### Install Tomoscan Library

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/usage.md

Install the tomoscan library by navigating to its source directory and running the setup script. This enables the tomoscan command-line interface.

```bash
cd ~/epics/synApps/support/tomoscan/
python setup.py install
```

--------------------------------

### Running a Vertical Scan with tomoscan-cli

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/demo.md

This example demonstrates how to run a vertical tomography scan with specific start, step, and points parameters using the tomoscan-cli. It also shows the expected log output during the scan.

```bash
$ 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
```

--------------------------------

### Build and Install Support Modules

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Commands to update the release file and build all support modules after configuration changes.

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

--------------------------------

### begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_pso.md

Performs the initial setup for a tomography scan, including motor speed, position computation, PSO driver programming, and initiating streaming.

```APIDOC
## begin_scan()

### Description
Performs the operations needed at the very start of a scan. This includes setting the rotation motor speed, computing scan positions, programming the Aerotech driver for PSO pulses, and beginning the data stream.

### Method
This is a method of the `TomoScanStreamPSO` class.
```

--------------------------------

### Running the Python Tomography Scan Demo

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/demo.md

This example shows how to execute the `scan_demo` Python function and its expected output, demonstrating a scan of an EPICS motor PV.

```python
>>> from scan_demo import scan_demo
>>> scan_demo('13BMDPG1:TS:', .01, '13BMD:m90', 5, 1, 5)
Completed dataset T:\tomo_user\2020\Run1\Test\Test_R_001.h5
Completed dataset T:\tomo_user\2020\Run1\Test\Test_R_002.h5
Completed dataset T:\tomo_user\2020\Run1\Test\Test_R_003.h5
Completed dataset T:\tomo_user\2020\Run1\Test\Test_R_004.h5
Completed dataset T:\tomo_user\2020\Run1\Test\Test_R_005.h5
```

--------------------------------

### Install Tomoscan Python Library

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Installs the Tomoscan Python package as a library after creating beamline-specific Python classes.

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

--------------------------------

### Tomoscan CLI Help

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/usage.md

Display general help for the tomoscan CLI, showing available commands and global options. Use this to get an overview of the CLI's capabilities.

```bash
tomoscan -h
```

--------------------------------

### begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_32id.md

Performs the operations needed at the very start of a scan, including setting the data directory, opening the front-end shutter, setting the PSO controller, and creating the theta array.

```APIDOC
## begin_scan()

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

This does the following:

- Set data directory.
- Calls the base class method.
- Opens the front-end shutter.
- Sets the PSO controller.
- Creates theta array using list from PSO.
```

--------------------------------

### Run assemble_synApps Script

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Execute the assemble_synApps.sh script to build a minimal synApps installation, specifying the output directory and EPICS base path.

```default
$ ./assemble_synApps.sh --dir=synApps --base=/home/beams/FAST/epics-ts/epics-base
```

--------------------------------

### Start EPICS IOC and MEDM Screen

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Commands to start the EPICS IOC and associated MEDM screen for Tomoscan. Ensure you are in the correct directory.

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

--------------------------------

### begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_step.md

Performs the operations needed at the very start of a scan. This includes calling the base class method and setting the HDF plugin.

```APIDOC
## begin_scan()

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

This does the following:

- Calls the base class method.
- Set the HDF plugin.
```

--------------------------------

### Install Tomoscan Python Package

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Installs the Tomoscan package using pip after setting up the conda environment and requirements.

