Merge pull request #261 from RobertGawron/feature/rev_5_0

Feature/rev 5 0

Documentation/Diagrams/UARTFrameFormat.tex

@@ -25,20 +25,21 @@
 
 
 \node (StartPoint) [text depth=13pt, text height=6pt]{};
-\shnode{StartPoint}{MsgId}{msg id};
-\shnode{MsgId}{MsgLen}{msg length};
-\lnode{MsgLen}{Configuration}{ADC configuration};
+\shnode{StartPoint}{MsgType}{msg type};
+\shnode{MsgType}{MsgLen}{msg length};
+\lnode{MsgLen}{MsgCounter}{msg \\ counter};
+\lnode{MsgCounter}{Configuration}{ADC configuration};
 \lnode{Configuration}{MSBADC}{MSB ADC value};
 \lnode{MSBADC}{LSBADC}{LSB ADC value};
 \lnode{LSBADC}{CRC}{CRC};
 
-\draw[decorate,decoration={brace,raise=3pt}] (MsgId.north west) -- node[above=4pt] {Preamble} (MsgLen.north east);
+\draw[decorate,decoration={brace,raise=3pt}] (MsgType.north west) -- node[above=4pt] {Preamble} (MsgCounter.north east);
 \draw[decorate,decoration={brace,raise=3pt}] (Configuration.north west) -- node[above=4pt] {Data} (LSBADC.north east);
 \draw[decorate,decoration={brace,raise=3pt}] (CRC.north west) -- node[above=4pt] {CRC} (CRC.north east);
 
-\draw (MsgId.south west) -- +(0,-1.2cm);
+\draw (MsgType.south west) -- +(0,-1.2cm);
 \draw (MsgLen.south east) -- +(0,-1.2cm);
-\draw[<->] ( $ (MsgId.south west) +(0,-0.6cm) $ ) -- node[fill=white] {1 Byte} ( $ (MsgLen.south east) +(0,-0.6cm) $ );
+\draw[<->] ( $ (MsgType.south west) +(0,-0.6cm) $ ) -- node[fill=white] {1 byte} ( $ (MsgLen.south east) +(0,-0.6cm) $ );
 
 
 \end{tikzpicture}

Simulation/main.py

@@ -1,13 +1,13 @@
 import sys
 sys.path.append('../Software/DataAcquisition')
 
-from hardware_connection import HardwareConnection  # noqa: E402
+from physical_layer import PhysicalLayer  # noqa: E402
 from state_machine import IonizationChamberStateMachine  # noqa: E402
 import config  # noqa: E402
 
 if __name__ == "__main__":
-    hardware = HardwareConnection(config)
-    machine = IonizationChamberStateMachine(hardware)
+    physicalLayer = PhysicalLayer(config)
+    machine = IonizationChamberStateMachine(physicalLayer)
 
     while True:
         machine.tick()

Simulation/physical_layer.py

@@ -0,0 +1,11 @@
+
+
+class PhysicalLayer:
+    def __init__(self, config):
+        pass
+
+    def connect(self):
+        pass
+
+    def getData(self):
+        return [1, 2, 3, 4, 5, 9]

Software/DataAcquisition/README.md

@@ -1,33 +1,61 @@
-# Firmware
+## Setting up development environment on Linux
 
 
-## Setup
+1.  Install tools via apt-get:
 
-* [Setting up development environment on Linux
-](https://github.com/RobertGawron/IonizationChamber/wiki/Setting-up-development-environment-on-Linux) 
+```console
+apt-get install screen git sdcc doxygen uncrustify libusb-1.0-0-dev python3-pip texlive-latex-base texlive-latex-extra texlive-extra-utils poppler-utils cmake cppcheck r-base-core shellcheck
+```
 
+3. Install python libraries.
+```console
+pip3 install pyserial
+pip3 install flake8 flake8-html
+```
 
-## Architecture
+4. Install R libraries, run R in command line:
+```console
+pi@raspberrypi:~/IonizationChamber/software/DataAcquisitionFromDevice $ R
+
+R version 3.5.2 (2018-12-20) -- "Eggshell Igloo"
+Copyright (C) 2018 The R Foundation for Statistical Computing
+Platform: arm-unknown-linux-gnueabihf (32-bit)
+```
+
+Type (write yes on next prompts):
+
+```
+install.packages('latticeExtra')
+```
+
+```
+install.packages('gridExtra')
+```
+
+```
+install.packages('Hmisc')
+```
 
-<img src="../../Documentation/Diagrams/HostArchitecture.svg"  width="100%">
 
 ## 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``.
+```
+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```
+```
+Rscript main.R
+```
 
 A new .png image with timestamp in its name will be created in directory where script is.
 
@@ -42,7 +70,9 @@ Below is example of such generated plot.
 2. Edit ```boxplot.R```, to match filenames of .cvs files and labels of measurements.
 3. Run:
 
-```Rscript boxplot.R```
+```
+Rscript boxplot.R
+```
 
 A new .png image with timestamp in its name will be created in directory where script is.
 

