ramutils

Bootstrapping a conda environment

conda create -y -n environment_name python=3
source activate environment_name
conda install -c pennmem ramutils

Usage with the RAM_maint account

For generating Ramulator configuration files, the RAM_maint account on rhino2 should be used. This account provides a managed conda environment and should only be updated by a responsible person from the Systems Development team.

The general workflow for users is the following:

Login to rhino using your normal account
Use sudo to open a shell with the RAM_maint user: sudo -s -u RAM_maint
Use qlogin to open an interactive session on an availabel node: qlogin
Activate the ramutils environment: source activate ramutils
Run the provided command line scripts

Ramulator experiment config generation

Ramulator experiment configuration files for stimulation experiments are generated via the ramulator-conf script:

usage: ramulator-conf [-h] [--root ROOT] [--dest DEST] [--cachedir CACHEDIR]
                      --subject SUBJECT [--use-cached] --experiment
                      {AmplitudeDetermination,PS4_FR5,PS4_CatFR5,PS5_FR,PS5_CatFR,FR3,CatFR3,PAL3,FR5,CatFR5,PAL5,FR6,CatFR6,FR1,CatFR1,PAL1}
                      [--vispath VISPATH] [--version]
                      [--localization LOCALIZATION] [--montage MONTAGE]
                      [--electrode-config-file ELECTRODE_CONFIG_FILE]
                      [--anodes ANODES [ANODES ...]]
                      [--cathodes CATHODES [CATHODES ...]]
                      [--min-amplitudes MIN_AMPLITUDES [MIN_AMPLITUDES ...]]
                      [--max-amplitudes MAX_AMPLITUDES [MAX_AMPLITUDES ...]]
                      [--target-amplitudes TARGET_AMPLITUDES [TARGET_AMPLITUDES ...]]
                      [--no-extended-blanking]
                      [--default-area DEFAULT_AREA | --area-file AREA_FILE]
                      [--clear-log]

Generate experiment configs for Ramulator

optional arguments:
  -h, --help            show this help message and exit
  --root ROOT           path to rhino root (default: /)
  --dest DEST, -d DEST  directory to write output to (default:
                        scratch/ramutils)
  --cachedir CACHEDIR   absolute path for caching dir
  --subject SUBJECT, -s SUBJECT
                        subject ID
  --use-cached          allow cached results from previous run to be reused
  --experiment {AmplitudeDetermination,PS4_FR5,PS4_CatFR5,PS5_FR,PS5_CatFR,FR3,CatFR3,PAL3,FR5,CatFR5,PAL5,FR6,CatFR6,FR1,CatFR1,PAL1}, -x {AmplitudeDetermination,PS4_FR5,PS4_CatFR5,PS5_FR,PS5_CatFR,FR3,CatFR3,PAL3,FR5,CatFR5,PAL5,FR6,CatFR6,FR1,CatFR1,PAL1}
                        experiment
  --vispath VISPATH     path to save task graph visualization to
  --version             show program's version number and exit
  --localization LOCALIZATION, -l LOCALIZATION
                        localization number (default: 0)
  --montage MONTAGE, -m MONTAGE
                        montage number (default: 0)
  --electrode-config-file ELECTRODE_CONFIG_FILE, -e ELECTRODE_CONFIG_FILE
                        path to existing electrode config CSV file
  --anodes ANODES [ANODES ...], -a ANODES [ANODES ...]
                        stim anode labels
  --cathodes CATHODES [CATHODES ...], -c CATHODES [CATHODES ...]
                        stim cathode labels
  --min-amplitudes MIN_AMPLITUDES [MIN_AMPLITUDES ...]
                        minimum stim amplitudes
  --max-amplitudes MAX_AMPLITUDES [MAX_AMPLITUDES ...]
                        maximum stim amplitudes
  --target-amplitudes TARGET_AMPLITUDES [TARGET_AMPLITUDES ...], -t TARGET_AMPLITUDES [TARGET_AMPLITUDES ...]
                        target stim amplitudes
  --no-extended-blanking
                        disable extended blanking
  --default-area DEFAULT_AREA, -A DEFAULT_AREA
                        default surface area to use for all contacts (default:
                        0.001)
  --area-file AREA_FILE
                    path to area.txt file relative to root

--clear-log clear the log

Report generation

Generating reports on the command line:

usage: ram-report [-h] [--root ROOT] [--dest DEST] [--cachedir CACHEDIR]
                  --subject SUBJECT [--use-cached] --experiment
                  {FR1,CatFR1,PAL1,PS4_FR5,PS4_CatFR5,PS5_FR,PS5_CatFR,FR3,CatFR3,PAL3,FR5,CatFR5,PAL5,FR6,CatFR6,AmplitudeDetermination,PS4_FR5,PS4_CatFR5,FR6,CatFR6}
                  [--vispath VISPATH] [--version]
                  [--sessions SESSIONS [SESSIONS ...]] [--retrain]
                  [--excluded-contacts EXCLUDED_CONTACTS [EXCLUDED_CONTACTS ...]]
                  [--joint-report] [--rerun]
                  [--report_db_location REPORT_DB_LOCATION]
                  [--trigger-electrode TRIGGER_ELECTRODE]

