields. Choices are ‘Start’, ‘End’, ‘Both’, ‘None’.
$(P)$(R)FlatFieldAxis	mbbo	Axis to move when collecting flat fields. Choices are ‘X’, ‘Y’, and ‘Both’.
$(P)$(R)FlatFieldValue	ao	A constant flat field value for every pixel, typically used when FlatFieldMode=None.
$(P)$(R)SampleInX	ao	Position of the X stage when the sample is in position for collecting projections.
$(P)$(R)SampleOutX	ao	Position of the X stage when the sample is out for collecting flat fields.
$(P)$(R)SampleInY	ao	Position of the Y stage when the sample is in position for collecting projections.
$(P)$(R)SampleOutY	ao	Position of the Y stage when the sample is out for collecting flat fields.
$(P)$(R)SampleOutAngle	ao	Position of the raotary stage when the sample is moved out for collecting flat fields.
$(P)$(R)SampleOutAngleEnable	bo	Flag controlling whether the flat fields are collected at the start/end position or at the value set by $(P)$(R)SampleOutAngle.

Frame type¶

Record name	Record type	Description
$(P)$(R)FrameType	mbbi	Type of the current frame. Choices are ‘DarkField’, ‘FlatField’, ‘Projection’. This record can be used as a detector attribute to indicate what type of data each frame contains.

Exposure time¶

Record name	Record type	Description
$(P)$(R)ExposureTime	ao	The exposure time in seconds. Currently the same time is used for dark fields and projections. The time for flat fields can be different, and is controlled by the following 2 records. Writing to this PV will copy the value to the camera AcquireTime PV.
$(P)$(R)FlatExposureTime	ao	The exposure time for flat fields in seconds if the value of the $(P)$(R)DifferentFlatExposure record is “Different”. Otherwise $(P)$(R)ExposureTime is also used for flat fields.
$(P)$(R)DifferentFlatExposure	bo	Controls whether $(P)$(R)ExposureTime or $(P)$(R)FlatExposureTime is used for the flat fields. Choices are “Same” (0) or “Different (1).

File path and name control¶

Record name	Record type	Description
$(P)$(R)FilePath	waveform	The file path to save data. Writing to this PV will copy the value to the file plugin.
$(P)$(R)FileName	waveform	The file name to save data. Writing to this PV will copy the value to the file plugin.
$(P)$(R)FilePathExists	bi	Flag indicating whether the specified FilePath exists. This is a mirror of the FilePathExists_RBV record in the file plugin.
$(P)$(R)OverwriteWarning	bi	Selects whether to open a dialog box to warn the user if the file to be written would overwrite an existing file. The user can then choose ‘Yes’ or ‘No’.
$(P)$(R)FullFileName	waveform	The last file name used to save data.

Location for data in HDF5 file¶

Record name	Record type	Description
$(P)$(R)HDF5ProjectionLocation	stringout	String defining the location in the HDF5 file to write projection frames. The default is `/exchange/data`.
$(P)$(R)HDF5DarkLocation	stringout	String defining the location in the HDF5 file to write dark field frames. The default is `/exchange/data_dark`.
$(P)$(R)HDF5FlatLocation	stringout	String defining the location in the HDF5 file to write flat field frames. The default is `/exchange/data_white`.
$(P)$(R)HDF5Location	stringout	String defining the location in the HDF5 file to write the current frame. This is updated by TomoScan depending on which type of frame is currently being collected. This PV should be used to define the HDF5FrameLocation attribute in the detector attributes XML file. The HDF5 layout XML file should use the HDF5FrameLocation attribute to control where the frame is written in the HDF5 file.

Scan control via Channel Access¶

Record name	Record type	Description
$(P)$(R)MoveSampleIn	ao	Setting this record to 1 moves the sample in.
$(P)$(R)MoveSampleOut	ao	Setting this record to 1 moves the sample out.
$(P)$(R)StartScan	busy	Setting this record to 1 starts a scan.
$(P)$(R)AbortScan	bo	Setting this record to 1 aborts a scan.

Scan status via Channel Access¶

Record name	Record type	Description
$(P)$(R)ScanStatus	waveform	This record will be updated with the scan status while scanning.
$(P)$(R)ImagesCollected	stringout	This record will be updated with the current projection number while scanning.
$(P)$(R)ImagesSaved	stringout	This record will be updated with the current projection number saved.
$(P)$(R)ElapsedTime	stringout	This record will be updated with the elapsed time while scanning.
$(P)$(R)RemainingTime	stringout	This record will be updated with the estimated time remaining while scanning.
$(P)$(R)ServerRunning	bi	This record will be `Running` if the Python server is running and `Stopped` if not. It is controlled by a watchdog timer, and will change from `Running` to `Stopped` within 5 seconds if the Python server exits.

