diff --git a/configs/config_mb_2023_4_mux_2023.py b/configs/config_mb_2023_4_mux_2023.py
new file mode 100644
index 0000000000000000000000000000000000000000..dbfe0b8f20ce1e846e41e0cd67170ecae8a5d776
--- /dev/null
+++ b/configs/config_mb_2023_4_mux_2023.py
@@ -0,0 +1,141 @@
+import logging
+from ohmpi.utils import get_platform
+
+from paho.mqtt.client import MQTTv31 # noqa
+
+_, on_pi = get_platform()
+# DEFINE THE ID OF YOUR OhmPi
+ohmpi_id = '0001' if on_pi else 'XXXX'
+# DEFINE YOUR MQTT BROKER (DEFAULT: 'localhost')
+mqtt_broker = 'localhost' if on_pi else 'NAME_YOUR_BROKER_WHEN_IN_SIMULATION_MODE_HERE'
+# DEFINE THE SUFFIX TO ADD TO YOUR LOGS FILES
+logging_suffix = ''
+
+# OhmPi configuration
+OHMPI_CONFIG = {
+ 'id': ohmpi_id, # Unique identifier of the OhmPi board (string)
+ 'settings': 'ohmpi_settings.json', # INSERT YOUR FAVORITE SETTINGS FILE HERE
+}
+
+HARDWARE_CONFIG = {
+ 'ctl': {'model': 'raspberry_pi'},
+ 'pwr': {'model': 'pwr_batt', 'voltage': 12., 'interface_name': 'none'},
+ 'tx': {'model': 'mb_2023_0_X',
+ 'voltage_max': 12., # Maximum voltage supported by the TX board [V]
+ 'adc_voltage_max': 4800., # Maximum voltage read by the current ADC on the TX board [mA]
+ 'r_shunt': 2., # Shunt resistance in Ohms
+ 'interface_name': 'i2c',
+ },
+ 'rx': {'model': 'mb_2023_0_X',
+ 'coef_p2': 2.50, # slope for conversion for ADS, measurement in V/V
+ 'sampling_rate': 50., # number of samples per second
+ 'interface_name': 'i2c',
+ },
+ 'mux': # default properties given in config are system properties that will be
+ # overwritten by properties defined in each the board dict below.
+ # if defined in board specs, values out of specs will be bounded to remain in specs
+ # omitted properties in config will be set to board specs default values if they exist
+ {'boards':
+ {'mux_A':
+ {'model': 'mux_2023_0_X',
+ 'mux_tca_address': 0x70,
+ 'roles': {'A': 'X'},
+ 'cabling': {(i, j): ('mux_A', i) for j in ['A'] for i in range(1, 65)},
+ 'voltage_max': 12.},
+ 'mux_B':
+ {'model': 'mux_2023_0_X',
+ 'mux_tca_address': 0x71,
+ 'roles': {'B': 'X'},
+ 'cabling': {(i, j): ('mux_B', i) for j in ['B'] for i in range(1, 65)},
+ 'voltage_max': 12.},
+ 'mux_M':
+ {'model': 'mux_2023_0_X',
+ 'mux_tca_address': 0x72,
+ 'roles': {'M': 'X'},
+ 'cabling': {(i, j): ('mux_M', i) for j in ['M'] for i in range(1, 65)},
+ 'voltage_max': 12.},
+ 'mux_N':
+ {'model': 'mux_2023_0_X',
+ 'mux_tca_address': 0x73,
+ 'roles': {'N': 'X'},
+ 'cabling': {(i, j): ('mux_N', i) for j in ['N'] for i in range(1, 65)},
+ 'voltage_max': 12.},
+ },
+ 'default': {'interface_name': 'i2c',
+ 'voltage_max': 12.,
+ 'current_max': 3.}
+ }
+}
+
+# SET THE LOGGING LEVELS, MQTT BROKERS AND MQTT OPTIONS ACCORDING TO YOUR NEEDS
+# Execution logging configuration
+EXEC_LOGGING_CONFIG = {
+ 'logging_level': logging.DEBUG, # TODO: set logging level back to INFO
+ 'log_file_logging_level': logging.DEBUG,
+ 'logging_to_console': True,
+ 'file_name': f'exec{logging_suffix}.log',
+ 'max_bytes': 262144,
+ 'backup_count': 30,
+ 'when': 'd',
+ 'interval': 1
+}
+
+# Data logging configuration
+DATA_LOGGING_CONFIG = {
+ 'logging_level': logging.INFO,
+ 'logging_to_console': True,
+ 'file_name': f'data{logging_suffix}.log',
+ 'max_bytes': 16777216,
+ 'backup_count': 1024,
+ 'when': 'd',
+ 'interval': 1
+}
+
+# State of Health logging configuration (For a future release)
+SOH_LOGGING_CONFIG = {
+ 'logging_level': logging.INFO,
+ 'logging_to_console': True,
+ 'log_file_logging_level': logging.DEBUG,
+ 'file_name': f'soh{logging_suffix}.log',
+ 'max_bytes': 16777216,
+ 'backup_count': 1024,
+ 'when': 'd',
+ 'interval': 1
+}
+
+# MQTT logging configuration parameters
+MQTT_LOGGING_CONFIG = {
+ 'hostname': mqtt_broker,
+ 'port': 1883,
+ 'qos': 2,
+ 'retain': False,
+ 'keepalive': 60,
+ 'will': None,
+ 'auth': {'username': 'mqtt_user', 'password': 'mqtt_password'},
+ 'tls': None,
+ 'protocol': MQTTv31,
+ 'transport': 'tcp',
+ 'client_id': f'{OHMPI_CONFIG["id"]}',
+ 'exec_topic': f'ohmpi_{OHMPI_CONFIG["id"]}/exec',
+ 'exec_logging_level': logging.DEBUG,
+ 'data_topic': f'ohmpi_{OHMPI_CONFIG["id"]}/data',
+ 'data_logging_level': DATA_LOGGING_CONFIG['logging_level'],
+ 'soh_topic': f'ohmpi_{OHMPI_CONFIG["id"]}/soh',
+ 'soh_logging_level': SOH_LOGGING_CONFIG['logging_level']
+}
+
+# MQTT control configuration parameters
+MQTT_CONTROL_CONFIG = {
+ 'hostname': mqtt_broker,
+ 'port': 1883,
+ 'qos': 2,
+ 'retain': False,
+ 'keepalive': 60,
+ 'will': None,
+ 'auth': {'username': 'mqtt_user', 'password': 'mqtt_password'},
+ 'tls': None,
+ 'protocol': MQTTv31,
+ 'transport': 'tcp',
+ 'client_id': f'{OHMPI_CONFIG["id"]}',
+ 'ctrl_topic': f'ohmpi_{OHMPI_CONFIG["id"]}/ctrl'
+}
diff --git a/configs/config_mb_2023_4_mux_2024.py b/configs/config_mb_2023_4_mux_2024.py
new file mode 100644
index 0000000000000000000000000000000000000000..19254ca112b0526895b64adb6afb23b1ace95ee0
--- /dev/null
