CreoptixFitting

Original documentation in gciscripts/README.md

Usage at DLS

Submitting jobs

From a DLS linux machine terminal (or NoMachine/ssh):

1. Connect to the SLURM cluster "wilson"

ssh wilson

2. Load the python environment:

source /dls/science/groups/i04-1/software/max/load_py310.sh

3. Navigate/create a working directory

e.g.

mkdir creoptix_test
cd creoptix_test
pwd

4. Place your input files inside:

• trace file, a text file exported from Creoptix containing response time-series for all channels
• schema file, a text file containing the copied and pasted table describing the channels from Creoptix

To use the example data:

cp -v $CREOPTIX/example/input/sample_*_3.txt .

5. Copy and edit your config file:

cp -v $CREOPTIX/config.json .
nano config.json

6. See the CLI help:

python -m gcifit.fit --help

7. Submit the fitting

python -m gcifit.fit sample_traces_3.txt sample_schema_3.txt config.json example_output

8. Track running jobs:

rq

Viewing outputs in a notebook

From a DLS linux machine terminal (or NoMachine):

1. Load the python environment:

source /dls/science/groups/i04-1/software/max/load_py310.sh

2. Change to a working directory:

e.g.

cd creoptix_test

3. Copy over the example notebook file

cp $CREOPTIX/show_outputs.ipynb .

4. Launch a jupyter notebook

jupyter lab

5. Open the address shown in the terminal in a browser (if it doesn't open automatically)

6. Try out the example notebook: show_outputs.ipynb