Scan Types¶

Record name	Record type	Description
$(P)$(R)ScanType	mbbo	Contains the scan type, e.g. ‘Single’, ‘Vertical’, ‘Horizontal’, ‘Mosaic’, “File’, ‘Energy’, “Helical’.
$(P)$(R)FlipStitch	bo	Tells if the scan is a Flip&Stitch or not.

tomoScan_settings.req¶

This is the autosave request file for tomoScan.template tomoScan_settings.req.

This file serves 2 purposes:

It is used by autosave to determine which PVs to save in the auto_settings.sav file.
It is read in the constructor of the TomoScan class to determine what PVs to read and write.

It contains 4 types of PVs:

Configuration PVs. These are PVs the control how tomography scans are collected, and provide metadata about the scan. An example is $(P)$(R)RotationStart. These have the following properties:

They are saved by autosave in the auto_settings.sav file.

They are saved by TomoScan in configuration files.

They do not contain the string “PVName” or “PVPrefix” in their PV names.

They appear as normal lines in the file, not in comment lines.

PVs that contain the name of another PV. These are used to configure TomoScan to control a particular motor for the rotation axis, sample X axis, etc. An example is $(P)$(R)RotationPVName. These have the following properties:

They contain the string “PVName” in their PV names.

They are saved by autosave in the auto_settings.sav file.

They are not saved by TomoScan in configuration files.

They appear as normal lines in the file, not in comment lines.

PVs that contain the PV prefix for a set of other PVs. These are used to configure TomoScan to control a particular areaDetector camera, etc. Examples are (P)$(R)CameraPVPrefix and $(P)$(R)FilePluginPVPrefix. These have the following properties:

They contain the string “PVPrefix” in their PV names.

They are saved by autosave in the auto_settings.sav file.

They are not saved by TomoScan in configuration files.

They appear as normal lines in the file, not in comment lines.

PVs that are required by TomoScan, but which should not be saved and restored by autosave, either because they are read-only, or because writing to them when the IOC starts might have unwanted consequences. These have the following properties:

They appear in comment lines in the file. The comment line must start with the string #controlPV followed by the PV name.

They do not contain the string “PVName” or “PVPrefix” in their PV names.

They are not saved by autosave in the auto_settings.sav file.

They are not saved by TomoScan in configuration files.

When the request file is read it is used to construct all of the EPICS PV names that are used by TomoScan. This allows TomoScan to avoid having any hard-coded PV names, and makes it easy to port to a new beamline.

Intermediate base class files¶

The following tables list all of the records in the tomoScan_PSO.template file. This class is used when an Aerotech controller runs the rotation stage and the PSO output is used to trigger the camera.

tomoScan_PSO.template¶

This is the database file that contains only the PVs required by the tomoscan_pso.py base class. These records cannot be modified at run-time, except for the asyn record. Configuration records are set in the tomoScan.subsitutions file for each IOC, and set when the IOC starts. Status records contain read-only status information.

tomoScan.template.

PSO configuration¶

Record name	Record type	Access type	Description
$(P)$(R)PSOControllerModel	mbbi	Configuration	The Aerotech controller model being used. This is needed because some PSO commands are controller dependent, and there appears to be no way to query the controller model. The choices are “Ensemble” (0), and “A3200” (1).
$(P)$(R)PSOStartTaxi	ai	Status	The starting “taxi” position. The taxi distance is used to allow the rotation stage to accelerate and reach the desired rotation speed before the first projection angle.
$(P)$(R)PSOEndTaxi	ai	Status	The ending “taxi” position. The taxi distance is used to allow the rotation stage to deccelerate to 0 after reaching the final projection angle.
$(P)$(R)PSOEncoderCountsPerStep	longin	Status	The number of encoder counts between projections.
$(P)$(R)PSOCommand	asyn	Write/read	This record is used to send PSO commands to the Aerotech controller. An EPICS drvAsynIPPort is created in the IOC startup script using the IP address of the Aerotech controller, and this record communicates using that asyn port. The record uses “Hybid” mode for both input and output, so that the strings can be longer than 40 characters. This means that it uses the .BOUT field for output and the .BINP field for input. The .BOUT field is a text-input widget in the medm screen so the user can type commands directly to the controller for debugging.
$(P)$(R)PSOAxisName	stringin	Configuration	The name of the rotation axis in the controller. This is the name that is displayed in the Aerotech Motion Composer software.
$(P)$(R)PSOCountsPerRotation	ai	Configuration	The number of encoder pulses per 360 degree rotation of the rotation stage. This is a signed number, and must be negative if the encoder direction and motor direction in the controller are different. On the A3200 this value is read from the controller in the constructor, and includes the correct sign. This overrides the value in the subsitutions file. On the Ensemble this value must be provided in the substitutions file.
$(P)$(R)PSOEncoderInput	longin	Configuration	Selects which encoder signal is used for the PSO control. This is hardware dependent, and is typically 2 or 3.
$(P)$(R)PSOPulsWidth	ao	Write/read	Sets the PSO output pulse width in microseconds. Different cameras may have different requirements for the trigger pulse width, so this value can be modified.
$(P)$(R)PSOKeepAlive	asyn	Write/read	This record is needed on the Ensemble to keep the socket from timing out. It is not needed on the A3200, but does not hurt. SCAN could be set to Passive on the A3200.
$(P)$(R)ProgramPSO	bo	Write/read	Enable PSO programming ‘Yes’.

