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Configfiles to support different operational modes #4

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15e0412
- adding device number to the error messages
zoltuz Feb 3, 2020
d05b000
Merge remote-tracking branch 'upstream/master' into develop
zoltuz Feb 3, 2020
6e324ef
- reading config file
zoltuz Feb 4, 2020
fc5e468
- adding configuration for two/four pump per chi.bio unit, this allow…
zoltuz Feb 4, 2020
4b88e1f
- default config file
zoltuz Feb 4, 2020
45c6044
- add logging event for successful config value check
zoltuz Feb 5, 2020
0b5dd84
- fixing typos
zoltuz Feb 6, 2020
eedd544
- making the device comm failure threshold configurable
zoltuz Feb 6, 2020
77b31b9
- bug fix for number of OD measurement
zoltuz Feb 10, 2020
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94 changes: 67 additions & 27 deletions app.py
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Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@


application = Flask(__name__)
application.config.from_pyfile('config/chibio_default.cfg', silent=True)
application.config['SEND_FILE_MAX_AGE_DEFAULT'] = 0 #Try this https://stackoverflow.com/questions/23112316/using-flask-how-do-i-modify-the-cache-control-header-for-all-output/23115561#23115561

lock=Lock()
Expand All @@ -34,6 +35,7 @@
'presentDevices' : { 'M0' : 0,'M1' : 0,'M2' : 0,'M3' : 0,'M4' : 0,'M5' : 0,'M6' : 0,'M7' : 0},
'Version' : {'value' : 'Turbidostat V3.0'},
'DeviceID' : '',
'DeviceName': '',
'time' : {'record' : []},
'LEDA' : {'WL' : '395', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
'LEDB' : {'WL' : '457', 'default': 0.1, 'target' : 0.0, 'max': 1.0, 'min' : 0.0,'ON' : 0},
Expand Down Expand Up @@ -370,10 +372,9 @@ def initialise(M):
scanDevices(M)
if(sysData[M]['present']==1):
turnEverythingOff(M)
print(str(datetime.now()) + " Initialised " + str(M) +', Device ID: ' + sysData[M]['DeviceID'])
print(str(datetime.now()) + " Initialised " + str(M) + ', (' + sysData[M]['DeviceName'] + ') Device ID: '
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@zoltuz zoltuz Jun 25, 2021

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remove device name feature

+ sysData[M]['DeviceID'])




def initialiseAll():
# Initialisation function which runs at when software is started for the first time.
Expand All @@ -382,6 +383,11 @@ def initialiseAll():
time.sleep(2.0) #This wait is to allow the watchdog circuit to boot.
print(str(datetime.now()) + ' Initialising devices')

check_config_value(config_key='TWO_PUMPS_PER_DEVICE', default_value=False)
check_config_value(config_key='NUMBER_OF_OD_MEASUREMENTS', default_value=4)
check_config_value(config_key='DEVICE_COMM_FAILURE_THRESHOLD', default_value=10)


for M in ['M0','M1','M2','M3','M4','M5','M6','M7']:
initialise(M)
scanDevices("all")
Expand All @@ -405,7 +411,13 @@ def turnEverythingOff(M):

I2CCom(M,'DAC',0,8,int('00000000',2),int('00000000',2),0)#Sets all DAC Channels to zero!!!
setPWM(M,'PWM',sysItems['All'],0,0)
setPWM(M,'Pumps',sysItems['All'],0,0)

if application.config['TWO_PUMPS_PER_DEVICE']:
chibios_to_shut_down = [0, 1, 2, 3]
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@zoltuz zoltuz Jun 25, 2021

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let's call the variable chibios_w_pumps

else:
chibios_to_shut_down = [0, 1, 2, 4, 5, 6, 7]
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@zoltuz zoltuz Jun 25, 2021

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number 3 is missing!

if int(M[1]) in chibios_to_shut_down:
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@zoltuz zoltuz Jun 25, 2021

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let's use f-string instead! printf(f'M{number}') in number

setPWM(M=M, device='Pumps', channels=sysItems['All'], fraction=0, ConsecutiveFails=0)

SetOutputOn(M,'Stir',0)
SetOutputOn(M,'Thermostat',0)
Expand Down Expand Up @@ -584,12 +596,12 @@ def SetOutputOn(M,item,force):
if (force==1):
sysData[M][item]['ON']=1
SetOutput(M,item)
return ('', 204)
return ('', 204)

elif(force==0):
sysData[M][item]['ON']=0;
SetOutput(M,item)
return ('', 204)
return ('', 204)

#Elsewise this is doing a flip operation (i.e. changes to opposite state to that which it is currently in)
if (sysData[M][item]['ON']==0):
Expand Down Expand Up @@ -681,7 +693,27 @@ def PumpModulation(M,item):
global sysData
global sysItems
global sysDevices


if application.config['TWO_PUMPS_PER_DEVICE']:
pump_mapping = {'M4': 'M0', 'M5': 'M1', 'M6': 'M2', 'M7': 'M3'}
if int(M[1]) in [0, 1, 2, 3]:
if item == 'Pump1' or item == 'Pump2':
MB = M
itemB = item
elif item == 'Pump3' or item == 'Pump4':
sysData[M][item]['ON'] = 0
return
else:
if item == 'Pump1' or item == 'Pump2':
MB = pump_mapping[M]
itemB = 'Pump' + str(int(item[4])+2)
elif item == 'Pump3' or item == 'Pump4':
sysData[M][item]['ON'] = 0
return
else:
MB = M
itemB = item

sysDevices[M][item]['threadCount']=(sysDevices[M][item]['threadCount']+1)%100 #Index of the particular thread running.
currentThread=sysDevices[M][item]['threadCount']