Generate a report

optional arguments:
  -h, --help            show this help message and exit
  --root ROOT           path to rhino root (default: /)
  --dest DEST, -d DEST  directory to write output to (default:
                        scratch/ramutils)
  --cachedir CACHEDIR   absolute path for caching dir
  --subject SUBJECT, -s SUBJECT
                        subject ID
  --use-cached          allow cached results from previous run to be reused
  --experiment {FR1,CatFR1,PAL1,PS4_FR5,PS4_CatFR5,PS5_FR,PS5_CatFR,FR3,CatFR3,PAL3,FR5,CatFR5,PAL5,FR6,CatFR6,AmplitudeDetermination,PS4_FR5,PS4_CatFR5,FR6,CatFR6}, -x {FR1,CatFR1,PAL1,PS4_FR5,PS4_CatFR5,PS5_FR,PS5_CatFR,FR3,CatFR3,PAL3,FR5,CatFR5,PAL5,FR6,CatFR6,AmplitudeDetermination,PS4_FR5,PS4_CatFR5,FR6,CatFR6}
                        experiment
  --vispath VISPATH     path to save task graph visualization to
  --version             show program's version number and exit
  --sessions SESSIONS [SESSIONS ...], -S SESSIONS [SESSIONS ...]
                        sessions to read data from (default: use all)
  --retrain, -R         retrain classifier rather than loading from disk
  --excluded-contacts EXCLUDED_CONTACTS [EXCLUDED_CONTACTS ...], -E EXCLUDED_CONTACTS [EXCLUDED_CONTACTS ...]
                        contacts to exclude from classifier
  --joint-report, -j    include CatFR/FR for FR reports (default: off)
  --rerun, -C           do not use previously generated output
  --report_db_location REPORT_DB_LOCATION
                        location of report data database
  --trigger-electrode TRIGGER_ELECTRODE, -t TRIGGER_ELECTRODE
                    Label of the electrode to use for triggering
                    stimulation in PS5

Aggregated Stim Report generation

Generating an aggregated stim report from the command line:

usage: ram-aggregated-report [-h] [--root ROOT] [--dest DEST]
                         [--cachedir CACHEDIR] [--use-cached]
                         [--vispath VISPATH] [--version]
                         [--subject SUBJECT [SUBJECT ...]]
                         [--experiment EXPERIMENT [EXPERIMENT ...]]
                         [--sessions SESSIONS [SESSIONS ...]]
                         [--fit-model]
                         [--report_db_location REPORT_DB_LOCATION]

Generate a report

optional arguments:
  -h, --help            show this help message and exit
  --root ROOT           path to rhino root (default: /)
  --dest DEST, -d DEST  directory to write output to (default:
                        scratch/ramutils)
  --cachedir CACHEDIR   absolute path for caching dir
  --use-cached          allow cached results from previous run to be reused
  --vispath VISPATH     path to save task graph visualization to
  --version             show program's version number and exit
  --subject SUBJECT [SUBJECT ...], -s SUBJECT [SUBJECT ...]
                        List of subjects
  --experiment EXPERIMENT [EXPERIMENT ...], -x EXPERIMENT [EXPERIMENT ...]
                        List of experiments
  --sessions SESSIONS [SESSIONS ...], -S SESSIONS [SESSIONS ...]
  --fit-model, -f
  --report_db_location REPORT_DB_LOCATION
                        location of report data database

Info for account maintainers

To update an existing conda environment to use the latest release:

conda update ramutils

To set up a conda environment for development purposes, execute the following commands from the top-level of the repository:

conda create -y -n ramutils_dev python=3
source activate ramutils_dev
conda install -c pennmem -c conda-forge --file=requirements.txt

Testing

Automated unit tests that do not require access to RHINO are run with every push to the remote repository or pull request. Longer running tests requiring local files can and should be run frequently. Please note that the full test suite takes appropximately 4 hours to complete. The full test suite should pass before any new release. Running the full test suite requires two additional arguments to be passed to pytest:

--rhino-root: The mount point for RHINO
--output-dest: Where output from blackbox tests will be saved

You will likely also need to set the environment variable:

MKL_THREADING_LAYER=GNU

Running the full test suite on rhino

To manually run the full test suite on rhino, first create a conda environment as described above. Build and install the conda package with the appropriate version of Python, for example:

$ maint/build.py -p 3.6
$ conda activate ramutils_dev
(ramutils_dev) $ conda install build/ramutils-*-py36*.bz2

Next, run the maint/run_tests_rhino.sh script:

..code-block:: shell-session

(ramutils_dev) $ maint/run_tests_rhino.sh

Older testing info

To run the full testing suite from a local copy of the repository, create a development environment as outlined above, then execute the following from top level of the repository:

qlogin
source activate ramutils_dev
pytest ramutils/ --rhino-root RHINO_ROOT --output-dest OUTPUT_DEST

The full set of tests are run nightly (5pm EST) from the RAM_maint account on RHINO by submitting ramutils/maint/run_tests.sh as a cron job. To update the timing of the automated tests, switch to the RAM_maint user account on rhino and edit the crontab file: crontab -e. To update what users receive the testing report or to modify anything related to the testing itself, update ramutils/maint/run_tests.sh.

Name		Name	Last commit message	Last commit date
Latest commit History 3,265 Commits
MatlabIO		MatlabIO
conda.recipe		conda.recipe
demos		demos
docs		docs
maint		maint
ramutils		ramutils
scripts		scripts
.gitignore		.gitignore
.travis.yml		.travis.yml
CHANGELOG.rst		CHANGELOG.rst
HOW_TO_RELEASE.rst		HOW_TO_RELEASE.rst
MANIFEST.in		MANIFEST.in
README.rst		README.rst
requirements.txt		requirements.txt
setup.cfg		setup.cfg
setup.py		setup.py

pennmem/ram_utils

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ramutils

Bootstrapping a conda environment

Usage with the RAM_maint account

Ramulator experiment config generation

Report generation

Aggregated Stim Report generation

Info for account maintainers

Testing

Running the full test suite on rhino

Older testing info

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