medm files¶

tomoScan.adl¶

The following is the MEDM screen tomoScan.adl during a scan. The status information is updating.

tomoScanEPICS_PVs.adl¶

The following is the MEDM screen tomoScanEPICS_PVs.adl. If these PVs are changed tomoscan must be restarted.

tomoScan_pso.adl¶

The following is the MEDM screen tomoScan_pso.adl. It contains the PVs that control the Aerotech PSO pulse control.

Beamline-specific files¶

The following files are for the beamline-specific derived classes.

Beamline 13BM¶

These are the files that are specific to the TomoScan13BM derived class used at APS beamline 13-BM-D.

tomoScan_13BM.template¶

This is database file for the TomoScan13BM derived class tomoScan_13BM.template.

The following tables list all of the records in the tomoScan_13BM.template file. This file is used for records needed by the tomoscan_13bm derived class, and also for metadata PVs that should be saved in the tomoscan configuration file and files written by the areaDetector file plugins.

SIS MCS Prefix¶

Record name	Record type	Description
$(P)$(R)MCSPVPrefix	stringout	Contains the prefix for the SIS MCS, e.g. 13BMD:SIS1:

Energy information¶

Record name	Record type	Description
$(P)$(R)EnergyMode	mbbo	Contains the energy mode of the beamline, e.g. ‘Mono’, ‘Pink’, ‘White’.

Beam status information¶

Record name	Record type	Description
$(P)$(R)BeamReadyPVName	stringout	Contains the name of the PV that indicates if beam is ready, e.g. 13BMA:mono_pid1Locked
$(P)$(R)BeamReadyValue	stringout	Contains the value of the beam ready PV when beam is ready.

Optics information¶

Record name	Record type	Description
$(P)$(R)ScintillatorType	stringout	Contains the type of scintillator being used.
$(P)$(R)ScintillatorThickness	ao	Contains the thickness of the scintillator in microns.
$(P)$(R)ImagePixelSize	ao	Contains the pixel size on the sample in microns (i.e. includes objective magnification)
$(P)$(R)DetectorPixelSize	ao	Contains the pixel size of the detector.
$(P)$(R)CameraObjective	stringout	Description of the camera objective
$(P)$(R)CameraTubeLength	stringout	Description of the camera objective

Sample information¶

Record name	Record type	Description
$(P)$(R)SampleName	stringout	Name of the sample
$(P)$(R)SampleDescription1	stringout	Description of the sample, part 1
$(P)$(R)SampleDescription2	stringout	Description of the sample, part 2
$(P)$(R)SampleDescription3	stringout	Description of the sample, part 3

User information¶

Record name	Record type	Description
$(P)$(R)UserName	stringout	User name
$(P)$(R)UserInstitution	stringout	User institution
$(P)$(R)UserBadge	stringout	User badge number
$(P)$(R)UserEmail	stringout	User email address
$(P)$(R)ProposalNumber	stringout	Proposal number
$(P)$(R)ProposalTitle	stringout	Proposal title
$(P)$(R)ESAFNumber	stringout	Experiment Safety Approval Form number

tomoScan_13BM_settings.req¶

This is the autosave request file for tomoScan_13BM.template tomoScan_13BM_settings.req.

It has the same usage and type of content as tomoScan_settings.req described above, except that it contains the PVs for the derived class TomoScan13BM.