+++ b/configs/config_mb_2023_4_mux_2024.py
@@ -0,0 +1,152 @@
+import logging
+from ohmpi.utils import get_platform
+from paho.mqtt.client import MQTTv31 # noqa
+
+_, on_pi = get_platform()
+# DEFINE THE ID OF YOUR OhmPi
+ohmpi_id = '0001' if on_pi else 'XXXX'
+# DEFINE YOUR MQTT BROKER (DEFAULT: 'localhost')
+mqtt_broker = 'localhost' if on_pi else 'NAME_YOUR_BROKER_WHEN_IN_SIMULATION_MODE_HERE'
+# DEFINE THE SUFFIX TO ADD TO YOUR LOGS FILES
+logging_suffix = ''
+
+# OhmPi configuration
+OHMPI_CONFIG = {
+ 'id': ohmpi_id, # Unique identifier of the OhmPi board (string)
+ 'settings': 'ohmpi_settings.json', # INSERT YOUR FAVORITE SETTINGS FILE HERE
+}
+
+HARDWARE_CONFIG = {
+ 'ctl': {'model': 'raspberry_pi'},
+ 'pwr': {'model': 'pwr_batt', 'voltage': 12., 'interface_name': 'none'},
+ 'tx': {'model': 'mb_2023_0_X',
+ 'voltage_max': 12., # Maximum voltage supported by the TX board [V]
+ 'adc_voltage_max': 4800., # Maximum voltage read by the current ADC on the TX board [mA]
+ 'r_shunt': 2., # Shunt resistance in Ohms
+ 'interface_name': 'i2c',
+ },
+ 'rx': {'model': 'mb_2023_0_X',
+ 'coef_p2': 2.50, # slope for conversion for ADS, measurement in V/V
+ 'sampling_rate': 50., # number of samples per second
+ 'interface_name': 'i2c',
+ },
+ 'mux': {'boards':
+ {'mux_02':
+ {'model': 'mux_2024_0_X',
+ 'tca_address': None,
+ 'tca_channel': 0,
+ 'addr2': 'up',
+ 'addr1': 'up',
+ # 'mcp_0': '0x26',
+ # 'mcp_1': '0x27',
+ 'roles': {'A': 'X', 'B': 'Y', 'M': 'XX', 'N': 'YY'},
+ 'cabling': {(i+8, j): ('mux_02', i) for j in ['A', 'B', 'M', 'N'] for i in range(1, 9)},
+ 'voltage_max': 12.},
+ 'mux_03':
+ {'model': 'mux_2024_0_X',
+ 'tca_address': None,
+ 'tca_channel': 0,
+ 'addr2': 'down',
+ 'addr1': 'up',
+ # 'mcp_0': '0x26',
+ # 'mcp_1': '0x27',
+ 'roles': {'A': 'X', 'B': 'Y', 'M': 'XX', 'N': 'YY'},
+ 'cabling': {(i+24, j): ('mux_03', i) for j in ['A', 'B', 'M', 'N'] for i in range(1, 9)},
+ 'voltage_max': 12.},
+ 'mux_05':
+ {'model': 'mux_2024_0_X',
+ 'tca_address': None,
+ 'tca_channel': 0,
+ 'addr2': 'up',
+ 'addr1': 'down',
+ 'roles': {'A': 'X', 'B': 'Y', 'M': 'XX', 'N': 'YY'},
+ 'cabling': {(i+0, j): ('mux_05', i) for j in ['A', 'B', 'M', 'N'] for i in range(1, 9)},
+ 'voltage_max': 12.},
+ 'mux_06':
+ {'model': 'mux_2024_0_X',
+ 'tca_address': None,
+ 'tca_channel': 0,
+ 'addr2': 'down',
+ 'addr1': 'down',
+ 'roles': {'A': 'X', 'B': 'Y', 'M': 'XX', 'N': 'YY'},
+ 'cabling': {(i+16, j): ('mux_06', i) for j in ['A', 'B', 'M', 'N'] for i in range(1, 9)},
+ 'voltage_max': 12.},
+ },
+ 'default': {'interface_name': 'i2c_ext',
+ 'voltage_max': 100.,
+ 'current_max': 3.}
+ }
+ }
+
+# SET THE LOGGING LEVELS, MQTT BROKERS AND MQTT OPTIONS ACCORDING TO YOUR NEEDS
+# Execution logging configuration
+EXEC_LOGGING_CONFIG = {
+ 'logging_level': logging.INFO,
+ 'log_file_logging_level': logging.DEBUG,
+ 'logging_to_console': True,
+ 'file_name': f'exec{logging_suffix}.log',
+ 'max_bytes': 262144,
+ 'backup_count': 30,
+ 'when': 'd',
+ 'interval': 1
+}
+
+# Data logging configuration
+DATA_LOGGING_CONFIG = {
+ 'logging_level': logging.INFO,
+ 'logging_to_console': True,
+ 'file_name': f'data{logging_suffix}.log',
+ 'max_bytes': 16777216,
+ 'backup_count': 1024,
+ 'when': 'd',
+ 'interval': 1
+}
+
+# State of Health logging configuration (For a future release)
+SOH_LOGGING_CONFIG = {
+ 'logging_level': logging.INFO,
+ 'logging_to_console': True,
+ 'log_file_logging_level': logging.DEBUG,
+ 'file_name': f'soh{logging_suffix}.log',
+ 'max_bytes': 16777216,
+ 'backup_count': 1024,
+ 'when': 'd',
+ 'interval': 1
+}
+
+# MQTT logging configuration parameters
+MQTT_LOGGING_CONFIG = {
+ 'hostname': mqtt_broker,
+ 'port': 1883,
+ 'qos': 2,
+ 'retain': False,
+ 'keepalive': 60,
+ 'will': None,
+ 'auth': {'username': 'mqtt_user', 'password': 'mqtt_password'},
+ 'tls': None,
+ 'protocol': MQTTv31,
+ 'transport': 'tcp',
+ 'client_id': f'{OHMPI_CONFIG["id"]}',
+ 'exec_topic': f'ohmpi_{OHMPI_CONFIG["id"]}/exec',
+ 'exec_logging_level': logging.DEBUG,
+ 'data_topic': f'ohmpi_{OHMPI_CONFIG["id"]}/data',
+ 'data_logging_level': DATA_LOGGING_CONFIG['logging_level'],
+ 'soh_topic': f'ohmpi_{OHMPI_CONFIG["id"]}/soh',
+ 'soh_logging_level': SOH_LOGGING_CONFIG['logging_level']
+}
+
+# MQTT control configuration parameters
+MQTT_CONTROL_CONFIG = {
+ 'hostname': mqtt_broker,
+ 'port': 1883,
+ 'qos': 2,
+ 'retain': False,
+ 'keepalive': 60,
+ 'will': None,
+ 'auth': {'username': 'mqtt_user', 'password': 'mqtt_password'},
+ 'tls': None,
+ 'protocol': MQTTv31,
+ 'transport': 'tcp',
+ 'client_id': f'{OHMPI_CONFIG["id"]}',
+ 'ctrl_topic': f'ohmpi_{OHMPI_CONFIG["id"]}/ctrl'
+}
diff --git a/dev/start_mqtt_html.py b/dev/start_mqtt_html.py
new file mode 100644
index 0000000000000000000000000000000000000000..67b66851c3edb9b0ca6fbec9a80c33da06e58e0d
--- /dev/null
+++ b/dev/start_mqtt_html.py
@@ -0,0 +1,18 @@
+
+# we need to start the OhmPi instance so that it listens
