tomoscan.tomoscan_stream_pso

Software for tomography scanning with EPICS

Classes

TomoScanStreamPSO

Derived class for tomography scanning with EPICS using Aerotech controllers and PSO trigger outputs in the streaming mode

Functions:

tomoscan.tomoscan_stream_pso

Software for tomography scanning with EPICS

class tomoscan.tomoscan_stream_pso.TomoScanStreamPSO(pv_files, macros)

Bases: TomoScan

Derived class used for tomography scanning with EPICS using Aerotech controllers and PSO trigger outputs

Parameters

• pv_files (list of str) – List of files containing EPICS pvNames to be used.

• macros (dict) – Dictionary of macro definitions to be substituted when reading the pv_files

begin_scan()

Performs the operations needed at the very start of a scan.

• Calls the base class method.

• Sets the speed of the rotation motor

• Computes the delta theta, start and stop motor positions for the scan

• Programs the Aerotech driver to provide pulses at the right positions

• Begin streaming

begin_stream()

Streaming settings adjustments at the beginning of the scan

• set dark/flat fields modes as None (do not take static dark/flat fields)

• set binning in ROI1 plugin

• set capturing status to Done for all capturing pvs

• set circular buffer

• add callbacks for capturing changing sizes pvs

broadcast_dark()

Broadcast dark fields

• read dark fields from the file

• take average and bin dark fields according to StreamBinning parameter

• broadcast dark field with the pv variable

broadcast_flat()

Broadcast flat fields

• read flat fields from the file

• take average and bin flat fields according to StreamBinning parameter

• broadcast flat field with the pv variable

capture_projections()

Monitor the capturing projections process: capture projections, save pre-buffer, dump angles, copy dark and flat fields. The result of this capturing process is 4 files, e.g. scan_045.h5 (captured projections), circular_buffer_scan_045.h5 (pre-buffer with projections), dark_fields_scan_045.h5 (dark fields), and flat_fields_scan_045.h5 (flat fields)

• set StreamMessage to ‘Capturing projections’

• disable cb plugin

• set number of captured frames in the hdf5 plugin as StreamNumCapture parameter

• set file name

• start capturing to the hdf5 file

• wait when capturing is started

• wait when capturing is finished

• dump angles

• take basename and dirname from full file name

NOTE: Temporarily: dont copy dark and flats // copy dark_flat fields file to the one having the same index as data (eg. copy dark_fields.h5 dark_fields_scan_045.h5) // copy dark_flat fields file to the one having the same index as data (eg. copy flat_fields.h5 flat_fields_scan_045.h5)

if circular buffer size > 0:

• set StreamMessage to ‘Capturing circular buffer’

• save file name, hdf5 plugin port name, autoincrement values

• change hdf5 file name to circular_buffer_*file_name*, set autoincrent to No

• switch input port of hdf5 plugin to the circular buffer port

• set the number of captured frames in the hdf5 as the currentQty value in cb

• start capturing to the hdf5 file

• set the number of post-count in cb plugin equal to currentQty

• press trigger button in cb plugin

• enable cb callbacks

• wait when trigger is finished

• start cb capturing again

• dump angles to hdf5 with data from cb

• switch input port for hdf plugin back to the initial

• change hdf5 file name and autoincrement values back to the initial

• compute total number of captured frames and show it the medm screen

• enable circular buffer (because if number of elements in CB == 0 then the plugin will automatically turn off)

• set StreamMessage to ‘Done’

• set capturing status to ‘Done’

change_binning()

Change binning for broadcasted projections and dark/flat fields

• change binning in the ROI1 plugin

• broadcast binned dark and flat fields

• cancel change_binning if StreamMessage!=’Done’

change_cbmessage()

Update status message for the circular buffer

change_cbqty()

Update current number of elements in the circular buffer

change_cbsize()

Change the circular buffer size

• stop cb capturing

• set precount in circular buffer to the new size

• start cb capturing

• if StreamMessage!=’Done’, cancel the entered value for the cb size

change_numcaptured()

Update current number of captured frames

cleanup_PSO()

Cleanup activities after a PSO scan. Turns off PSO and sets the speed back to default. Same as in TomoScanPSO

collect_projections()

Collects projections in fly scan mode.

