Scanning

A regular tomographic scan at 2-BM consists of a series of projections collected in fly scan mode and a set of dark/flat images collected before/after/both the projections. These tasks are accomplished by tomoScan. 2-BM can also collect tomographic data in streaming mode. In this case projections and dark/flat images are broadcasted as EPICS PVs and the actual data saving only occurs on-demand. The data collected in streaming mode is accomplished by tomoScanStream. During the streaming data collection, a real-time 3-orthogonal slice reconstruction is also generated using tomoStream

Since at 2-BM we have two startion (A and B), tomoScan and tomoStream are installed at both station. To access the main control screens

[user2bmb@arcturus]$ start_epics
2bma_beamline 2bmb_beamline

To start the main tomography control screens for 2-BM-A or 2-BM-B for scanning or streaming data collection select in the main beamline control screens the corresponding screen for user, admin, tomoscan, tomoscan 2-BM:

tomo_01 tomo_02 tomo_03

TomoScan

There are 2 installation of tomoScan at 2-BM to support tomography in the A and B stations.

Startup

For experiments in 2-BM-A:

[user2bmb@arcturus]$ ~/tomoscan_start_A.sh

for experiments in 2-BM-B:

[user2bmb@arcturus]$ ~/tomoscan_start_B.sh

a_tomoscan_start.sh and b_tomoscan_start.sh for scripts content.

The tomoscan startup steps executed by a_tomoscan_start.sh for experiments in 2-BM-A are described in detail below.

Data collection

Support for tomography data collection is provided by tomoScan_2bm a tomoScan derived classes to implement the data collection at 2-BM. To run tomoScan in 2-BM-A:

Start area detector - EPICS IOC

[user2bmb@pg10ge]$ 2bmSP2 start

  • medm screen

[user2bmb@pg10ge]$ 2bmSP2 medm

Start tomoScan

  • EPICS IOC

[user2bmb@pg10ge]$ cd /local/user2bmb/epics/synApps/support/tomoscan/iocBoot/iocTomoScan_2BMA/
[user2bmb@pg10ge]$ ./start_IOC

  • tomoscan_2bm python server

[user2bmb@pg10ge]$ bash
[user2bmb@pg10ge]$ cd /local/user2bmb/epics/synApps/support/tomoscan/iocBoot/iocTomoScan_2BMA/
[user2bmb@pg10ge]$ python -i start_tomoscan.py

  • medm screen

[user2bmb@pg10ge]$ cd /local/user2bmb/epics/synApps/support/tomoscan/iocBoot/iocTomoScan_2BMA/
[user2bmb@pg10ge]$ ./start_medm
tomoScan

The tomoScan allows to configure and collect a single tomographic dataset.

Command-line-interface

[user2bmb@pg10ge]$ tomoscan -h
usage: tomoscan [-h] [--config FILE] [--version]  ...
optional arguments:
  -h, --help     show this help message and exit
  --config FILE  File name of configuration file
  --version      show program's version number and exit

  Commands:

init         Create configuration file
status       Show tomoscan status
single       Run a single tomographic scan
vertical     Run a vertical tomographic scan
horizontal   Run a horizontal tomographic scan
mosaic       Run a mosaic tomographic scan

each command help is accessible with -h:

Usage: tomoscan vertical [-h] [--scan-type SCAN_TYPE]
                       [--tomoscan-db-home FILE]
                       [--tomoscan-prefix TOMOSCAN_PREFIX]
                       [--in-situ-pv IN_SITU_PV]
                       [--in-situ-pv-rbv IN_SITU_PV_RBV]
                       [--in-situ-start IN_SITU_START]
                       [--in-situ-step-size IN_SITU_STEP_SIZE]
                       [--sleep-steps SLEEP_STEPS] [--sleep-time SLEEP_TIME]
                       [--vertical-start VERTICAL_START]
                       [--vertical-step-size VERTICAL_STEP_SIZE]
                       [--vertical-steps VERTICAL_STEPS] [--config FILE]
                       [--in-situ] [--logs-home FILE] [--sleep] [--testing]
                       [--verbose]

