diff --git a/ohmpi/ohmpi.py b/ohmpi/ohmpi.py
index 825ce6d995f6cf40f525b8fcd10c73bfa81c893b..b25add816ed5beb3c191c1131eb917a4dd179368 100644
--- a/ohmpi/ohmpi.py
+++ b/ohmpi/ohmpi.py
@@ -15,6 +15,7 @@ from copy import deepcopy
import numpy as np
import csv
import time
+import pandas as pd
from shutil import rmtree, make_archive
from threading import Thread
from inspect import getmembers, isfunction
@@ -51,8 +52,7 @@ class OhmPi(object):
Dictionnary of parameters. Possible parameters with their default values:
`{'injection_duration': 0.2, 'nb_meas': 1, 'sequence_delay': 1,
'nb_stack': 1, 'sampling_interval': 2, 'tx_volt': 5, 'duty_cycle': 0.5,
- 'strategy': 'constant', 'export_path': None, 'export_dir': 'data',
- 'export_name': 'measurement.csv'`.
+ 'strategy': 'constant', 'export_path': None
sequence : str, optional
Path of the .csv or .txt file with A, B, M and N electrodes.
Electrode index starts at 1. See `OhmPi.load_sequence()` for full docstring.
@@ -74,9 +74,10 @@ class OhmPi(object):
self._hw = OhmPiHardware(**{'exec_logger': self.exec_logger, 'data_logger': self.data_logger,
'soh_logger': self.soh_logger})
self.exec_logger.info('Hardware configured...')
-
+
# default acquisition settings
- self.update_settings('settings/default.json')
+ self.settings = {}
+ self.update_settings(os.path.join(os.path.split(os.path.dirname(__file__))[0],'settings/default.json'))
# read in acquisition settings
self.update_settings(settings)
@@ -169,18 +170,17 @@ class OhmPi(object):
Unique command identifier.
"""
# check if directory 'data' exists
- ddir = os.path.join(os.path.dirname(__file__), '../data/')
+ ddir = os.path.split(filename)[0]
if os.path.exists(ddir) is not True:
os.mkdir(ddir)
last_measurement = deepcopy(last_measurement)
- # TODO need to make all the full data of the same size (pre-populate
- # readings with NaN in hardware_system.OhmPiHardware.read_values())
+ # save full waveform data in a long .csv file
if fw_in_zip:
fw_filename = filename.replace('.csv', '_fw.csv')
if not os.path.exists(fw_filename): # new file, write headers first
- with open(fw_filane, 'w') as f:
+ with open(fw_filename, 'w') as f:
f.write('A,B,M,N,t,pulse,polarity,current,voltage\n')
# write full data
with open(fw_filename, 'a') as f:
@@ -191,10 +191,9 @@ class OhmPi(object):
df['M'] = last_measurement['M']
df['N'] = last_measurement['N']
df.to_csv(f, index=False, header=False)
- print('--------', fw_filename)
if fw_in_csv:
- d = last_measurement['fulldata']
+ d = last_measurement['full_waveform']
n = d.shape[0]
if n > 1:
idic = dict(zip(['i' + str(i) for i in range(n)], d[:, 0]))
@@ -256,7 +255,8 @@ class OhmPi(object):
# get all .csv file in data folder
if survey_names is None:
survey_names = []
- ddir = os.path.join(os.path.dirname(__file__), '../data/')
+ # ddir = os.path.join(os.path.dirname(__file__), '../data/')
+ ddir = self.settings['export_dir']
fnames = [fname for fname in os.listdir(ddir) if fname[-4:] == '.csv']
ddic = {}
if cmd_id is None:
@@ -397,20 +397,10 @@ class OhmPi(object):
"""
self.exec_logger.debug('Getting hardware config')
self.id = OHMPI_CONFIG['id'] # ID of the OhmPi
- # self.r_shunt = OHMPI_CONFIG['R_shunt'] # reference resistance value in ohm
- # self.Imax = OHMPI_CONFIG['Imax'] # maximum current
- # self.exec_logger.debug(f'The maximum current cannot be higher than {self.Imax} mA')
- # self.coef_p2 = OHMPI_CONFIG['coef_p2'] # slope for current conversion for ads.P2, measurement in V/V
- # self.nb_samples = OHMPI_CONFIG['nb_samples'] # number of samples measured for each stack
- # self.version = OHMPI_CONFIG['version'] # hardware version
- # self.max_elec = OHMPI_CONFIG['max_elec'] # maximum number of electrodes
- # self.board_addresses = OHMPI_CONFIG['board_addresses']
- # self.board_version = OHMPI_CONFIG['board_version']
- # self.mcp_board_address = OHMPI_CONFIG['mcp_board_address']
self.exec_logger.debug(f'OHMPI_CONFIG = {str(OHMPI_CONFIG)}')
def remove_data(self, cmd_id=None):
- """Remove all data in the ´data/´ folder on the raspberrypi.
