removed old utils virtualenv

.gitignore

@@ -0,0 +1,129 @@
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+pip-wheel-metadata/
+share/python-wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+*.py,cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+db.sqlite3-journal
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# pipenv
+#   According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
+#   However, in case of collaboration, if having platform-specific dependencies or dependencies
+#   having no cross-platform support, pipenv may install dependencies that don't work, or not
+#   install all needed dependencies.
+#Pipfile.lock
+
+# pyflow
+__pypackages__/
+
+# Celery stuff
+celerybeat-schedule
+celerybeat.pid
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

.pylintrc

@@ -0,0 +1,2 @@
+[MASTER]
+disable = c0103

LICENSE.txt

@@ -0,0 +1,14 @@
+Copyright (c) 2018, 2019, Kristjan Komloši, Jakob Kosec, Juš Dolžan,
+TeraHz development team
+
+Permission to use, copy, modify, and/or distribute this software for any
+purpose with or without fee is hereby granted, provided that the above
+copyright notice and this permission notice appear in all copies.
+
+THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
+WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
+MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY
+SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
+WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN ACTION
+OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF OR IN
+CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.

README.md

@@ -0,0 +1,23 @@
+# TeraHz
+
+[![Documentation Status](https://readthedocs.org/projects/terahz/badge/?version=latest)](https://terahz.readthedocs.io/en/latest/?badge=latest)
+
+TeraHz is a low-cost spectrometer based on a Raspberry Pi 3 or 3 B+ and three sensors:
+ + [__AS7265x__](https://www.tindie.com/products/onehorse/compact-as7265x-spectrometer/)
+ is a 18 channel spectrometer chipset that provides the device with spectral data
+ + [__VEML6075__](https://www.sparkfun.com/products/15089) is an
+ UVA/UVB sensor
+ + [__APDS-9301__](https://www.sparkfun.com/products/14350) is a calibrated illuminance (lux) meter that provides the device with reliable readings
+
+## Why?
+Because people and institutions could use an affordable and accurate light-analysing device that is also portable, easy to use and simple to assemble. TeraHz was started as an answer to our high school not being able to afford a commercially available solution. One TeraHz spectrometer costs around 150$ in parts, which makes it a competitive alternative to other solutions on the market today.
+
+## Development team
+Copyright 2018, 2019
+
+- Kristjan "cls-02" Komloši (electronics, sensor drivers, backend)
+- Jakob "D3m1j4ck" Kosec (frontend)
+
+
+I would also like to thank Juš "ANormalPerson" Dolžan, who decided to leave the
+team, but helped me a lot with backend development.

backend/app.py

@@ -0,0 +1,17 @@
+# app.py - main backend program
+'''Main TeraHz backend program'''
+# All code in this file is licensed under the ISC license, provided in LICENSE.txt
+from flask import Flask
+import flask
+import sensors
+
+app = Flask(__name__)
+@app.route('/data')
+def sendData():
+    '''Responder function for /data route'''
+    s = sensors.Spectrometer(path='/dev/serial0', baudrate=115200, tout=1)
+    u = sensors.UVSensor()
+    l = sensors.LxMeter()
+    response = flask.jsonify([s.getData(), l.getData(), u.getABI()])
+    response.headers.add('Access-Control-Allow-Origin', '*')
+    return response

backend/run.sh

@@ -0,0 +1,4 @@
+#!/bin/bash
+# run.sh - run the backend server
+cd `dirname $0`
+sudo gunicorn app:app -b 0.0.0.0:5000 &

