diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7501d059267552b510b5eb1e2a6529b57428e592..6e1207196a145cf6525fbe61067b13e19bd9cb53 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -6,15 +6,16 @@ pages:
script:
- apt-get update
- apt-get install --assume-yes pandoc
- - pip install sphinx numpydoc sphinx_rtd_theme sphinx_nbexamples pandoc
+ - pip install numpy pandas termcolor # top import of Ohmpi.py
+ - pip install sphinx numpydoc sphinx_rtd_theme pandoc recommonmark
- cd doc
- make html
# also make latex? pdf?
- cd ..
- - mv doc/_build_html/ public/
+ - mv doc/build/html/ public/
- ls public/
artifacts:
paths:
- public/
only:
- - master
\ No newline at end of file
+ - master
diff --git a/Ohmpi.py b/Ohmpi.py
index c7302d1f9a68cc2ad09940988639307e2adf21e7..81ca7339364e9487f2e4e1f813a860fea3357c58 100644
--- a/Ohmpi.py
+++ b/Ohmpi.py
@@ -1,7 +1,9 @@
+# -*- coding: utf-8 -*-
"""
created on January 6, 2020
Update February 2022
-Ohmpi.py is a program to control a low-cost and open hardward resistivity meter OhmPi that has been developed by Rémi CLEMENT(INRAE),Vivien DUBOIS(INRAE),Hélène GUYARD(IGE), Nicolas FORQUET (INRAE), and Yannick FARGIER (IFSTTAR).
+Ohmpi.py is a program to control a low-cost and open hardward resistivity meter OhmPi that has been developed by Rémi CLEMENT (INRAE),Vivien DUBOIS (INRAE),Hélène GUYARD (IGE), Nicolas FORQUET (INRAE), Yannick FARGIER (IFSTTAR)
+and Guillaume BLANCHY (ILVO).
"""
VERSION = '2.0.0'
@@ -28,16 +30,6 @@ from datetime import datetime
from termcolor import colored
import threading
-if True:
- import board, busio, adafruit_tca9548a
- import adafruit_ads1x15.ads1115 as ADS
- from adafruit_ads1x15.analog_in import AnalogIn
- from adafruit_mcp230xx.mcp23008 import MCP23008
- from adafruit_mcp230xx.mcp23017 import MCP23017
- import digitalio
- from digitalio import Direction
- from gpiozero import CPUTemperature
-
current_time = datetime.now()
print(current_time.strftime("%Y-%m-%d %H:%M:%S"))
@@ -50,22 +42,22 @@ print(current_time.strftime("%Y-%m-%d %H:%M:%S"))
class OhmPi(object):
+ """Create the main OhmPi object.
+
+ Parameters
+ ----------
+ config : str, optional
+ Path to the .json configuration file.
+ sequence : str, optional
+ Path to the .txt where the sequence is read. By default, a 1 quadrupole
+ sequence: 1, 2, 3, 4 is used.
+ onpi : bool, optional
+ True if running on the RaspberryPi. False for testing (random data generated).
+ output : str, optional
+ Either 'print' for a console output or 'mqtt' for publication onto
+ MQTT broker.
+ """
def __init__(self, config=None, sequence=None, onpi=True, output='print'):
- """Create the main OhmPi object.
-
- Parameters
- ----------
- config : str, optional
- Path to the .json configuration file.
- sequence : str, optional
- Path to the .txt where the sequence is read. By default, a 1 quadrupole
- sequence: 1, 2, 3, 4 is used.
- onpi : bool, optional
- True if running on the RaspberryPi. False for testing (random data generated).
- output : str, optional
- Either 'print' for a console output or 'mqtt' for publication onto
- MQTT broker.