Expand All @@ -690,10 +722,10 @@ def PumpModulation(M,item):

if (abs(sysData[M][item]['target']*sysData[M][item]['ON'])!=1 and currentThread==sysDevices[M][item]['threadCount']): #In all cases we turn things off to begin
sysDevices[M][item]['active']=1
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In2'],0.0*float(sysData[M][item]['ON']),0)
sysDevices[M][item]['active']=0
if (sysData[M][item]['ON']==0):
return
Expand All @@ -711,23 +743,23 @@ def PumpModulation(M,item):

if (sysData[M][item]['target']>0 and currentThread==sysDevices[M][item]['threadCount']): #Turning on pumps in forward direction
sysDevices[M][item]['active']=1
setPWM(M,'Pumps',sysItems[item]['In1'],1.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In1'],1.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In2'],0.0*float(sysData[M][item]['ON']),0)
sysDevices[M][item]['active']=0
elif (sysData[M][item]['target']<0 and currentThread==sysDevices[M][item]['threadCount']): #Or backward direction.
sysDevices[M][item]['active']=1
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],1.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In2'],1.0*float(sysData[M][item]['ON']),0)
sysDevices[M][item]['active']=0

time.sleep(Ontime)

if(abs(sysData[M][item]['target'])!=1 and currentThread==sysDevices[M][item]['threadCount']): #Turning off pumps at appropriate time.
sysDevices[M][item]['active']=1
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(M,'Pumps',sysItems[item]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In2'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In1'],0.0*float(sysData[M][item]['ON']),0)
setPWM(MB,'Pumps',sysItems[itemB]['In2'],0.0*float(sysData[M][item]['ON']),0)
sysDevices[M][item]['active']=0

Time2=datetime.now()
Expand Down Expand Up @@ -1336,7 +1368,7 @@ def I2CCom(M,device,rw,hl,data1,data2,SMBUSFLAG):

global sysDevices
if(sysData[M]['present']==0): #Something stupid has happened in software if this is the case!
print(str(datetime.now()) + ' Trying to communicate with absent device - bug in software!. Disabling hardware and software!')
print(str(datetime.now()) + ' Trying to communicate with M%s absent device - bug in software!. Disabling hardware and software!' % M)
sysItems['Watchdog']['ON']=0 #Basically this will crash all the electronics and the software.
out=0
tries=-1
Expand Down Expand Up @@ -1420,11 +1452,12 @@ def I2CCom(M,device,rw,hl,data1,data2,SMBUSFLAG):
out=0
sysData[M]['present']=0
tries=-1
if tries>10: #In this case something else has gone wrong, so we panic.
if tries >= application.config['DEVICE_COMM_FAILURE_THRESHOLD']: #In this case something else has gone wrong, so we panic.
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@zoltuz zoltuz Jun 25, 2021

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remove this!

sysItems['Watchdog']['ON']=0 #Basically this will crash all the electronics and the software.
out=0
sysData[M]['present']=0
print('Failed to communicate to a device 10 times. Disabling hardware and software!')
print('Failed to communicate to a device %d times. Disabling hardware and software!' %
application.config['DEVICE_COMM_FAILURE_THRESHOLD'])
tries=-1
os._exit(4)

Expand Down Expand Up @@ -2066,13 +2099,13 @@ def runExperiment(M,placeholder):

sysData[M]['OD']['Measuring']=1 #Begin measuring - this flag is just to indicate that a measurement is currently being taken.

#We now meausre OD 4 times and take the average to reduce noise when in auto mode!
ODV=0.0
for i in [0, 1, 2, 3]:
# We now measure OD N times and take the average to reduce noise when in auto mode!
ODV = 0.0
for _ in range(0, application.config['NUMBER_OF_OD_MEASUREMENTS']):
MeasureOD(M)
ODV=ODV+sysData[M]['OD']['current']
time.sleep(0.25)
sysData[M]['OD']['current']=ODV/4.0
sysData[M]['OD']['current'] = ODV/float(application.config['NUMBER_OF_OD_MEASUREMENTS'])

MeasureTemp(M,'Internal') #Measuring all temperatures
MeasureTemp(M,'External')
Expand Down Expand Up @@ -2187,7 +2220,14 @@ def runExperiment(M,placeholder):
addTerminal(M,'Experiment Stopped')



def check_config_value(config_key, default_value, critical=False):
if config_key not in application.config.keys():
if critical:
raise ValueError('config value for %s was not found, it must be set for safe operations' % config_key)
application.config[config_key] = default_value
application.logger.warning('config value %s was not found and set to default: %d' % (config_key, default_value))
else:
application.logger.info('config found: %s=%s' % (config_key, application.config[config_key]))

if __name__ == '__main__':
initialiseAll()
Expand Down
4 changes: 4 additions & 0 deletions config/chibio_default.cfg
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Original file line number Diff line number Diff line change
@@ -0,0 +1,4 @@
NUMBER_OF_OD_MEASUREMENTS = 4
TWO_PUMPS_PER_DEVICE = False
DEVICE_COMM_FAILURE_THRESHOLD = 10
CONTINUOUS_STIRRING = False