backend/sensors.py

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+# sensors.py - a module for interfacing to the sensors
+'''Module for interfacing with TeraHz sensors'''
+# Copyright 2019 Kristjan Komloši
+# All code in this file is licensed under the ISC license, provided in LICENSE.txt
+import serial as ser
+import pandas as pd
+import smbus2
+
+class Spectrometer:
+    '''Class representing the AS7265X specrometer'''
+    def initializeSensor(self):
+        '''confirm the sensor is responding and proceed\
+         with spectrometer initialization'''
+        try:
+            rstring = 'undefined'  # just need it set to a value
+            self.setParameters({'gain': 0})
+            self.serialObject.write(b'AT\n')
+            rstring = self.serialObject.readline().decode()
+            if rstring == 'undefined':
+                raise Exception  # sensor didn't respond
+            if rstring == 'OK':
+                pass  # handshake passed
+            if rstring == 'ERROR':
+                raise Exception  # sensor is in error state
+        except:
+            raise Exception(
+                'An exception ocurred when performing spectrometer handshake')
+
+    def setParameters(self, parameters):
+        '''applies the parameters like LED light and gain to the spectrometer'''
+        try:
+            if 'it_time' in parameters:
+                it_time = int(parameters['it_time'])
+                if it_time <= 0:
+                    it_time = 1
+                self.serialObject.write(
+                    'ATINTTIME={}\n'.format(str(it_time)).encode())
+                self.serialObject.readline()
+
+            if 'gain' in parameters:
+                gain = int(parameters['gain'])
+                if gain < 0 or gain > 3:
+                    gain = 1
+                self.serialObject.write('ATGAIN={}\n'.format(gain).encode())
+                self.serialObject.readline()
+
+            if 'led' in parameters:
+                led = bool(parameters['led'])
+                if led:
+                    led = 1
+                else:
+                    led = 0
+                self.serialObject.write('ATLED3={}\n'.format(led).encode())
+                self.serialObject.readline()
+        except:
+            raise Exception(
+                'An exception occured during spectrometer initialization')
+
+    def getData(self):
+        '''Returns spectral data in a pandas DataFrame.'''
+        try:
+            self.serialObject.write(b'ATCDATA\n')
+            rawresp = self.serialObject.readline().decode()
+        except:
+            raise Exception(
+                'An exception occurred when polling for spectrometer data')
+        else:
+            responseorder = [i for i in 'RSTUVWGHIJKLABCDEF']
+            realorder = [i for i in 'ABCDEFGHRISJTUVWKL']
+            response = pd.Series(
+                [float(i) / 35.0 for i in rawresp[:-3].split(',')], index=responseorder)
+            return pd.DataFrame(response, index=realorder, columns=['uW/cm^2']).to_dict()['uW/cm^2']
+
+    def __init__(self, path='/dev/ttyUSB0', baudrate=115200, tout=1):
+        self.path = path
+        self.baudrate = baudrate
+        self.timeout = 1
+        try:
+            self.serialObject = ser.Serial(path, baudrate, timeout=tout)
+        except:
+            raise Exception(
+                'An exception occured when opening the serial port at {}'.format(path))
+        else:
+            self.initializeSensor()
+
+
+class LxMeter:
+    '''Class representing the APDS-9301 digital photometer.'''
+    def __init__(self, busNumber=1, addr=0x39):
+        self.addr = addr
+        try:
+            # initialize the SMBus interface
+            self.bus = smbus2.SMBus(busNumber)
+        except:
+            raise Exception(
+                'An exception occured opening the SMBus {}'.format(self.bus))
+
+        try:
+            self.bus.write_byte_data(
+                self.addr, 0xa0, 0x03)  # enable the sensor
+            self.setGain(16)
+        except:
+            raise Exception('An exception occured when enabling lux meter')
+
+    def setGain(self, gain):
+        '''Set the sensor gain. Either 1 or 16.'''
+        if gain == 1:
+            try:
+                temp = self.bus.read_byte_data(self.addr, 0xa1)
+                self.bus.write_byte_data(self.addr, 0xa1, 0xef & temp)
+            except:
+                raise Exception(
+                    'An exception occured when setting lux meter gain')
+        if gain == 16:
+            try:
+                temp = self.bus.read_byte_data(self.addr, 0xa1)
+                self.bus.write_byte_data(self.addr, 0xa1, 0x10 | temp)
+            except:
+                raise Exception(
+                    'An exception occured when setting lux meter gain')
+        else:
+            raise Exception('Invalid gain')
+
+    def getGain(self):
+        '''Get the gain from the sensor.'''
+        try:
+            if self.bus.read_byte_data(self.addr, 0xa1) & 0x10 == 0x10:
+                return 16
+            if self.bus.read_byte_data(self.addr, 0xa1) & 0x10 == 0x00:
+                return 1
+            raise Exception('An error occured when getting lux meter gain')
+            # Under normal conditions, this raise is unreachable.
+        except:
+            raise Exception('An error occured when getting lux meter gain')
+
+    def setIntTime(self, time):
+        '''Set the lux sensor integration time. 0 to including 2'''
+        if time < 0 or time > 2:
+            raise Exception('Invalid integration time')
+        try:
+            temp = self.bus.read_byte_data(self.addr, 0xa1)
+            self.bus.write_byte_data(self.addr, 0xa1, (temp & 0xfc) | time)
+        except:
+            raise Exception(
+                'An exception occured setting lux integration time')
+
+    def getIntTime(self):
+        '''Get the lux sensor integration time.'''
+        try:
+            return self.bus.read_byte_data(self.addr, 0xa1) & 0x03
+        except:
+            raise Exception(
+                'An exception occured getting lux integration time')
+
+    def getData(self):
+        '''return the calculated lux value'''
+        try:
+            chA = self.bus.read_word_data(self.addr, 0xac)
+            chB = self.bus.read_word_data(self.addr, 0xae)
+        except:
+            raise Exception('An exception occured fetching lux channels')
+
+        # scary computations ahead! refer to the apds-9301 datasheet!
+        if chB / chA <= 0.5 and chB / chA > 0:
+            lux = 0.0304 * chA - 0.062 * chA * (chB / chA)**1.4
+        elif chB / chA <= 0.61 and chB / chA > 0.5:
+            lux = 0.0224 * chA - 0.031 * chB
+        elif chB / chA <= 0.8 and chB / chA > 0.61:
+            lux = 0.0128 * chA - 0.0153 * chB
+        elif chB / chA <= 1.3 and chB / chA > 0.8:
+            lux = 0.00146 * chA - 0.00112 * chB
+        else:
+            lux = 0
+        return lux
+
+
+class UVSensor:
+    '''Class representing VEML6075 UVA/B meter'''
+    def __init__(self, bus=1, addr=0x10):
+        self.addr = addr
+        try:
+            self.bus = smbus2.SMBus(bus)
+        except:
+            raise Exception(
+                'An exception occured opening SMBus {}'.format(bus))
+
+        try:
+            # enable the sensor and set the integration time
+            self.bus.write_byte_data(self.addr, 0x00, 0b00010000)
+        except:
+            raise Exception(
+                'An exception occured when initalizing the UV Sensor')
+
+    def getABI(self):
+        '''Calculates the UVA and UVB irradiances,
+        along with UV index. Returns [a,b,i]'''
+
+        try:
+            # read the raw UVA, UVB and compensation values from the sensor
+            aRaw = self.bus.read_word_data(self.addr, 0x07)
+            bRaw = self.bus.read_word_data(self.addr, 0x09)
+            c1 = self.bus.read_word_data(self.addr, 0x0a)
+            c2 = self.bus.read_word_data(self.addr, 0x0b)
+        except:
+            raise Exception('An exception occured when fetching raw UV data')
+        # scary computations ahead! refer to Vishay app note 84339 and Sparkfun
+        # VEML6075 documentation.
+
+        # compensate for visible and IR noise
+        aCorr = aRaw - 2.22 * c1 - 1.33 * c2
+        bCorr = bRaw - 2.95 * c1 - 1.74 * c2
+
+        # convert values into irradiances
+        a = aCorr * 1.06
+        b = bCorr * 0.48
+
+        # zero out negative results (readings with no uv)
+        if a < 0:
+            a = 0
+        if b < 0:
+            b = 0
+        # last, calculate the UV index
+        i = (a + b) / 2
+
+        return [a, b, i]
+
+    def getA(self):
+        '''Returns UVA value. A getABI() wrapper.'''
+        return self.getABI()[0]
+
+    def getB(self):
+        '''Returns UVB value. A getABI() wrapper.'''
+        return self.getABI()[1]
+
+    def getI(self):
+        '''Returns UV index. A getABI() wrapper.'''
+        return self.getABI()[2]
+
+    def on(self):
+        '''Turns the UV sensor on after shutdown.'''
+        try:
+            # write the default value for power on
+            # no configurable params = no bitmask
+            self.bus.write_byte_data(self.addr, 0x00, 0x10)
+        except:
+            raise Exception(
+                'An exception occured when turning the UV sensor on')
+
+    def off(self):
+        '''Shuts the UV sensor down.'''
+        try:
+            # write the default value + the shutdown bit
+            # no configurable params = no bitmask
+            self.bus.write_byte_data(self.addr, 0x00, 0x11)
+        except:
+            raise Exception(
+                'An exception occured when shutting the UV sensor down')

