Merge pull request #7 from mgalardini/new-server

New client for new server/arduino configuration

experiment/template/custom_script.py

@@ -1,19 +1,23 @@
-import eVOLVER_module
+#!/usr/bin/env python3
+
 import numpy as np
+import logging
 import os.path
 import time
 
+# logger setup
+logger = logging.getLogger(__name__)
+
 ##### USER DEFINED GENERAL SETTINGS #####
 
 #set new name for each experiment, otherwise files will be overwritten
 EXP_NAME = 'test_expt'
-GUI_NAME = 'eVOLVER Experiment'
 EVOLVER_IP = '192.168.1.2'
 EVOLVER_PORT = 8081
 
 ##### Identify pump calibration files, define initial values for temperature, stirring, volume, power settings
 
-TEMP_INITIAL = [30] * 16 #degrees C, makes 16-value list 
+TEMP_INITIAL = [30] * 16 #degrees C, makes 16-value list
 #Alternatively enter 16-value list to set different values
 #TEMP_INITIAL = [30,30,30,30,32,32,32,32,34,34,34,34,36,36,36,36]
 
@@ -24,12 +28,13 @@
 VOLUME =  25 #mL, determined by vial cap straw length
 OD_POWER = 2125 #must match value used for OD calibration
 PUMP_CAL_FILE = 'pump_cal.txt' #tab delimited, mL/s with 16 influx pumps on first row, etc.
-OPERATION_MODE = 'chemostat' #use to choose between 'turbidostat' and 'chemostat' functions
+OPERATION_MODE = 'turbidostat' #use to choose between 'turbidostat' and 'chemostat' functions
+# if using a different mode, name your function as the OPERATION_MODE variable
 
 ##### END OF USER DEFINED GENERAL SETTINGS #####
 
-
-def turbidostat (OD_data, temp_data, vials, elapsed_time):
+def turbidostat(eVOLVER, input_data, vials, elapsed_time):
+    OD_data = input_data['transformed']['od_90']
 
     ##### USER DEFINED VARIABLES #####
 
@@ -39,7 +44,7 @@ def turbidostat (OD_data, temp_data, vials, elapsed_time):
     lower_thresh = [0.2] * len(vials) #to set all vials to the same value, creates 16-value list
     upper_thresh = [0.4] * len(vials) #to set all vials to the same value, creates 16-value list
 
-    #Alternatively, use 16 value list to set different thresholds, use 9999 for vials not being used 
+    #Alternatively, use 16 value list to set different thresholds, use 9999 for vials not being used
     #lower_thresh = [0.2, 0.2, 0.3, 0.3, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999]
     #upper_thresh = [0.4, 0.4, 0.4, 0.4, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999, 9999]
 
@@ -51,37 +56,38 @@ def turbidostat (OD_data, temp_data, vials, elapsed_time):
     #Tunable settings for overflow protection, pump scheduling etc. Unlikely to change between expts
 
     time_out = 5 #(sec) additional amount of time to run efflux pump
-    pump_wait = 3 # (min) minimum amount of time to wait between pump events 
+    pump_wait = 3 # (min) minimum amount of time to wait between pump events
 
     ##### End of Turbidostat Settings #####
 
-    control = np.power(2,range(0,32)) #vial addresses
     save_path = os.path.dirname(os.path.realpath(__file__)) #save path
-    flow_rate = eVOLVER_module.get_flow_rate() #read from calibration file
+    flow_rate = eVOLVER.get_flow_rate() #read from calibration file
 
 
     ##### Turbidostat Control Code Below #####
 
+    # fluidic message: initialized so that no change is sent
+    MESSAGE = ['--'] * 48
     for x in turbidostat_vials: #main loop through each vial
 
         # Update turbidostat configuration files for each vial
         # initialize OD and find OD path
 
         file_name =  "vial{0}_ODset.txt".format(x)
-        ODset_path = os.path.join(save_path,EXP_NAME,'ODset',file_name)
+        ODset_path = os.path.join(save_path, EXP_NAME, 'ODset', file_name)
         data = np.genfromtxt(ODset_path, delimiter=',')
         ODset = data[len(data)-1][1]
         ODsettime = data[len(data)-1][0]
         num_curves=len(data)/2;
 
         file_name =  "vial{0}_OD.txt".format(x)
-        OD_path = os.path.join(save_path,EXP_NAME,'OD',file_name)
+        OD_path = os.path.join(save_path, EXP_NAME, 'OD', file_name)
         data = np.genfromtxt(OD_path, delimiter=',')
         average_OD = 0
 
         # Determine whether turbidostat dilutions are needed
         enough_ODdata = (len(data) > 7) #logical, checks to see if enough data points (couple minutes) for sliding window
-        collecting_more_curves = (num_curves <= (stop_after_n_curves+2)) #logical, checks to see if enough growth curves have happened
+        collecting_more_curves = (num_curves <= (stop_after_n_curves + 2)) #logical, checks to see if enough growth curves have happened
 
         if enough_ODdata:
             # Take median to avoid outlier
@@ -92,16 +98,17 @@ def turbidostat (OD_data, temp_data, vials, elapsed_time):
 