- """
# flags and attributes
self.onpi = onpi # True if run from the RaspberryPi with the hardware, otherwise False for random data
self.output = output # type of output print
@@ -73,6 +65,18 @@ class OhmPi(object):
self.run = False # flag is True when measuring
self.thread = None # contains the handle for the thread taking the measurement
self.path = 'data/' # wher to save the .csv
+
+ # finish import (done only when class is instantiated as some libs are
+ # only available on arm64 platform)
+ if self.onpi:
+ import board, busio, adafruit_tca9548a
+ import adafruit_ads1x15.ads1115 as ADS
+ from adafruit_ads1x15.analog_in import AnalogIn
+ from adafruit_mcp230xx.mcp23008 import MCP23008
+ from adafruit_mcp230xx.mcp23017 import MCP23017
+ import digitalio
+ from digitalio import Direction
+ from gpiozero import CPUTemperature
# read in hardware parameters (seetings.py)
self._read_hardware_parameters()
@@ -590,8 +594,8 @@ class OhmPi(object):
self.dump('status = ' + self.status)
# test
-ohmpi = OhmPi(config='ohmpi_param.json')
-ohmpi.measure()
-time.sleep(4)
-ohmpi.stop()
+#ohmpi = OhmPi(config='ohmpi_param.json')
+#ohmpi.measure()
+#time.sleep(4)
+#ohmpi.stop()
diff --git a/Ohmpi_4elec.py b/Ohmpi_4elec.py
deleted file mode 100644
index ce3b060c1a32fa3b78366cd634655f0d701e05fe..0000000000000000000000000000000000000000
--- a/Ohmpi_4elec.py
+++ /dev/null
@@ -1,285 +0,0 @@
-"""
-created on september , 2021
-Update september 2021
-Ohmpi_4elec.py is a program to control a low-cost and open hardward resistivity meter OhmPi that has been developed by Rémi CLEMENT(INRAE),Vivien DUBOIS(INRAE),Hélène GUYARD(IGE), Nicolas FORQUET (INRAE), Oliver KAUFMANN (UMONS) and Yannick FARGIER (IFSTTAR).
-"""
-
-print('\033[1m'+'\033[31m'+' ________________________________')
-print('| _ | | | || \/ || ___ \_ _|')
-print('| | | | |_| || . . || |_/ / | |' )
-print('| | | | _ || |\/| || __/ | |')
-print('\ \_/ / | | || | | || | _| |_')
-print(' \___/\_| |_/\_| |_/\_| \___/ ')
-print('\033[0m')
-print('OhmPi 4 elec start' )
-print('Vers: 1.01')
-print('Import library')
-
-
-
-import time , board, busio, numpy, os, sys, json, glob,os.path,adafruit_tca9548a
-import adafruit_ads1x15.ads1115 as ADS
-from adafruit_ads1x15.analog_in import AnalogIn
-from pandas import DataFrame
-from datetime import datetime
-from adafruit_mcp230xx.mcp23008 import MCP23008
-from adafruit_mcp230xx.mcp23017 import MCP23017
-from termcolor import colored
-import digitalio
-from digitalio import Direction
-from gpiozero import CPUTemperature
-current_time = datetime.now()
-print(current_time.strftime("%Y-%m-%d %H:%M:%S"))
-"""
-hardware parameters
-"""
-R_shunt = 2# reference resistance value in ohm
-Imax=4800/50/2
-print(colored(('The maximum current cannot be higher than ',Imax, 'mA'), 'red'))
-
-coef_p2 = 2.50# slope for current conversion for ADS.P2, measurement in V/V
-coef_p3 = 2.50 # slope for current conversion for ADS.P3, measurement in V/V
-offset_p2= 0
-offset_p3= 0
-integer=2 #Max value 10
-meas=numpy.zeros((3,integer))
-
-"""
-import parameters
-"""
-
-with open('ohmpi_param.json') as json_file:
- pardict = json.load(json_file)
-
-
-i2c = busio.I2C(board.SCL, board.SDA) #activation du protocle I2C
-mcp = MCP23008(i2c, address=0x20) #connexion I2C MCP23008, injection de courant
-ads_current = ADS.ADS1115(i2c, gain=2/3,data_rate=128, address=0X48)# connexion ADS1115, pour la mesure de courant
-ads_voltage = ADS.ADS1115(i2c, gain=2/3,data_rate=128, address=0X49)# connexion ADS1115, pour la mesure de voltage
-#initialisation desvoie pour la polarité
-pin0 = mcp.get_pin(0)
-pin0.direction = Direction.OUTPUT
-pin1 = mcp.get_pin(1)
-pin1.direction = Direction.OUTPUT
-pin0.value = False
-pin1.value = False
-"""
-functions
-"""
-# function swtich_mux select the right channels for the multiplexer cascade for electrodes A, B, M and N.
