Offline Calibration

The offline calibration is a package that consists of different services, responsible for applying most of the offline calibration and characterization for the detectors.

Offline Calibration Installation

It's recommended to install the offline calibration (pycalibration) package on maxwell, using the suggested python virtual environment.

The following instructions clone from the EuXFEL GitLab instance using SSH remote URLs, this assumes that you have set up SSH keys for use with GitLab already. If you have not then read the appendix section on SSH Key Setup for GitLab for instructions on how to do this .

Installation using python virtual environment - recommended

pycalibration uses Python 3.11. Currently the default python installation on Maxwell is still Python 3.9, so Python 3.11 needs to be loaded from a different location.

We use pyenv to manage different Python versions. A pyenv installation is provided at /gpfs/exfel/sw/calsoft/.pyenv.

To install pycalibration, follow these steps:

# Activate pyenv
source /gpfs/exfel/sw/calsoft/.pyenv/bin/activate

# Clone the repository
git clone ssh://git@git.xfel.eu:10022/detectors/pycalibration.git
cd pycalibration

# Set up Python environment
pyenv shell 3.11.9
python3 -m venv .venv
source .venv/bin/activate

# Install pycalibration
python3 -m pip install --upgrade pip
# Use 'pip install -e .' for editable install
python3 -m pip install .

Installation into user home directory

Warning: This method is not recommended as pycalibration has pinned dependencies for stability. Installing directly into your user's home environment may downgrade/upgrade your local packages, potentially causing major issues and breaking your local environment. It is highly recommended to use the venv installation method instead.

If you still wish to proceed with a user home directory installation, follow these steps:

# Activate pyenv
source /gpfs/exfel/sw/calsoft/.pyenv/bin/activate

# Clone the repository
git clone ssh://git@git.xfel.eu:10022/detectors/pycalibration.git
cd pycalibration

# Set up Python environment
pyenv shell 3.11.9

# Install pycalibration
# Use 'pip install --user -e .' for editable install
pip install --user .

# Update PATH
export PATH=$HOME/.local/bin:$PATH

Working with Jupyter Notebooks

If you plan to work with Jupyter notebooks interactively, you have two main options:

Option 1: Install Jupyter Notebook locally

if you prefer to run Jupyter notebooks on your local machine or on Maxwell, you can install the notebook package in your virtual environment:

python3 -m pip install notebook==6.2.0

After installation, you can start a Jupyter notebook server by running:

jupyter notebook

Option 2: Use max-jhub (Recommended)

Alternatively, we recommend using max-jhub, a JupyterHub instance available at DESY. This option provides a convenient web-based environment for running Jupyter notebooks without needing to set up everything locally.

For detailed instructions on how to use max-jhub, please refer to these documentations:

• Max-jhub DESY Documentation
• Max-jhub EuXFEL User Documentation

To use max-jhub effectively with pycalibration, make sure you've created an ipython kernel as described in the Creating an ipython kernel for virtual environments section below.

Creating an ipython kernel for virtual environments

To create an ipython kernel with pycalibration available you should (if using a venv) activate the virtual environment first, and then run:

# If not using a venv add `--user` flag
python3 -m pip install ipykernel
# If not using a venv pick different name
python3 -m ipykernel install --user --name pycalibration --display-name "pycalibration"

Offline Calibration Configuration

The offline calibration package is configured with three configuration files:

• webservice/config/webservice.yaml - configuration for the web service
• webservice/config/serve_overview.yaml - configuration for the overview page
• src/cal_tools/restful_config.yaml - configuration for RESTful access to myMDC and CalCat by cal tools

These configuration files should not be modified directly, instead you should create a file $CONFIG.secrets.yaml (e.g. webservice.secrets.yaml) in the configuration directory, and then add any modifications, such as secrets, to this file.

Alternatively, configurations are also searched for in ~/.config/pycalibration/$MODULE/$CONFIG.yaml (e.g. ~/.config/pycalibration/webservice/serve_overview.yaml), which is a useful place to store configurations like secrets so that they are present even if you delete the pycalibration directory, or if you have multiple pycalibration repos checked out, as you no longer need to copy/paste the configurations each time.

Finally, you can use environment variables to override the configuration without modifying any files, which is useful for one-off changes or if you are running tests in a CI environment. The environment variables should be prefixed with:

• webservice/config/webservice.yaml - CAL_WEBSERVICE
• webservice/config/serve_overview.yaml - CAL_SERVE_OVERVIEW
• src/cal_tools/restful_config.yaml - CAL_CAL_TOOLS

Followed by an underscore and the configuration key you wish to change. Nested keys can be accessed with two underscores, e.g. CAL_WEBSERVICE_CONFIG_REPO__URL would modify the config-repo: url: value.