+ """Remove all data in the ´export_path´ folder on the raspberrypi.
Parameters
----------
@@ -418,7 +408,8 @@ class OhmPi(object):
Unique command identifier.
"""
self.exec_logger.debug(f'Removing all data following command {cmd_id}')
- datadir = os.path.join(os.path.dirname(__file__), '../data')
+ datadir = os.path.split(self.settings['export_path'])
+ #datadir = os.path.join(os.path.dirname(__file__), '../data')
rmtree(datadir)
os.mkdir(datadir)
@@ -436,7 +427,8 @@ class OhmPi(object):
def download_data(self, cmd_id=None):
"""Create a zip of the data folder to then download it easily.
"""
- datadir = os.path.join(os.path.dirname(__file__), '../data/')
+ datadir = os.path.split(self.settings['export_path'])
+ # datadir = os.path.join(os.path.dirname(__file__), '../data/')
make_archive(datadir, 'zip', 'data')
self.data_logger.info(json.dumps({'download': 'ready'}))
@@ -911,10 +903,7 @@ class OhmPi(object):
- nb_stack (number of stack for each quadrupole measurement)
- strategy (injection strategy: constant, vmax, vmin)
- duty_cycle (injection duty cycle comprised between 0.5 - 1)
- - export_dir (directory where to export the data)
- - export_name (name of exported file, timestamp will be added to filename)
- - export_path (path where to export the data, timestamp will be added to filename ;
- if export_path is given, it goes over export_dir and export_name)
+ - export_path (path where to export the data, timestamp will be added to filename)
Parameters
----------
@@ -942,10 +931,11 @@ class OhmPi(object):
self.exec_logger.warning('Settings are missing...')
if self.settings['export_path'] is None:
- self.settings['export_path'] = os.path.join(self.settings['export_dir'], self.settings['export_name'])
- else:
- self.settings['export_dir'] = os.path.split(self.settings['export_path'])[0]
- self.settings['export_name'] = os.path.split(self.settings['export_path'])[1]
+ self.settings['export_path'] = os.path.join("data", "measurement.csv")
+
+ if not os.path.isabs(self.settings['export_path']):
+ export_dir = os.path.split(os.path.dirname(__file__))[0]
+ self.settings['export_path'] = os.path.join(export_dir, self.settings['export_path'])
def run_inversion(self, survey_names=None, elec_spacing=1, **kwargs):
"""Run a simple 2D inversion using ResIPy (https://gitlab.com/hkex/resipy).
@@ -999,7 +989,7 @@ class OhmPi(object):
# get absolule filename
fnames = []
for survey_name in survey_names:
- fname = os.path.join(pdir, '../data', survey_name)
+ fname = os.path.join(self.settings['export_path'], survey_name)
if os.path.exists(fname):
fnames.append(fname)
else:
diff --git a/settings/default.json b/settings/default.json
new file mode 100644
index 0000000000000000000000000000000000000000..8e0510fa52c8ef3326f3671ed094dc658e8ec8d6
--- /dev/null
+++ b/settings/default.json
@@ -0,0 +1,12 @@
+{
+ "injection_duration": 0.2,
+ "nb_meas": 1,
+ "sequence_delay": 1,
+ "nb_stack": 1,
+ "sampling_interval": 2,
+ "tx_volt": 5,
+ "duty_cycle": 0.5,
+ "strategy": "constant",
+ "fulldata": false,
+ "export_path": "data/measurements.csv"
+}
\ No newline at end of file