+# to message from the MQTT broker
+
+import subprocess
+# launch webserver
+
+from ohmpi.utils import change_config
+change_config('../configs/config_mb_2023.py', verbose=False)
+
+from ohmpi.ohmpi import OhmPi
+from ohmpi.config import OHMPI_CONFIG
+ohmpi = OhmPi(settings=OHMPI_CONFIG['settings'])
+if ohmpi.controller is not None:
+ ohmpi.controller.loop_forever()
+
+# restore default config
+change_config('../configs/config_default.py', verbose=False)
diff --git a/dev/test_inv.py b/dev/test_inv.py
index b212d585b5f0fa9156a9b84fce37ddf10f95d479..40a5791e541d8e8a1412ed8c53209de23f4297bb 100644
--- a/dev/test_inv.py
+++ b/dev/test_inv.py
@@ -1,12 +1,32 @@
-#
+import matplotlib.pyplot as plt
+import matplotlib
+matplotlib.use('TkAgg')
+
+import numpy as np
from ohmpi.utils import change_config
change_config('../configs/config_mb_2023.py', verbose=False)
from ohmpi.ohmpi import OhmPi
k = OhmPi()
-k.run_inversion(['measurement_20220206T194552.csv'])
+# single inversion
+#k.run_inversion(['measurement_20220206T194552.csv'])
+
+# batch inversion
+xzv = k.run_inversion([
+ 'measurement_20220206T194752.csv',
+ 'measurement_20220206T194852.csv',
+], reg_mode=0)
+# make a contour figure with the output
+fig, axs = plt.subplots(len(xzv), 1, sharex=True, sharey=True, figsize=(10, 6))
+axs = [axs] if len(xzv) == 1 else axs
+for i, dic in enumerate(xzv):
+ ax = axs[i]
+ x, z = np.meshgrid(dic['x'], dic['z'])
+ cax = ax.contourf(x, z, dic['rho'])
+ fig.colorbar(cax, ax=ax, label=r'$\rho$ [$\Omega$.m]')
+plt.show(block=True)
# restore default config
change_config('../configs/config_default.py', verbose=False)
diff --git a/dev/test_mb_2023_4_mux_2023.py b/dev/test_mb_2023_4_mux_2023.py
new file mode 100644
index 0000000000000000000000000000000000000000..057c3bba07d4d45f84e97a62dc0d20cf49f3c13a
--- /dev/null
+++ b/dev/test_mb_2023_4_mux_2023.py
@@ -0,0 +1,108 @@
+import matplotlib
+matplotlib.use('TkAgg')
+from ohmpi.utils import change_config
+change_config('../configs/config_mb_2023_4_mux_2023.py', verbose=False)
+import importlib
+import os
+import time
+import logging
+from ohmpi.config import HARDWARE_CONFIG
+
+stand_alone = False
+part_of_hardware_system = False
+within_ohmpi = True
+
+# Stand alone
+if stand_alone:
+
+ ctl_module = importlib.import_module(f'ohmpi.hardware_components.{HARDWARE_CONFIG["ctl"].pop("model")}')
+ pwr_module = importlib.import_module(f'ohmpi.hardware_components.{HARDWARE_CONFIG["pwr"].pop("model")}')
+ tx_module = importlib.import_module(f'ohmpi.hardware_components.{HARDWARE_CONFIG["tx"].pop("model")}')
+ rx_module = importlib.import_module(f'ohmpi.hardware_components.{HARDWARE_CONFIG["rx"].pop("model")}')
+
+ ctl = ctl_module.Ctl()
+ HARDWARE_CONFIG['tx'].update({'ctl': ctl, 'exec_logger': ctl.exec_logger, 'soh_logger': ctl.soh_logger})
+ HARDWARE_CONFIG['rx'].update({'ctl': ctl, 'exec_logger': ctl.exec_logger, 'soh_logger': ctl.soh_logger})
+ HARDWARE_CONFIG['tx'].update({'connection': HARDWARE_CONFIG['tx'].pop('connection',
+ ctl.interfaces[
+ HARDWARE_CONFIG['tx'].pop(
+ 'interface_name', 'i2c')])})
+ HARDWARE_CONFIG['rx'].update({'connection': HARDWARE_CONFIG['rx'].pop('connection',
+ ctl.interfaces[
+ HARDWARE_CONFIG['rx'].pop(
+ 'interface_name', 'i2c')])})
+
+ HARDWARE_CONFIG['pwr'].update({'connection': HARDWARE_CONFIG['pwr'].pop('connection',
+ ctl.interfaces[
+ HARDWARE_CONFIG['pwr'].pop(
+ 'interface_name', None)])})
+
+
+ rx = rx_module.Rx(**HARDWARE_CONFIG['rx'])
+ tx = tx_module.Tx(**HARDWARE_CONFIG['tx'])
+ pwr = pwr_module.Pwr(**HARDWARE_CONFIG['pwr'])
+
+ role = 'A'
+ mux_id = f'mux_{role}'
+ mux_boards = []
+ mux_module = importlib.import_module(
+ f'ohmpi.hardware_components.{HARDWARE_CONFIG["mux"]["boards"][mux_id].pop("model")}')
+
+ MUX_CONFIG = HARDWARE_CONFIG['mux']['boards'][mux_id]
+
+ MUX_CONFIG.update({'ctl': ctl, 'connection': MUX_CONFIG.pop('connection', ctl.interfaces[
+ MUX_CONFIG.pop('interface_name', 'i2c_ext')]), 'exec_logger': ctl.exec_logger,
+ 'soh_logger': ctl.soh_logger})
+ MUX_CONFIG.update({'id': mux_id})
+ mux = mux_module.Mux(**MUX_CONFIG)
+ mux.reset()
+
+ mux.test({role: [i for i in range(1, 65)]}, activation_time=.5)
+ mux.reset()
+
+# mux as part of a OhmPiHardware system
+if part_of_hardware_system:
+ from ohmpi.hardware_system import OhmPiHardware
+ print('Starting test of as part of an OhmPiHardware system.')
+ # mux_id = 'mux_03'
+ k = OhmPiHardware()
+ k.exec_logger.setLevel(logging.DEBUG)
+ # Test mux switching
+ k.reset_mux()
+ # k.switch_mux(electrodes=[1, 4, 2, 3], roles=['A', 'B', 'M', 'N'], state='on')
+ # time.sleep(1.)
+ # k.switch_mux(electrodes=[1, 4, 2, 3], roles=['A', 'B', 'M', 'N'], state='off')
+ # k.mux_boards[mux_id].test(activation_time=.4)
+ k.test_mux()
+ k.reset_mux()
+
+if within_ohmpi:
+ from ohmpi.ohmpi import OhmPi
+ # from ohmpi.plots import plot_exec_log
+
+ print('Starting test with OhmPi.')