-def switch_mux_on(quadripole):
- elec_adress=[0x76,0X71,0x74,0x70]
-
- for i in range(0,4):
- tca= adafruit_tca9548a.TCA9548A(i2c, elec_adress[i]) #choose MUX A B M or N
-
- if quadripole[i] < 17:
- nb_i2C=7
- a=quadripole[i]
- elif quadripole[i] > 16 and quadripole[i] < 33:
- nb_i2C=6
- a=quadripole[i]-16
- elif quadripole[i] > 32 and quadripole[i] < 49:
- nb_i2C=5
- a=quadripole[i]-32
- elif quadripole[i] > 48 and quadripole[i] < 65:
- nb_i2C=4
- a=quadripole[i]-48
-
- mcp2 = MCP23017(tca[nb_i2C])
- mcp2.get_pin(a-1).direction=digitalio.Direction.OUTPUT
- mcp2.get_pin(a-1).value=True
-
-def switch_mux_off(quadripole):
- elec_adress=[0x76,0X71,0x74,0x70]
-
- for i in range(0,4):
- tca= adafruit_tca9548a.TCA9548A(i2c, elec_adress[i]) #choose MUX A B M or N
-
- if quadripole[i] < 17:
- nb_i2C=7
- a=quadripole[i]
- elif quadripole[i] > 16 and quadripole[i] < 33:
- nb_i2C=6
- a=quadripole[i]-16
- elif quadripole[i] > 32 and quadripole[i] < 49:
- nb_i2C=5
- a=quadripole[i]-32
- elif quadripole[i] > 48 and quadripole[i] < 65:
- nb_i2C=4
- a=quadripole[i]-48
-
- mcp2 = MCP23017(tca[nb_i2C])
- mcp2.get_pin(a-1).direction=digitalio.Direction.OUTPUT
- mcp2.get_pin(a-1).value=False
-
-
-#function to switch off mux
-def ZERO_mux(nb_elec):
- elec_adress=[0x76,0X71,0x74,0x70]
- for i in range(0,4):
- tca= adafruit_tca9548a.TCA9548A(i2c, elec_adress[i]) #choose MUX A B M or N
- for y in range(0,nb_elec):
- qd=y+1
- if qd < 17:
- nb_i2C=7
- a=qd
- elif qd > 16 and qd < 33:
- nb_i2C=6
- a=qd-16
- elif qd > 32 and qd < 49:
- nb_i2C=5
- a=qd-32
- elif qd > 48 and qd < 65:
- nb_i2C=4
- a=qd-48
-
- mcp2 = MCP23017(tca[nb_i2C])
- mcp2.get_pin(a-1).direction=digitalio.Direction.OUTPUT
- mcp2.get_pin(a-1).value= False
-
-# function to find rows with identical values in different columns
-def find_identical_in_line(array_object):
- output = []
- if array_object.ndim == 1:
- temp = numpy.zeros(4)
- for i in range(len(array_object)):
- temp[i] = numpy.count_nonzero(array_object == array_object[i])
- if any(temp > 1):
- output.append(0)
- else:
- for i in range(len(array_object[:,1])):
- temp = numpy.zeros(len(array_object[1,:]))
- for j in range(len(array_object[1,:])):
- temp[j] = numpy.count_nonzero(array_object[i,:] == array_object[i,j])
- if any(temp > 1):
- output.append(i)
- return output
-#
-# read quadripole file and apply tests
-def read_quad(filename, nb_elec):
- output = numpy.loadtxt(filename, delimiter=" ",dtype=int) # load quadripole file
- # locate lines where the electrode index exceeds the maximum number of electrodes
- test_index_elec = numpy.array(numpy.where(output > nb_elec))
- # locate lines where an electrode is referred twice
- test_same_elec = find_identical_in_line(output)
- # if statement with exit cases (rajouter un else if pour le deuxième cas du ticket #2)
- if test_index_elec.size != 0:
- for i in range(len(test_index_elec[0,:])):
- print("Error: An electrode index at line "+ str(test_index_elec[0,i]+1)+" exceeds the maximum number of electrodes")
- sys.exit(1)
- elif len(test_same_elec) != 0:
- for i in range(len(test_same_elec)):
- print("Error: An electrode index is used twice at line " + str(test_same_elec[i]+1))
- sys.exit(1)
- else:
- return output
-
-
-def run_measurement(nb_stack, injection_deltat, R_shunt, coefp2, coefp3):
- start_time=time.time()
- # inner variable initialization
- sum_I=0
- sum_Vmn=0
- sum_Ps=0
- # injection courant and measure
- mcp = MCP23008(i2c, address=0x20)
- pin0 = mcp.get_pin(0)
- pin0.direction = Direction.OUTPUT
- pin1 = mcp.get_pin(1)
- pin1.direction = Direction.OUTPUT
- pin0.value = False
- pin1.value = False
- for n in range(0,3+2*nb_stack-1) :
- # current injection
-
- if (n % 2) == 0:
-
- pin1.value = True
