Merge pull request #239 from RobertGawron/feature/travis_to_github_actions_transition

Feature/travis to GitHub actions transition

ContinousIntegration/.gitignore

@@ -0,0 +1 @@
+python_lint_repport/

Software/DataAcquisition/.gitignore

@@ -0,0 +1 @@
+__pycache__/

Software/DataAcquisition/IonizationChamber.py

@@ -1,20 +1,24 @@
 from serial import Serial
 import mcp3425
 
+
 class IonizationChamber:
     def __init__(self, config):
         self.config = config
 
-
     def connect(self):
-        self.serialPort = Serial(self.config.myDeviceId, baudrate = self.config.myBaudrate, timeout=None)
+        self.serialPort = Serial(
+            self.config.myDeviceId,
+            baudrate=self.config.myBaudrate,
+            timeout=None)
+
         self.serialPort.isOpen()
         self.serialPort.flushInput()
 
-
     def getMeasurement(self):
         dataIn = self.serialPort.read(5)
-        (msb, lsb) = (dataIn[2], dataIn[3]) 
-        deviceMeasurement = mcp3425.convert(msb, lsb, mcp3425.MCP3425_RESOLUTION.R14)
-        return deviceMeasurement
+        (msb, lsb) = (dataIn[2], dataIn[3])
+        deviceMeasurement = mcp3425.convert(
+            msb, lsb, mcp3425.MCP3425_RESOLUTION.R14)
 
+        return deviceMeasurement

Software/DataAcquisition/README.md

@@ -1,7 +1,52 @@
 # Firmware
 
-* ["Data processing and firmware flashing" node architecture
-](https://github.com/RobertGawron/IonizationChamber/wiki/%22Data-processing-and-firmware-flashing%22-node-architecture
-)
+
+## Setup
+
 * [Setting up development environment on Linux
 ](https://github.com/RobertGawron/IonizationChamber/wiki/Setting-up-development-environment-on-Linux) 
+
+
+## Architecture
+
+![architecture of the component](https://raw.githubusercontent.com/RobertGawron/IonizationChamber/master/Documentation/Diagrams/HostArchitecture-1.png)
+
+
+## Collecting measurements
+
+1. **Edit config.py** to select the correct COM port of Ionization Chamber. Note that **useDMM flag should be set to False**, is experimental and was supposed to be used to check the correlation of Ionization Chamber with other factors (measured by DMM with SCPI support), such factors could be e.g. temperature.
+
+2. **Run data acquisition script**, it will log Ionization Chamber output on the screen and also it will save it to data.csv for further processing.
+
+```python main.py```
+
+3. When all data is logged, terminate ```python main.py``.
+
+## Plotting signal value in domain time + plotting histogram
+
+This mode is useful to look on measurement changes over time.
+
+After collecting data run script to post-process it and generate diagrams:
+
+```Rscript main.R```
+
+A new .png image with timestamp in its name will be created in directory where script is.
+
+Below is example of such generated plot.
+
+![boxplot](https://raw.githubusercontent.com/RobertGawron/IonizationChamber/master/Documentation/Plots/time_domain_example.png)
+
+
+## Plotting values from different measurements [(box plot)](https://en.wikipedia.org/wiki/Box_plot)
+
+1. Collect data from different samples as different .csv files.
+2. Edit ```boxplot.R```, to match filenames of .cvs files and labels of measurements.
+3. Run:
+
+```Rscript boxplot.R```
+
+A new .png image with timestamp in its name will be created in directory where script is.
+
+Below is example of such generated plot.
+
+![boxplot](https://raw.githubusercontent.com/RobertGawron/IonizationChamber/master/Documentation/Plots/box_plot_example.png)

Software/DataAcquisition/boxplot.R

@@ -1,10 +1,10 @@
 inputFileName ="DataNoSample.csv" 
 fileNoSample <- read.delim(inputFileName, , sep=",")
 
-inputFileName ="DataAmSample1.csv" 
+inputFileName ="DataSample1.csv" 
 fileAmSample1 <- read.delim(inputFileName, , sep=",")
 
-inputFileName ="DataRaSample2.csv" 
+inputFileName ="DataSample2.csv" 
 fileAmSample2 <- read.delim(inputFileName, , sep=",")
 
 

Software/DataAcquisition/config.py

@@ -1,10 +1,9 @@
 # ionization chamber
 myDeviceId = '/dev/ttyUSB0'
-myBaudrate = 9600 
+myBaudrate = 9600
 
 # dmm
 idDMM = "USB0::0x2A8D::0x1601::INSTR"
 testCommand = "READ?"
 
-
-useDMM = True
+useDMM = False

Software/DataAcquisition/dmm.py

@@ -1,14 +1,12 @@
 import usbtmc
 
+
 class DMM:
     def __init__(self, config):
         self.config = config
 
-
     def connect(self):
         self.device = usbtmc.Instrument(self.config.idDMM)
 