+ k = OhmPi()
+ k.load_sequence(os.path.join(os.path.dirname(__file__), '../sequences/01_GRAD_8_s4_a4.txt'))
+ k.reset_mux()
+ # k.test_mux(mux_id=None, activation_time=0.2)
+ # k._hw.switch_mux([A, B, M, N], state='on')
+ # k._hw.vab_square_wave(12.,1., cycles=2)
+ # k._hw.switch_mux([A, B, M, N], state='off')
+ # k._hw.calibrate_rx_bias() # electrodes 1 4 2 3 should be connected to a reference circuit
+ # k._hw.rx._bias = -1.38
+ # print(f'Resistance: {k._hw.last_rho :.2f} ohm, dev. {k._hw.last_dev:.2f} %, rx bias: {k._hw.rx._bias:.2f} mV')
+ # k._hw._plot_readings()
+ # k._hw.switch_mux([A, B, M, N], state='on')
+ # k._hw.vab_square_wave(12., cycle_duration=10., cycles=3)
+ # k._hw.switch_mux([A, B, M, N], state='off')
+ # print(f'OhmPiHardware Resistance: {k._hw.last_rho :.2f} ohm, dev. {k._hw.last_dev:.2f} %, rx bias: {k._hw.rx._bias:.2f} mV')
+ # k._hw._plot_readings()
+ A, B, M, N = (1, 4, 2, 3)
+ d = k.run_measurement([A, B, M, N], injection_duration=2., nb_stack=2, duty_cycle=0.5)
+ print(d)
+ # k._hw._plot_readings()
+ print(f'OhmPiHardware: Resistance: {k._hw.last_resistance() :.2f} ohm, dev. {k._hw.last_dev():.2f} %, sp: {k._hw.sp:.2f} mV, rx bias: {k._hw.rx._bias:.2f} mV')
+ print(f'OhmPi: Resistance: {d["R [ohm]"] :.2f} ohm, dev. {d["R_std [%]"]:.2f} %, rx bias: {k._hw.rx._bias:.2f} mV')
+ k._hw._plot_readings(save_fig=False)
+ # plot_exec_log('ohmpi/logs/exec.log')
+change_config('../configs/config_default.py', verbose=False)
diff --git a/html/index.html b/html/index.html
deleted file mode 100644
index b334d18b47d1f8ab64e32028a15fac4c0b513d7e..0000000000000000000000000000000000000000
--- a/html/index.html
+++ /dev/null
@@ -1,704 +0,0 @@
-<!DOCTYPE html>
-<html>
-<head>
- <meta charset="utf8"/>
- <title>OhmPi Acquisition Board</title>
- <link rel="shortcut icon" type="image/jpg" href="logo_ohmpi.jpg"/>
-
- <!-- dependencies (need to be local as no internet in AP mode)-->
- <script src="js/plotly-basic-2.8.3.min.js"></script>
- <script src="js/jquery-3.4.1.min.js"></script>
- <link type="text/css" href="css/bootstrap.min.css" rel="stylesheet">
- <!-- <script src="https://code.jquery.com/jquery-3.4.1.min.js"></script> -->
- <!-- <link href="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/css/bootstrap.min.css" rel="stylesheet" integrity="sha384-eOJMYsd53ii+scO/bJGFsiCZc+5NDVN2yr8+0RDqr0Ql0h+rP48ckxlpbzKgwra6" crossorigin="anonymous"> -->
- <!-- <script src="js/danfojs/bundle.min.js"></script> -->
-</head>
-<body>
- <div class='container'>
- <h1>OhmPi Acquisition Board</h1>
- <!-- nb stacks, on-time -->
- <button id="update_settingsBtn" type="button" class="btn btn-secondary" data-toggle="modal" data-target="#exampleModal">Settings</button>
- <button id='runBtn' type="button" class="btn btn-primary">▶</button>
- <button id='stopBtn' type="button" class="btn btn-warning">◼</button>
- <!-- upload button for csv which display the table ABMN -->
- <button id="removeDataBtn" type="button" class="btn btn-danger">Clear data</button>
- <button id="getDataBtn" type="button" class="btn btn-info">Get data</button>
- <div class="form-check">
- <input id="dataRetrievalCheck" class="form-check-input" type="checkbox" value="">
- <label class="form-check-label" for="dataRetrievalCheck">
- Automaticaly get data every 1 second
- </label>
- </div>
- <div id='output'>Status: idle</div>
-
- <!-- Pseudo section -->
- <select id='surveySelect' class='custom-select'>
- </select>
- <input id="cmin" type="number" value=""/>
- <input id="cmax" type="number" value=""/>
- <button id="capplyBtn" type="button" class="btn btn-info">Apply</button>
- <div id="gd"></div>
- <div id="hoverinfo" style="margin-left:80px;"></div>
- <div class="mb3 row">
- <label for="quadSelect">Quadrupole:</label>
- <div class="col-sm-10">
- <select id='quadSelect' class='custom-select'></select>
- </div>
- </div>
-
- <!-- trace figure -->
- <button id="addTraceBtn" type="button" class="btn btn-info">Add trace</button>
- <button id="removeTracesBtn" type="button" class="btn btn-info">Remove all traces</button>
- <div id="ts"></div>
-
- <!-- RS check -->
- <button id="rsBtn" type="button" class="btn btn-info">Check contact resistance</button>
- <button id="getRsBtn" type="button" class="btn btn-info">Get contact resistance</button>
- <button id="rsClearBtn" type="button" class="btn btn-info">Clear plot</button>
- <div id="rs"></div>
-
- <!-- Additional buttons -->
- <button id="downloadBtn" type="button" class="btn btn-primary">Download data</button>
- <!-- <button id="invertBtn" type="button" class="btn btn-primary">Invert</button> -->
- <a id="download"></a>
-
- <!-- Modal for settings -->
- <div class="modal fade" id="exampleModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
- <div class="modal-dialog" role="document">
- <div class="modal-content">
- <div class="modal-header">
- <h5 class="modal-title" id="exampleModalLabel">OhmPi settings</h5>
- <button type="button" class="close" data-dismiss="modal" aria-label="Close">
- <span aria-hidden="true">×</span>
- </button>
- </div>
- <div class="modal-body">
- <form>
- <div class="form-group row">
- <label for="nbElectrodes" class="col-sm-2 col-form-label">Nb electrodes</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbElectrodes" value=64>
- </div>
- </div>
- <div class="form-group row">
- <label for="injectionDuration" class="col-sm-2 col-form-label">Injection duration [s]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="injectionDuration" value=0.2>
- </div>
- </div>
- <div class="form-group row">
- <label for="nbMeasurements" class="col-sm-2 col-form-label">Nb Measurements</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbMeasurements" value="1">
- </div>
- </div>
- <div class="form-group row">
- <label for="sequenceDelay" class="col-sm-2 col-form-label">Sequence delay [s]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="sequenceDelay" value="100">
- </div>
- </div>
- <div class="form-group row">
- <label for="nbStack" class="col-sm-2 col-form-label">Nb stack</label>
- <div class="col-sm-10">
- <input type="number" class="form-control-number" id="nbStack" value="1">
- </div>
- </div>
- <div class="form-group row">
- <label for="sequence" class="col-sm-2 col-form-label">Sequence</label>
- <div class="col-sm-10">
- <input type="file" class="form-control" id="sequence">
- </div>
- </div>
- <div class="form-group row">
- <label for="elecSpacing" class="col-sm-2 col-form-label">Electrode spacing [m]</label>
- <div class="col-sm-10">
- <input type="number" class="form-control" id="elecSpacing", value="1">
- </div>
- </div>
- </form>
- </div>
- <div class="modal-footer">
- <button type="button" class="btn btn-secondary" data-dismiss="modal">Cancel</button>
- <button id="saveConfigBtn" type="button" data-dismiss="modal" class="btn btn-primary">Save</button>
- </div>
- </div>
- </div>
- </div>
- <button id="restartBtn" type="button" class="btn btn-danger">Restart</button>
- <button id="shutdownBtn" type="button" class="btn btn-danger">Shutdown</button>
- <footer>v0.2.0</footer>
- </div>
-
- <script type="text/javascript">
- //let serverUrl = 'http://10.3.141.1:8080'
- //let serverUrl = 'http://0.0.0.0:8080'
- //let serverUrl = 'http://localhost:8080'
- let serverUrl = 'http://' + window.location.host
- console.log('serverUrl =', serverUrl)
- let output = document.getElementById('output')
- let data = {} // hold data of all surveys
- let interv = null // hold interval for automatic data retrieval
- let quads = [] // available quadrupoles for time-serie figure
- let squads = [] // selected quadrupoles for time-serie figure
- let elecSpacing = 1 // 1 m
-
- // useful functions
- function sendCommand(query, callback=null) {
- // dic in the form: {'cmd': X, ...} as JSON
- if (callback == null) {
- function callback(x) {
- console.log('default callback:', x)
- }
- }
- let xhr = new XMLHttpRequest();
- xhr.onreadystatechange = function() {
- if (this.readyState == 4) {
- if (xhr.status == 200) {
- callback(JSON.parse(xhr.response))
- }
- }
- }
- xhr.open('POST', serverUrl)
- xhr.setRequestHeader('Content-Type', 'application/json')
- xhr.send(query)
- }
-
- // run button
- function runBtnFunc() {
- sendCommand('{"cmd": "run_multiple_sequences"}', function(x) {
- console.log(x['ohmpi_status'])
- if (x['ohmpi_status'] == 'running') {
- output.innerHTML = 'Status: measuring...'