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

--------------------------------

### Basic tomoscan-cli Command

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/demo.md

This command initiates a single tomography scan using the tomoscan-cli. It's the simplest way to start a scan with the tool.

```bash
$ tomoscan single
```

--------------------------------

### begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_pso.md

Performs the operations needed at the very start of a scan, including setting motor speed, computing positions, and programming the Aerotech driver for pulses.

```APIDOC
## begin_scan()

### Description
Performs the operations needed at the very start of a scan.
This does the following:

- 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
```

--------------------------------

### Busy Record for Start Scan

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan.template.md

Manages the 'Start Scan' process, with states for 'Done' and 'Acquire'.

```EPICS
record(busy,"$(P)$(R)StartScan")
{
   field(ZNAM,"Done")
   field(ZSV, "NO_ALARM")
   field(ONAM,"Acquire")
   field(OSV, "MINOR")
   field(VAL, "0")
}
```

--------------------------------

### Navigate to IOC Boot Directory

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Changes the current directory to the IOC boot directory.

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

--------------------------------

### collect_projections()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_pso.md

Collects projections in fly scan mode, including taxiing to start, setting camera trigger mode, moving to end, computing motor speed, and starting PSO capture.

```APIDOC
## collect_projections()

### Description
Collects projections in fly scan mode.

This does the following:

- Call the superclass collect_projections() function
- Taxi to the start position
- Set the trigger mode on the camera
- Move the stage to the end position
- Computes and sets the speed of the rotation motor so that it reaches the next projection
  angle just after the current exposure and readout are complete.
- These will be used by the PSO to calculate the Taxi distance and rotary stage acceleration.
- Starts the file plugin capturing in stream mode.
- Starts the camera acquiring in external trigger mode.
- Starts the PSOfly.
- Wait on the PSO done.
```

--------------------------------

### Create EPICS Base Directory

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Create a directory for EPICS base and navigate into it.

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

--------------------------------

### Navigate to EPICS Directory

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Navigate to the EPICS timestamp directory before building synApps.

```default
$ cd ~/epics-ts
```

--------------------------------

### Build and Compile Tomoscan Module

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Navigate to the synApps support directory and run make release followed by make -sj to build and compile the tomoscan module.

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

--------------------------------

### begin_stream()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_pso.md

Configures streaming settings at the beginning of a scan, such as disabling static dark/flat fields, setting binning, and managing capturing status.

```APIDOC
## begin_stream()

### Description
Adjusts streaming settings at the beginning of the scan. This involves setting dark/flat field modes to None, configuring binning in the ROI1 plugin, resetting capturing statuses, setting up a circular buffer, and adding callbacks for capturing size changes.

### Method
This is a method of the `TomoScanStreamPSO` class.
```

--------------------------------

### Control Outlets via HTTP

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_2bm.md

Demonstrates powering outlets on/off and checking their status using the NetBooter_Control class over an HTTP connection.

```python
NetBooter.power_on(2)                              #Return (True,'') for set Outlet 2 ON success
```

```python
NetBooter.power_off(4)                             #Return (True,'') for set Outlet 4 OFF success
```

```python
Outlet3_Status = NetBooter.check_outlet_status(3)  #Return (True,'') for Outlet 3 is ON | (False,'') for OFF
```

--------------------------------

### update_status

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan.md

Updates scan status including images collected, images saved, elapsed time, and remaining time. It requires a start time to calculate the elapsed duration.

```APIDOC
## update_status(start_time)

### Description
When called updates `ImagesCollected`, `ImagesSaved`, `ElapsedTime`, and `RemainingTime`.

### Method
Not specified (assumed to be a method call within a library/SDK)

### Parameters
#### Path Parameters
None

#### Query Parameters
None

#### Request Body
None

### Parameters
* **start_time** (time) - Required - Start time to calculate elapsed time.

### Response
#### Success Response
* **elapsed_time** (float) - Elapsed time to be used for time out.

### Request Example
```
update_status(start_time='2023-10-27T10:00:00Z')
```

### Response Example
```json
{
  "elapsed_time": 120.5
}
```
```

--------------------------------

### TomoScan2BMSTEP.begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Initiates a new scan sequence with the TomoScan2BMSTEP device. This prepares the system for data acquisition.

```APIDOC
## TomoScan2BMSTEP.begin_scan()

### Description
Initiates a new scan sequence.

### Method
Not specified (likely a method call within a Python class)

### Endpoint
Not applicable (Python method)

### Parameters
Parameters are not detailed in the source.

### Request Example
Not specified.

### Response
Response details are not specified.
```