Software/DataAcquisition/application_layer.py

@@ -0,0 +1,45 @@
+from transport_layer import TransportLayer
+from enum import Enum
+
+
+class ADC_RESOLUTION(Enum):
+    R12 = 1
+    R13 = 2
+    R14 = 3
+
+
+def convert(upperByte, lowerByte, resolution):
+    """
+    based on https://ww1.microchip.com/downloads/en/DeviceDoc/22072b.pdf
+    assumed that gain = 1
+    """
+    def digitalToAnalog(value, lsb, pga):
+        return (value * (lsb / pga))
+
+    digitalOutput = (upperByte << 8) | lowerByte
+
+    if resolution == ADC_RESOLUTION.R12:
+        return digitalToAnalog(digitalOutput, (1 * 0.01), 1)
+
+    if resolution == ADC_RESOLUTION.R13:
+        return digitalToAnalog(digitalOutput, (250 * 0.0000001), 1)
+
+    if resolution == ADC_RESOLUTION.R14:
+        return digitalToAnalog(digitalOutput, (62.5 * 0.000001), 1)
+
+
+class ApplicationLayer:
+    def __init__(self, physicalLayer):
+        self.transportLayer = TransportLayer(physicalLayer)
+
+    def connect(self):
+        self.transportLayer.connect()
+
+    def getMeasurement(self):
+        dataIn = self.transportLayer.getFrame()
+
+        (msb, lsb) = (dataIn[2], dataIn[3])
+        deviceMeasurement = convert(
+            msb, lsb, ADC_RESOLUTION.R14)
+
+        return deviceMeasurement

Software/DataAcquisition/main.py

@@ -1,11 +1,11 @@
 
-from hardware_connection import HardwareConnection
+from physical_layer import PhysicalLayer
 from state_machine import IonizationChamberStateMachine
 import config
 
 if __name__ == "__main__":
-    hardware = HardwareConnection(config)
-    machine = IonizationChamberStateMachine(hardware)
+    physicalLayer = PhysicalLayer(config)
+    machine = IonizationChamberStateMachine(physicalLayer)
 
     while True:
         machine.tick()

Software/DataAcquisition/measurement_storage.py

@@ -0,0 +1,15 @@
+import csv
+
+
+class MeasurementStorage:
+    def __init__(self):
+        self.CVS_FileName = "data.csv"
+        self.CVS_Header = ['Time', 'Counter']
+
+    def connect(self):
+        CVS_Handler = open(self.CVS_FileName, 'w', encoding='UTF8', newline='')
+        self.CVS_Writter = csv.writer(CVS_Handler)
+        self.CVS_Writter.writerow(self.CVS_Header)
+
+    def saveMeasurement(self, date, measurement):
+        self.CVS_Writter.writerow([date, measurement])

Software/DataAcquisition/hardware_connection.py → Software/DataAcquisition/physical_layer.py

@@ -1,7 +1,7 @@
 from serial import Serial
 
 
-class HardwareConnection:
+class PhysicalLayer:
     def __init__(self, config):
         self.config = config
 
@@ -14,6 +14,7 @@ def connect(self):
         self.serialPort.isOpen()
         self.serialPort.flushInput()
 
-    def getMeasurement(self):
-        dataIn = self.serialPort.read(5)
+    def getData(self):
+        msgLength = 6
+        dataIn = self.serialPort.read(msgLength)
         return dataIn

Software/DataAcquisition/state_machine.py

@@ -1,39 +1,40 @@
 import datetime
-from ionization_chamber import IonizationChamber
+from application_layer import ApplicationLayer
+from measurement_storage import MeasurementStorage
 
 
 class IonizationChamberStateMachine:
-    def __init__(self, hardware):
-        self.hardware = hardware
+    def __init__(self, physicalLayer):
+        self.applicationLayer = ApplicationLayer(physicalLayer)
         self.deviceMeasurement = 0.0
+        self.measurementStorage = MeasurementStorage()
+
         self.nextState = self.initIonizationChamber
 
     def tick(self):
         self.nextState()
 
     def initIonizationChamber(self):
-        self.chamber = IonizationChamber(self.hardware)
-        self.chamber.connect()
-        self.nextState = self.initOutputFile
+        self.applicationLayer.connect()
+
+        self.nextState = self.initMeasurementStorage
+
+    def initMeasurementStorage(self):
+        self.measurementStorage.connect()
 
-    def initOutputFile(self):
-        self.logFile = open('data.csv', 'w')
-        self.logFile.write("Time,Counter,DMM\n")
         self.nextState = self.getMeasurementFromIonizationChamber
 
     def getMeasurementFromIonizationChamber(self):
-        self.deviceMeasurement = self.chamber.getMeasurement()
+        self.deviceMeasurement = self.applicationLayer.getMeasurement()
+
         self.nextState = self.saveMeasurement
 
     def saveMeasurement(self):
         now = datetime.datetime.now()
-        self.logFile.write("{0},{1}\n".format(
-            now, self.deviceMeasurement))
-
-        self.logFile.flush()
-
+        self.measurementStorage.saveMeasurement(now, self.deviceMeasurement)
         self.nextState = self.showMeasurementToUser
 
     def showMeasurementToUser(self):
         print("{0}".format(self.deviceMeasurement))
+
         self.nextState = self.getMeasurementFromIonizationChamber

Software/DataAcquisition/transport_layer.py

@@ -0,0 +1,23 @@
+
+
+class InvalidCRC(Exception):
+    pass
+
+
+class MissingFrame(Exception):
+    pass
+
+
+class InvalidMsgLength(Exception):
+    pass
+
+
+class TransportLayer:
+    def __init__(self, physicalLayer):
+        self.physicalLayer = physicalLayer
+
+    def connect(self):
+        self.physicalLayer.connect()
+
+    def getFrame(self):
+        return self.physicalLayer.getData()