tomoscan.tomoscan_stream_7bm

Software for tomography stream scanning with EPICS at APS beamline 2-BM

This class support tomoStream by providing:

• Dark-flat field image PVs broadcasting

  Dark-flat field images are broadcasted using PVaccess. Dark-flat field images are also saved in a temporary hdf5 file that are re-written whenever new flat/dark fields are acquired. Acquisition of dark and flat fields is performed without stopping rotation of the stage. Dark-flat field images can also be binned setting the binning parameter in ROI1 plugin.

• On-demand capturing to an hdf5 file

  The capturing/saving to an hdf5 file can be done on-demand by pressing the Capture proj button in the Stream MEDM control screen. Whenever capturing is done, dark/flat fields from the temporarily hdf5 file are added to the file containing the projections and the experimental meta data. In addition, the circular buffer plugin (CB1) of AreaDetector is used to store a set of projections acquired before capturing is started. This allows to save projections containing information about the sample right before a sample change is detected. Data from the circular buffer is also added to the hdf5 after capturing is done. The resulting hdf5 file has the same format as in regular single tomoscan file.

Classes

TomoScanStream2BM

Derived class for tomography scanning in streaming mode with EPICS at APS beamline 2-BM

Functions:

tomoscan.tomoscan_stream_7bm

class tomoscan.tomoscan_stream_7bm.TomoScanStream7BM(pv_files, macros)

Bases: TomoScanStreamPSO

Derived class used for tomography scanning in streamaing mode with EPICS at APS beamline 2-BM

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

add_theta()

Add theta at the end of a scan.

auto_copy_data()

Copies data from detector computer to analysis computer.

close_shutter()

Closes the shutter to collect dark fields and at the end of a scan This does the following:

• Checks if we are in testing mode. If we are, do nothing

• Closes the 7-BM-B fast shutter.

• Closes the beamline shutter.

end_scan()

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

This does the following: - 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.

• Calls move_sample_in().

• Calls the base class method.

• Closes shutter.

move_sample_in()

Moves the sample to the in beam position for collecting projections.

The in-beam position is defined by the SampleInX and SampleInY PVs.

Which axis to move is defined by the FlatFieldAxis PV, which can be X, Y, or Both.

move_sample_out()

Moves the sample to the out of beam position for collecting flat fields.

The out of beam position is defined by the SampleOutX and SampleOutY PVs.

Which axis to move is defined by the FlatFieldAxis PV, which can be X, Y, or Both.

open_shutter()

Opens the shutter to collect flat fields or projections.

This does the following:

• Checks if we are in testing mode. If we are, do nothing.

• Opens the front end shutter, waiting for it to indicate it is open.

  This is copied from the 2-BM implementation 9/2020

• Opens the 7-BM-B fast shutter.

set_trigger_mode(trigger_mode, num_images)

Sets the trigger mode for the camera.

Parameters

• trigger_mode (str) – Choices are: “FreeRun”, “Internal”, or “PSOExternal”

• num_images (int) – Number of images to collect. Ignored if trigger_mode=”FreeRun”. This is used to set the NumImages PV of the camera.

wait_pv(epics_pv, wait_val, timeout=numpy.inf, delta_t=0.01)

Wait on a pv to be a value until max_timeout (default forever) delay for pv to change