Lab PC Setup Guide#

This guide provides installation and setup instructions for the PHOTONICS bench laboratory computer.

Camera (C-Red 3)#

Driver for the EDT PCI Board#

The C-Red 3 camera communicates through an EDT PCI board that must be properly configured.

Dependencies#

Install the required libraries:

  • EDT PDV SDK: Available from /opt/EDTpdv/

  • libImageStreamIO: For shared memory image streaming

  • commander: Camera control interface

Starting the C-Red 1 Server#

After a reboot, the PCI board must be reconfigured to recognize the camera type:

cd ~/Progs/repos/dcs/asgard-cred1-server
/opt/EDTpdv/initcam -f cred3_edt_config.cfg

Start the C-Red 1 server:

cd ~/Progs/repos/dcs/asgard-cred1-server
./asgard_cam_server

Camera Control Commands#

Grab Frames#

In the C-Red 1 server prompt:

fetch

View Images with shmview#

In the “photonic” Python environment:

shmview

  • Navigate to File > Open SHM

  • Select cred1.im.shm

  • The camera image should appear

Stop Grabbing#

stop

Get Camera Status#

status

Returns idle if not running, running otherwise.

Get Framerate#

cli "fps"

Returns the frame rate in Hz.

Set Framerate#

cli "set fps XXX"

Replace XXX with the desired frame rate in Hz.

Other Commands#

Check the C-Red 3 documentation for available commands, then use:

cli "your_command"

Troubleshooting Camera Issues#

Camera Information Shows Zeros#

If the server displays frame size, timeout, or FPS as 0, restart the PCI board:

cd ~/Progs/repos/dcs/asgard-cred1-server
/opt/EDTpdv/initcam -f cred3_edt_config.cfg

Segmentation Fault on “fetch” Command#

Restart the PCI board using the same command as above.

Segmentation Fault on Server Start#

Swap the cables behind the camera, then reinitialize:

cd ~/Progs/repos/dcs/asgard-cred1-server
/opt/EDTpdv/initcam -f cred3_edt_config.cfg
./asgard_cam_server

USB Device Assignment#

To ensure USB devices are assigned to consistent ttyUSB ports for phobos:

Create the udev rules file:

sudo nano /etc/udev/rules.d/99-usbserial.rules

Add the following rules:

ACTION=="add",ENV{ID_BUS}=="usb",ENV{ID_SERIAL_SHORT}=="AC01ZP6W",SYMLINK+="ttyUSBzaber"
ACTION=="add",ENV{ID_BUS}=="usb",ENV{ID_SERIAL_SHORT}=="TP02052235-13923",SYMLINK+="ttyUSBthorlabs"
ACTION=="add",ENV{ID_BUS}=="usb",ENV{ID_SERIAL_SHORT}=="37001886",SYMLINK+="ttyUSBFlipMount"
ACTION=="add",ENV{ID_BUS}=="usb",ENV{ID_SERIAL_SHORT}=="A64MV77S",SYMLINK+="ttyUSBnewport"
ACTION=="add",ENV{ID_BUS}=="usb",ENV{ID_SERIAL_SHORT}=="c6db877177fded11906c6919f9a91825",SYMLINK+="ttyUSBNkt"

Apply the rules:

sudo udevadm control --reload-rules

Or reboot the computer.

Device mappings:

  • ttyUSBzaber: Zaber linear stages

  • ttyUSBthorlabs: Thorlabs filter wheel

  • ttyUSBFlipMount: Thorlabs MFF101 flip mount

  • ttyUSBnewport: Newport mask wheel

  • ttyUSBNkt: NKT photonics supercontinuum source

phobos reads these device IDs from the config.yml file.

Flip Mount Troubleshooting (MFF101)#

If FlipMount() fails with a timeout-like traceback similar to:

ThorlabsBackendError: read returned less than expected: 0 instead of 1

try a full power cycle of the flip mount power supply (turn it off, wait a few seconds, then turn it back on).

This has been observed to recover communication immediately in cases where USB enumeration succeeds but the device does not respond to APT commands.

Deformable Mirror (BMC)#

Software Download#

The BMC SDK can be downloaded directly from the Boston Micromachines website:

https://bostonmicromachines.com/DMSDK/BMC-DMSDK.zip

Note

The SDK requirements tie us to a specific version of Ubuntu Linux.

After successful installation, files will be added to the /opt/Boston Micromachines/ directory.

Verify installation by checking that the Linux kernel module is loaded:

lsmod | grep bmc

Expected output:

bmc_mdrv         16384  0

Configuration Files#

Each BMC DM is identified by an 11-digit serial number.

PHOTONICS bench DM serial number: 27BW007#051

Two configuration files must be copied to the appropriate locations:

sudo cp 27BW007#051.dm /opt/Boston\ Micromachines/Profiles/
sudo cp LUT_27BW007#051.mat /opt/Boston\ Micromachines/Calibration/

Note

The .dm profile file is mandatory. The .mat calibration file may only be used by MATLAB-based tools.

These files are located in the config/calibration/ directory of this repository.

Testing the Installation#

BMC provides command-line test tools in /opt/Boston Micromachines/bin/.

Test DM communication:

/opt/Boston\ Micromachines/bin/BmcExampleC -s 27BW007#051

This runs through a sequence of actuator activations to verify proper operation.

Python Environment Setup#

Lab PC (Linux)#

Install all dependencies including hardware-specific libraries:

# Install base package with lab dependencies
pip install -r requirements-lab.txt
pip install -e .

This installs:

  • Core dependencies (numpy, scipy, etc.)

  • xaosim (for camera shared memory interface)

  • Development tools (pytest, jupyter, etc.)

Development/Sandbox Mode (Windows/Linux without hardware)#

For development without hardware access:

pip install -e .

This installs only the base dependencies. The package will automatically run in sandbox mode with mock hardware interfaces.

Verifying Installation#

Test the installation in Python:

import phobos

# Check mode
print(f"Sandbox mode: {phobos.SANDBOX_MODE}")

# Try initializing hardware (uses mocks if in sandbox mode)
dm = phobos.DM()
fw = phobos.FilterWheel()
chip = phobos.Chip(6)
camera = phobos.Cred3()

If BMC SDK is not installed, you’ll see:

❌ BMC lib not found. Install it via the BMC SDK.
⛱️ Running in sandbox mode.

Additional Resources#