[update] change table name project_report -> project_reports & project_meta -> project_metas

README.md

@@ -158,8 +158,8 @@ reboot
 
 ###### Set pi password
 ```
-$cd ~
-$passwd
+cd ~
+passwd
 Current password:raspberry
 New password:5k6zj454778225
 Retype new password:5k6zj454778225
@@ -198,11 +198,11 @@ exit 0
 ### MQTT broker install
 
 ###### 1.Install mosquitto
-$sudo apt-get install mosquitto mosquitto-clients
+sudo apt-get install mosquitto mosquitto-clients
 
 
 ###### 2.Enable Remote Access
-$sudo vim /etc/mosquitto/conf.d/default.conf
+sudo vim /etc/mosquitto/conf.d/default.conf
 
 add the code following as:
 ```
@@ -213,13 +213,13 @@ protocol websockets
 allow_anonymous true
 ```
 ###### 3.restart mqtt broker
-$sudo systemctl restart mosquitto
+sudo systemctl restart mosquitto
 
 ###### 4.Robust MQTT
 create mosquitto_restart.sh
 
-$cd ~
-$sudo vim mosquitto_restart.sh
+cd ~
+sudo vim mosquitto_restart.sh
 
 
 add the code following as:
@@ -236,16 +236,16 @@ echo "$SERVICE is currently running" >> /home/ubuntu/cron.log
 exit 0
 ```
 ###### 5.add mosquitto_restart.sh to root routing
-$sudo chmod +x mosquitto_restart.sh
-$sudo  -i
-$crontab -e
+sudo chmod +x mosquitto_restart.sh
+sudo  -i
+crontab -e
 
 add the code following as:
 ```
 */5 * * * * /home/pi/mosquitto_restart.sh
 ```
 ###### 6.Auto run MQTT broker when when pi-start
-$sudo vim /etc/rc.local
+sudo vim /etc/rc.local
 
 add the code following as:
 ```
@@ -254,31 +254,31 @@ sudo nohup systemctl restart mosquitto
 
 ### Setting up a Routed Wireless Access Point
 ###### 1.Install AP and Management Software
-$sudo apt install hostapd
-$sudo systemctl unmask hostapd
-$sudo systemctl enable hostapd
-$sudo apt install dnsmasq
-$sudo DEBIAN_FRONTEND=noninteractive apt install -y netfilter-persistent iptables-persistent
+sudo apt install hostapd
+sudo systemctl unmask hostapd
+sudo systemctl enable hostapd
+sudo apt install dnsmasq
+sudo DEBIAN_FRONTEND=noninteractive apt install -y netfilter-persistent iptables-persistent
 
 ###### 2.Set up the Network Router
-$sudo nano /etc/dhcpcd.conf
+sudo nano /etc/dhcpcd.conf
 ```
 interface wlan0
     static ip_address=192.168.2.1/24
     nohook wpa_supplicant
 ```
-$sudo nano /etc/sysctl.d/routed-ap.conf
+sudo nano /etc/sysctl.d/routed-ap.conf
 ```
 # Enable IPv4 routing
 net.ipv4.ip_forward=1
 ```
 
-$sudo iptables -t nat -A POSTROUTING -o eth0 -j MASQUERADE
-$sudo netfilter-persistent save
-$sudo mv /etc/dnsmasq.conf /etc/dnsmasq.conf.orig
+sudo iptables -t nat -A POSTROUTING -o eth0 -j MASQUERADE
+sudo netfilter-persistent save
+sudo mv /etc/dnsmasq.conf /etc/dnsmasq.conf.orig
 
 
-$sudo nano /etc/dnsmasq.conf
+sudo nano /etc/dnsmasq.conf
 
 ```
 interface=wlan0 # Listening interface
@@ -289,10 +289,10 @@ address=/gw.wlan/192.168.2.1
                 # Alias for this router
 ```
 ###### 3.Ensure Wireless Operation
-$sudo rfkill unblock wlan
+sudo rfkill unblock wlan
 
 ###### 4.Configure the AP Software
-$sudo nano /etc/hostapd/hostapd.conf
+sudo nano /etc/hostapd/hostapd.conf
 
 ```
 country_code=TW
@@ -317,11 +317,13 @@ wme_enabled=1
 ht_capab=[HT40+][SHORT-GI-40]
 ```
 ###### 5.Running the new Wireless AP
-$sudo systemctl reboot
+sudo systemctl reboot
 
+### Install Apache2
+sudo apt install apache2
 
-### Set web site
-$sudo vim ./sites-available/000-default.conf
+### Deploy web site
+sudo vim /etc/apache2/sites-available/000-default.conf
 ```
 <VirtualHost *:8080> #80------>8080
         # The ServerName directive sets the request scheme, hostname and port that
@@ -363,6 +365,11 @@ $sudo vim ./sites-available/000-default.conf
 > https://www.raspberrypi.org/documentation/configuration/wireless/access-point-routed.md
 
