update html documentation

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public/_sources/index.rst.txt

@@ -6,6 +6,20 @@
 OHMPI: Open source and open hardware resitivity-meter 
 ===================================================== 
 
+.. sidebar:: Summary
+
+    :Release: |release|
+    :Date: |today|
+    :Authors: **Rémi CLEMENT, Nicolas FORQUET, Julien GANCE, Yannick FARGIER, Vivien DUBOIS, Hélène GUYARD**
+    :Target: users, researchers and developers 
+    :status: some mature, some in progress
+
+.. topic:: OhmPi Document Center
+
+    * OhmPi offcial documents
+    * Release guidelines
+    * General tutorials
+
 .. image:: logo_ohmpi.JPG
    :width: 200px
    :height: 150px
@@ -19,9 +33,5 @@ Contents:
    page0 
    page1
 
-Indices and tables
-==================
 
-* :ref:`genindex`
-* :ref:`modindex`
 

public/_sources/page0.rst.txt

@@ -26,7 +26,6 @@ Parteners:
    +-------------------------------+-----------------------------------+-------------------------------+-----------------------------------+
    |   .. image:: logo_inrae.jpg   |  .. image:: logo_univ_gustave.png |   .. image:: logo-iris.jpg    |  .. image:: ige.png               | 
    +-------------------------------+-----------------------------------+-------------------------------+-----------------------------------+
-   
 
 
 Creation date : Juillet 2020.
@@ -37,8 +36,7 @@ Status of document: In progress.
 
    
 **Introduction to OhmPi** 
-************************* 
-
+=========================
 
 This documentation presents the development of a low-cost, open hardware \ 
 resistivity meter to provide the scientific community with a robust \
@@ -47,7 +45,6 @@ features current injection and measurement functions associated with a multiplex
 that allows performing automatic measurements with up to 32 electrodes.\ 
 OhmPi's philosophy is to provide a fully open source and open hardware tool /
 to the near surface scientific community.
-
  
 
 .. note:: 

public/_sources/page1.rst.txt

@@ -211,6 +211,85 @@ This same operation must be repeated for the other three multiplexers as well.
 The next step consists of connecting the relay card inputs to the Raspberry Pi according to Table 5 for all four multiplexers.
 
 
++-------------------------------+-------------------------------------------+---------------------+
+|                               |Relay shield n°1                           |Relay Shield n°2     |                      
+|                               +----------+----------+----------+----------+---------------------+
+|                               |Pin 1     |Pin 2-3   |Pin 4-7   |Pin 8-16  |Pin 1- 16            |
++-------------------------------+----------+----------+----------+----------+---------------------+
+| Multiplexer A                 |12        |16        |20        |21        |26                   |
++-------------------------------+----------+----------+----------+----------+---------------------+
+| Multiplexer B                 |18        |23        |24        |25        |19                   |
++-------------------------------+----------+----------+----------+----------+---------------------+
+| Multiplexer M                 |06        |13        |04        |17        |27                   |
++-------------------------------+----------+----------+----------+----------+---------------------+
+| Multiplexer N                 |22        |10        |09        |11        |05                   |
++-------------------------------+----------+----------+----------+----------+---------------------+
+    
+	Connection of the GPIOs to each multiplexer
+
+
+Electrode connection
+*************************
+At this point, all that remains is to connect the electrodes of each multiplexer to a terminal block (Fig. 13). In our set-up, screw terminals assembled on a din rail were used. 
+According to the chosen multiplexer configuration, all the relays of each multiplexer will be connected to an electrode and, consequently, each electrode will have four incoming 
+connections. Instead of having four cables connecting an electrode terminal to each multiplexer, we recommend using the cable assembly shown in the following Figure.
+
+.. figure:: cable.jpg
+   :width: 800px
+   :align: center
+   :height: 300px
+   :alt: alternate text
+   :figclass: align-center
+
+the next figure provides an example of multiplexer relay connections for electrode no. 1: this electrode of multiplexer MUX A must be connected to electrode no. 1 of MUX B. Moreover, electrode no. 1 of MUX B 
+must be connected to electrode no. 1 of MUX N, which in turn must be connected to electrode no. 1 of MUX M. Lastly, electrode no. 1 of MUX M is connected to the terminal block. 
+This operation must be repeated for all 32 electrodes.
+
+.. figure:: electrode_cable.jpg
+   :width: 800px
+   :align: center
+   :height: 800px
+   :alt: alternate text
+   :figclass: align-center
+
+Operating instruction
+*************************
+
+Preliminary procedure (Only for the initial operation)
+======================================================
+The open source code must be downloaded at the Open Science Framework source file repository for this manuscript (https://osf.io/dzwb4/) 
+or at the following Gitlab repository address: https://gitlab.irstea.fr/reversaal/OhmPi. The code must be then unzipped into a selected folder (e.g. OhmPi-master). A “readme” file 
+is proposed in the directory to assist with installation of the software and required python packages. It is strongly recommended to create a python virtual environment for installing 
+the required packages and running the code.
+ 
+ 
+Startup procedure
+==================
+As an initial operating instruction, the 12-V battery must be disconnected before any hardware handling. Ensure that the battery is charged at full capacity. Plug all the electrodes (32 or fewer)
+into the screw terminals. The Raspberry Pi must be plugged into a computer screen, with a mouse and keyboard accessed remotely. The Raspberry Pi must then be plugged into the power supply 
+(for laboratory measurements) or a power bank (5V - 2A for field measurements). At this point, you'll need to access the Raspbian operating system. Inside the previously created folder “ohmPi”, 
+the protocol file “ABMN.txt” must be created or modified; this file contains all quadrupole ABMN numeration (an example is proposed with the source code). Some input parameters of the main “ohmpi.py” 
+function may be adjusted/optimized depending on the measurement attributes. For example, both the current injection duration and number of stacks can be adjusted. At this point, the 12-V battery can be 
+plugged into the hardware; the "ohmpi.py" source code must be run within a python3 environment (or a virtual environment if one has been created) either in the terminal or using Thonny. You should now 
+hear the characteristic sound of a relay switching as a result of electrode permutation. After each quadrupole measurement, the potential difference as well as the current intensity and resistance 
+are displayed on the screen. A measurement file is automatically created and named "measure.csv"; it will be placed in the same folder.
+
+Electrical resistivity measurement parameters description
+==========================================================
+
+.. code-block:: python
+	:linenos:
+	:lineno-start: 27
+
+	 """
+	 measurement parameters
+	 """
+	 nb_electrodes = 32 # maximum number of electrodes on the resistivity meter
+	 injection_duration = 0.5 # Current injection duration in second
+	 nbr_meas= 1 # Number of times the quadripole sequence is repeated
+	 sequence_delay= 30 # Delay in seconds between 2 sequences
+	 stack= 1 # repetition of the current injection for each quadripole
+
+The measurement parameters can be adjusted in lines 27 to 30 of the ohmpi.py code.
 