- pin0.value = False # current injection polarity n°1
- else:
- pin0.value = True
- pin1.value = False# injection de courant polarity n°2
- start_delay=time.time()#stating measurement time
- time.sleep(injection_deltat) # delay depending on current injection duration
-
-# mesureament of i and u
- for k in range(0,integer):
- meas[0,k] = ((AnalogIn(ads_current,ADS.P0).voltage/50)/R_shunt)*1000 # reading current value on ADS channel A0
- meas[1,k] = AnalogIn(ads_voltage,ADS.P0).voltage * coefp2*1000
- meas[2,k] = AnalogIn(ads_voltage,ADS.P1).voltage * coefp3*1000 # reading voltage value on ADS channel A2
- pin1.value = False; pin0.value = False# stop current injection
- end_delay=time.time()
- sum_I=sum_I+(numpy.mean(meas[0,:]))
- Vmn1=((numpy.mean(meas[1,:]))-(numpy.mean(meas[2,:])))
- if (n % 2) == 0:
- sum_Vmn=sum_Vmn-Vmn1
- sum_Ps=sum_Ps+Vmn1
- else:
- sum_Vmn=sum_Vmn+Vmn1
- sum_Ps=sum_Ps+Vmn1
-
- cpu = CPUTemperature()
-
- end_calc=time.time()
- time.sleep(2*(end_delay-start_delay)-(end_calc-start_delay))
- #end_sleep2=time.time()
- #print(['sleep=',((end_sleep2-start_delay))])
-
- #print(['true delta=',((end_delay-start_delay)-injection_deltat)])
- #print(['time stop=',((2*(end_delay-start_delay)-(end_calc-start_delay)))])
- # return averaged values
-# cpu= CPUTemperature()
- output = DataFrame({
- "time":[datetime.now()],
- "A":[(1)],
- "B":[(2)],
- "M":[(3)],
- "N":[(4)],
- "inj time [ms]" : (end_delay-start_delay)*1000,
- "Vmn [mV]":[(sum_Vmn/(3+2*nb_stack-1))],
- "I [mA]":[(sum_I/(3+2*nb_stack-1))],
- "R [ohm]":[( (sum_Vmn/(3+2*nb_stack-1)/(sum_I/(3+2*nb_stack-1))))],
- "Ps [mV]":[(sum_Ps/(3+2*nb_stack-1))],
- "nbStack":[nb_stack],
- "CPU temp [°C]":[cpu.temperature],
- "Time [S]":[(-start_time+time.time())],
- "Integer [-]": [integer]
-
-
-
- # Dead time equivalent to the duration of the current injection pulse
- })
- output=output.round(2)
- print(output.to_string())
- time.sleep(1)
- return output
-
-# save data
-def append_and_save(path, last_measurement):
-
- if os.path.isfile(path):
- # Load data file and append data to it
- with open(path, 'a') as f:
- last_measurement.to_csv(f, header=False)
- else:
- # create data file and add headers
- with open(path, 'a') as f:
- last_measurement.to_csv(f, header=True)
-
-
-"""
-Main loop
-"""
-for g in range(0,pardict.get("nbr_meas")): # for time-lapse monitoring
-
-
-
-
- current_measurement = run_measurement(pardict.get("stack"), pardict.get("injection_duration"), R_shunt, coef_p2, coef_p3)
-
- append_and_save(pardict.get("export_path"), current_measurement)
-
-
-
- time.sleep(pardict.get("sequence_delay")) #waiting next measurement (time-lapse)
diff --git a/doc/docker.sh b/doc/docker.sh
new file mode 100644
index 0000000000000000000000000000000000000000..ba1ccdee08c7b8c407031638c1ae9db692fd28e9
--- /dev/null
+++ b/doc/docker.sh
@@ -0,0 +1,4 @@
+# to test documentation build using same environemnet as gitlab doc runner
+
+docker run -it -v /media/jkl/data/ilvo/ohmpi/OhmP:/OhmPi python:3.9-bullseye bash
+
diff --git a/doc/running_html.py b/doc/running_html.py
deleted file mode 100644
index 27194cada6965c089aea87a7e4dbdf46e3bb473b..0000000000000000000000000000000000000000
--- a/doc/running_html.py
+++ /dev/null
@@ -1,9 +0,0 @@
-# -*- coding: utf-8 -*-
-"""
-Created on Mon Jul 13 21:48:00 2020
-
-@author: remi.clement
-"""
-
-import shutil
-
diff --git a/doc/source/Ohmpi.rst b/doc/source/Ohmpi.rst
index 9eb52792be48c3ef115bcbf4ee0caaa0740d2595..5a3cab23f61497ada19f9b7bceedf3980a3155ad 100644
--- a/doc/source/Ohmpi.rst
+++ b/doc/source/Ohmpi.rst
@@ -13,12 +13,12 @@ OhmPi project
**Authors:**
------------
-| Rémi CLEMENT,Vivien DUBOIS,Nicolas Forquet, INRAE, REVERSAAL, Villeurbanne, France.