--------------------------------

### Initialize NetBooter_Control via HTTP

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_2bm.md

Instantiate the NetBooter_Control class for HTTP communication. Provide the IP address of the NetBooter device.

```python
NetBooter = NetBooter_Control(mode='http',ip='192.168.1.101')
```

--------------------------------

### TomoScan Default Substitution Configuration

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan.substitutions.md

Defines the default mapping of parameters for tomoScan, including camera, file plugin, rotation, and shutter settings. This is used for standard scanning setups.

```default
file "$(TOP)/db/tomoScan.template"
{
pattern
{  P,        R,    CAMERA,    FILE_PLUGIN,   ROTATION,   SAMPLE_X,    SAMPLE_Y,      CLOSE_SHUTTER,        CLOSE_VALUE,        OPEN_SHUTTER,         OPEN_VALUE}
{13BMDPG1:,  TS:, 13BMDPG1:, 13BMDPG1:HDF1:, 13BMD:m119, 13BMD:m114, 13BMD:m115, 13BMA:CloseBMDShutter.PROC,    1,        13BMA:OpenBMDShutter.PROC,      1}
}
```

--------------------------------

### Copy IOC Configuration for New Beamline

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Copies the default IOC configuration to a new directory for a specific beamline (e.g., iocTomoScan_2BM).

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

--------------------------------

### TomoScan 13BM Substitution Configuration

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan.substitutions.md

Defines the beam ready and ready value parameters for the 13BM beamline's tomoScan setup. This configuration is specific to the 13BM beamline's operational requirements.

```default
file "$(TOP)/db/tomoScan_13BM.template"
{
pattern
{  P,      R,      BEAM_READY,         READY_VALUE,}
{13BMDPG1:, TS:,  13BMA:mono_pid1Locked,     1,}
}
```

--------------------------------

### Navigate to SynApps Support Directory

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Change directory to the synApps support directory after the build process.

```default
$ cd synApps/support/
```

--------------------------------

### TomoScan 13BM PSO Substitution Configuration

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan.substitutions.md

A minimal substitution configuration for the 13BM beamline's PSO setup, defining only the primary and record parameters. This is a streamlined version for specific 13BM configurations.

```default
file "$(TOP)/db/tomoScan_13BM_PSO.template"
{
pattern
{  P,        R}
{13BMDPG1:, TS:}
}
```

--------------------------------

### Initialize NetBooter_Control via Serial

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_2bm.md

Instantiate the NetBooter_Control class for serial communication. Specify the serial port to use.

```python
NetBooter = NetBooter_Control(mode='serial',serial_port='COM1')
```

--------------------------------

### Control Outlets via Serial

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_2bm.md

Demonstrates powering outlets on/off and checking their status using the NetBooter_Control class over a serial connection. Note that rebooting an outlet has no return value.

```python
NetBooter.power_on(1)                              #Return (True,'') for set Outlet 1 ON success
```

```python
NetBooter.power_off(5)                             #Return (True,'') for set Outlet 5 OFF success
```

```python
NetBooter.reboot(3)                                #No return, use NetBooter internal reboot function, don’t suggest to use it
```

```python
Outlet3_Status = NetBooter.check_outlet_status(3)  #Return (True,'') for Outlet 3 is ON | (False,'') for OFF
```

--------------------------------

### TomoScan PSO Substitution Configuration

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan.substitutions.md

Configures parameters related to the PSO (Position Sensitive Output) model for tomoScan, including model, port, axis name, and encoder input. This is specifically for setups requiring PSO integration.

```default
file "$(TOP)/db/tomoScan_PSO.template"
{
pattern
{  P,       R,   PSO_MODEL, PSO_PORT, PSO_AXIS_NAME, PSO_ENC_INPUT, PSO_ENC_PER_ROTATION}
{13BMDPG1:, TS:,    1,      PSO_PORT,      THETA,         2,             0}
}
```

--------------------------------

### Configure Minimal SynApps Build

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Edit the assemble_synApps.sh script to include only ASYN, AUTOSAVE, and BUSY modules for a minimal synApps build.