optional arguments:
-h, --help            show this help message and exit
--scan-type SCAN_TYPE
                      For internal use to log the tomoscan status (default: )
--tomoscan-db-home FILE
                      Log file directory
                      (default: /home/user2bmb/epics/synApps/support/tomoscan/db/)
--tomoscan-prefix TOMOSCAN_PREFIX
                      The tomoscan prefix, i.e.'13BMDPG1:TS:' or
                      '2bma:TomoScan:' (default: 2bma:TomoScan:)
--in-situ-pv IN_SITU_PV
                      Name of the in-situ EPICS process variable to set
                      (default: )
--in-situ-pv-rbv IN_SITU_PV_RBV
                      Name of the in-situ EPICS process variable to read back (default: )
--in-situ-start IN_SITU_START
                      In-situ start (default: 0)
--in-situ-step-size IN_SITU_STEP_SIZE
                      In-situ step size (default: 1)
--sleep-steps SLEEP_STEPS
                      Number of sleep/in-situ steps (default: 1)
--sleep-time SLEEP_TIME
                      Wait time (s) between each data collection scan (default: 0)
--vertical-start VERTICAL_START
                      Vertical start position (mm) (default: 0)
--vertical-step-size VERTICAL_STEP_SIZE
                      Vertical step size (mm) (default: 1)
--vertical-steps VERTICAL_STEPS
                      Number of vertical steps (default: 1)
--config FILE         File name of configuration file
                      (default: /home/user2bmb/tomoscan.conf)
--in-situ             Enable in-situ PV scan during sleep time (default: False)
--logs-home FILE      Log file directory (default: /home/user2bmb/logs)
--sleep               Enable sleep time between tomography scans (default: False)
--testing             Enable test mode, tomography scan will not run (default: False)
--verbose             Verbose output (default: False)

to run a single scan with the parameters set in the tomoScan IOC and the tomoscan-cli:

[user2bmb@pg10ge]$ tomoscan single

tomoscan supports also vertical, horizontal and mosaic tomographic scans with:

[user2bmb@pg10ge]$ tomoscan vertical
[user2bmb@pg10ge]$ tomoscan horizontal
[user2bmb@pg10ge]$ tomoscan mosaic

to run a vertical scan:

$ [user2bmb@pg10ge]$ tomoscan vertical --vertical-start 0 --vertical-step-size 0.1 --vertical-steps 2

2020-05-29 16:54:03,354 - vertical scan start
2020-05-29 16:54:03,356 - vertical positions (mm): [0.  0.1]
2020-05-29 16:54:03,358 - SampleInY stage start position: 0.000 mm
2020-05-29 16:54:03,362 - single scan start
2020-05-29 16:54:51,653 - single scan time: 0.805 minutes
2020-05-29 16:54:51,654 - SampleInY stage start position: 0.100 mm
2020-05-29 16:54:51,658 - single scan start
2020-05-29 16:55:47,607 - single scan time: 0.932 minutes
2020-05-29 16:55:47,607 - vertical scan time: 1.738 minutes
2020-05-29 16:55:47,608 - vertical scan end

tomoscan-cli always stores the last used set of paramters so to repeat the above vertical scan:

[user2bmb@pg10ge]$ tomoscan vertical

use -h for the list of supported parameters.

To repeat the vertical scan 5 times with 60 s wait time between each:

[user2bmb@pg10ge]$ tomoscan vertical --sleep --sleep-steps 10 --sleep-time 60

to repeat the same:

[user2bmb@pg10ge]$ tomoscan vertical --sleep

while:

[user2bmb@pg10ge]$ tomoscan vertical

repeats a single vertical scan with –vertical-start 0 –vertical-step-size 0.1 –vertical-steps 5.

To reset the tomoscan-cli status:

[user2bmb@pg10ge]$ tomoscan init

after deleting the tomoscan.conf file if already exists.

TomoStream

There are 2 major components supporting streaming at 2-BM:

  • Streaming data collection

  • Streaming data reconstruction

Startup

To start streaming data collection and streaming data reconstruction run tomostream_start.sh,

for experiments in 2-BM-A:

[tomo@handyn]$ ~/tomostream_start.sh

for experiments in 2-BM-B:

[user2bmb@arcturus]$ ~/tomostream_start.sh

a_tomostream_start.sh and b_tomostream_start.sh for scripts content.

The streaming data collection and streaming data reconstruction startup steps executed by b_tomostream_start.sh for experiments in 2-BM-B are described in detail below.