 # ChangeLog
+[2022.12.28]
+change meta_project_info to project_metas
+change project_report to project_reports
+alter table project_meta column cycle type string to jsonb
+
 [2022.11.16]
 add python package SQLAlchemy
 add new column project(int4) in postgresSQL table recording_meta_datas

python/biopro/db/project_meta.py

@@ -6,11 +6,11 @@ from sqlalchemy.dialects.postgresql import JSONB
 from .base import Base
 
 class MetaProjectInfo(Base):
-    __tablename__ = "meta_project_info"
+    __tablename__ = "project_metas"
 
     id = Column(Integer, primary_key=True)
     project = Column(String(36))
-    cycle = Column(String)
+    cycle = Column(JSONB)
     task = Column(JSONB)
     serial_number = Column(Integer)
     deleted = Column(Boolean, default = False)

python/biopro/db/project_report.py

@@ -6,7 +6,7 @@ from sqlalchemy.dialects.postgresql import JSONB
 from .base import Base
 
 class ProjectReport(Base):
-    __tablename__ = "project_report"
+    __tablename__ = "project_reports"
 
     id = Column(Integer, primary_key=True)
     name = Column(String)

python/biopro/devlib/data.py

@@ -1360,7 +1360,6 @@ class EISZeroOneDataDecoder(RecDataDecoder):
         self._mode_stop = 0
 
         self._cycle_start_time = []
-        self._ac_amp: int = 0
         self._mode: int = 0
         self._last_phase = 0
         self._first_phase_flag = 1
@@ -1488,14 +1487,14 @@ class EISZeroOneDataDecoder(RecDataDecoder):
             phase_coeff[3][g] = struct.unpack('>i', cali_coeff[index+9:index+13])[0]
             phase_offset[3][g] = struct.unpack('>i', cali_coeff[index+13:index+17])[0]
 
-            # print('cutoff_freq', cutoff_freq)
-            # print('hsrtia_a', hsrtia_a)
-            # print('hsrtia_b', hsrtia_b)
-            # print('hsrtia_c', hsrtia_c)
-            # print('phase_coeff')
-            # print(phase_coeff)
-            # print('phase_offset')
-            # print(phase_offset)
+            print('cutoff_freq', cutoff_freq)
+            print('hsrtia_a', hsrtia_a)
+            print('hsrtia_b', hsrtia_b)
+            print('hsrtia_c', hsrtia_c)
+            print('phase_coeff')
+            print(phase_coeff)
+            print('phase_offset')
+            print(phase_offset)
 
             cali_table.append((cutoff_freq, phase_coeff, phase_offset, hsrtia_a, hsrtia_b, hsrtia_c, hsrtia_d))
 
@@ -1528,8 +1527,13 @@ class EISZeroOneDataDecoder(RecDataDecoder):
         cycle_number = struct.unpack('>H', data[17+3:19+3])[0]
         d19 = data[19+3]
         gain = data[20+3]
-        finishMode = (d19 & 0x80) >> 7        
+        finishMode = (d19 & 0x80) >> 7  
+        ch4 = struct.unpack('<i', data[21+3:25+3])[0] # Amp[uV]
         
+        notify_one = struct.unpack('<i', data[25+3:29+3])[0]
+        notify_two = struct.unpack('<i', data[29+3:33+3])[0]
+        notify_three = struct.unpack('<i', data[33+3:37+3])[0]
+
         if time_stamp == 0:
             self._start_return_data = True
 
@@ -1553,13 +1557,12 @@ class EISZeroOneDataDecoder(RecDataDecoder):
                     hsrtia_d = []
                     cutoff_freq, phase_coeff, phase_offset, hsrtia_a, hsrtia_b, hsrtia_c, hsrtia_d = self.cali_coeff[0]
 
-                    voltage_amp = round(self._ac_amp * 800 / 2047) # use UI value
-
                 if (self._mode == 0 or self._mode == 5):
                     img = ch1
                     real = ch2
                     freq = ch3
                     fre_idx = 0
+                    voltage_amp = round(ch4 / 1000) # Amp[mV]
 
