cs_jiffies

A personal respository for short scripts to do things in CryoSPARC

Usage:

Dependencies:

• cryosparc-tools
• jupyter notebook
• python-dotenv

Install:

conda create -n cs_jiffies python=3.11
conda activate cs_jiffies
pip install -r requirements.txt

Create a .env in the repository's directory for the constants

cs_license = 'asdf1348-replace-me-123lkj12'
cs_hostname = 'mycryosparcinstance.mysupercoolinstitution.com'
cs_port = 39000

Instructions:

For Jupyter Notebooks files (files ending in .ipnyb, in a Python environment with cryosparc-tools and Jupyter Notebooks installed, open a new Jupyter notebook instance with jupyter notebook. Load the .ipnyb file in the Jupyter notebook, and follow the prompts from top to bottom.

For Python scripts (files ending in .py), typically make sure you have cryosparc-tools available (if using conda, load the conda environment)

python cs_mdoc_image_shift.py -h
usage: cs_mdoc_image_shift.py [-h] [--email EMAIL] [--project PROJECT] [--workspace WORKSPACE] [--job JOB] [--mdoc_dir MDOC_DIR] [--recursive]

options:
  -h, --help            show this help message and exit
  --email EMAIL, -e EMAIL
                        Email or account used in cryosparc
  --project PROJECT, -p PROJECT
                        Cryosparc project. i.e. P83
  --workspace WORKSPACE, -w WORKSPACE
                        Workspace number, i.e. W1
  --job JOB, -j JOB     Input job number, i.e. J56
  --mdoc_dir MDOC_DIR, -d MDOC_DIR
                        Directory where the exposures mdoc files are located
  --recursive, -r       Whether to look for the mdoc file recursively from the mdoc_dir.

You will need to be on a filesystem that has access to the data at the same path as CryoSPARC.