Streaming data collection

Support for streaming data collection is provided by tomoScanStream a tomoScan derived classes to implement the streaming data collection. To run tomoScanStream in 2-BM-B:

Start area detector

  • EPICS IOC

[user2bmb@lyra]$ 2bmbSP2 start
[user2bmb@lyra]$ 2bmbSP2 console

  • medm screen

[user2bmb@lyra]$ 2bmbSP2 medm

Note: the IOC prefix for [user2bmb@lyra]$ 2bmbSP2 start is 2bmbSP1:

Start tomoScanStream

  • EPICS IOC

[user2bmb@lyra]$ cd /local/user2bmb/epics/synApps/support/tomoscan/iocBoot/iocTomoScanStream_2BMB/
[user2bmb@lyra]$ ./start_IOC

  • tomoscan_stream python server

[user2bmb@lyra]$ bash
[user2bmb@lyra]$ cd /local/user2bmb/epics/synApps/support/tomoscan/iocBoot/iocTomoScanStream_2BMB/
[user2bmb@lyra]$ python -i start_tomoscan_stream.py

  • medm screen

[user2bmb@lyra]$ cd /local/user2bmb/epics/synApps/support/tomoscan/iocBoot/iocTomoScanStream_2BMB/
[user2bmb@lyra]$ ./start_medm
../../_images/tomoScanStream.png

Streaming data collection features can be controlled from the Streaming Control section and includes:

  • On-demand data capturing with saving in a standard Data Exchange hdf5file

  • Set a number of projectons (“Pre count”) collected before a triggered data capturing event to be also saved in the same hdf5 file

  • binning data streaming

dark-flat field images can be re-taken on-demand at any time during data collection by selecting Now next to the Collect flat (dark) fields.

When collecting data in streaming mode, projections, dark and flat images are broadcasted using PVaccess and can be retrieved as EPICS PVs. Projections are streamed by the detector PVA1 plugin while dark and flat are streamed by tomoScanStream with a dark/flat Stream Prefix configurable under tomoScan/Epics PV names PVs screen:

../../_images/tomoScanStreamEPICS_PVs.png

Using the dark/flat Stream Prefix above, the PVs for data and flat are:

2bmb:TomoScanStream:flat
2bmb:TomoScanStream:dark

These PVs together with the projection PV (in this case 2bmbSP1:Pva1:) will be passed as input to the tomography streaming reconstruction tool tomoStream.

Streaming data reconstruction

The projection, dark and flat image broadcast provided by tomoScanStream can be used to reconstruct in real-time 3 orthogonal slices. This task is accomplished by tomoStream.

Start tomoStream

  • EPICS IOC

[tomo@handyn]$ cd /local/tomo/epics/synApps/support/tomostream/iocBoot/iocTomoStream/
[tomo@handyn]$ ./start_IOC

  • tomostream python server

[tomo@handyn]$ bash
[tomo@handyn]$ cd /local/tomo/epics/synApps/support/tomostream/iocBoot/iocTomoStream/
[tomo@handyn]$ source activate streaming
[tomo@handyn]$ python -i start_tomostream.py

  • medm screen

[tomo@handyn]$ bash
[tomo@handyn]$ cd /local/tomo/epics/synApps/support/tomostream/iocBoot/iocTomoStream/
[tomo@handyn]$ ./start_medm
../../_images/tomoStream.png

Streaming data reconstruction features are:

  • Streaming reconstruction of 3 (X-Y-Z) ortho-slices through the sample

  • On demand adjustment of the

    • X Y Z ortho-slice positions

    • reconstruction rotation center

    • reconstruction filter

and can be controlled from the main tomoStream control screen.

The output of tomostream is a live reconstruction:

../../_images/tomoStreamRecon.png

This is broadcasted as a PVA that can be diplayed by ImageJ using the EPICS_NTNDA_Viewer plug-in:

../../_images/ImageJ_NTNDA_01.png ../../_images/ImageJ_NTNDA_02.png

The PVA name broadcasting the recontruction can be set in the tomoStream/Epics PV names under Recon PVA screen:

../../_images/tomoStreamEPICS_PVs.png

While the sample is rotating is possible to optimize instrument (alignment, focus, sample to detector distance etc.) and beamline (energy etc.) conditions and monitor the effect live on the 3 orthogonal slices. It is also possible to automatically trigger data capturing based on events occurring in the sample and its environment as a result of segmentation or machine learning.