Update to the documentation

README.rst

@@ -5,23 +5,21 @@
 Preparing Novonix Data
 ======================
 
-**preparenovonix** is a Python package that handles common issues encountered in files generated with a range of software versions from the `Novonix`_
-battery-testers. The code can also add extra information that makes
-easier coulombic counting and relating a measurement to the experimental
-protocol. The code provides a master function, *prepare_novonix*, that can run at once all the available features, providing also flexibility to choose only some. 
+**preparenovonix** is a Python package that handles common issues encountered in data files generated with a range of software versions from the `Novonix`_ battery-testers. This package can also add extra information that makes easier coulombic counting and relating a measurement to the experimental protocol. The package provides a master function, *prepare_novonix*, that can run at once the cleaning and adding derived information, with flexibility to choose only some features. There is a separate function to simply read a column by its given name.
+
 
 Example
 -------
 
-The **example.py** runs over the given example data. To run this
+The **example.py** runs over the given example data, producing a new file and a plot that compares the original and the prepared data. To run this
 example, simply type: :code:`python example.py`.
 
 Requirements and Installation
 -----------------------------
 
 This code has been developed in Python 3.7.1 and it is compatible with Python above 3.5 versions. The code has been tested to run in Windows, OSX and Linux operating systems. 
 
-This code uses numpy and pathlib as specified in docs/requirements.txt.
+This code uses numpy as specified in docs/requirements.txt. The ploting routine from the *example.py* also requires the use of matplotlib.
 
 The code can be run directly from a cloned GitHub `repository`_ or it can also be installed as a python `package`_ through pip:
 
@@ -47,7 +45,7 @@ In your code you can add the following lines that will call the master function
 .. code-block:: Matlab
 
    try
-	py.preparenovonix.novonix_add.prepare_novonix(file_to_open,...
+	py.preparenovonix.novonix_prep.prepare_novonix(file_to_open,...
 		pyargs('addstate','True',...
 		'lprotocol','True',...
                 'overwrite','True',...
@@ -59,6 +57,9 @@ In your code you can add the following lines that will call the master function
         end
    end
 
+
+.. _compability:
+
 Compatibility
 -------------
 
@@ -86,7 +87,7 @@ List of the `Novonix`_ software versions the code has been tested against:
 .. |build| image:: https://travis-ci.org/BatLabLancaster/preparenovonix.svg?branch=master
     :target: https://travis-ci.org/BatLabLancaster/preparenovonix
 
-.. |coverage| image:: https://codecov.io/gh/codecov/preparenovonix/branch/master/graph/badge.svg
+.. |coverage| image:: https://codecov.io/gh/BatLabLancaster/preparenovonix/branch/master/graph/badge.svg
     :target: https://codecov.io/gh/BatLabLancaster/preparenovonix
 
 .. |docs| image:: https://readthedocs.org/projects/prepare-novonix-data/badge/?version=latest