- }
- })
- }
- let runBtn = document.getElementById('runBtn')
- runBtn.addEventListener('click', runBtnFunc)
-
- // interrupt button
- function stopBtnFunc() {
- sendCommand('{"cmd": "interrupt"}', function(x) {
- output.innerHTML = 'Status: ' + x['ohmpi_status']
- clearInterval(interv)
- getData()
- })
- }
- let stopBtn = document.getElementById('stopBtn')
- stopBtn.addEventListener('click', stopBtnFunc)
-
- // set configuration
- function saveSettingsBtnFunc() {
- // collect values from modal
- let formVals = {}
- formVals['nb_electrodes'] = parseInt(document.getElementById('nbElectrodes').value)
- formVals['injection_duration'] = parseFloat(document.getElementById('injectionDuration').value)
- formVals['nb_meas'] = parseInt(document.getElementById('nbMeasurements').value)
- formVals['sequence_delay'] = parseInt(document.getElementById('sequenceDelay').value)
- formVals['nb_stack'] = parseInt(document.getElementById('nbStack').value)
- formVals['elec_spacing'] = parseFloat(document.getElementById('elecSpacing').value)
- console.log(formVals)
- elecSpacing = formVals['elec_spacing']
-
- // define callback to send settigs to Pi
- function settingsCallback() {
- sendCommand(JSON.stringify({
- 'cmd': 'update_settings',
- 'config': formVals
- }), function(x) {
- console.log('update_settings', x)
- })
- }
-
- // deal with the potential file containing the sequence
- // https://stackoverflow.com/questions/19038919/is-it-possible-to-upload-a-text-file-to-input-in-html-js
- if (!window.FileReader) {
- alert('Your browser is not supported');
- return false;
- }
- let input = document.getElementById('sequence')
- if (input.files.length) {
- const reader = new FileReader()
- reader.readAsText(input.files[0])
- reader.addEventListener('load', () => {
- formVals['sequence'] = reader.result
- console.log('file==', reader.result)
- settingsCallback()
- }, false)
- } else {
- console.log('no sequence uploaded')
- formVals['sequence'] = ''
- settingsCallback()
- }
-
-
- }
- let saveConfigBtn = document.getElementById('saveConfigBtn')
- saveConfigBtn.addEventListener('click', saveSettingsBtnFunc)
-
- // make pseudo plot
- var trace = {}
- let layout = {}
- let tdata = []
- let layout2 = {}
- let rsdata = []
- let rslayout = {}
-
- // initialize all plots
- function initPlots() {
- trace = {
- x: [],
- y: [],
- mode: 'markers',
- marker: {
- size: 40,
- color: [],
- colorbar: {
- title: 'App. res. [Ohm.m]',
- cmin: 0,
- cmax: 100,
- }
- }
- }
- layout = {
- title: 'Pseudo-section',
- yaxis: {
- title: 'Pseudo-depth',
- autorange: 'reversed'
- },
- xaxis: {
- title: 'X'
- }
-
- }
- Plotly.newPlot('gd', [trace], layout)
-
- // make time-serie plot
- tdata = []
- layout2 = {
- title: 'Time-serie',
- yaxis: {
- title: 'App. res. [Ohm.m]'
- },
- xaxis: {
- title: 'Sampling time'
- }
- }
- Plotly.newPlot('ts', tdata, layout2)
-
- // bar chart for contact resistance
- rsdata = []
- rslayout = {
- title: 'Contact resistances',
- yaxis: {
- title: 'Resistance [kOhm]'
- },
- xaxis: {
- title: 'Consecutive electrodes'
- }
- }
- Plotly.newPlot('rs', rsdata, rslayout)
- }
- initPlots()
-
- // hover function
- var hoverInfo = document.getElementById('hoverinfo')
- document.getElementById('gd').on('plotly_hover', function(data){
- var infotext = data.points.map(function(d){
- return (Math.round(d.data.marker.color[d.pointIndex], 2) + ' Ohm.m');
- });
- hoverInfo.innerHTML = infotext.join('<br/>');
- })
- .on('plotly_unhover', function(data){
- hoverInfo.innerHTML = '';
- });
-
- // add trace to time-serie plot
- function addTraceBtnFunc() {
- let val = document.getElementById('quadSelect').value
- squads.push(val.split(', '))
- tdata.push({
- x: [],
- y: [],
- name: val,
- type: 'scatter'
- })
- Plotly.newPlot('ts', tdata, layout2)
- getData()
- }
- let addTraceBtn = document.getElementById('addTraceBtn')
- addTraceBtn.addEventListener('click', addTraceBtnFunc)
-
- // remove all traces from time-serie plot
- function removeTracesBtnFunc() {
- squads = []
- tdata = []
- Plotly.newPlot('ts', tdata, layout2)
- }
- let removeTracesBtn = document.getElementById('removeTracesBtn')
- removeTracesBtn.addEventListener('click', removeTracesBtnFunc)
-
- // callback function to draw the plot
- function surveySelectFunc(el) {
- let surveyName = el['target'].value
- let df = data[surveyName]
- if (df != undefined) {
- // let's assume electrodes are 1 m distance
- // compute pseudo-depth (assume no topo)
- // compute app res (assumping flat, line survey)
- let xpos = []
- let ypos = []
- let app = []
- for (let i = 0; i < df['a'].length; i++) {
- let a = df['a'][i]
- let b = df['b'][i]
- let m = df['m'][i]
- let n = df['n'][i]
-
- // compute geometric factor assuming flat 2D surface
- let am = Math.abs(a - m)*elecSpacing
- let bm = Math.abs(b - m)*elecSpacing
- let an = Math.abs(a - n)*elecSpacing
- let bn = Math.abs(b - n)*elecSpacing
- let K = 2*Math.PI/((1/am)-(1/bm)-(1/an)+(1/bn))
- app.push(df['rho'][i]*K)
- //console.log(K) // same as resipy for the wenner case
-
- // computing pseudo-depth assuming 2D flat array
- // let's sort the electrodes AB are the two left, MN, the two right
- let abmn = [a, b, m, n]
- abmn = abmn.sort((a, b) => a - b)
- let ab = (abmn[0] + abmn[1])/2
- let mn = (abmn[2] + abmn[3])/2
- let dist = Math.abs(ab - mn)
- xpos.push((Math.min(ab, mn) + dist/2)*elecSpacing)
- ypos.push((Math.sqrt(2)/2*dist)*elecSpacing)
-
- /*
- lookupDict = dict(zip(self.elec['label'], np.arange(self.elec.shape[0])))
- array = self.df[['a','b','m','n']].replace(lookupDict).values.astype(int)
- elecm = self.elec[['x','y','z']].values.astype(float).copy() # electrode matrix - should be array of floats so np.inf work properly
-
- ### first determine if measurements are nested ###
- #find mid points of AB
- AB = (elecm[array[:,0]] + elecm[array[:,1]]) / 2 # mid points of AB
- MN = (elecm[array[:,2]] + elecm[array[:,3]]) / 2 # mid points of MN
- ABrad = np.sqrt(np.sum((elecm[array[:,0]] - AB)**2,axis=1)) # radius of AB circle
- MNrad = np.sqrt(np.sum((elecm[array[:,2]] - MN)**2,axis=1)) # radius of MN circle
-
- Amn = np.sqrt(np.sum((elecm[array[:,0]] - MN)**2,axis=1)) # distance of A to mid point of MN