backend/storage.py

@@ -0,0 +1,37 @@
+# storage.py - storage backend for TeraHz
+'''TeraHz storage backend'''
+# Copyright Kristjan Komloši 2019
+# All code in this file is licensed under the ISC license,
+# provided in LICENSE.txt
+
+
+import sqlite3
+class jsonStorage:
+    '''Class for simple sqlite3 database of JSON entries'''
+    def __init__(self, dbFile):
+        '''Storage object constructor. Argument is filename'''
+        self.db = sqlite3.connect(dbFile)
+
+    def listJSONs(self):
+        '''Returns a list of all existing entries.'''
+        c = self.db.cursor()
+        c.execute('SELECT * FROM storage')
+        result = c.fetchall()
+        c.close()
+        return result
+
+    def storeJSON(self, jsonString, comment):
+        '''Stores a JSON entry along with a timestamp and a comment.'''
+        c = self.db.cursor()
+        c.execute(('INSERT INTO storage VALUES (datetime'
+                   '(\'now\', \'localtime\'), ?, ?)'), (comment, jsonString))
+        c.close()
+        self.db.commit()
+
+    def retrieveJSON(self, timestamp):
+        '''Retrieves a JSON entry. Takes a timestamp string'''
+        c = self.db.cursor()
+        c.execute('SELECT * FROM storage WHERE timestamp = ?', (timestamp,))
+        result = c.fetchall()
+        c.close()
+        return result

backend/terahz.fcgi

@@ -0,0 +1,7 @@
+#!/usr/bin/python3
+# Minimal flup configuration for Flask
+from flup.server.fcgi import WSGIServer
+from app import app
+
+if __name__ == '__main__':
+    WSGIServer(app, bindAddress='/var/www/api/terahz.sock').run()