-| Yannick FARGIER, GERS-RRO, Univ Gustave Eiffel, IFSTTAR, Lyon, France.
-| Julien GANCE, IRIS Instruments, Orléans, France.
-| Hélène GUYARD, IGE Grenoble, Université Grenoble Alpes, Grenoble, France.
+| Rémi CLEMENT,Vivien DUBOIS,Nicolas Forquet, INRAE, REVERSAAL, Villeurbanne, France
+| Yannick FARGIER, GERS-RRO, Univ Gustave Eiffel, IFSTTAR, Lyon, France
+| Julien GANCE, IRIS Instruments, Orléans, France
+| Hélène GUYARD, IGE Grenoble, Université Grenoble Alpes, Grenoble, France
| Olivier Kaufmann, Université de Mons, Mons, Belgium
-| Guillaume Banchy, ILVO,Merelbeke, Belgium
+| Guillaume Banchy, ILVO, Merelbeke, Belgium
|
@@ -62,4 +62,4 @@ to the near surface scientific community.
.. note::
- Everyone willing to get involved is welcome in OhmPi Project!.
\ No newline at end of file
+ Everyone willing to get involved is welcome in OhmPi Project!.
diff --git a/doc/source/api.rst b/doc/source/api.rst
new file mode 100644
index 0000000000000000000000000000000000000000..c1157b20f6f7090299118d1b70501ae0202d961a
--- /dev/null
+++ b/doc/source/api.rst
@@ -0,0 +1,9 @@
+API reference
+=============
+.. toctree::
+ :maxdepth: 2
+ :caption: Contents:
+.. automodule:: Ohmpi
+ :members:
+
+
diff --git a/doc/source/conf.py b/doc/source/conf.py
index 803d3705b28c413470cba85220848998b722eb16..d40917b39b5b6356a9a2ea5929b02072cf67942d 100644
--- a/doc/source/conf.py
+++ b/doc/source/conf.py
@@ -1,3 +1,5 @@
+# -*- coding: utf-8 -*-
+
# Configuration file for the Sphinx documentation builder.
#
# This file only contains a selection of the most common options. For a full
@@ -12,15 +14,16 @@
#
import os
import sys
-# sys.path.insert(0, os.path.abspath('.'))
+sys.path.append(os.path.abspath('../..'))
+import Ohmpi # import Ohmpi module to be documented in api.rst by numpydoc
import sphinx_rtd_theme
from shutil import copyfile
# -- Project information -----------------------------------------------------
-project = 'Ohmpi:'
-copyright = '2022, INRAE, Team Ohmpi'
+project = 'OhmPi'
+copyright = '2022, INRAE, Team OhmPi'
author = 'Rémi CLEMENT'
# The full version, including alpha/beta/rc tags
@@ -30,8 +33,17 @@ release = 'open hardware resistivity-meter'
# -- General configuration ---------------------------------------------------
-extensions = ['recommonmark']
+extensions = [
+ 'sphinx.ext.autodoc',
+ 'sphinx.ext.coverage',
+ 'sphinx.ext.mathjax',
+ 'numpydoc',
+ 'recommonmark'
+]
+
+
+numpydoc_show_class_members = False
# Add any paths that contain templates here, relative to this directory.
diff --git a/doc/source/index.rst b/doc/source/index.rst
index 7ae7b05dc7509c2e505a4953a7b9efc74767d368..ccbf3e772af1caef76011d907450b62688bddd5a 100644
--- a/doc/source/index.rst
+++ b/doc/source/index.rst
@@ -37,6 +37,7 @@ Contents:
V1_01
V1_02
V2_00
+ api