Note that the order of priority is:

• default configuration - e.g. webservice/config/webservice.yaml
• local configuration - e.g. webservice/config/webservice.secrets.yaml
• user configuration - e.g. ~/.config/pycalibration/webservice/webservice.yaml
• environment variables - e.g. export CAL_WEBSERVICE_*=...

Examples

For example, webservice/config/webservice.yaml has:

config-repo:
    url:  "@note add this to secrets file"
    local-path: "@format {env[HOME]}/calibration_config"
...
metadata-client:
    user-id: "@note add this to secrets file"
    user-secret: "@note add this to secrets file"
    user-email: "@note add this to secrets file"

So you would create a file webservice/config/webservice.secrets.yaml:

config-repo:
    url: "https://USERNAME:TOKEN@git.xfel.eu/gitlab/detectors/calibration_configurations.git"

metadata-client:
    user-id: "id..."
    user-secret: "secret..."
    user-email: "calibration@example.com"

Alternatively, this file could be placed at ~/.config/pycalibration/webservice/webservice.yaml

Checking Configurations

Having multiple nested configurations can get a bit confusing, so dynaconf includes a command to help view what a configuration will be resolved to. Once you have activated the python environment pycalibration is installed in, you can run the command dynaconf -i webservice.config.webservice list to list the current configuration values:

> dynaconf -i webservice.config.webservice list
Working in main environment
WEBSERVICE_DIR<PosixPath> PosixPath('/home/roscar/work/git.xfel.eu/detectors/pycalibration/webservice')
CONFIG-REPO<dict> {
  'local-path': '/home/roscar/calibration_config',
  'url': 'https://haufs:AAABBBCCCDDDEEEFFF@git.xfel.eu/gitlab/detectors/calibration_configurations.git'
}
WEB-SERVICE<dict> {
  'allowed-ips': '131.169.4.197, 131.169.212.226',
  'bind-to': 'tcp://*',
  'job-db': '/home/roscar/work/git.xfel.eu/detectors/pycalibration/webservice/webservice_jobs.sqlite',
  'job-timeout': 3600,
  'job-update-interval': 60,
  'port': 5556
}
METADATA-CLIENT<dict> {
  'auth-url': 'https://in.xfel.eu/test_metadata/oauth/authorize',
  'base-api-url': 'https://in.xfel.eu/metadata/api/',
  'metadata-web-app-url': 'https://in.xfel.eu/test_metadata',
  'refresh-url': 'https://in.xfel.eu/test_metadata/oauth/token',
  'scope': '',
  'token-url': 'https://in.xfel.eu/test_metadata/oauth/token',
  'user-email': 'calibration@example.com',
  'user-id': 'AAABBBCCCDDDEEEFFF',
  'user-secret': 'AAABBBCCCDDDEEEFFF'\
}
KAFKA<dict> {
  'brokers': [
    'it-kafka-broker01.desy.de',
    'it-kafka-broker02.desy.de',
    'it-kafka-broker03.desy.de'
  ],
  'topic': 'xfel-test-offline-cal'
}
CORRECT<dict> {
  'cmd': 'python -m xfel_calibrate.calibrate {detector} CORRECT '
         '--slurm-scheduling {sched_prio} --slurm-mem 750 --request-time '
         '{request_time} --slurm-name '
         '{action}_{instrument}_{detector}_{cycle}_p{proposal}_{runs} '
        '--report-to /gpfs/exfel/exp/{instrument}/{cycle}/p{proposal}/usr/Reports/{runs}/{det_instance}_{action}_{proposal}_{runs}_{time_stamp} '
        '--cal-db-timeout 300000 --cal-db-interface '
        'tcp://max-exfl-cal001:8015#8044',
  'in-folder': '/gpfs/exfel/exp/{instrument}/{cycle}/p{proposal}/raw','out-folder': '/gpfs/exfel/d/proc/{instrument}/{cycle}/p{proposal}/{run}',
 'sched-prio': 80
}
DARK<dict> {
  'cmd': 'python -m xfel_calibrate.calibrate {detector} DARK --concurrency-par '
         'karabo_da --slurm-scheduling {sched_prio} --request-time '
         '{request_time} --slurm-name '
         '{action}_{instrument}_{detector}_{cycle}_p{proposal}_{runs} '
         '--report-to /gpfs/exfel/d/cal/caldb_store/xfel/reports/{instrument}/{det_instance}/{action}/{action}_{proposal}_{runs}_{time_stamp} '
         '--cal-db-interface tcp://max-exfl-cal001:8015#8044 --db-output',
  'in-folder': '/gpfs/exfel/exp/{instrument}/{cycle}/p{proposal}/raw',
  'out-folder': '/gpfs/exfel/u/usr/{instrument}/{cycle}/p{proposal}/dark/runs_{runs}',
  'sched-prio': 10
}

And here you can see that metadata-client: user-id: contains the ID now instead of the note "add this to secrets file", so the substitution has worked correctly.