docs/build.md

@@ -0,0 +1,9 @@
+# TeraHz build guide
+In its early development phase, TeraHz was hard and time-consuming to compile and install.
+This is not case now, as the more optimized DietPi Linux distribution allows
+better performance and simpler configuration than formerly used Raspbian.
+
+## Downloading the preconfigured image
+DietPi needs some initial configuration to support TeraHz. To shorten the process,
+Preconfigured SD card images are available for download under the release tab in
+the Github repository

docs/dependencies.md

@@ -0,0 +1,26 @@
+# Development-stable dependencies
+The current development version of TeraHz has been verified to work with:
+
+  - Raspbian Stretch (9)
+  - Python 3.6.8 (built from source code and altinstall'd)
+  - Module versions (direct `pip3.6 list` output):
+
+```
+      Package         Version  
+      --------------- ---------
+      Click           7.0      
+      Flask           1.0.3    
+      itsdangerous    1.1.0    
+      Jinja2          2.10.1   
+      MarkupSafe      1.1.1    
+      numpy           1.16.4   
+      pandas          0.24.2   
+      pip             18.1     
+      pyserial        3.4      
+      python-dateutil 2.8.0    
+      pytz            2019.1   
+      setuptools      40.6.2   
+      six             1.12.0   
+      smbus           1.1.post2
+      Werkzeug        0.15.4   
+```

docs/dev-guide.md

@@ -0,0 +1,95 @@
+# TeraHz developer's guide
+This document explains how TeraHz works. It's a good starting point for developers
+and an interesting read for the curious.
+
+# Hardware
+TeraHz was developed on and for the Raspberry Pi 3 Model B+. Compatibility with
+other Raspberries can probably be achieved by tweaking the device paths in the
+`app.py` file, but isn't confirmed at this point. Theoretically, 3 Model B and
+Zero W should work out of the box, but models without Wi-Fi will need an
+external Wi-Fi adapter if Wi-Fi functionality is desired. The practicality of
+compiling Python on the first generation of Raspberry Pis is also very
+questionable.
+
+Sensors required for operation are:
++ AS7265x
++ VEML6075
++ APDS-9301
+
+They provide the spectrometry data, UV data and illuminance data, respectively.
+They all support I2C, AS7265x supports UART in addition.
+
+The sensors leech power from the GPIO connector, thus eliminating the need for a
+separate power supply. The necessary power for the whole system is delivered through
+the Raspberry's USB port. This also allows for considerable versatility, as it
+enables the resulting device to be either wall-powered or battery-powered.
+In a portable configuration, I used a one-cell power bank, which allowed for
+about 45 minutes of continuous operation.
+
+## AS7265x chipset
+_[Datasheet][1ds] [Buy breakout board][1]_
+
+This chipset supports either I2C or UART. Because transferring large amounts of
+data over I2C is rather cumbersome, TeraHz uses AS7265x in UART mode.
+
+This chipset consists of three rather small surface-mounted chips and requires
+an EEPROM. To lower the complexity of assembly for the end-user, I recommend
+using a breakout board.
+
+The serial UART connection operates at 115200 baud, which seems to be the
+standard for most recent embedded peripherals. As with most serial hardware,
+the TxD and RxD lines must be crossed over when connecting to the processor.
+
+Communication with the sensor is simple and clear through AT commands. There's
+a lot of them, all documented inside the datasheet, but the most important one
+is `ATGETCDATA`, which returns the calibrated spectral data from the sensors.
+
+The data is returned in the form of a comma-separated list of floating point
+values, ending with a newline. The order is alphabetical, which is __different
+from wavelength order__. See the datasheet for more information.
+
+## VEML6075
+_[Datasheet][2ds] [Buy breakout board][2]_
+
+This chip communicates through I2C and provides TeraHz with UVA and UVB
+irradiance readings. It's not an ideal chip for this task, as it's been marked
+End-of-Life by Vishay and it'll have to be replaced with a better one in future
+hardware versions of TeraHz.
+
+The chip resides at the I2C address `0x10`. There's not a lot of communication
+required: at initialization, the integration time has to be set and after that,
+the sensor is ready to go.
+
+16-bit UV values lie in two two-byte registers, `0x07` for UVA and `0x09` for
+UVB. For correct result conversion, there are also two correction registers,
+UVCOMP_1 and 2, located at `0x0A` and `0x0B`, respectively.
+
+To convert these four values into irradiances, they must be multiplied by
+certain constants, somewhat loosely defined in the sensor datasheet. Keep in
+mind that the way of computing the "irradiance" is very much experimentally
+derived, and even Vishay's tech support doesn't know how exactly to calculate
+the irradiance.
+
+## APDS-9301
+_[Datasheet][3ds] [Buy breakout board][3]_
+This chip measures illuminance in luxes and like the VEML6075, connects through
+I2C. Unlike the VEML6075, this chip is very good at its job, providing accurate
+and fast results without undefined mathematics or required calibration.
+
+At power-on, it needs to be enabled and the sensor gain set to the high setting,
+as the formula for Lux calculation is only defined for that setting. This
+initialization is handled by the sensors module.
+
+The lux reading is derived from two channels, descriptively called CH0 and CH1,
+residing in respective 16-bit registers at addresses `0xAC` and `0xAE`. After a
+successful read of both data registers, the lux value can be derived using the
+formula in the sensor's datasheet.
+
+
+
+[1]: https://www.tindie.com/products/onehorse/compact-as7265x-spectrometer/
+[2]: https://www.sparkfun.com/products/15089
+[3]: https://www.sparkfun.com/products/14350
+[1ds]: sensor-docs/AS7265x.pdf
+[2ds]: sensor-docs/veml6075.pdf
+[3ds]: sensor-docs/APDS-9301.pdf

