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* Bug fixes after v0.2.2, heading to v0.2.3
* Updating url of GitHub repository, previously INM-6, now NeuralEnsemble
* Typo fix
* RegEx fix for t_start and t_stop
Copy file name to clipboardExpand all lines: cobrawap/pipeline/README.rst
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@@ -40,7 +40,7 @@ Manual Installation For Developers
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----------------------------------
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For working on the source code, it is recommended to fork the Cobrawap repository from Github, and clone it or set it as a submodule to another project repository.
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`Create a fork <https://docs.github.com/en/get-started/quickstart/fork-a-repo>`_ in your github domain of the upstream location `github.com/INM-6/cobrawap <https://github.com/INM-6/cobrawap>`_ and clone the repository to your local machine (:code:`git clone [email protected]:<your-github-handle>/cobrawap.git`).
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`Create a fork <https://docs.github.com/en/get-started/quickstart/fork-a-repo>`_ in your github domain of the upstream location `github.com/NeuralEnsemble/cobrawap <https://github.com/NeuralEnsemble/cobrawap>`_ and clone the repository to your local machine (:code:`git clone [email protected]:<your-github-handle>/cobrawap.git`).
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Then use pip to install the module from your local directory in an editable mode.
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.. code-block:: bash
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cobrawap create
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This will prompt the setting of a profile name and optionally a parent profile name from which to copy the parameter presets. The parent profile name will be prepended to the profile name (see :ref:`config_profiles`). Optionally, these names can be directly passed to the :code:`create` command with :code:`--profile` and :code:`--parent_profile`.
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The profile and parent name will be used to create correspondingly named config files for each stage: ``config_<parent>_<profile>.yaml`` for the first stage and ``config_<parent>.yaml`` for all other stages.
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The profile and parent name will be used to create correspondingly named config files for each stage: ``config_<parent>_<profile>.yaml`` for the first stage and ``config_<parent>.yaml`` for all other stages.
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For specifying the data entry into the pipeline :code:`create` also asks for the path to the dataset and a name for the corresponding loading script. This information can also be passed to the :code:`create` command with :code:`--data_path` and :code:`--loading_script_name`.
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Both information are written into the corresponding config file of the first stage. Furthermore, a template loading script is created in ``<config_path>/stage01_data_entry/scripts/`` which has to be adapted to load the specific dataset.
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This will prompt the setting of a profile and parent profile name just as for :code:`cobrawap create`. Additionally, it requires to specify the stages for which to create new config files (can be directly passed with :code:`--stages`).
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Consequently, this will create new config files ``config_<parent>_<profile>.yaml`` for the selected stages, copying the parameter presents from ``config_<parent>.yaml``.
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If the stage selection includes the first stage, this will again prompt the additional setting of a :code:`--data_path` and :code:`--loading_script_name` as for :code:`cobrawap create`.
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If the stage selection includes the first stage, this will again prompt the additional setting of a :code:`--data_path` and :code:`--loading_script_name` as for :code:`cobrawap create`.
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Running the Pipeline
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--------------------
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cobrawap run_block
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This command allows to execute the python script of a specific block. The block should be specified as :code:`<stage_name>.<block_name>` and can be passed with :code:`--block`. Any additional command line arguments are passed to the script.
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This command allows to execute the python script of a specific block. The block should be specified as :code:`<stage_name>.<block_name>` and can be passed with :code:`--block`. Any additional command line arguments are passed to the script.
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To display the help text of the block script add :code:`--block_help`.
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Config Profiles
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---------------
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Config profiles make it possible to group specific parameter configurations for different datasets or applications across stages, and easily switch between them. You can set the ``PROFILE`` parameter in the top-level config file (or via the command line when running the pipeline). The corresponding pipeline output will be stored in ``{output_path}/{profile}/``, and for each stage the specific config file ``{stage}/configs/config_{profile}.yaml`` is used.
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Config profiles make it possible to group specific parameter configurations for different datasets or applications across stages, and easily switch between them. You can set the ``PROFILE`` parameter in the top-level config file (or via the command line when running the pipeline). The corresponding pipeline output will be stored in ``{output_path}/{profile}/``, and for each stage the specific config file ``{stage}/configs/config_{profile}.yaml`` is used.
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To reduce redundancy and the number of config files, profiles use a hierachical naming convention where each subgroup is seperated with an underscore ``_``, for example, ``config_ecog_session1_trial7.yaml``. When a stage does not contain this exact file name, it falls back onto the parent group (``config_ecog_session1.yaml``) and when it also doesn't exist onto its parent group (``config_ecog.yaml``) and so on. Thus, config specialization is only applied in the stages where it is needed. Furthermore, you can add variants to the profile name with a ``|`` delimiter to additionally switch analysis types, for example, ``config_caimg_session1|subsampled.yaml``.
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The selection order is the following:
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Block Outputs
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-------------
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All output from blocks (data and figures) is stored in ``{output_path}/{profile}/{STAGE_NAME}/{block_name}/``.
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* Set the additional metadata for the config parameter as required (*can be revisited when writing the loading script*)
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3. Create the corresponding loading script.
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* Copy the ``enter_data_template.py`` in ``cobrawap/pipeline/stage01_data_entry/scripts/`` and and name it as specified in the just created config file.
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* Copy the ``enter_data_template.py`` in ``cobrawap/pipeline/stage01_data_entry/scripts/`` and and name it as specified in the just created config file.
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* Put the script either in the same folder or in ``<configs_dir>/stage01_data_entry/scripts/`` if defined.
Copy file name to clipboardExpand all lines: cobrawap/pipeline/stage04_wave_detection/README.rst
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@@ -4,11 +4,11 @@ Stage 04 - Wave Detection
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**This stage detects individual propagating waves based on the local transition times and optionally complements the wave description with additionally derived properties.**
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Usage
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=====
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In this stage, any number of blocks can be selected via the ``MEASURES`` parameter and are applied on the stage input (*choose any*).
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To include specific metadata in the output table, select the corresponding annotation keys with ``INCLUDE_KEYS``, or to include all available metadata execept some specifiy only the corresponding annotations keys in ``IGNORE_KEYS``.
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In this stage, any number of blocks can be selected via the ``MEASURES`` parameter and are applied on the stage input (*choose any*).
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To include specific metadata in the output table, select the corresponding annotation keys with ``INCLUDE_KEYS``, or to include all available metadata execept some specifiy only the corresponding annotations keys in ``IGNORE_KEYS``.
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Usage
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=====
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In this stage, any number of blocks can be selected via the ``MEASURES`` parameter and are applied on the stage input (*choose any*).
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To include specific metadata in the output table, select the corresponding annotation keys with ``INCLUDE_KEYS``, or to include all available metadata execept some specifiy only the corresponding annotations keys in ``IGNORE_KEYS``.
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In this stage, any number of blocks can be selected via the ``MEASURES`` parameter and are applied on the stage input (*choose any*).
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To include specific metadata in the output table, select the corresponding annotation keys with ``INCLUDE_KEYS``, or to include all available metadata execept some specifiy only the corresponding annotations keys in ``IGNORE_KEYS``.
Describe type and format of the stage output data and metadata, eventual intermediate output, and where it is stored.
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Usage
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=====
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Describe the functionality of the stage, what type of blocks are used and how they can be arranged, and eventually special stage parameters. However, an account of the exact blocks and their features should be placed into the Snakefile's and scripts' docstring.
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Describe the functionality of the stage, what type of blocks are used and how they can be arranged, and eventually special stage parameters. However, an account of the exact blocks and their features should be placed into the Snakefile's and scripts' docstring.
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