- Bmn = np.sqrt(np.sum((elecm[array[:,1]] - MN)**2,axis=1)) # distance of B to mid point of MN
- Nab = np.sqrt(np.sum((elecm[array[:,2]] - AB)**2,axis=1)) # distance of N to mid point of AB
- Mab = np.sqrt(np.sum((elecm[array[:,3]] - AB)**2,axis=1)) # distance of M to mid point of AB
-
- iABinMN = (Amn < MNrad) & (Bmn < MNrad)
- iMNinAB = (Nab < ABrad) & (Mab < ABrad)
- inested = iABinMN | iMNinAB #if AB encompasses MN or MN encompasses AB
-
- # so it will never be taken as minimium
- elecm[self.elec['remote'].values,:] = np.inf
-
- # compute midpoint position of AB and MN dipoles
- elecx = elecm[:,0]
- elecy = elecm[:,1]
-
- #CURRENT ELECTRODE MIDPOINTS
- caddx = np.abs(elecx[array[:,0]]-elecx[array[:,1]])/2
- caddy = np.abs(elecy[array[:,0]]-elecy[array[:,1]])/2
- caddx[np.isinf(caddx)] = 0
- caddy[np.isinf(caddy)] = 0
- cmiddlex = np.min([elecx[array[:,0]], elecx[array[:,1]]], axis=0) + caddx
- cmiddley = np.min([elecy[array[:,0]], elecy[array[:,1]]], axis=0) + caddy
-
- #POTENTIAL ELECTRODE MIDPOINTS
- paddx = np.abs(elecx[array[:,2]]-elecx[array[:,3]])/2
- paddy = np.abs(elecy[array[:,2]]-elecy[array[:,3]])/2
- paddx[np.isinf(paddx)] = 0
- paddy[np.isinf(paddy)] = 0
- pmiddlex = np.min([elecx[array[:,2]], elecx[array[:,3]]], axis=0) + paddx
- pmiddley = np.min([elecy[array[:,2]], elecy[array[:,3]]], axis=0) + paddy
-
-
- # for non-nested measurements
- xposNonNested = np.min([cmiddlex, pmiddlex], axis=0) + np.abs(cmiddlex-pmiddlex)/2
- yposNonNested = np.min([cmiddley, pmiddley], axis=0) + np.abs(cmiddley-pmiddley)/2
- pcdist = np.sqrt((cmiddlex-pmiddlex)**2 + (cmiddley-pmiddley)**2)
-
- # zposNonNested = np.sqrt(2)/2*pcdist
- zposNonNested = pcdist/4
-
- if np.all(cmiddley-pmiddley == 0):
- zposNonNested = 0.25*pcdist
- else: # for 3D arrays where there are mid-line measurements, this works closer to inversion results
- zposNonNested = np.sqrt(2)/2*pcdist
-
- # for nested measurements use formula of Dalhin 2006
- xposNested = np.zeros(len(pmiddlex))
- yposNested = np.zeros(len(pmiddlex))
- outerElec1 = np.zeros((len(pmiddlex), 2)) # position of one electrode of outer dipole
- outerElec2 = np.zeros((len(pmiddlex), 2)) # position of one electrode of outer dipole
- # innerMid = np.zeros((len(pmiddlex), 2)) # middle of inner dipole
- if np.sum(iMNinAB) > 0:
- xposNested[iMNinAB] = pmiddlex[iMNinAB]
- yposNested[iMNinAB] = pmiddley[iMNinAB]
- outerElec1[iMNinAB] = np.c_[elecx[array[iMNinAB,0]], elecy[array[iMNinAB,0]]]
- outerElec2[iMNinAB] = np.c_[elecx[array[iMNinAB,1]], elecy[array[iMNinAB,1]]]
-
- if np.sum(iABinMN) > 0:
- xposNested[iABinMN] = cmiddlex[iABinMN]
- yposNested[iABinMN] = cmiddley[iABinMN]
- outerElec1[iABinMN] = np.c_[elecx[array[iABinMN,2]], elecy[array[iABinMN,2]]]
- outerElec2[iABinMN] = np.c_[elecx[array[iABinMN,3]], elecy[array[iABinMN,3]]]
-
- innerMid = np.c_[pmiddlex, pmiddley] # always use potential dipole
-
- apdist = np.sqrt(np.sum((outerElec1-innerMid)**2, axis=1))
- bpdist = np.sqrt(np.sum((outerElec2-innerMid)**2, axis=1))
- zposNested = np.min([apdist, bpdist], axis=0)/3
-
- xpos = np.zeros_like(pmiddlex)
- ypos = np.zeros_like(pmiddlex)
- zpos = np.zeros_like(pmiddlex)
-
- xpos[~inested] = xposNonNested[~inested]
- xpos[inested] = xposNested[inested]
-
- ypos[~inested] = yposNonNested[~inested]
- ypos[inested] = yposNested[inested]
-
- zpos[~inested] = zposNonNested[~inested]
- zpos[inested] = zposNested[inested]
-
- */
- }
- //console.log(app)
- // update the trace and redraw the figure
- trace['x'] = xpos
- trace['y'] = ypos
- trace['marker']['color'] = app
- trace['marker']['cmax'] = document.getElementById('cmax').value
- trace['marker']['cmin'] = document.getElementById('cmin').value
- Plotly.redraw('gd')
- }
- }
- let surveySelect = document.getElementById('surveySelect')
-
- // run RS check
- function rsBtnFunc() {
- sendCommand('{"cmd": "rsCheck"}', function (a) {})
- }
- let rsBtn = document.getElementById('rsBtn')
- rsBtn.addEventListener('click', rsBtnFunc)
-
- // get RS check data
- function getRsBtnFunc() {
- sendCommand('{"cmd": "getRsCheck"}', function(res) {
- // update the bar plot
- rsdata.push({
- x: res['data']['AB'],
- y: res['data']['res'],
- name: 'RS',
- type: 'bar'
- })
- Plotly.redraw('rs')
- })
- }
- let getRsBtn = document.getElementById('getRsBtn')
- getRsBtn.addEventListener('click', getRsBtnFunc)
-
- // clear RS graph
- function rsClearBtnFunc() {
- rsdata = []
- Plotly.newPlot('rs', rsdata, rslayout)
- }
- let rsClearBtn = document.getElementById('rsClearBtn')
- rsClearBtn.addEventListener('click', rsClearBtnFunc)
-
- // getData
- function getData() {
- let surveyNames = []
- sendCommand(JSON.stringify({
- 'cmd': 'getData',
- 'surveyNames': surveyNames
- // last survey is often partial so we download it again
- }), function(ddic) {
- // update status
- //output.innerHTML = 'Status: ' + ddic['status']
-
- // update data dic with new data
- data = { // destructuring assignement (magic! :o)
- ...data,
- ...ddic['data'] // value from second dic are preferred
- }
-
- // dropdown with number of surveys
- surveyNames = Object.keys(data).sort()
-
- // remove listener as we will replace the choices
- surveySelect.removeEventListener('change', surveySelectFunc)
- surveySelect.innerHTML = '' // clearing all child nodes
-
- // add choices again
- for (let surveyName of surveyNames) {
- let option = document.createElement('option')
- option.innerText = surveyName
- option.value = surveyName
- surveySelect.appendChild(option)
- }
-
- // listener again
- surveySelect.addEventListener('change', surveySelectFunc)
-
- // plot last one by default
- surveySelect.value = surveyNames[surveyNames.length - 1]
-
- // call the function directly
- // (as progammatically chaging the value does not trigger the event)
- surveySelectFunc({'target': surveySelect})
-
- // update list of quadrupoles if any
- let idiff = false
- if (data[surveyNames[0]] != undefined) {
- idiff = quads.length != data[surveyNames[0]]['a'].length
- }
- //console.log('idiff=', idiff, quads.length, data[surveyNames[0]]['a'].length)
- if (((quads.length == 0) | idiff) & (data[surveyNames[0]] != undefined)){