docs/electrical.md

@@ -0,0 +1,55 @@
+# TeraHz Electrical Guide
+This section briefly explains the neccessary electrical connections between the
+Raspberry Pi and the sensors you'll need to make to ensure correct and safe
+operation.
+
+As mentioned before, TeraHz requires 3 sensors to operate. The simpler UVA/UVB
+sensor and the ambient light analyzer connect to the Raspberry's SMBus (I2C)
+bus, while the spectrometer connects via high-speed UART.
+
+![pinout](imgs/raspi-pinout.png)
+
+## PCBs vs breakout boards & jumpers
+The Raspberry Pi GPIO port includes enough power pins to require only jumper
+cables to connect the sensors to the Raspberry Pi. However, this is not a great
+idea. During development, jumper cables have repeatedly been proven to be an
+unreliable nuisance, and their absolute lack of rigidity helped me fry one of my
+development Raspberry Pis. For this reason, I wholeheartedly recommend using a
+simple PCB to route the connections from the Pi to the sensors. At this time,
+there is no official TeraHz PCB, but it shall be announced and included in the
+project when basic testing will be done.
+
+GPIO can be routed to the PCB with a standard old IDE disk cable, and terminated
+with another 40-pin connector at the PCB. Sensor breakouts should be mounted
+<<<<<<< HEAD
+through standard 0.1" connectors, male on the sensor breakout and female on the
+PCB. A shitty add-on header and a shitty add-on header v1.69bis can't hurt, either.
+=======
+through standard 0.1" connectors, male on the sensor brakout and female on the
+PCB. A shitty addon header and a shitty addon header v1.69bis can't hurt, either.
+>>>>>>> fd1f07d40dace3e003e49377d4771de53f8bdeb8
+
+## SMBus sensors
+SMBus is a well-defined version of the well-known I2C bus, widely used
+in computer motherboards for low-band bandwidth communication with various ICs,
+especially sensors and power-supply related devices. This bus is broken out on
+the Raspberry Pi GPIO port as the "I2C1" bus (see picture).
+
+Pins are familiarly marked as SDA and SCL, the same as with classic I2C. They
+connect to the SDA and SCL pins on the VEML6075 and APDS-9301 sensor.
+
+## UART sensor
+<<<<<<< HEAD
+Spectral sensor attaches through the UART port on the Raspberry pi (see picture).
+=======
+Spectrometry sensor attaches through the UART port on the Raspberry pi (see picture).
+>>>>>>> fd1f07d40dace3e003e49377d4771de53f8bdeb8
+
+The Tx and Rx lines must cross over, connecting the sensor's Tx line to the
+computer's Rx line and vice versa.
+
+## Power supply
+As the sensors require only a small amount of power, they can be powered directly from the Raspberry Pi itself, leeching power from the 3.3V lines.
+
+## Ground
+There's not a lot to say here, connect sensor GND to Pi's GND.

docs/index.md

@@ -0,0 +1,3 @@
+<img alt="TeraHz logo" src="imgs/logo-sq.png" width="200px">
+# TeraHz documentation - index
+This is the starting point of TeraHz documentation.

etcs/dnsmasq.conf

@@ -0,0 +1,3 @@
+interface=wlan0
+	dhcp-range=192.168.1.10,192.168.1.100,255.255.255.0,24h
+	address=/terahz.site/192.168.1.1

etcs/hostapd/edit_ssid.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+# edit_ssid.sh - edits hostapd.conf and sets a MAC address-based SSID
+cd `dirname $0`
+ssid=`ip link | awk '/wlan0/ {getline; print $2}' | awk -v FS=':' '{printf("TeraHz_%s%s%s\n", $4, $5, $6)}'`
+sed "/ssid=.*/s/ssid=.*/ssid=$ssid/" hostapd.conf > newconf
+mv newconf hostapd.conf

