Install directions¶

Build EPICS base¶

Warning

Make sure the disk partition hosting ~/epics is not larger than 2 TB. See tech talk and Diamond Data Storage document.

$ mkdir ~/epics-ts
$ cd epics-ts

Download EPICS base latest release, i.e. 7.0.3.1., from https://github.com/epics-base/epics-base:

$ git clone https://github.com/epics-base/epics-base.git
$ cd epics-base
$ git submodule init
$ git submodule update
$ make distclean (do this in case there was an OS update)
$ make -sj

Warning

if you get a configure/os/CONFIG.rhel9-x86_64.Common: No such file or directory error issue this in your csh termimal: $ setenv EPICS_HOST_ARCH linux-x86_64

Build a minimal synApps¶

To build a minimal synApp:

$ cd ~/epics-ts

Download in ~/epics-ts assemble_synApps.sh

Edit the assemble_synApps.sh script to include only:

$modules{'ASYN'} = 'R4-44-2';
$modules{'AUTOSAVE'} = 'R5-11';
$modules{'BUSY'} = 'R1-7-4';

You can comment out all of the other modules (ALLENBRADLEY, ALIVE, etc.)

Run:

$ cd ~/epics-ts
$ ./assemble_synApps.sh --dir=synApps --base=/home/beams/FAST/epics-ts/epics-base

This will create a synApps/support directory:
```
$ cd synApps/support/
```

Clone the tomoscan module into synApps/support:

$ git clone https://github.com/tomography/tomoscan.git

Warning

If you are a tomoScan developer you should clone your fork.

Edit configure/RELEASE add this line to the end:
```
TOMOSCAN=$(SUPPORT)/tomoscan
```

Verify that synApps/support/tomoscan/configure/RELEASE:

EPICS_BASE=/home/beams/FAST/epics-ts/epics-base
SUPPORT=/home/beams/FAST/epics-ts/synApps/support

are set to the correct EPICS_BASE and SUPPORT directories and that:

BUSY
AUTOSAVE
ASYN

point to the version installed.

Run the following commands:

$ cd ~/epics-ts/synApps/support/
$ make release
$ make -sj

Testing the installation¶

Start the epics ioc and associated medm screen with:

$ cd ~/epics-ts/synApps/support/tomoscan/iocBoot/iocTomoScan_13BM_PSO
$ start_IOC
$ start_medm

Python server¶

create a dedicated conda environment:

$ conda create --name tomoscan python=3.9
$ conda activate tomoscan

and install all packages listed in the requirements.txt file then

$ cd ~/epics-ts/synApps/support/tomoscan
$ pip install .
$ cd ~/epics-ts/synApps/support/tomoscan/iocBoot/iocTomoScan_13BM_PSO/
$ python -i start_tomoscan.py

Beamline customization¶

tomoScan¶

Below are the customization steps for 2-BM, you can use these as templates for your beamline.

Create in ~/epics-ts/synApps/support/tomoscan/tomoScanApp/Db
- tomoScan_2BM_settings.req
- tomoScan_2BM.template
Create in ~/epics-ts/synApps/support/tomoscan/tomoScanApp/op/adl
- tomoScan_2BM.adl

add here custom PVs required to run tomography at your beamline.

$ mkdir ~/epics-ts/synApps/support/tomoscan/iocBoot/iocTomoScan_2BM
$ cd ~/epics-ts/synApps/support/tomoscan/iocBoot/
$ cp -r iocTomoScan_13BM/* iocTomoScan_2BM/

$ cd ~/epics-ts/synApps/support/tomoscan/iocBoot/

Edit iocBoot/iocTomoScan_2BM/auto_settings.req
- file “tomoScan_settings.req”, P=$(P), R=$(R)
- file “tomoScan_2BM_settings.req”, P=$(P), R=$(R)
Edit iocBoot/iocTomoScan_2BM/st.cmd to match the name you want to assign to the TomoScan ioc
- epicsEnvSet(“P”, “2bma:”)
- epicsEnvSet(“R”, “TomoScan:”)
Edit iocBoot/iocTomoScan_2BM/start_medm to match the name assigned to the TomoScan ioc
- medm -x -macro “P=2bma:,R=TomoScan:,BEAMLINE=tomoScan_2BM” ../../tomoScanApp/op/adl/tomoScan.adl &
Edit iocBoot/iocTomoScan_2BM/start_tomoscan_2bm.py
- from tomoscan.tomoscan_2bm import TomoScan2BM
- ts = TomoScan2BM([“../../db/tomoScan_settings.req”,”../../db/tomoScan_2BM_settings.req”], {“$(P)”:”2bma:”, “$(R)”:”TomoScan:”})
Edit iocBoot/iocTomoScan_2BM/tomoScan.substitutions
- to match the custom PVs required to run tomography at your beamline.

file "$(TOP)/db/tomoScan.template"
{
pattern
{  P,      R,      CAMERA,    FILE_PLUGIN,   ROTATION,  SAMPLE_X,  SAMPLE_Y,      CLOSE_SHUTTER,        CLOSE_VALUE,        OPEN_SHUTTER,         OPEN_VALUE}
{2bma:, TomoScan:, 2bmbSP1:, 2bmbSP1:HDF1:,  2bma:m82,   2bma:m49,  2bma:m20,  2bma:A_shutter:close.VAL,    1,        2bma:A_shutter:open.VAL,      1}
}

# For the Ensemble PSO_ENC_PER_ROTATION is a signed number containing the number of encoder pulses per rotation in positive dial coordinates
file "$(TOP)/db/tomoScan_PSO.template"
{
pattern
{  P,       R,     PSO_MODEL, PSO_PORT, PSO_AXIS_NAME, PSO_ENC_INPUT, PSO_ENC_PER_ROTATION}
{2bma:, TomoScan:,    0,      PSO_PORT,      X,             3,            11840158.}
}

file "$(TOP)/db/tomoScan_2BM.template"
{
pattern
{  P,      R,           BEAM_READY,     READY_VALUE,    CLOSE_FAST_SHUTTER,  CLOSE_FAST_VALUE,   OPEN_FAST_SHUTTER,  OPEN_FAST_VALUE,         SHUTTER_STATUS,}
{2bma:, TomoScan:, ACIS:ShutterPermit,       1,             2bma:m23,               0,                 2bma:m23,              1,           PA:02BM:STA_A_FES_OPEN_PL,}
}

then:

$ cd ~/epics-ts/synApps/support
$ make release
$ make -sj

Python class¶

Create in ~/epics-ts/synApps/support/tomoscan/tomoscan/
- tomoscan_2bm.py

to implemented a derived classes that inherit from ~/epics-ts/synApps/support/tomoscan/tomoscan/tomoscan.py This derived class will handle any beamline specific hardware (fast shutter, fly scan hardware etc.)

To install the python class as a libray:

$ cd ~/epics-ts/synApps/support/tomoscan/
$ conda activate tomoscan
$ pip install .