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

--------------------------------

### Rotation Axis Configuration

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan.template.md

Configure the rotation axis parameters including start angle, step, number of angles, and stop angle calculation. Uses analog output (ao), calculation (calc), long output (longout), and multi-button output (mbbo) records.

```default
record(ao, "$(P)$(R)RotationStart")
{
   field(PREC,  "3")
}
```

```default
record(ao, "$(P)$(R)RotationStep")
{
   field(PREC,  "3")
}
```

```default
record(calc, "$(P)$(R)RotationStop")
{
   field(INPA, "$(P)$(R)RotationStart CP")
   field(INPB, "$(P)$(R)RotationStep CP")
   field(INPC, "$(P)$(R)NumAngles CP")
   field(CALC, "A+B*(C-1)")
   field(PREC,  "3")
}
```

```default
record(longout, "$(P)$(R)NumAngles")
{
}
```

```default
record(mbbo, "$(P)$(R)ReturnRotation")
{
   field(ZRVL, "0")
   field(ZRST, "No")
   field(ONVL, "1")
   field(ONST, "Yes")
   field(TWVL, "2")
   field(TWST, "Home")
}
```

--------------------------------

### Dark Field Control PVs

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan.template.md

Configure parameters for dark field acquisition, including the number of dark fields, mode of acquisition (start, end, both, none), and the value to set for dark fields. Uses long output (longout), multi-button output (mbbo), and analog output (ao) records.

```default
record(longout, "$(P)$(R)NumDarkFields")
{
}
```

```default
record(mbbo, "$(P)$(R)DarkFieldMode")
{
   field(ZRVL, "0")
   field(ZRST, "Start")
   field(ONVL, "1")
   field(ONST, "End")
   field(TWVL, "2")
   field(TWST, "Both")
   field(THVL, "3")
   field(THST, "None")
}
```

```default
record(ao, "$(P)$(R)DarkFieldValue")
{
   field(PREC,  "0")
}
```

--------------------------------

### Verify SynApps Support RELEASE Settings

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Verify that the EPICS_BASE and SUPPORT directories in synApps/support/tomoscan/configure/RELEASE are set correctly and that the versions for BUSY, AUTOSAVE, and ASYN are specified.

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

--------------------------------

### TomoScan2BM Class Initialization

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_2bm.md

Initializes the TomoScan2BM class with PV files and macro definitions.

```APIDOC
## class tomoscan.tomoscan_2bm.TomoScan2BM(pv_files, macros)

### Description
Derived class used for tomography scanning 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
```

--------------------------------

### TomoScan2BM.begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Initiates a new scan sequence with the TomoScan2BM device. This prepares the system for data acquisition.

```APIDOC
## TomoScan2BM.begin_scan()

### Description
Initiates a new scan sequence.

### Method
Not specified (likely a method call within a Python class)

### Endpoint
Not applicable (Python method)

### Parameters
Parameters are not detailed in the source.

### Request Example
Not specified.

### Response
Response details are not specified.
```

--------------------------------

### Sample Information PVs

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan_13BM.template.md

Configures PVs to store sample metadata, including name and up to three description fields.

```EPICS
record(stringout, "$(P)$(R)SampleName")
{
   field(VAL,  "Unknown")
}

record(stringout, "$(P)$(R)SampleDescription1")
{
   field(VAL,  "Unknown")
}

record(stringout, "$(P)$(R)SampleDescription2")
{
   field(VAL,  "Unknown")
}

record(stringout, "$(P)$(R)SampleDescription3")
{
   field(VAL,  "Unknown")
}
```

