{"id":18420617,"url":"https://github.com/openworm/org.geppetto.recording","last_synced_at":"2026-03-05T16:46:56.279Z","repository":{"id":15030224,"uuid":"17756037","full_name":"openworm/org.geppetto.recording","owner":"openworm","description":"Python project allowing to create a recording for Geppetto","archived":false,"fork":false,"pushed_at":"2015-05-12T19:29:10.000Z","size":32243,"stargazers_count":5,"open_issues_count":5,"forks_count":0,"subscribers_count":23,"default_branch":"master","last_synced_at":"2025-03-22T19:43:12.409Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":"http://www.geppetto.org/","language":"Python","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/openworm.png","metadata":{"files":{"readme":"README.rst","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-03-14T18:31:40.000Z","updated_at":"2023-07-04T06:41:52.000Z","dependencies_parsed_at":"2022-09-07T08:01:21.693Z","dependency_job_id":null,"html_url":"https://github.com/openworm/org.geppetto.recording","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2Forg.geppetto.recording","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2Forg.geppetto.recording/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2Forg.geppetto.recording/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/openworm%2Forg.geppetto.recording/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/openworm","download_url":"https://codeload.github.com/openworm/org.geppetto.recording/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":247661890,"owners_count":20975141,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":[],"created_at":"2024-11-06T04:22:26.806Z","updated_at":"2026-03-05T16:46:56.241Z","avatar_url":"https://github.com/openworm.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"org.geppetto.recording\n======================\n\nThis Python project creates recordings for `Geppetto \u003chttp://www.geppetto.org/\u003e`_.\nA recording is a file that contains all the raw data processed during a simulation run.\nThe recording files are based on the popular binary file format `HDF5 \u003chttp://www.hdfgroup.org/HDF5/\u003e`_\n(more information to come).\n\nRequirements\n------------\n\n- **Python 2.7**: `Download \u003chttps://www.python.org/download\u003e`_ and install\n  (Tip: Use the 32bit version, it will save you a lot of trouble if you want to install NEURON and Brian later).\n  Make sure that the *Python27* and *Python27/Scripts* directories are in your PATH environment variable.\n\n- **Python packages** (h5py, numpy, enum34): If you use pip to install org.geppetto.recording (see below), these\n  packages will be installed automatically as needed. If you want to install them manually, use pip\n  (`Get it here \u003chttp://pip.readthedocs.org/en/latest/installing.html\u003e`_).\n  and type on the command line::\n\n    pip install h5py\n    pip install numpy\n    pip install enum34\n\n- **NEURON and Brian (optional)**: Required to record simulations or read binary recordings\n  from `NEURON \u003chttp://www.neuron.yale.edu/neuron/\u003e`_ or `Brian \u003chttp://briansimulator.org/\u003e`_.\n  Note that for NEURON, the standard installer is not enough - you need to be able to run ``import neuron`` or\n  ``import brian``, respectively, from the Python console.\n  For installation instructions, see the `Appendix: Installing NEURON and Brian`_.\n\nInstallation\n------------\nIf you installed all requirements, use pip (`Get it here \u003chttp://pip.readthedocs.org/en/latest/installing.html\u003e`_) to\ninstall org.geppetto.recording::\n\n    pip install org.geppetto.recording\n\nAlternatively, download or clone the source code from this repository. Fire up the command line, navigate into\nthe org.geppetto.recording folder (the one containing this *README*) and type::\n\n    python setup.py install\n\nUsage\n-----\nDetailed instructions on how to create and replay a recording are in the\n`Geppetto documentation \u003chttp://docs.geppetto.org/en/latest/recordingandreplaying.html\u003e`_.\n\nIf you can't await it, fire up the Python console and type:\n\n\u003e\u003e\u003e from org.geppetto.recording.creators import RecordingCreator, MetaType\n\u003e\u003e\u003e c = RecordingCreator('recording_file.h5')\n\u003e\u003e\u003e c.add_values('cell.voltage', [-60.0, -59.9, -59.8], 'mV', MetaType.STATE_VARIABLE)\n\u003e\u003e\u003e c.set_time_step(0.1, 'ms')\n\u003e\u003e\u003e c.create()\n\nThis will create a simple recording named *recording_file.h5* in you current directory.\nYou can look at it with `HDFView \u003chttp://www.hdfgroup.org/products/java/hdfview/\u003e`_.\n\nFeedback\n--------\nGot a great idea for a new feature? Found something you don't like? We are happy to hear from you!\nGet in touch through the `OpenWorm mailing list \u003chttps://groups.google.com/forum/#!forum/openworm-discuss\u003e`_,\nopen an issue on `GitHub \u003chttps://github.com/openworm/org.geppetto.recording\u003e`_ or create a fork of this repository\nand start coding!\n\nAppendix: Installing NEURON and Brian\n-------------------------------------\n\n**NEURON**\n\nUnfortunately, the standard installer for NEURON isn't enough, you need to be able to run ``import neuron`` from the\nPython console.\n\nFor OSX and Linux, there are some (unofficial)\n`installers \u003chttp://neuralensemble.org/people/eilifmuller/software.html\u003e`_ from Eilif Muller that work.\n\nFor Windows, there is the `pyNEURON \u003chttps://bitbucket.org/uric/pyneuron/wiki/Home\u003e`_ package.\nIf you have pip, simply run::\n\n    pip install pyNEURON\n\nNote that pyNEURON only works completely with a 32bit version of Python.\nIf your NEURON simulation loads any of the built-in hoc files (for example nrngui, NEURON's graphical user interface),\nset the NEURONHOME environment variable to the directory of your (standard) NEURON installation.\npyNEURON can then execute your model file, however, it will not actually show you the user interface!\nHence, make sure that your simulation starts without it.\n\nAt the very last resort, you can build NEURON from source (on all operating systems),\nsee the `instructions \u003chttp://www.neuron.yale.edu/neuron/download/getstd\u003e`_.\nKeep in mind that this is not the easiest thing to do; if possible, use any of the options above.\n\n**Brian**\n\nIf you have pip, simply run::\n\n    pip install brian\n\nNote that this may not work with a 64bit version of Python. Alternatively, have a look at Brian's excellent\n`installation instructions \u003chttp://www.briansimulator.org/docs/installation.html\u003e`_. In the end, you should be able\nto run ``import brian`` on the Python console.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenworm%2Forg.geppetto.recording","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fopenworm%2Forg.geppetto.recording","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fopenworm%2Forg.geppetto.recording/lists"}