- console.log('updating list of quadrupoles')
- quads = []
- let df = data[surveyNames[0]]
- let quadSelect = document.getElementById('quadSelect')
- quadSelect.innerHTML = ''
- for (let i = 0; i < df['a'].length; i++) {
- quad = [df['a'][i], df['b'][i], df['m'][i], df['n'][i]]
- quads.push(quad)
- let option = document.createElement('option')
- option.value = quad.join(', ')
- option.innerText = quad.join(', ')
- quadSelect.appendChild(option)
- }
- console.log('quads=', quads)
- }
-
- // update time-serie figure
- if (squads.length > 0) {
-
- // transform all surveyNames to datetime
- let xt = []
- for (surveyName of surveyNames) {
- let a = surveyName.split('_').slice(-1)[0]
- xt.push(a.slice(0, 4) + '-'
- + a.slice(4, 6) + '-'
- + a.slice(6, 8) + ' '
- + a.slice(9, 11) + ':'
- + a.slice(11, 13) + ':'
- + a.slice(13, 15))
- }
- //console.log(xt)
-
- // create one new trace per selected quadrupole
- for (let k = 0; k < squads.length; k++) {
- squad = squads[k]
- let x = []
- let y = []
- for (let i = 0; i < surveyNames.length; i++) {
- df = data[surveyNames[i]]
- for (let j = 0; j < df['a'].length; j++) {
- if (df['a'][j] == squad[0]
- && df['b'][j] == squad[1]
- && df['m'][j] == squad[2]
- && df['n'][j] == squad[3]) {
- y.push(df['rho'][j])
- x.push(xt[i])
- break
- }
- }
- }
-
- // update trace dictionnary
- tdata[k]['x'] = x
- tdata[k]['y'] = y
- }
- //console.log(tdata)
- Plotly.redraw('ts')
- }
- })
- }
- let getDataBtn = document.getElementById('getDataBtn')
- getDataBtn.addEventListener('click', getData)
-
- // apply new colorscale
- let capplyBtn = document.getElementById('capplyBtn')
- capplyBtn.addEventListener('click', function() {
- surveySelectFunc({'target': surveySelect})
- })
-
- // checkbox interaction for data download
- function dataRetrievalCheckFunc(x) {
- if (x['target'].checked == true) {
- interv = setInterval(getData, 1000) // every 5s
- } else {
- clearInterval(interv)
- }
- }
- let dataRetrievalCheck = document.getElementById('dataRetrievalCheck')
- dataRetrievalCheck.addEventListener('change', dataRetrievalCheckFunc)
-
- // remove data
- function removeDataBtnFunc() {
- sendCommand('{"cmd": "removeData"}',function(x) {
- data = {}
- output.innerHTML = 'Status: ' + x['ohmpi_status'] + ' (all data cleared)'
- console.log('all data removed')
- initPlots() // reset all plots
- })
- }
- let removeDataBtn = document.getElementById('removeDataBtn')
- removeDataBtn.addEventListener('click', removeDataBtnFunc)
-
- // shutdown Pi
- function shutdownBtnFunc() {
- sendCommand('{"cmd": "shutdown"}', function(x) {
- console.log('shuting down...')
- })
- }
- let shutdownBtn = document.getElementById('shutdownBtn')
- shutdownBtn.addEventListener('click', shutdownBtnFunc)
-
- // restart Pi
- function restartBtnFunc() {
- sendCommand('{"cmd": "restart"}', function(x) {
- console.log('rebooting...')
- })
- }
- let restartBtn = document.getElementById('restartBtn')
- restartBtn.addEventListener('click', restartBtnFunc)
-
- // invert data
- // function invertBtnFunc() {
- // sendCommand('{"cmd": "invert"}', function(x) {
- // console.log('inversion results', x)
- // })
- // }
- // let invertBtn = document.getElementById('invertBtn')
- // invertBtn.addEventListener('click', invertBtnFunc)
-
- // download data
- function downloadBtnFunc() {
- sendCommand('{"cmd": "download"}', function(x) {
- let dwl = document.getElementById('download')
- dwl.setAttribute('href', serverUrl + '/data.zip')
- dwl.setAttribute('download', 'data.zip')
- dwl.click()
- })
- }
- let downloadBtn = document.getElementById('downloadBtn')
- downloadBtn.addEventListener('click', downloadBtnFunc)
-
-
- </script>
-
- <!-- Boostrap scripts (at the end of the page for faster loading time)-->
- <script src="js/bootstrap.bundle.min.js"></script>
- <!-- <script src="https://cdn.jsdelivr.net/npm/bootstrap@5.0.0-beta3/dist/js/bootstrap.bundle.min.js" integrity="sha384-JEW9xMcG8R+pH31jmWH6WWP0WintQrMb4s7ZOdauHnUtxwoG2vI5DkLtS3qm9Ekf" crossorigin="anonymous"></script> -->
-</body>
-</html>
diff --git a/html/index-mqtt.html b/index-mqtt.html
similarity index 88%
rename from html/index-mqtt.html
rename to index-mqtt.html
index 7c121aea79adcce5d3177f0c3e56e78e122f244a..e90f129f3271c51698a607f6b2d0248fbdc13c77 100755
--- a/html/index-mqtt.html
+++ b/index-mqtt.html
@@ -1,4 +1,7 @@
<!DOCTYPE html>
+<!-- debugging instruction to see the messages passing on the RPi
+mosquitto_sub -h raspberrypi.local -t ohmpi_0001/ctrl
+-->
<html>
<head>
<meta charset="utf8"/>
@@ -40,14 +43,14 @@
<input id="cmax" type="number" value="150"/>
<button id="capplyBtn" type="button" class="btn btn-info">Apply</button>
<div id="gd"></div>
+
+ <!-- trace figure -->
<div class="mb3 row">
<label for="quadSelect">Quadrupole:</label>
<div class="col-sm-10">
<select id='quadSelect' class='custom-select'></select>
</div>
</div>
-
- <!-- trace figure -->
<button id="addTraceBtn" type="button" class="btn btn-info">Add trace</button>
<button id="removeTracesBtn" type="button" class="btn btn-info">Remove all traces</button>
<div id="ts"></div>
@@ -57,9 +60,22 @@
<button id="rsClearBtn" type="button" class="btn btn-info">Clear plot</button>
<div id="rs"></div>
+ <!-- Inversion plot -->
+ <select id="surveySelectInv" class='custom-select'>
+ <option>measurement_20220206T194552.csv</option>
+ </select>
+ <button id="invertBtn" type="button" class="btn btn-info">Run inversion</button>
+ <input id="cminInv" type="number" value="0"/>
+ <input id="cmaxInv" type="number" value="150"/>
+ <button id="capplyBtnInv" type="button" class="btn btn-info">Apply</button>
+ <div id="inv"></div>
+
<!-- Additional buttons -->
<button id="downloadBtn" type="button" class="btn btn-primary">Download data</button>
<a id="download"></a>
+
+ <button id="restartBtn" type="button" class="btn btn-danger">Restart</button>
+ <button id="shutdownBtn" type="button" class="btn btn-danger">Shutdown</button>
<!-- Modal for configuration -->
<div class="modal fade" id="exampleModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
@@ -124,9 +140,7 @@
</div>
</div>
</div>
- <button id="restartBtn" type="button" class="btn btn-danger">Restart</button>