                     # rolloff_cali = cutoff_freq/1e5
                     rolloff_cali = hsrtia_c[gain]
@@ -1573,15 +1576,9 @@ class EISZeroOneDataDecoder(RecDataDecoder):
                     # current = voltage_mag ** 2 * hsrtia_a[gain] + voltage_mag * hsrtia_b[gain] + hsrtia_c[gain]
                     
 
-                    # print(current)
-                    # print(voltage_mag)
-                    # print(hsrtia_a[gain])
-                    # print(hsrtia_b[gain])
-                    # print(hsrtia_c[gain])
-
                     if (current != 0):
-                        # impedance = voltage_amp * 1000_000 / 1.414213 / current 
-                        impedance = voltage_amp * 707106.78 / current 
+                        # impedance[mOhm] = voltage_amp[mv] * 1000000 / 1.414213 / current[nA]       #RMS=amp*SQRT(2), SQRT(2)=1.414213
+                        impedance = voltage_amp * 707106.78 / current
                     else:
                         impedance = 0
 
@@ -1612,25 +1609,33 @@ class EISZeroOneDataDecoder(RecDataDecoder):
                     #     phase = self._last_phase + diff
                     # self._last_phase = phase
 
-                    imag_after_cal = impedance * math.sin(round(phase) * math.pi / 180)
-                    real_after_cal = impedance * math.cos(round(phase) * math.pi / 180)
+                    imag_after_cal = impedance * math.sin(phase * math.pi / 180)
+                    real_after_cal = impedance * math.cos(phase * math.pi / 180)
 
                 if self._show_data:
                     if (self._mode == 0 or self._mode == 5):
                         print('|', '{:10}'.format(time_stamp),
-                            '|', '{:5}'.format(delta),
-                            '|', '{:6}'.format(ch1),
-                            '|', '{:6}'.format(ch2),
-                            '|', '{:8}'.format(ch3 / 100),
-                            '|', '{:6}'.format(round(voltage_mag)),
-                            '|', '{:5}'.format(int(imag_after_cal)),
-                            '|', '{:5}'.format(int(real_after_cal)),
-                            '|', '{:5}'.format(round(impedance)),
-                            '|', '{:5}'.format(round(phase, 1)),
-                            '|', '{:5}'.format(round(current, 3)),
-                            '|', '{:1}'.format(gain),
-                            '|', '{:1}'.format(finishMode),
-                            '@', str(self.device), '|', flush = True)
+                              '|', '{:5}'.format(delta),
+                              '|', '{:5}'.format(ch1),                            #raw_img
+                              '|', '{:5}'.format(ch2),                            #raw_real
+                              '|', '{:8}'.format(ch3 * 10), '[mHz]',              #Frequency [mHz]
+                              '|', '{:5}'.format(cycle_number),                   #cycle
+                              '|', '{:5}'.format(round(imag_after_cal)), '[Ohm]', #Z_imag [Ohm]
+                              '|', '{:5}'.format(round(real_after_cal)), '[Ohm]', #Z_real [Ohm]
+                              '|', '{:5}'.format(round(impedance)), '[Ohm]',      #Impedance [Ohm]
+                              '|', '{:5}'.format(round(phase*1000)), '[mdegree]', #Phase [millidegree]
+                              '|', '{:5}'.format(round(current)), '[nA]',         #Current [nA]
+                              '|', '{:1}'.format(gain),                           #gain
+                              '|', '{:1}'.format(finishMode),                     #finishMode
+                              '@', str(self.device), '|', flush = True)
+
+                        print('|', '{:10}'.format(time_stamp),
+                              '|', '{:5}'.format(delta),
+                              '|', '{:5}'.format(notify_one),
+                              '|', '{:5}'.format(notify_two),
+                              '|', '{:5}'.format(notify_three),
+                              '|', '{:5}'.format(voltage_amp),                    #amp[mV]
+                              '|', flush = True)
                         pass
                     else:
                         print('|', '{:10}'.format(time_stamp),
@@ -1652,16 +1657,24 @@ class EISZeroOneDataDecoder(RecDataDecoder):
 