etcs/hostapd/hostapd.conf

@@ -0,0 +1,9 @@
+interface=wlan0
+hw_mode=g
+channel=8
+wpa=2
+wpa_key_mgmt=WPA-PSK
+wpa_pairwise=TKIP
+rsn_pairwise=CCMP
+ssid=TeraHz
+wpa_passphrase=terahertz

etcs/install.sh

@@ -0,0 +1,18 @@
+# install.sh - install TeraHz onto a Raspbian or DietPi installation
+apt -y update
+apt -y full-upgrade
+apt install -y python3 python3-pip lighttpd dnsmasq hostapd libatlas-base-dev
+pip3 install numpy pandas flask smbus2 pyserial gunicorn
+
+cp -R hostapd/ /etc
+chmod +rx /etc/hostapd/edit_ssid.sh
+cp dnsmasq.conf /etc
+cp rc.local /etc
+cp interfaces-terahz /etc/network/interfaces.d/
+
+cp -R ../frontend/* /var/www/html
+mkdir -p /usr/local/lib/terahz
+cp -R ../backend/* /usr/local/lib/terahz
+
+systemctl unmask dnsmasq hostapd lighttpd
+systemctl enable dnsmasq hostapd lighttpd

etcs/interfaces-terahz

@@ -0,0 +1,3 @@
+iface wlan0 inet static
+  address 192.168.1.1
+  netmask 255.255.255.0

etcs/lighttpd/lighttpd.conf

@@ -0,0 +1,27 @@
+server.modules = (
+	"mod_access",
+	"mod_alias",
+	"mod_compress",
+ 	"mod_redirect"
+)
+
+server.document-root        = "/var/www/html"
+server.upload-dirs          = ( "/var/cache/lighttpd/uploads" )
+server.errorlog             = "/var/log/lighttpd/error.log"
+server.pid-file             = "/var/run/lighttpd.pid"
+server.username             = "www-data"
+server.groupname            = "www-data"
+server.port                 = 80
+
+
+index-file.names            = ( "index.php", "index.html", "index.lighttpd.html" )
+url.access-deny             = ( "~", ".inc" )
+static-file.exclude-extensions = ( ".php", ".pl", ".fcgi" )
+
+compress.cache-dir          = "/var/cache/lighttpd/compress/"
+compress.filetype           = ( "application/javascript", "text/css", "text/html", "text/plain" )
+
+# default listening port for IPv6 falls back to the IPv4 port
+include_shell "/usr/share/lighttpd/use-ipv6.pl " + server.port
+include_shell "/usr/share/lighttpd/create-mime.assign.pl"
+include_shell "/usr/share/lighttpd/include-conf-enabled.pl"

etcs/rc.local

@@ -0,0 +1,16 @@
+#!/bin/sh -e
+#
+# rc.local
+#
+# This script is executed at the end of each multiuser runlevel.
+# Make sure that the script will "exit 0" on success or any other
+# value on error.
+#
+# In order to enable or disable this script just change the execution
+# bits.
+#
+# By default this script does nothing.
+/etc/hostapd/edit_ssid.sh &
+/usr/local/lib/terahz/run.sh &
+sleep 3
+service hostapd restart # restart hostapd to prevent a weird startup race condition

frontend/frontend.js

@@ -0,0 +1,46 @@
+// All code in this file is licensed under the ISC license, provided in LICENSE.txt
+$('#update').click(function () {
+  updateData();
+});
+// jQuery event binder
+
+function updateData () {
+  const url = 'http://' + window.location.hostname + ':5000/data';
+  $.ajax({ // spawn an AJAX request
+    url: url,
+    success: function (data, status) {
+      console.log(data);
+      graphSpectralData(data[0], 0);
+      fillTableData(data);
+    },
+    timeout: 2500 // this should be a pretty sane timeout
+  });
+}
+
+function graphSpectralData (obj, dom) {
+  // graph spectral data in obj into dom
+  var graphPoints = [];
+  var graphXTicks = [];
+
+  Object.keys(obj).forEach((element, index) => {
+    graphPoints.push([index, obj[element]]); // build array of points
+    graphXTicks.push([index, element]); // build array of axis labels
+  });
+  // console.log(graphPoints);
+  const options = {
+    grid: {color: 'white'},
+    xaxis: {ticks: graphXTicks}
+  };
+  $.plot('#graph', [graphPoints], options);
+  // flot expects an array of arrays (lines) of 2-element arrays (points)
+}
+
+function fillTableData (obj) {
+  // fill the obj data into HTML tables
+  Object.keys(obj[0])
+    .forEach((element) => { $('#' + element).text(obj[0][element]); });
+  $('#lx').text(obj[1]);
+  $('#uva').text(obj[2][0]);
+  $('#uvb').text(obj[2][1]);
+  $('#uvi').text(obj[2][2]);
+}