docs/features.rst

@@ -2,62 +2,44 @@
 Code Features
 =============
 
-The `preparenovonix`_ package prepares exported files produced by
-`Novonix`_ battery-testers (or ’Novonix files’) by (i) cleaning them and (ii) adding
-derived information to the file. The package also allows reading a
-column given its name. The list of functions available in the package
-can be found below in alphabetical order. This functions are presented
-with the expected input parameters in brackets and further details are
-given here for some of them and otherwise go to the `module index`_ for full details and examples of usage.
-
--  ``cleannovonix(infile)``: Given a ’Novonix file’ clean it as it is
-   described below.
-
--  ``isnovonix(infile)``: Given a file, check if it is or not a ’Novonix
-   file’.
-
--  ``icolumn(infile,column_name)``: Given the name of a column, find the
-   position of this column within a cleaned ’Novonix file’.
-
--  ``novonix_add_loopnr(infile,verbose=False)``: Given a cleaned
-   ’Novonix file’, add a reduced protocol to the header and the columns
-   ’Protocol line’ and ’Loop number’.
-
--  ``novonix_add_state(infile,verbose=False)``: Given a cleaned ’Novonix
-   file’, add the ’State’.
-
--  ``prepare_novonix(infile,addstate=False,lprotocol=False,``\ ``overwrite=False,verbose=False)``:
-   Master function of the package that can call the cleaning and adding
-   derived information functions directly. This function follows the
-   flow chart presented in the :ref:`chart`. Running all the
-   available features from the `preparenovonix`_ package can take form
+The main functions available in the `preparenovonix`_ package are
+listed below in alphabetical order. The list contains the module name
+followed by the function name with the expected input parameters in
+brackets.
+
+-  ``novonix_add.create_reduced_protocol(infile,verbose=False)``: Given
+   a cleaned Novonix data file, ``infile``, generate a reduced protocol.
+
+-  ``novonix_add.novonix_add_loopnr(infile,verbose=False)``: Given a
+   cleaned Novonix data file, ``infile``, add a reduced protocol to the
+   header and the columns Protocol line and Loop number.
+
+-  ``novonix_add.novonix_add_state(infile,verbose=False)``: Given a
+   cleaned Novonix data file, ``infile``, add the State column.
+
+-  ``novonix_clean.cleannovonix(infile)``: Given a Novonix data file,
+   ``infile``, clean it as it is described below.
+
+-  ``novonix_io.isnovonix(infile)``: Given a file, ``infile``, check if
+   it is or not a Novonix data file.
+
+-  ``novonix_io.read_column(infile,column_name,outtype=’float’)``: Given
+   a column name, ``column_name``, read it from a cleaned Novonix data
+   file, ``infile``, as a numpy array of the type given in ``outtype``.
+
+-  ``novonix_prep.prepare_novonix(infile,addstate=False,lprotocol=False,``\ ``overwrite=False,verbose=False)``:
+   Master function of the ``preparenovonix`` package that prepares a
+   Novonix data file by cleaning it and adding to it derived
+   information. This function follows the flow chart presented in
+   :ref:`chart`. Running all the available features from
+   the `preparenovonix`_ package through this function can take form
    few seconds to up to few minutes depending on the size of the input
    file.
 
--  ``read_column(infile,column_name,outtype=’float’)``: Given a column
-   name, read it from a cleaned ’Novonix file’ as a numpy array of the
-   type given in ``outtype``.
-
--  ``reduced_protocol(infile,verbose=False)``: Given a cleaned ’Novonix
-   file’, generate a reduced protocol.
-
--  ``select_com_val(index)``: Auxiliary function of
-   ``novonix_add_loopnr``.
-
-As it is shown in the :ref:`chart`, the derived information
-is only added on ’cleaned’ files and only files that the code considers
-as ’Novonix files’ can be cleaned. The master function
-``prepare_novonix`` allows the user to call either the cleaning process
-or the addition of extra columns ensuring that the dependencies
-previously defined are taken into account. This function requires as
-input parameters: the path to a file and four boolean optional
-parameters. These boolean parameters are: ``addstate``, ``lprotocol``,
-``overwrite`` and ``verbose``. The last parameter provides the option to
-output more information about the run. If the ``overwrite`` parameter is
-set to False, a new file will be generated with a name similar to the
-input one, except for the addition of ``_prep`` before the extension of
-the file.
+In what follows, the above functions will be referred by simply their
+name, without stating the modules they belong to.
 
+   
 .. _chart:
 
 Flow chart
@@ -67,40 +49,66 @@ Flow chart
    :align: center
    :alt: Flow chart
 