--------------------------------

### NetBooter_Control.login()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Logs into the NetBooter_Control system. This is typically required before performing other control operations.

```APIDOC
## NetBooter_Control.login()

### Description
Logs into the NetBooter_Control system.

### Method
Not specified (likely a method call within a Python class)

### Endpoint
Not applicable (Python method)

### Parameters
Parameters are not detailed in the source.

### Request Example
Not specified.

### Response
Response details are not specified.
```

--------------------------------

### TomoScan2BMSTEP.wait_frontend_shutter_open()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Waits until the front-end shutter of the TomoScan2BMSTEP is confirmed to be open. This is useful for synchronizing operations.

```APIDOC
## TomoScan2BMSTEP.wait_frontend_shutter_open()

### Description
Waits until the front-end shutter is confirmed to be open.

### Method
Not specified (likely a method call within a Python class)

### Endpoint
Not applicable (Python method)

### Parameters
Parameters are not detailed in the source.

### Request Example
Not specified.

### Response
Response details are not specified.
```

--------------------------------

### Clone and Build EPICS Base

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Download the EPICS base latest release, initialize and update submodules, clean the build, and compile EPICS base.

```default
$ 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
```

--------------------------------

### Configure Tomoscan RELEASE File

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Add the TOMOSCAN path to the configure/RELEASE file and verify EPICS_BASE and SUPPORT paths, ensuring ASYN, AUTOSAVE, and BUSY versions are correctly set.

```default
TOMOSCAN=$(SUPPORT)/tomoscan
```

--------------------------------

### NetBooter_Control.power_on()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Powers on a connected device or outlet managed by NetBooter_Control.

```APIDOC
## NetBooter_Control.power_on()

### Description
Powers on a connected device or outlet.

### Method
Not specified (likely a method call within a Python class)

### Endpoint
Not applicable (Python method)

### Parameters
Parameters are not detailed in the source.

### Request Example
Not specified.

### Response
Response details are not specified.
```

--------------------------------

### File Path and Name Configuration

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan.template.md

Configure PVs for file path, file name, and full file name using waveform records. Includes boolean input (bi) records to check file path existence and overwrite warnings.

```default
record(waveform, "$(P)$(R)FilePath")
{
   field(FTVL, "UCHAR")
   field(NELM, "256")
}
```

```default
record(waveform, "$(P)$(R)FileName")
{
   field(FTVL, "UCHAR")
   field(NELM, "256")
}
```

```default
record(bi, "$(P)$(R)FilePathExists")
{
    field(ZNAM, "No")
    field(ZSV,  "MAJOR")
    field(ONAM, "Yes")
    field(OSV,  "NO_ALARM")
}
```

```default
record(bi, "$(P)$(R)OverwriteWarning")
{
    field(ZNAM, "No")
    field(ZSV,  "MAJOR")
    field(ONAM, "Yes")
    field(OSV,  "NO_ALARM")
}
```

```default
record(waveform, "$(P)$(R)FullFileName")
{
   field(FTVL, "UCHAR")
   field(NELM, "256")
}
```

--------------------------------

### TomoScanStreamPSO Constructor

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_pso.md

Initializes the TomoScanStreamPSO class, setting up the scanning parameters with EPICS PVs and macros.

```APIDOC
## class tomoscan.tomoscan_stream_pso.TomoScanStreamPSO(pv_files, macros)

### Description
Initializes the TomoScanStreamPSO class, which is derived from TomoScan and used for tomography scanning with EPICS using Aerotech controllers and PSO trigger outputs in streaming mode.

### 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
```