-
     def getMeasurement(self):
-         return self.device.ask(self.config.testCommand)
-
+        return self.device.ask(self.config.testCommand)

Software/DataAcquisition/main.R

@@ -10,6 +10,6 @@ samples <- read.delim(inputFileName, , sep=",")
 drawDiagramSingle(samples)
 
 # TODO move to a separate module
-library(Hmisc)
-rcorr(samples$Counter,samples$DMM, type="pearson")
+#library(Hmisc)
+#rcorr(samples$Counter,samples$DMM, type="pearson")
 

Software/DataAcquisition/main.py

@@ -1,76 +1,70 @@
 import datetime
-
-from IonizationChamber import IonizationChamber 
+from IonizationChamber import IonizationChamber
 from dmm import DMM
 import config
 
+
 class IonizationChamberStateMachine:
     def __init__(self, config):
         self.config = config
         self.deviceMeasurement = 0.0
         self.dmmMeasurement = 0.0
-        
-        self.nextState = self.initIonizationChamber
 
+        self.nextState = self.initIonizationChamber
 
     def tick(self):
         self.nextState()
 
-
     def initIonizationChamber(self):
         self.chamber = IonizationChamber(config)
         self.chamber.connect()
-        
+
         if config.useDMM:
             self.nextState = self.initDMM
         else:
             self.nextState = self.initOutputFile
 
-
     def initDMM(self):
         self.dmm = DMM(config)
         self.dmm.connect()
-        
-        self.nextState = self.initOutputFile
 
+        self.nextState = self.initOutputFile
 
     def initOutputFile(self):
         self.logFile = open('data.csv', 'w')
         self.logFile.write("Time,Counter,DMM\n")
-        
-        self.nextState = self.getMeasurementFromIonizationChamber
 
+        self.nextState = self.getMeasurementFromIonizationChamber
 
     def getMeasurementFromIonizationChamber(self):
         self.deviceMeasurement = self.chamber.getMeasurement()
-        
+
         if config.useDMM:
             self.nextState = self.getMeasurementFromDMM
         else:
             self.nextState = self.saveMeasurement
 
-
     def getMeasurementFromDMM(self):
         self.dmmMeasurement = self.dmm.getMeasurement()
-        
-        self.nextState = self.saveMeasurement
 
+        self.nextState = self.saveMeasurement
 
     def saveMeasurement(self):
         now = datetime.datetime.now()
-        self.logFile.write("{0},{1},{2}\n".format(now, self.deviceMeasurement, self.dmmMeasurement))
-        self.logFile.flush()
-        
-        self.nextState = self.showMeasurementToUser
+        self.logFile.write("{0},{1},{2}\n".format(
+            now, self.deviceMeasurement, self.dmmMeasurement))
 
+        self.logFile.flush()
+
+        self.nextState = self.showMeasurementToUser
 
     def showMeasurementToUser(self):
         print("{0}, {1}".format(self.deviceMeasurement, self.dmmMeasurement))
-        
+
         self.nextState = self.getMeasurementFromIonizationChamber
 
 
-if __name__=="__main__":
+if __name__ == "__main__":
     machine = IonizationChamberStateMachine(config)
 
     while True:

Software/DataAcquisition/mcp3425.py

@@ -1,24 +1,27 @@
-# based on https://ww1.microchip.com/downloads/en/DeviceDoc/22072b.pdf
-# assumed that gain = 1
-
+"""
+based on https://ww1.microchip.com/downloads/en/DeviceDoc/22072b.pdf
+assumed that gain = 1
+"""
 from enum import Enum
 
+
 class MCP3425_RESOLUTION(Enum):
     R12 = 1
     R13 = 2
     R14 = 3
 
-def convert(upperByte, lowerByte, resolution):
-    digitalToAnalog = lambda value, lsb, pga: (value * (lsb / pga))
 
-    digitalOutput = (upperByte << 8) | lowerByte;
+def convert(upperByte, lowerByte, resolution):
+    def digitalToAnalog(value, lsb, pga):
+        return (value * (lsb / pga))
+
+    digitalOutput = (upperByte << 8) | lowerByte
 
     if resolution == MCP3425_RESOLUTION.R12:
         return digitalToAnalog(digitalOutput, (1 * 0.01), 1)
-        
+
     if resolution == MCP3425_RESOLUTION.R13:
         return digitalToAnalog(digitalOutput, (250 * 0.0000001), 1)
- 
+
     if resolution == MCP3425_RESOLUTION.R14:
         return digitalToAnalog(digitalOutput, (62.5 * 0.000001), 1)
-