frontend/index.html

@@ -0,0 +1,162 @@
+<!DOCTYPE html>
+<html>
+
+<head>
+  <meta charset="utf8">
+  <link rel="stylesheet" href="lib/bootstrap.min.css">
+  <link rel="stylesheet" href="stylesheet.css">
+  <title>TeraHz</title>
+</head>
+
+<body>
+  <div class="container text-center">
+    <h1><img src="lib/logo-sq.png" height="64px">TeraHz</h1>
+
+  </div>
+  <div class="container">
+    <button id="update" class="btn btn-primary m-1 float-right">Get data</button>
+    <p id="debug">
+    </p>
+    <h3>Spectrogram</h3>
+    <div id="graph" style="height:480px;width:720px"></div>
+    <h3>Spectral readings</h3>
+    <table class="table table-dark table-sm" id="specter">
+      <thead class="thead-dark">
+        <tr>
+          <th>Band</th>
+          <th>Wavelength [nm]</th>
+          <th>Irradiance [μW/cm²]</th>
+        </tr>
+      </thead>
+      <tr>
+        <td>A</td>
+        <td>410 nm</td>
+        <td id="A">---</td>
+      </tr>
+      <tr>
+        <td>B</td>
+        <td>435 nm</td>
+        <td id="B">---</td>
+      </tr>
+      <tr>
+        <td>C</td>
+        <td>460 nm</td>
+        <td id="C">---</td>
+      </tr>
+      <tr>
+        <td>D</td>
+        <td>485 nm</td>
+        <td id="D">---</td>
+      </tr>
+      <tr>
+        <td>E</td>
+        <td>510 nm</td>
+        <td id="E">---</td>
+      </tr>
+      <tr>
+        <td>F</td>
+        <td>535 nm</td>
+        <td id="F">---</td>
+      </tr>
+      <tr>
+        <td>G</td>
+        <td>560 nm</td>
+        <td id="G">---</td>
+      </tr>
+      <tr>
+        <td>H</td>
+        <td>585 nm</td>
+        <td id="H">---</td>
+      </tr>
+      <tr>
+        <td>R</td>
+        <td>610 nm</td>
+        <td id="R">---</td>
+      </tr>
+      <tr>
+        <td>I</td>
+        <td>645 nm</td>
+        <td id="I">---</td>
+      </tr>
+      <tr>
+        <td>S</td>
+        <td>680 nm</td>
+        <td id="S">---</td>
+      </tr>
+      <tr>
+        <td>J</td>
+        <td>705 nm</td>
+        <td id="J">---</td>
+      </tr>
+      <tr>
+        <td>T</td>
+        <td>730 nm</td>
+        <td id="T">---</td>
+      </tr>
+      <tr>
+        <td>U</td>
+        <td>760 nm</td>
+        <td id="U">---</td>
+      </tr>
+      <tr class="table-secondary">
+        <td>V</td>
+        <td>810 nm</td>
+        <td id="V">---</td>
+      </tr>
+      <tr class="table-secondary">
+        <td>W</td>
+        <td>860 nm</td>
+        <td id="W">---</td>
+      </tr>
+      <tr class="table-secondary">
+        <td>K</td>
+        <td>900 nm</td>
+        <td id="K">---</td>
+      </tr>
+      <tr class="table-secondary">
+        <td>L</td>
+        <td>940 nm</td>
+        <td id="L">---</td>
+      </tr>
+    </table>
+    <br>
+    <h3>Lux and UV readings</h3>
+    <table class="table-dark table" id="luxuv">
+      <thead class="thead-dark">
+        <tr>
+          <th>Parameter</th>
+          <th>Value</th>
+        </tr>
+      </thead>
+      <tr>
+        <td>Illuminance [lx]</td>
+        <td id="lx">---</td>
+      </tr>
+      <tr>
+        <td>UVA irradiance [μW/cm²]</td>
+        <td id="uva">---</td>
+      </tr>
+      <tr>
+        <td>UVB irradiance [μW/cm²]</td>
+        <td id="uvb">---</td>
+      </tr>
+      <tr>
+        <td>UVA/UVB average [μW/cm²]</td>
+        <td id="uvi">---</td>
+      </tr>
+    </table>
+  </div>
+  <script src="lib/bootstrap.bundle.min.js"></script>
+  <script src="lib/jquery-3.4.1.min.js"></script>
+  <script src="lib/flot/jquery.flot.js"></script>
+  <script src="frontend.js"></script>
+  <script src="lib/flot/jquery.canvaswrapper.js"></script>
+  <script src="lib/flot/jquery.colorhelpers.js"></script>
+  <script src="lib/flot/jquery.flot.js"></script>
+  <script src="lib/flot/jquery.flot.saturated.js"></script>
+  <script src="lib/flot/jquery.flot.browser.js"></script>
+  <script src="lib/flot/jquery.flot.drawSeries.js"></script>
+  <script src="lib/flot/jquery.flot.uiConstants.js"></script>
+</body>
+
+</html>