--------------------------------

### wait_frontend_shutter_open(timeout=-1)

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_2bm.md

Waits for the front end shutter to open, with an optional timeout, and handles potential abort signals or timeouts.

```APIDOC
## wait_frontend_shutter_open(timeout=-1)

### Description
Waits for the front end shutter to open, or for `abort_scan()` to be called.
While waiting this method periodically tries to open the shutter..

### Parameters
**timeout** (*float*) – The maximum number of seconds to wait before raising a ShutterTimeoutError exception.
* **Raises:**
  * [**ScanAbortError**](tomoscan.md#tomoscan.tomoscan.ScanAbortError) – If `abort_scan()` is called
  * **ShutterTimeoutError** – If the open shutter has not completed within timeout value.
```

--------------------------------

### Create TomoScan Object

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/usage.md

Initializes the TomoScan13BM_PSO object with database request files and macro substitution values. These arguments configure the scan settings and PV prefixes.

```python
ts = TomoScan13BM_PSO(["../../db/tomoScan_settings.req",
                       "../../db/tomoScan_PSO_settings.req",
                       "../../db/tomoScan_13BM_settings.req"],
                      {"$(P)":"13BMDPG1:", "$(R)":"TS:"})
```

--------------------------------

### Import TomoScan Class

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/usage.md

Imports the TomoScan13BM_PSO class from the tomoscan_13bm_pso library. This class is used for setting up and running tomography scans.

```python
>>> from tomoscan_13bm_pso import TomoScan13BM_PSO
```

--------------------------------

### open_frontend_shutter()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_32id.md

Opens the shutters to collect flat fields or projections, specifically opening the 2-BM-A front-end shutter, with a check for testing mode.

```APIDOC
## open_frontend_shutter()

### Description
Opens the shutters to collect flat fields or projections.

This does the following:

- Checks if we are in testing mode. If we are, do nothing else opens the 2-BM-A front-end shutter.
```

--------------------------------

### Create and Activate Conda Environment

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/install.md

Steps to create a dedicated conda environment for Tomoscan with Python 3.9 and activate it.

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

--------------------------------

### wait_frontend_shutter_open(timeout=-1)

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_32id.md

Waits for the front end shutter to open or for abort_scan() to be called, with an optional timeout.

```APIDOC
## wait_frontend_shutter_open(timeout=-1)

### Description
Waits for the front end shutter to open, or for `abort_scan()` to be called.

While waiting this method periodically tries to open the shutter..

### Parameters
**timeout** (*float*) – The maximum number of seconds to wait before raising a ShutterTimeoutError exception.
* **Raises:**
  * [**ScanAbortError**](tomoscan.md#tomoscan.tomoscan.ScanAbortError) – If `abort_scan()` is called
  * **ShutterTimeoutError** – If the open shutter has not completed within timeout value.
```

--------------------------------

### TomoScan2BMSTEP.open_frontend_shutter()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Opens the front-end shutter for the TomoScan2BMSTEP. This allows light or radiation to pass through before or during a scan.

```APIDOC
## TomoScan2BMSTEP.open_frontend_shutter()

### Description
Opens the front-end shutter.

### Method
Not specified (likely a method call within a Python class)

### Endpoint
Not applicable (Python method)

### Parameters
Parameters are not detailed in the source.

### Request Example
Not specified.

### Response
Response details are not specified.
```

--------------------------------

### reinit_camera(camera=None)

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_2bm.md

Re-initializes camera PVs based on the selected optics.

```APIDOC
## reinit_camera(camera=None)

### Description
Init camera PVs based on the mctOptics selection.

### Parameters
**camera** (*int, optional*) – The camera to use. Optique Peter system support 2 cameras
```

--------------------------------

### TomoScan32IDSTEP.wait_frontend_shutter_open()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Waits for the frontend shutter of the TomoScan32IDSTEP to open. Ensures synchronization before proceeding.

```APIDOC
## TomoScan32IDSTEP.wait_frontend_shutter_open()

### Description
Waits for the frontend shutter of the TomoScan32IDSTEP to open. Ensures synchronization before proceeding.

### Method
Not specified (likely a Python method call)

### Endpoint
Not applicable (Python method)

### Parameters
Not specified in the source text.

### Request Example
Not specified in the source text.

### Response
Not specified in the source text.
```