• Call the superclass collect_projections() function

• Taxi to the start position

• Set the External trigger mode on the camera

• Starts the camera acquiring in external trigger mode.

• Assign fly angular positions to theta depending on the stream type (‘backforth’ or ‘continuous’)

• Broadcast angles in a pva variable

compute_frame_time()

Redefine the one from Tomoscan, set no readout

Returns

float – The frame time, which is the minimum time allowed between triggers for the value of the ExposureTime PV.

compute_positions_PSO()

Computes several parameters describing the fly scan motion. Computes the spacing between points, ensuring it is an integer number of encoder counts. Uses this spacing to recalculate the end of the scan, if necessary. Computes the taxi distance at the beginning and end of scan to allow the stage to accelerate to speed. Same as in TomoScanPSO except angles are not initiated here

copy_flat_dark_to_hdf()

Copies the flat and dark field data to the HDF5 file with the projection data. This allows the file to be a fully valid DXchange file. Once the file is created it will be copied to the remote data analysis computer (if CopyToAnalysisDir is set to yes)

dump_theta()

Add theta to the hdf5 file by using unique ids stored in the same hdf5 file

• read unique projection ids from the hdf5 file

• take angles by ids from the PSO

• dump angles into hdf5 file

end_scan()

Performs the operations needed at the very end of a scan.

• End streaming

• Calls save_configuration().

• Put the camera back in “FreeRun” mode and acquiring so the user sees live images.

• Sets the speed of the rotation stage back to the maximum value.

• Stop rotation with Jog

• Calls the base class method.

end_stream()

Stream settings adjustments at the end of the scan

• set capturing status to Done for all capturing pvs

• remove callbacks

program_PSO()

Performs programming of PSO output on the Aerotech driver. Same as in TomoScanPSO, but with adding RotationSpeedJog

pv_callback_stream(pvname=None, value=None, char_value=None, **kw)

Callback functions for capturing in the streaming mode

retake_dark()

Recollect dark fields while in the streaming mode

• set StreamMessage to ‘Captruing dark fields’

• save file_name, template, autoincrement values

• change file name to dark_fields.h5, autoincrement to No, template to %s%s

• set frame type to DarkField

• disable circular buffer plugin

• close shutter

• collect dark fields

• enable circular buffer plugin

• return file name to the initial one

• set the frame type to ‘Projection’

• set the retake dark button to Done

• broadcast dark fields

• set StreamMessage to ‘Done’

• set capturing status to ‘Done’

retake_flat()

Recollect flat fields while in the streaming mode

• set StreamMessage to ‘Captruing flat fields’

• save file_name, template, autoincrement values

• change file name to flat_fields.h5, autoincrement to No, template to %s%s

• set frame type to DarkField

• disable circular buffer plugin

• close shutter

• collect flat fields

• enable circular buffer plugin

• return file name to the initial one

• set the frame type to ‘Projection’

• set the retake dark button to Done

• broadcast flat fields

• set StreamMessage to ‘Done’

• set capturing status to ‘Done’

stop_capture_projections()

Stop capturing projections

stream_sync()

Synchronize new angular step and exposure with rotation speed. Broadcast new array of angles for streaming reconstruction

• cleanup PSO

• save last unique ID of projection

• program pso (base part)

• change the JOG speed wrt exposure and angular step

• initiate DATAACQ in aerotech for saving encoder values

• ARM PSO

• wait exposure time to acquire 1 projection

• read encoder value for the projection unique_id + 1

• convert encoder value to the angle, form array of angles

• broadcast array of angles for streaming

NOTE: currently doesn’t work for backforth scans