             #if recently exceeded upper threshold, note end of growth curve in ODset, allow dilutions to occur and growthrate to be measured
             if (average_OD > upper_thresh[x]) and (ODset != lower_thresh[x]):
-                text_file = open(ODset_path,"a+")
-                text_file.write("{0},{1}\n".format(elapsed_time, lower_thresh[x]))
+                text_file = open(ODset_path, "a+")
+                text_file.write("{0},{1}\n".format(elapsed_time,
+                                                   lower_thresh[x]))
                 text_file.close()
                 ODset = lower_thresh[x]
                 # calculate growth rate
-                eVOLVER_module.calc_growth_rate(x, ODsettime, elapsed_time)
+                eVOLVER.calc_growth_rate(x, ODsettime, elapsed_time)
 
             #if have approx. reached lower threshold, note start of growth curve in ODset
-            if (average_OD < (lower_thresh[x]+(upper_thresh[x] - lower_thresh[x])/3)) and (ODset != upper_thresh[x]):
-                text_file = open(ODset_path,"a+")
+            if (average_OD < (lower_thresh[x] + (upper_thresh[x] - lower_thresh[x]) / 3)) and (ODset != upper_thresh[x]):
+                text_file = open(ODset_path, "a+")
                 text_file.write("{0},{1}\n".format(elapsed_time, upper_thresh[x]))
                 text_file.close()
                 ODset = upper_thresh[x]
@@ -116,21 +123,38 @@ def turbidostat (OD_data, temp_data, vials, elapsed_time):
 
                 time_in = round(time_in, 2)
 
-                save_path = os.path.dirname(os.path.realpath(__file__))
                 file_name =  "vial{0}_pump_log.txt".format(x)
-                file_path = os.path.join(save_path,EXP_NAME,'pump_log',file_name)
+                file_path = os.path.join(save_path, EXP_NAME,
+                                         'pump_log', file_name)
                 data = np.genfromtxt(file_path, delimiter=',')
                 last_pump = data[len(data)-1][0]
                 if ((elapsed_time - last_pump)*60) >= pump_wait: # if sufficient time since last pump, send command to Arduino
-                    MESSAGE = {'pumps_binary':"{0:b}".format(control[x]), 'pump_time': time_in, 'efflux_pump_time': time_out, 'delay_interval': 0, 'times_to_repeat': 0, 'run_efflux': 1}
-                    eVOLVER_module.fluid_command(MESSAGE, x, elapsed_time, pump_wait *60, time_in, 'y')
+                    logger.info('turbidostat dilution for vial %d' % x)
+                    # influx pump
+                    MESSAGE[x] = str(time_in)
+                    # efflux pump
+                    MESSAGE[x + 16] = str(time_in + time_out)
+
+                    file_name =  "vial{0}_pump_log.txt".format(x)
+                    file_path = os.path.join(save_path, EXP_NAME, 'pump_log', file_name)
+
+                    text_file = open(file_path, "a+")
+                    text_file.write("{0},{1}\n".format(elapsed_time, time_in))
+                    text_file.close()
+        else:
+            logger.debug('not enough OD measurements for vial %d' % x)
+
+    # send fluidic command only if we are actually turning on any of the pumps
+    if MESSAGE != ['--'] * 48:
+        eVOLVER.fluid_command(MESSAGE)
 
         # your_FB_function_here() #good spot to call feedback functions for dynamic temperature, stirring, etc for ind. vials
     # your_function_here() #good spot to call non-feedback functions for dynamic temperature, stirring, etc.
 
     # end of turbidostat() fxn
 
-def chemostat (OD_data, temp_data, vials, elapsed_time):
+def chemostat(eVOLVER, input_data, vials, elapsed_time):
+    OD_data = input_data['transformed']['od_90']
 
     ##### USER DEFINED VARIABLES #####
     start_OD = 0 # ~OD600, set to 0 to start chemostate dilutions at any positive OD
@@ -139,10 +163,10 @@ def chemostat (OD_data, temp_data, vials, elapsed_time):
 
     chemostat_vials = vials #vials is all 16, can set to different range (ex. [0,1,2,3]) to only trigger tstat on those vials
 
-    rate_config = [0.5] * len(vials) #to set all vials to the same value, creates 16-value list
+    rate_config = [0.5] * 16 #to set all vials to the same value, creates 16-value list
     #UNITS of 1/hr, NOT mL/hr, rate = flowrate/volume, so dilution rate ~ growth rate, set to 0 for unused vials
 
-    #Alternatively, use 16 value list to set different rates, use 0 for vials not being used 
+    #Alternatively, use 16 value list to set different rates, use 0 for vials not being used
     #rate_config = [0.1,0.2,0.3,0.4,0.5,0.6,0.7,0.8,0.9,1.0,1.1,1.2,1.3,1.4,1.5,1.6]
 