 
- 
\ No newline at end of file

public/genindex.html

@@ -82,7 +82,6 @@
             
               <ul>
 <li class="toctree-l1"><a class="reference internal" href="page0.html"><strong>OhmPi project</strong></a></li>
-<li class="toctree-l1"><a class="reference internal" href="page0.html#introduction-to-ohmpi"><strong>Introduction to OhmPi</strong></a></li>
 <li class="toctree-l1"><a class="reference internal" href="page1.html">OhmPi V 1.01 (limited to 32 electrodes)</a></li>
 </ul>
 

public/html/.buildinfo

-# Sphinx build info version 1
-# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: c73cd0e1ac8a8c304acd5706bcab5918
-tags: 645f666f9bcd5a90fca523b33c5a78b7

public/html/_sources/index.rst.txt

-.. Ohmpi documentation master file, created by
-   sphinx-quickstart on Tue Jun 30 20:22:03 2020.
-   You can adapt this file completely to your liking, but it should at least
-   contain the root `toctree` directive.
-
-OHMPI: Open source and open hardware resitivity-meter 
-===================================================== 
-
-.. sidebar:: Summary
-
-    :Release: |release|
-    :Date: |today|
-    :Authors: **Rémi CLEMENT, Nicolas FORQUET, Julien GANCE, Yannick FARGIER, Vivien DUBOIS, Hélène GUYARD**
-    :Target: users, researchers and developers 
-    :status: some mature, some in progress
-
-.. topic:: OhmPi Document Center
-
-    * OhmPi offcial documents
-    * Release guidelines
-    * General tutorials
-
-.. image:: logo_ohmpi.JPG
-   :width: 200px
-   :height: 150px
-   :align: center
-
-Contents: 
-
-.. toctree:: 
-   :maxdepth: 2 
-
-   page0 
-   page1
-
-
-

public/html/_sources/page0.rst.txt

-************ 
-Premiere page 
-************* 
-**OhmPi project** 
-************************* 
- 
-.. image:: logo_ohmpi.JPG
-   :width: 350 px
-   :align: center
-   :height: 250 px
-   :alt: Logo OhmPi
-  
-
-Authors: 
-
-| Rémi CLEMENT,Vivien DUBOIS,Nicolas Forquet, INRAE, REVERSAAL, F-69626, Villeurbanne Cedex, France.
-| Yannick FARGIER, GERS-RRO, Univ Gustave Eiffel, IFSTTAR, Univ Lyon, F-69675 Lyon, France.
-| Julien GANCE, IRIS Instruments, 45100 Orléans, France.
-| Hélène GUYARD, IGE Grenoble, Université Grenoble Alpes, Grenoble.
-
-Parteners:
-
-.. table::
-   :align: center
-  
-   +-------------------------------+-----------------------------------+-------------------------------+-----------------------------------+
-   |   .. image:: logo_inrae.jpg   |  .. image:: logo_univ_gustave.png |   .. image:: logo-iris.jpg    |  .. image:: ige.png               | 
-   +-------------------------------+-----------------------------------+-------------------------------+-----------------------------------+
-
-
-Creation date : Juillet 2020.
-
-Update : 21 août 2020.
-
-Status of document: In progress.
-
-   
-**Introduction to OhmPi** 
-=========================
-
-This documentation presents the development of a low-cost, open hardware \ 
-resistivity meter to provide the scientific community with a robust \
-and flexible tool for small-scale experiments. Called OhmPi, this basic resistivity meter\
-features current injection and measurement functions associated with a multiplexer \
-that allows performing automatic measurements with up to 32 electrodes.\ 
-OhmPi's philosophy is to provide a fully open source and open hardware tool /
-to the near surface scientific community.
- 
-
-.. note:: 
-   Everyone willing to get involved is  welcome in ohmPi Project!.
\ No newline at end of file