--------------------------------

### wait_frontend_shutter_open()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_2bm.md

Waits for the front end shutter to open, with a timeout and error handling for ScanAbortError and ShutterTimeoutError.

```APIDOC
## wait_frontend_shutter_open(timeout=-1)

### Description
Waits for the front end shutter to open, or for `abort_scan()` to be called.

While waiting this method periodically tries to open the shutter..

### Parameters
**timeout** (*float*) – The maximum number of seconds to wait before raising a ShutterTimeoutError exception.

### Raises:
* [**ScanAbortError**](tomoscan.md#tomoscan.tomoscan.ScanAbortError) – If `abort_scan()` is called
* **ShutterTimeoutError** – If the open shutter has not completed within timeout value.
```

--------------------------------

### Beam Status PV Configuration

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/tomoScan_6BM.template.md

Sets up PVs to report beam readiness and testing status. Includes string outputs for the beam ready PV name and value, and a boolean output for testing mode.

```EPICS
record(stringout, "$(P)$(R)BeamReadyPVName")
{
   field(VAL,  "$(BEAM_READY)")
}

record(stringout, "$(P)$(R)BeamReadyValue")
{
   field(VAL,  "$(READY_VALUE)")
}

record(bo, "$(P)$(R)Testing")
{
   field(ZNAM, "No")
   field(ONAM, "Yes")
}
```

--------------------------------

### open_shutter

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_7bm.md

Opens the front end and 7-BM-B fast shutters for collecting flat fields or projections.

```APIDOC
## open_shutter()

### Description
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.
```

--------------------------------

### TomoScanPSO Class Initialization

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_pso.md

Initializes the TomoScanPSO class, a derived class for tomography scanning with EPICS using Aerotech controllers and PSO trigger outputs.

```APIDOC
## class tomoscan.tomoscan_pso.TomoScanPSO(pv_files, macros)

### Description
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
```

--------------------------------

### TomoScan2BM.wait_frontend_shutter_open()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Waits until the front-end shutter of the TomoScan2BM is confirmed to be open. This is useful for synchronizing operations.

```APIDOC
## TomoScan2BM.wait_frontend_shutter_open()

### Description
Waits until the front-end shutter is confirmed to be open.

### Method
Not specified (likely a method call within a Python class)

### Endpoint
Not applicable (Python method)

### Parameters
Parameters are not detailed in the source.

### Request Example
Not specified.

### Response
Response details are not specified.
```

--------------------------------

### begin_scan

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_7bm.md

Performs initial scan operations, including setting motor speeds and programming the rotation motor.

```APIDOC
## begin_scan()

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

This is an override of the begin_scan in TomoScanPSO to account for the extra frames due to saving camera gains.
This does the following:

- 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
```

--------------------------------

### TomoScanStream7BM.open_shutter()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Opens the shutter for the TomoScanStream7BM.

```APIDOC
## TomoScanStream7BM.open_shutter()

### Description
Opens the shutter for the TomoScanStream7BM.

### Method
(Not specified in source, assumed to be a method call)

### Endpoint
(Not applicable, this is an SDK method)

### Parameters
(Parameters not specified in source)

### Request Example
(Not specified in source)

### Response
(Response details not specified in source)
```

--------------------------------

### TomoScanStream32ID.begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Initiates a new scan sequence for the TomoScanStream32ID.

```APIDOC
## TomoScanStream32ID.begin_scan()

### Description
Initiates a new scan sequence for the TomoScanStream32ID.

### Method
(Not specified in source, assumed to be a method call)

### Endpoint
(Not applicable, this is an SDK method)

### Parameters
(Parameters not specified in source)

### Request Example
(Not specified in source)

### Response
(Response details not specified in source)
```