         ret = RecordingData(self.device, int(time_stamp * 1000 / 2), 0)
         if self._mode == 0 or self._mode == 5:                           #EIS Mode
-            ret.append_data(0, ch1)                     #Raw Imag  
-            ret.append_data(1, ch2)                     #Raw Real
+            ret.append_data(0, ch1)                     #raw_img
+            ret.append_data(1, ch2)                     #raw_real
             ret.append_data(2, ch3 * 10)                #Frequency [mHz]
-            ret.append_data(3, cycle_number)
+            ret.append_data(3, cycle_number)            #cycle
             ret.append_data(4, round(imag_after_cal))   #Z_imag [Ohm]
             ret.append_data(5, round(real_after_cal))   #Z_real [Ohm]
             ret.append_data(6, round(impedance))        #Impedance [Ohm]
-            ret.append_data(7, round(phase))            #Phase [degree]
+            ret.append_data(7, round(phase*1000))       #Phase [millidegree]
             ret.append_data(8, round(current))          #Current [nA]
-            ret.append_data(9, gain)                    #Gain Level
+            ret.append_data(9, gain)                    #gain
+            
+            #debug data
+            ret.append_data(10, notify_one)
+            ret.append_data(11, notify_two)
+            ret.append_data(12, notify_three)
+            ret.append_data(13, voltage_amp)            #amp[mV]
+
+
 
         else:                                           #CV Mode
             ret.append_data(0, ch1)                     #Iin     [nA]

python/biopro/project/project.py

@@ -57,7 +57,7 @@ class Project(threading.Thread):
     self.setup_device(self._device)
 
     # create log file handler
-    fh = logging.FileHandler(f'{self.uuid}.log', mode="w")
+    fh = logging.FileHandler(f'/home/pi/logger/project/{self.uuid}.log', mode="w")
     fh.setFormatter(self._formatter)
     self._logger.addHandler(fh)
     
@@ -259,13 +259,13 @@ class Project(threading.Thread):
                     self.log_verbose('file name ' + task_info['file_name'])
                     
                   if instruction_set != None and self.get_device_parameter_set(action.target) != None:
-                    if action.type == 'start':
-                      self._count += 1
                     for instruction in instruction_set:
                       print('instruction 1', device, instruction, datetime.now())
                       args = list(map(lambda arg: task_info[arg], instruction['arguments']))
                       target=getattr(device, instruction['method'])(*args)
                       print('instruction 2', device, instruction, datetime.now())
+                    if action.type == 'start':
+                      self._count += 1
             
             delay_time += (time() - now)
 

python/biopro/server/database.py

@@ -553,7 +553,7 @@ class DataBaseProcess(Process):
         return True
     
     def project_insert(self, device_id, _data):
-        sql_str = 'INSERT INTO "public"."meta_project_info" ('
+        sql_str = 'INSERT INTO "public"."project_metas" ('
         sql_set = []
         for item in _data.keys():
             sql_str = sql_str + str(item) + ', '

python/biopro/server/main.py

@@ -34,7 +34,7 @@ from biopro.api.device import DeviceAPI
 from biopro.project.project_manager import ProjectManager
 from biopro.db.base import Base, Session, engine
 from biopro.db.project_report import ProjectReport
-from biopro.db.meta_project_info import MetaProjectInfo
+from biopro.db.project_meta import MetaProjectInfo
 
 
 _RUNTIME_COMPILE = False

python/biopro/server/recording.py

@@ -158,7 +158,6 @@ class RecordingProcess(Process):
         elif isinstance(decoder, EISZeroOneDataDecoder):
             # get amp_gain from meta file
             decoder._mode = self._meta_file.configuration.get_parameter('MODE')
-            decoder._ac_amp = self._meta_file.configuration.get_parameter('EIS_AC_AMP')
 
         return decoder
 

update_db_package.sh

@@ -7,8 +7,23 @@ sudo apt-get install python3-numpy
 # install python module SQLAlchemy
 pip3 install SQLAlchemy
 
+# create folder to save project logger
+mkdir -p /home/pi/logger/project
+
 # add column cycle in projects
 sudo su -c "psql -d postgres -c \"ALTER TABLE projects ADD COLUMN IF NOT EXISTS cycle JSONB;\"" postgres
 
 # add column project in recording_data_metas
 sudo su -c "psql -d postgres -c \"ALTER TABLE recording_data_metas ADD COLUMN IF NOT EXISTS project Int4;\"" postgres
+
+# remove default controller info
+sudo su -c "psql -d postgres -c \"DELETE FROM controllers WHERE name='WTP_NONE';\"" postgres
+
+# change table name from meta_project_info to project_metas
+sudo su -c "psql -d postgres -c \"ALTER TABLE IF EXISTS meta_project_info RENAME TO project_metas;\"" postgres
+
+# change table name from project_report to project_reports
+sudo su -c "psql -d postgres -c \"ALTER TABLE IF EXISTS project_report RENAME TO project_reports;\"" postgres
+
+# change table project_meta column cycle to type jsonb
+sudo su -c "psql -d postgres -c \"ALTER TABLE project_metas ALTER COLUMN cycle type jsonb USING (cycle::jsonb);\"" postgres