Contributing

Guidelines

Development guidelines can be found on the GitLab Wiki page here: https://git.xfel.eu/gitlab/detectors/pycalibration/wikis/GitLab-Guidelines

Basics

If you are installing the package for development purposes then you should install the optional dependencies as well. Follow the instructions as above, but instead of pip install . use pip install ".[test,dev]" to install both the extras.

The installation instructions above assume that you have set up SSH keys for use with GitLab to allow for passwordless clones from GitLab, this way it's possible to run pip install git+ssh... commands and install packages directly from GitLab.

To do this check the settings page here: https://git.xfel.eu/gitlab/profile/keys

Pre-Commit Hooks

This repository uses pre-commit hooks automatically run some code quality and standard checks, this includes the following:

a. identity - The 'identity' meta hook prints off a list of files that the hooks will execute on b. 'Standard' file checks

1. check-added-large-files - Ensures no large files are committed to repo
2. check-ast - Checks that the python AST is parseable
3. check-json - Checks json file formatting is parseable
4. check-yaml - Checks yaml file formatting is parseable
5. check-toml - Checks toml file formatting is parseable
6. rstcheck - Checks rst file formatting is parseable
7. end-of-file-fixer - Fixes EoF to be consistent
8. trailing-whitespace - Removes trailing whitespaces from lines
9. check-merge-conflict - Checks no merge conflicts remain in the commit
10. mixed-line-ending - Fixes mixed line endings

c. Code checks

1. flake8 - Code style checks
2. isort - Sorts imports in python files
3. check-docstring-first - Ensures docstrings are in the correct place

d. Notebook checks

1. nbqa-flake8 - Runs flake8 on notebook cells
2. nbqa-isort - Runs isort on notebook cells
3. nbstripoutput - Strips output from ipynb files

To install these checks, set up you environment as mentioned above and then run the command:

pre-commit install-hooks

This will set up the hooks in git locally, so that each time you run the command git commit the hooks get executed on the staged files only, beware that if the pre-commit hooks find required changes some of them will modify your files, however they only modify the current working files, not the ones you have already staged. This means that you can look at the diff between your staged files and the ones that were modified to see what changes are suggested.

Run Checks Only On Diffs

Typically pre-commit is ran on --all-files within a CI, however as this is being set up on an existing codebase these checks will always fail with a substantial number of issues. Using some creative workarounds, the CI has been set up to only run on files which have changed between a PR and the target branch.

If you want to run the pre-commit checks as they would run on the CI, then you can use the bin/pre-commit-diff.sh to execute the checks as on the CI pipeline.

A side effect of this is that the checks will run on all of the differences between the 'local' and target branch. This means that if changes have recently been merged into the target branch, and there is divergence between the two, then the tests will run on all the differences.

If this happens and the hooks in the CI (or via the script) run on the wrong files then you should rebase onto the target branch to prevent the checks from running on the wrong files/diffs.

Skipping Checks

If the checks are failing and you want to ignore them on purpose then you have two options:

• use the --no-verify flag on your git commit command to skip them, e.g. git commit -m "Commit skipping hooks" --no-verify
• use the variable SKIP=hooks,to,skip before the git commit command to list hooks to skip, e.g. SKIP=flake8,isort git commit -m "Commit skipping only flake8 and isort hooks"

In the CI pipeline the pre-commit check stage has allow_failure: true set so that it is possible to ignore errors in the checks, and so that subsequent stages will still run even if the checks have failed. However there should be a good reason for allowing the checks to fail, e.g. checks failing due to unmodified sections of code being looked at.