-   Flow chart for the ``prepare_novonix`` function. Besides the name of the input file, this function has four optional boolean input parameters: ``addstate``, ``lprotocol``, ``overwrite`` and ``verbose``. The last two parameters are not included in the flow chart, but they are described in the text. In this chart rectangle shapes indicate a process, rounder rectangles the end of a process and diamonds a decision. Note that for simplicity not all the decisions made in the code are shown here.
+Flow chart for the ``prepare_novonix`` function (within the
+``novonix_prep`` module) which contains all the functionality of the
+`preparenovonix`_ package presented here. Besides the name of the input
+file, this function has four optional boolean input parameters:
+``addstate``, ``lprotocol``, ``overwrite`` and ``verbose``. The last two
+parameters are not included in the flow chart, but they are described in
+the text. In this chart rectangle shapes indicate processes, rounder
+rectangles end of processes and diamonds decisions. Note that for
+simplicity not all the decisions made in the code are shown here.
+
+.. _prepare_novonix:
+
+The ``prepare_novonix`` function
+--------------------------------
+As it is shown in :ref:`chart`, the `preparenovonix`_ package only cleans data files that are consider to
+be exported from the Novonix battery-testers and it only derives
+information for cleaned Novonix files. The master function ``prepare_novonix`` allows the user to
+call either the cleaning process or the addition of extra columns
+ensuring that these dependencies are taken into account. The input
+parameters for this function are the path to a file and four boolean
+optional parameters: ``addstate``, ``lprotocol``, ``overwrite`` and
+``verbose``. The last parameter provides the option to output more
+information about the run. If the ``overwrite`` parameter is set to
+``False``, a new file will be generated with a name similar to the input
+one, except for the addition of ``_prep`` before the extension of the
+file.
 
 
 The ``isnovonix`` function
 --------------------------
-The function ``isnovonix`` decides if a file has the expected structure
-(including a full header) for an exported file produced by the Novonix
-battery-testers (or ’Novonix files’). If the file is lacking the header
-or if it has not been exported with a Novonix battery-tester using the
-covered software (see section ’Quality control’), the code will exit
-with an error message and without generating a new file.
+The function ``isnovonix`` decides if a file has the expected structure (including a full header)
+for an exported file produced by the Novonix battery-testers. If the
+file is lacking the header or if it has not been exported with a Novonix
+battery-tester using the covered software (see the section :ref:`compability`), the code will exit with
+an error message and without generating a new file.
+
 
 The ``cleannovonix`` function
 -----------------------------
-The function ``cleannovonix`` produces a new ’Novonix type’ file after
-performing the following tasks:
+The function ``cleannovonix`` produces a new Novonix type file after performing the following tasks:
+
+-  Delete failed tests within a single file, adding the final capacity
+   of all failed tests to the capacity column of the finished test.
 
--  Delete failed tests within one file, adding the final capacity of all
-   failed tests to the capacity column of the finished test.
+-  Remove individual measurements for which the run time goes backwards.
 
 -  Remove blank lines from the header.
 
--  Remove eventual trailing characters from the header produced when the
-   file was previously open with certain programs, such as Excel.
+-  Remove any trailing characters from the header produced when the file
+   has been previously open with certain programs, such as Excel.
 
 -  Add a dummy header name (``dum[number]``) for each data column
    lacking a header name.
 
-The ’State’ column
-------------------
-A ’State’ column can be added to a cleaned Novonix file by calling the
-function ``novonix_add_state`` or setting to True the parameter
-``addstate`` when calling the function ``prepare_novonix``. This ’State’
-column can have the following values:
+The ``State`` column
+--------------------
+A ``State`` column can be added to a cleaned Novonix file by calling the function
+``novonix_add_state`` or setting to ``True`` the parameter ``addstate``
+when calling the function ``prepare_novonix``. This State column can
+have the following values:
 
 -  0 for the first measurement of a given type (for example, a constant
    current charge).
@@ -110,29 +118,29 @@ column can have the following values:
 -  2 for the last measurement of a given type.
 
 -  -1 for single measurements. This can happen under different
-   conditions. A type of measurement can end after a single measurement
-   when some conditions are met (this usually happens while the time
-   resolution is coarse). At times, the current can overshoot from
-   negative to positive values at the beginning of a measurement. A bug
-   in the Novonix software that locks certain values, etc. If two single
-   measurements happen together, the two lines are discarded in the new
-   file containing the additional ’State’ column.
-
-The ’State’ column is generated based on the quantities provided in
-’Novonix files’: ’Step’ (integer indicating the type of measurement) and
-’Step time’ (time that resets to 0 each time a new type of measurement
-starts).
+   circumstances. A type of measurement can end after a single
+   measurement when some experimental conditions are met, this usually
+   happens while the time resolution is coarse. At times, the current
+   can overshoot from negative to positive values at the beginning of a
+   measurement. A bug in the Novonix software that locks certain values,
+   etc. If two single measurements happen together, the two lines are
+   discarded in the new file containing the additional State column.
+
+The State column is generated based on the following quantities provided
+in the raw Novonix data files: Step number (integer indicating the type
+of measurement) and Step time (this time is assumed to reset to 0 each
+time a new type of measurement starts).
 