--------------------------------

### TomoScan32IDSTEP.begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Initiates the tomography scan process using TomoScan32IDSTEP. This method prepares the system for data acquisition.

```APIDOC
## TomoScan32IDSTEP.begin_scan()

### Description
Initiates the tomography scan process using TomoScan32IDSTEP. This method prepares the system for data acquisition.

### Method
Not specified (likely a Python method call)

### Endpoint
Not applicable (Python method)

### Parameters
Not specified in the source text.

### Request Example
Not specified in the source text.

### Response
Not specified in the source text.
```

--------------------------------

### TomoScan32ID.open_frontend_shutter()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Opens the frontend shutter for the TomoScan32ID.

```APIDOC
## TomoScan32ID.open_frontend_shutter()

### Description
Opens the frontend shutter for the TomoScan32ID.

### Method
(Not specified in source, assumed to be a method call)

### Endpoint
(Not applicable, this is an SDK method)

### Parameters
(Parameters not specified in source)

### Request Example
(Not specified in source)

### Response
(Response details not specified in source)
```

--------------------------------

### show_pvs()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan.md

Prints the current values of all EPICS PVs currently in use by TomoScan.

```APIDOC
## show_pvs()

### Description
Prints the current values of all EPICS PVs in use.

### Method
This is a method within a class, not an HTTP endpoint.

### Output Sections
- `config_pvs`: PVs part of the scan configuration, saved by `save_configuration()`.
- `control_pvs`: PVs for EPICS control and status, not saved by `save_configuration()`.
- `pv_prefixes`: Prefixes for PVs related to the areaDetector camera, file plugin, etc.
```

--------------------------------

### Python Script for Tomography Scan Demo

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/demo.md

This Python function demonstrates collecting tomography datasets while scanning an EPICS PV. It requires the 'epics' library and configures exposure time, file numbering, and auto-increment before initiating scans.

```python
import epics
def scan_demo(tomo_prefix, exposure_time, scan_pv, start, step, points):
    """Demonstrates collecting a series of tomography datasets while scanning an EPICS PV.

       Parameters
       ----------
       tomo_prefix : str
          The EPICS PV prefix for the tomoScan database
       exposure_time : float
          The exposure time per projection for the tomography datasets
       scan_pv : str
          The name of the EPICS PV to scan
       start : float
          The starting value for the scanned PV
       step : float
          The step size for the scanned PV
       points : int
          The number of points in the scan
    """

    epics.caput(tomo_prefix + 'ExposureTime', exposure_time, wait=True)
    file_plugin_prefix = epics.caget(tomo_prefix + 'FilePluginPVPrefix')
    # Set the initial file number back to 1 and make sure AutoIncrement is enables
    epics.caput(file_plugin_prefix + 'FileNumber', 1)
    epics.caput(file_plugin_prefix + 'AutoIncrement', 'Yes')

    for i in range(1, points+1):
        epics.caput(scan_pv, start + step*i, wait=True)
        epics.caput(tomo_prefix + 'StartScan', 1, wait=True, timeout=100)
        print('Completed dataset %s' % epics.caget(file_plugin_prefix + 'FullFileName_RBV', as_string=True))
```

--------------------------------

### TomoScan32ID.begin_scan()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api.md

Initiates a new scan sequence for the TomoScan32ID.

```APIDOC
## TomoScan32ID.begin_scan()

### Description
Initiates a new scan sequence for the TomoScan32ID.

### Method
(Not specified in source, assumed to be a method call)

### Endpoint
(Not applicable, this is an SDK method)

### Parameters
(Parameters not specified in source)

### Request Example
(Not specified in source)

### Response
(Response details not specified in source)
```

--------------------------------

### open_shutter()

Source: https://github.com/tomography/tomoscan/blob/master/docs/source/api/tomoscan_stream_32id.md

Opens the shutters to collect flat fields or projections by opening the 32-ID-C fast shutter.

```APIDOC
## open_shutter()

### Description
Opens the shutters to collect flat fields or projections.

This does the following:

- Opens the 32-ID-C fast shutter.
```