Python Scripted Calibration

To launch correction or characterisation jobs, run something like this

xfel-calibrate AGIPD CORRECT \
--in-folder /gpfs/exfel/exp/SPB/202131/p900215/raw --run 591 \
--out-folder /gpfs/exfel/data/scratch/kluyvert/agipd-calib-900215-591 \
--karabo-id SPB_DET_AGIPD1M-1 --karabo-id-control SPB_IRU_AGIPD1M1 \
--karabo-da-control AGIPD1MCTRL00 --modules 0-4

The first two arguments refer to a detector and an action, and are used to find the appropriate notebook to run. Most of the optional arguments are translated into parameter assignments in the notebook, e.g. --modules 0-4 sets modules = [0, 1, 2, 3] in the notebook.

This normally submits jobs to Slurm to do the work; you can check their status with squeue --me. If you are working on a dedicated node, you can use the --no-cluster-job option to run all the work on that node instead.

The notebooks will be used to create a PDF report after the jobs have run. This will be placed in --out-folder by default, though it can be overridden with the --report-to option.

Reproducing calibration

The information to run the calibration code again is saved to a directory next to the PDF report, named starting with slurm_out_. It can be run as a new job like this

python3 -m xfel_calibrate.repeat /gpfs/exfel/data/scratch/kluyvert/ agipd-calib-900215-591/slurm_out_AGIPDOfflineCorrection \
--out-folder /gpfs/exfel/data/scratch/kluyvert/agipd-calib-900215-591-repro

The information in the directory includes a Pip requirements.txt file listing the packages installed when this task was first set up. For better reproducibility, use this to create a similar environment, and pass --python path/to/bin/python to run notebooks in that environment. Future work will automate this step.

Note Our aim here is to run the same code as before, with the same parameters, in a similar software environment. This should produce essentially the same results, but not necessarily exactly identical. The code which runs may use external resources, or involve some randomness, and even different hardware may make small differences.

Appendix

Important information that doesn't really fit in as part of the readme.

SSH Key Setup for GitLab

It is highly recommended to set up SSH keys for access to GitLab as this simplifies the setup process for all of our internal software present on GitLab.

To set up the keys:

1. Connect to Maxwell
2. Generate a new keypair with ssh-keygen -o -a 100 -t ed25519, you can either leave this in the default location (~/.ssh/id_ed25519) or place it into a separate directory to make management of keys easier if you already have multiple ones. If you are using a password for your keys please check this page to learn how to manage them: https://docs.github.com/en/github/authenticating-to-github/generating-a-new-ssh-key-and-adding-it-to-the-ssh-agent#adding-your-ssh-key-to-the-ssh-agent
3. Add the public key (id_ed25519.pub) to your account on GitLab: https://git.xfel.eu/gitlab/profile/keys
4. Add the following to your ~/.ssh/config file

# Special flags for gitlab over SSH
Host git.xfel.eu
    User git
    Port 10022
    ForwardX11 no
    IdentityFile ~/.ssh/id_ed25519

Once this is done you can clone repositories you have access to from GitLab without having to enter your password each time. As pycalibration requirements are installed from SSH remote URLs having SSH keys set up is a requirement for installing pycalibration.

GitLab Access for xcaltst and xcal

To make it easier to work with and deploy software via xcaltst/xcal, we have created an xcal account for gitlab with the following details:

• Full Name: ReadOnly Gitlab Calibration External
• User ID: 423
• Username: xcalgitlab
• Password: ask Robert Rosca

This account is intended to be used as a read only account which can be given access to certain repos to make it easier to clone them when using our functional accounts on Maxwell.

The xcaltst account has an ed25519 keypair under ~/.ssh/gitlab/, the public key has been added to the xcalgitlab's approved SSH keys.

Additionally this block has been added to ~/.ssh/config:

# Special flags for gitlab over SSH
Host git.xfel.eu
    User git
    Port 10022
    ForwardX11 no
    IdentityFile ~/.ssh/gitlab/id_ed25519

Now any repository that xcalgitlab has read access to, e.g. if it is added as a reporter, can be cloned on Maxwell without having to enter a password.

For example, xcalgitlab is a reporter on the pycalibration https://git.xfel.eu/gitlab/detectors/pycalibration repository, so now xcalgitlab can do passwordless clones with SSH:

[xcaltst@max-exfl-cal002 tmp]$ git clone ssh://git@git.xfel.eu:10022/detectors/pycalibration.git
Cloning into 'pycalibration'...
remote: Enumerating objects: 9414, done.
remote: Counting objects: 100% (9414/9414), done.
remote: Compressing objects: 100% (2858/2858), done.
remote: Total 9414 (delta 6510), reused 9408 (delta 6504)
Receiving objects: 100% (9414/9414), 611.81 MiB | 54.87 MiB/s, done.
Resolving deltas: 100% (6510/6510), done.