     ##### END OF USER DEFINED VARIABLES #####
@@ -155,32 +179,21 @@ def chemostat (OD_data, temp_data, vials, elapsed_time):
 
     ##### End of Chemostat Settings #####
 
-    control = np.power(2,range(0,32)) #vial addresses
-
     save_path = os.path.dirname(os.path.realpath(__file__)) #save path
-    flow_rate = eVOLVER_module.get_flow_rate() #read from calibration file
+    flow_rate = eVOLVER.get_flow_rate() #read from calibration file
     period_config = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0] #initialize array
     bolus_in_s = [0,0,0,0,0,0,0,0,0,0,0,0,0,0,0,0] #initialize array
-    
+
 
     ##### Chemostat Control Code Below #####
 
     for x in chemostat_vials: #main loop through each vial
 
-        #calculate time needed to pump bolus for each pump
-        bolus_in_s[x] = bolus/flow_rate[x]
-
-        # calculate the period (i.e. frequency of dilution events) based on user specified growth rate and bolus size
-        if rate_config[x] > 0:
-            period_config[x] = (3600*bolus)/((rate_config[x])*VOLUME) #scale dilution rate by bolus size and volume  
-        else: # if no dilutions needed, then just loops with no dilutions
-            period_config[x] = 0
-
         # Update chemostat configuration files for each vial
 
         #initialize OD and find OD path
         file_name =  "vial{0}_OD.txt".format(x)
-        OD_path = os.path.join(save_path,EXP_NAME,'OD',file_name)
+        OD_path = os.path.join(save_path, EXP_NAME, 'OD', file_name)
         data = np.genfromtxt(OD_path, delimiter=',')
         average_OD = 0
         enough_ODdata = (len(data) > 7) #logical, checks to see if enough data points (couple minutes) for sliding window
@@ -189,13 +202,14 @@ def chemostat (OD_data, temp_data, vials, elapsed_time):
 
             #calculate median OD
             od_values_from_file = []
-            for n in range(1,7):
+            for n in range(1, 7):
                 od_values_from_file.append(data[len(data)-n][1])
             average_OD = float(np.median(od_values_from_file))
 
             # set chemostat config path and pull current state from file
-            file_name =  "vial{0}_chemoconfig.txt".format(x)
-            chemoconfig_path = os.path.join(save_path,EXP_NAME,'chemo_config',file_name)
+            file_name =  "vial{0}_chemo_config.txt".format(x)
+            chemoconfig_path = os.path.join(save_path, EXP_NAME,
+                                            'chemo_config', file_name)
             chemo_config = np.genfromtxt(chemoconfig_path, delimiter=',')
             last_chemoset = chemo_config[len(chemo_config)-1][0] #should t=0 initially, changes each time a new command is written to file
             last_chemophase = chemo_config[len(chemo_config)-1][1] #should be zero initially, changes each time a new command is written to file
@@ -204,20 +218,35 @@ def chemostat (OD_data, temp_data, vials, elapsed_time):
             # once start time has passed and culture hits start OD, if no command has been written, write new chemostat command to file
             if ((elapsed_time > start_time) & (average_OD > start_OD)):
 
+                #calculate time needed to pump bolus for each pump
+                bolus_in_s[x] = bolus/flow_rate[x]
+
+                # calculate the period (i.e. frequency of dilution events) based on user specified growth rate and bolus size
+                if rate_config[x] > 0:
+                    period_config[x] = (3600*bolus)/((rate_config[x])*VOLUME) #scale dilution rate by bolus size and volume
+                else: # if no dilutions needed, then just loops with no dilutions
+                    period_config[x] = 0
+
                 if  (last_chemorate != period_config[x]):
                     print('Chemostat updated in vial {0}'.format(x))
+                    logger.info('chemostat initiated for vial %d, period %.2f'
+                                % (x, period_config[x]))
                     # writes command to chemo_config file, for storage
-                    text_file = open(chemoconfig_path,"a+")
-                    text_file.write("{0},{1},{2}\n".format(elapsed_time,(last_chemophase+1),period_config[x])) #note that this changes chemophase
+                    text_file = open(chemoconfig_path, "a+")
+                    text_file.write("{0},{1},{2}\n".format(elapsed_time,
+                                                           (last_chemophase+1),
+                                                           period_config[x])) #note that this changes chemophase
                     text_file.close()
+        else:
+            logger.debug('not enough OD measurements for vial %d' % x)
 
         # your_FB_function_here() #good spot to call feedback functions for dynamic temperature, stirring, etc for ind. vials
-    # your_function_here() #good spot to call non-feedback functions for dynamic temperature, stirring, etc. 
+    # your_function_here() #good spot to call non-feedback functions for dynamic temperature, stirring, etc.
 
-    eVOLVER_module.update_chemo(vials, bolus_in_s) #uses values stored in chemo_config files
+    eVOLVER.update_chemo(input_data, chemostat_vials, bolus_in_s, period_config) #compares computed chemostat config to the remote one
     # end of chemostat() fxn
 
 # def your_function_here(): # good spot to define modular functions for dynamics or feedback
 
 if __name__ == '__main__':
-    print('Please run main_eVOLVER.py instead')
+    print('Please run eVOLVER.py instead')