Merge pull request #268 from scottclowe/doc_change-functional

DOC: Change functional to function-based

README.rst

@@ -74,7 +74,7 @@ Note that the Suite2p notebook is housed in its own `repository <suite2p_example
 +---------------------------+-------------------------------------------------------------------------------------+---------------------------------------------------------------+
 | Workflow                  |                                  Jupyter Notebook                                   |                            Script                             |
 +===========================+==========================+===============================+==========================+================================+==============================+
-| Functional (ImageJ_)      | `NBViewer <func_html_>`_ | `Launch Binder <func_bind_>`_ | `Download <func_down_>`_ | `Linux/Mac <func_nixscript_>`_ | `Windows <func_winscript_>`_ |
+| Function-based (ImageJ_)  | `NBViewer <func_html_>`_ | `Launch Binder <func_bind_>`_ | `Download <func_down_>`_ | `Linux/Mac <func_nixscript_>`_ | `Windows <func_winscript_>`_ |
 +---------------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
 | Object-oriented (ImageJ_) | `NBViewer <basichtml_>`_ | `Launch Binder <basicbind_>`_ | `Download <basicdown_>`_ | `Linux/Mac <basicnixscript_>`_ | `Windows <basicwinscript_>`_ |
 +---------------------------+--------------------------+-------------------------------+--------------------------+--------------------------------+------------------------------+
@@ -87,10 +87,10 @@ Note that the Suite2p notebook is housed in its own `repository <suite2p_example
 
 .. _Binder: https://mybinder.org/v2/gh/rochefort-lab/fissa/master?filepath=examples
 
-.. _func_bind: https://mybinder.org/v2/gh/rochefort-lab/fissa/master?filepath=examples/Basic%20usage%20-%20Functional.ipynb
+.. _func_bind: https://mybinder.org/v2/gh/rochefort-lab/fissa/master?filepath=examples/Basic%20usage%20-%20Function.ipynb
 .. _func_html: https://rochefort-lab.github.io/fissa/examples/Basic%20usage%20-%20Functional.html
-.. _func_view: https://github.com/rochefort-lab/fissa/blob/master/examples/Basic%20usage%20-%20Functional.ipynb
-.. _func_down: https://raw.githubusercontent.com/rochefort-lab/fissa/master/examples/Basic%20usage%20-%20Functional.ipynb
+.. _func_view: https://github.com/rochefort-lab/fissa/blob/master/examples/Basic%20usage%20-%20Function.ipynb
+.. _func_down: https://raw.githubusercontent.com/rochefort-lab/fissa/master/examples/Basic%20usage%20-%20Function.ipynb
 .. _func_nixscript: https://github.com/rochefort-lab/fissa/blob/master/examples/basic_usage_func.py
 .. _func_winscript: https://github.com/rochefort-lab/fissa/blob/master/examples/basic_usage_func_windows.py
 

examples/Basic usage - Functional.ipynb → examples/Basic usage - Function.ipynb

@@ -11,7 +11,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This notebook contains a step-by-step example of how to use the functional interface to the [FISSA](https://github.com/rochefort-lab/fissa) toolbox.\n",
+    "This notebook contains a step-by-step example of how to use the function-based interface to the [FISSA](https://github.com/rochefort-lab/fissa) toolbox.\n",
     "\n",
     "For more details about the methodology behind FISSA, please see our paper:\n",
     "> S. W. Keemink, S. C. Lowe, J. M. P. Pakan, E. Dylda, M. C. W. van Rossum, and N. L. Rochefort. FISSA: A neuropil decontamination toolbox for calcium imaging signals, *Scientific Reports*, **8**(1):3493, 2018. doi: [10.1038/s41598-018-21640-2](https://www.doi.org/10.1038/s41598-018-21640-2).\n",
@@ -63,7 +63,7 @@
    "source": [
     "## Running FISSA\n",
     "\n",
-    "With the functional interface to FISSA, everything is handled in a single function call to ``fissa.run_fissa``, which returns the decontaminated signals.\n",
+    "With the function-based interface to FISSA, everything is handled in a single function call to ``fissa.run_fissa``, which returns the decontaminated signals.\n",
     "\n",
     "The mandatory inputs to `fissa.run_fissa` are:\n",
     "- the experiment images\n",
@@ -111,15 +111,15 @@
     "images_location = \"exampleData/20150529\"\n",
     "rois_location = \"exampleData/20150429.zip\"\n",
     "\n",
-    "# Call FISSA using the functional interface\n",
+    "# Call FISSA using the function-based interface\n",
     "result, raw = fissa.run_fissa(images_location, rois_location)"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Note that although the functional interface is very straight forward, you can only access the result which is returned by the function.\n",
+    "Note that although the function-based interface is very straight forward, you can only access the result which is returned by the function.\n",
     "\n",
     "If you need to access the raw traces, ROI masks, or demixing matrix, you need to use the more flexible [object-oriented (class based) interface](https://rochefort-lab.github.io/fissa/examples/Basic%20usage.html), with [fissa.Experiment](https://fissa.readthedocs.io/en/stable/source/packages/fissa.core.html#fissa.core.Experiment), instead."
    ]

examples/basic_usage_func.py

@@ -4,10 +4,10 @@
 Basic FISSA usage example.
 
 This file contains a step-by-step example workflow for using the FISSA toolbox
-with a functional interface.
+with a function-based interface.
 
 An example notebook is provided here:
-https://github.com/rochefort-lab/fissa/blob/master/examples/Basic%20usage%20-%20Functional.ipynb
+https://github.com/rochefort-lab/fissa/blob/master/examples/Basic%20usage%20-%20Function.ipynb
 """
 
 import fissa

examples/basic_usage_func_windows.py

@@ -4,10 +4,10 @@
 Basic FISSA usage example.
 
 This file contains a step-by-step example workflow for using the FISSA toolbox
-with a functional interface.
+with a function-based interface.
 
 An example notebook is provided here:
-https://github.com/rochefort-lab/fissa/blob/master/examples/Basic%20usage%20-%20Functional.ipynb
+https://github.com/rochefort-lab/fissa/blob/master/examples/Basic%20usage%20-%20Function.ipynb
 """
 
 import fissa

fissa/core.py

@@ -417,7 +417,7 @@ def separate_trials(
 
 class Experiment:
     r"""
-    FISSA Experiment.
+    Class-based interface for running FISSA on experiments.
 
     Uses the methodology described in
     `FISSA: A neuropil decontamination toolbox for calcium imaging signals <doi_>`_.
@@ -1874,7 +1874,7 @@ def run_fissa(
     **kwargs
 ):
     r"""
-    Functional interface to run FISSA.
+    Function-based interface to run FISSA on an experiment.
 
     .. versionadded:: 1.0.0