 The ``reduced_protocol`` function
 ---------------------------------
-The ``reduced_protocol`` function reads the complete header from the
-input file and generates (or reads) the reduced protocol. This function
-returns the reduce protocol itself and a boolean flag, ``viable_prot``.
-The reduced protocol consist of an array of strings. Each string
-contains a line of the experimental protocol with a structure as
-follows: line number,’:’,command,’:’,trip conditions. An example:
-``[4 : Repeat 49 times :]``. Only commands referring to the following
-processes will appear in the reduced protocol (note that commands that do not produce measurements are ignored here):
+The ``reduced_protocol`` function reads the complete header from the input file and generates (or reads)
+the reduced protocol. This function returns the reduce protocol itself
+and a boolean flag, ``viable_prot``. The reduced protocol consist of an
+array of strings. Each string contains a line number, a command from the
+experimental protocol and the corresponding experimental conditions (if
+aplicable); for example: ``[4 : Repeat 49 times :]``. Only commands
+referring to the following processes will appear in the reduced
+protocol (note that the commands corresponding to incrementing the cycle counter and global emergency limits are ignored in the reduced protocol as there are no measurements associated with those):
 
 -  Open circuit storage (or rest)
 
@@ -143,25 +151,25 @@ processes will appear in the reduced protocol (note that commands that do not pr
 -  (End) Repeat
 
 The reduced protocol is tested against the number of unique measurements
-in the file, determined using the column ’State’. If the number of
+in the file, determined using the column State. If the number of
 measurements expected from the protocol is less than the actual number
-of measurements, the flag ``viable_prot`` is set to false, indicating
-that the construction of the reduced protocol was not viable.
-
-The ’Protocol line’ and ’Loop number’ columns
----------------------------------------------
-The ’Protocol line’ and ’Loop number’ columns can be generated by either
-calling directly the function ``novonix_add_loopnr`` or by setting to
-True the parameter ``lprotocol`` when calling the function
-``prepare_novonix``. The column ’Protocol line’ associates a measurment
-with the its corresponding line in the reduced protocol previously
-produced. The ’Loop number’ column has a value of 0 if a measurement
-does not correspond to any repetition statement in the protocol and
-otherwise it grows monotonically with each repetition.
-
-If the flag ``viable_prot`` was set to false by the ``reduced_protocol``
-function, the ’Protocol line’ and ’Loop number’ columns are populated
-with the value -999.
+of measurements, the flag ``viable_prot`` is set to ``False``,
+indicating that the construction of the reduced protocol was not viable.
+
+The ``Protocol line`` and ``Loop number`` columns
+-------------------------------------------------
+The ``Protocol line`` and ``Loop number`` columns can be generated by either calling directly the function
+``novonix_add_loopnr`` or by setting to ``True`` the parameter
+``lprotocol`` when calling the function ``prepare_novonix``. The column
+Protocol line associates a measurment with its corresponding line in the
+reduced protocol. The Loop number column has a value of 0 if a
+measurement does not correspond to any repetition statement in the
+protocol and otherwise it grows monotonically with each repetition (see
+:ref:`chart`).
+
+If the flag ``viable_prot`` was set to ``False`` by the
+``reduced_protocol`` function, the Protocol line and Loop number columns
+are populated with the value -999.
 
 .. _preparenovonix: https://github.com/BatLabLancaster/preparenovonix
 

docs/index.rst

@@ -15,6 +15,7 @@ Documentation for ``preparenovonix``
    :maxdepth: 2
 
    readme_include.rst
+   overview.rst
    features.rst
    source/modules.rst