- <button id="shutdownBtn" type="button" class="btn btn-danger">Shutdown</button>
- <footer>v0.2.0</footer>
+ <footer>v0.3.0</footer>
</div>
<script type="text/javascript">
@@ -142,6 +156,15 @@
let squads = [] // selected quadrupoles for time-serie figure
let commands = {} // store commands and their id
let callbacks = {} // store callback (might not be needed)
+ let invertData = [{
+ rho: [[10, 10.625, 12.5, 15.625, 20],
+ [5.625, 6.25, 8.125, 11.25, 15.625],
+ [2.5, 3.125, 5., 8.125, 12.5],
+ [0.625, 1.25, 3.125, 6.25, 10.625],
+ [0, 0.625, 2.5, 5.625, 10]],
+ x: [-9, -6, -5 , -3, -1],
+ y: [0, 1, 4, 5, 7],
+ }] // store inverted data
// function with MQTT
let topic = 'ohmpi_0001' // we could change this through a drop-down to connect to a different ohmpi
@@ -153,12 +176,15 @@
let clientId = 'ohmpi_0001_html'
let message = null
let msg = ''
+ let userName = 'jkl' // can be ask to the user
+ let password = 'jkl'
// create client
- client = new Paho.MQTT.Client(hostname, port, clientId);
- client.onConnectionLost = onConnectionLost;
- client.onMessageArrived = onMessageArrived;
- client.connect({onSuccess:onConnect});
+ client = new Paho.MQTT.Client(hostname, port, clientId)
+ client.onConnectionLost = onConnectionLost
+ client.onMessageArrived = onMessageArrived
+ client.connect({onSuccess: onConnect})
+// client.connect({userName: username, password: password, onSuccess:onConnect})
function onConnect() {
console.log("onConnect")
@@ -187,7 +213,7 @@
let ddic = JSON.parse(payload.split('INFO:')[1])
// check cmd_id is any
- processData(ddic)
+ processMessage(ddic)
// usually these don't have a cmd_id so we are not sure when
@@ -476,6 +502,19 @@
)
}
+ // processMessage
+ function processMessage(ddic) {
+ if ('status' in ddic) {
+ // acquisition related
+ processData(ddic)
+ } else {
+ // inversion related
+ console.log('--------', ddic)
+ let invertData = ddic[0]
+ showInvFunc()
+ }
+ }
+
// processData
function processData(ddic) {
// update status
@@ -582,6 +621,58 @@
surveySelectFunc({'target': surveySelect})
})
+ // plot inverted data
+ function showInvFunc() {
+ let cmin = document.getElementById('cminInv').value
+ let cmax = document.getElementById('cmaxInv').value
+
+ var data = [{
+ z: invertData[0]['rho'],
+ x: invertData[0]['x'],
+ y: invertData[0]['z'],
+ type: 'contour',
+ colorscale: 'Jet',
+ autocontour: true, // set to false if cmin is given
+ contours: {
+ start: cmin,
+ end: cmax,
+ size: 10
+ },
+ }]
+
+ var layout = {
+ title: 'Inverted section',
+ yaxis: {
+ title: 'Z [m]',
+ },
+ xaxis: {
+ title: 'X [m]'
+ }
+ }
+ Plotly.newPlot('inv', data, layout)
+ }
+
+ //invert data
+ function invertBtnFunc() {
+ let survey_name = document.getElementById('surveySelectInv').value
+ sendCommand(JSON.stringify({
+ 'cmd': 'run_inversion',
+ 'kwargs': {
+ 'survey_names': [survey_name]
+ }
+ }), function(x) {
+ console.log('inversion results', x)
+ })
+ }
+ let invertBtn = document.getElementById('invertBtn')
+ invertBtn.addEventListener('click', invertBtnFunc)
+
+ // apply new colorscale for inversion
+ let capplyBtnInv = document.getElementById('capplyBtnInv')
+ capplyBtnInv.addEventListener('click', function() {
+ showInvFunc()
+ })
+
// checkbox interaction for data download
function dataRetrievalCheckFunc(x) {
if (x['target'].checked == true) {
@@ -622,15 +713,6 @@
let restartBtn = document.getElementById('restartBtn')
restartBtn.addEventListener('click', restartBtnFunc)
- // invert data
- // function invertBtnFunc() {
- // sendCommand('{"cmd": "invert"}', function(x) {
- // console.log('inversion results', x)
- // })
- // }
- // let invertBtn = document.getElementById('invertBtn')
- // invertBtn.addEventListener('click', invertBtnFunc)
-
// download data
function downloadBtnFunc() {
sendCommand('{"cmd": "download"}', function(x) {
diff --git a/ohmpi/ohmpi.py b/ohmpi/ohmpi.py
index 2035c81d14c505ca8becc2e761880c3a24c8737f..efecdb58c85a7aa5a70350340757c440ee468aee 100644
--- a/ohmpi/ohmpi.py
+++ b/ohmpi/ohmpi.py
@@ -940,7 +940,7 @@ class OhmPi(object):
"""
# check if we have any files to be inverted
if len(survey_names) == 0:
- self.exec_logger('No file to invert')
+ self.exec_logger.error('No file to invert')
return []
# check if user didn't provide a single string instead of a list
@@ -957,12 +957,13 @@ class OhmPi(object):
pdir = os.path.dirname(__file__)
# import resipy if available
try:
+ from scipy.interpolate import griddata
import pandas as pd
import sys
sys.path.append(os.path.join(pdir, '../../resipy/src/'))
from resipy import Project
except Exception as e:
- self.exec_logger.error('Cannot import ResIPy or Pandas, error: ' + str(e))
+ self.exec_logger.error('Cannot import ResIPy, scipy or Pandas, error: ' + str(e))
return []
# get absolule filename
@@ -1001,18 +1002,29 @@ class OhmPi(object):
self.exec_logger.info('ResIPy: invert survey')
k.invert(param=kwargs)
- # read data
+ # read data and regrid on a regular grid for a plotly contour plot
self.exec_logger.info('Reading inverted surveys')
k.getResults()
xzv = []
for m in k.meshResults:
df = m.df
+ x = np.linspace(df['X'].min(), df['X'].max(), 20)
+ z = np.linspace(df['Z'].min(), df['Z'].max(), 20)
+ grid_x, grid_z = np.meshgrid(x, z)
+ grid_z = griddata(df[['X', 'Z']].values, df['Resistivity(ohm.m)'].values,
+ (grid_x, grid_z), method='linear')
+
+ # set nan to -1
+ inan = np.isnan(grid_z)
+ grid_z[inan] = -1
+
xzv.append({
- 'x': df['X'].values.tolist(),
- 'z': df['Z'].values.tolist(),
- 'rho': df['Resistivity(ohm.m)'].values.tolist(),
+ 'x': x.tolist(),
+ 'z': z.tolist(),
+ 'rho': grid_z.tolist(),
})
+ self.data_logger.info(json.dumps(xzv)) # limited to one survey
return xzv
# Properties
diff --git a/requirements-optional.txt b/requirements-optional.txt
new file mode 100644
index 0000000000000000000000000000000000000000..952b0be7f8527cac80e716fa70e7318599e9bff2
--- /dev/null
+++ b/requirements-optional.txt
@@ -0,0 +1,16 @@
+RPi.GPIO
+adafruit-blinka
+adafruit-circuitpython-ads1x15
+adafruit-circuitpython-tca9548a
+adafruit-circuitpython-mcp230xx
+adafruit_extended_bus
+minimalmodbus
+gpiozero
+numpy
+paho-mqtt
+termcolor
+pandas
+matplotlib
+scipy
+requests
+psutil
\ No newline at end of file