frontend/stylesheet.css

@@ -0,0 +1,69 @@
+body {
+  background: rgb(2,0,36);
+  background: linear-gradient(138deg, rgba(2,0,36,1) 0%, rgba(5,5,209,1) 51%, rgba(0,212,255,1) 100%);
+  color: white;
+}
+#A {
+  background-color: #7e00db;
+  color: white;
+}
+
+#B {
+  background-color: #2300ff;
+  color: white;
+}
+
+#C {
+  background-color: #007bff;
+  color: white;
+}
+
+#D {
+  background-color: #00eaff;
+}
+
+#E {
+  background-color: #00ff00;
+}
+
+#F {
+  background-color: #70ff00;
+}
+
+#G {
+  background-color: #c3ff00;
+}
+
+#H {
+  background-color: #ffef00;
+}
+
+#R {
+  background-color: #ff9b00;
+}
+
+#I, #S {
+  background-color: #ff0000;
+}
+
+#J {
+  background-color: #f60000;
+}
+
+#T {
+  background-color: #c80000;
+  color: white;
+}
+
+#U {
+  background-color: #8d0000;
+  color: white;
+}
+
+.table-secondary {
+  color: black;
+}
+
+.flot-tick-label {
+  fill: white;
+}

mkdocs.yml

@@ -0,0 +1,9 @@
+site_name: TeraHz Documentation
+theme: readthedocs
+nav:
+- Start page: 'index.md'
+- Advanced guides:
+  - Build guide: 'build.md'
+  - Developer's guide: 'dev-guide.md'
+  - Electrical connections: 'electrical.md'
+  - Latest dependencies: 'dependencies.md'

readthedocs.yml

@@ -0,0 +1,3 @@
+version: 2
+mkdocs:
+  configuration: mkdocs.yml

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sensor_docs/sysprep.md

@@ -0,0 +1 @@
+# sysprep - How to prepare a Raspberry Pi 3 B+ to run TeraHz

utils/getcdata.py

@@ -0,0 +1,45 @@
+# getcdata.py - fetch the calibrated data from the AS7265x module
+# All code in this file is licensed under the ISC license, provided in LICENSE.txt
+
+import serial as ser
+import pandas as pd
+import numpy as np
+import matplotlib.pyplot as plt
+import time
+#global variables
+uartpath = '/dev/ttyUSB0'
+uartbaud = 115200
+uarttout = 5
+
+wl = [410, 435, 460, 485, 510, 535, 560, 585, 610, 645, 680, 705, 730, 760, 810, 860, 900, 940]
+responseorder = [i for i in 'RSTUVWGHIJKLABCDEF'] # works, do NOT touch!
+realorder = [i for i in 'ABCDEFGHRISJTUVWKL']
+
+
+print('getcdata')
+print('This utility is part of the TeraHz project')
+
+wavelens = pd.Series(realorder)
+
+
+plt.ion()
+win = plt.figure()
+spectrum=win.add_subplot(111)
+
+
+with ser.Serial(uartpath, uartbaud, timeout=uarttout) as sensor:
+    while True:
+        sensor.write(b'ATCDATA\n')
+        rawresp = sensor.readline().decode()
+        # parses, calculates and saves the data
+        response = pd.Series([float(i)/35.0 for i in rawresp[:-3].split(',')], index=responseorder)
+        data = pd.DataFrame(response, index=realorder, columns = ['uW/cm^2']) # puts data into a DataFrame
+        data.insert(0, 'wavelenght', wl) #inserts a legend
+        print(data)
+        spectrum.cla()
+        spectrum.plot(data['wavelenght'], data['uW/cm^2'])
+        spectrum.set_xlabel('Valovna dolžina')
+        spectrum.set_ylabel('uW/cm2')
+        win.canvas.draw()
+
+        time.sleep(0.1)

utils/smbus-test.py

@@ -0,0 +1,12 @@
+import smbus2
+
+bus = smbus2.SMBus(1)
+
+result = bus.read_byte_data(0x39, 0x8a)
+print('LUX Meter ID = {}'.format(result))
+
+result = bus.read_word_data(0x10, 0x0c)
+print('UV sensor ID = {}'.format(result))
+
+result = bus.read_word_data(0x39, 0xec)
+print('LUX chan 0 = {}'.format(result))

utils/tinter-demo.py

@@ -0,0 +1,22 @@
+from serial import Serial
+import tkinter as tk
+import pandas as pd
+
+from matplotlib.backends.backend_tkagg import (FigureCanvasTkAgg, NavigationToolbar2Tk)
+from matplotlib.backend_bases import key_press_handler
+from matplotlib.figure import Figure
+
+uartpath = '/dev/ttyUSB0'
+uartbaud = 115200
+uarttout = 5
+
+wl = [410, 435, 460, 485, 510, 535, 560, 585, 610, 645, 680, 705, 730, 760, 810, 860, 900, 940]
+responseorder = [i for i in 'RSTUVWGHIJKLABCDEF'] # works, do NOT touch!
+realorder = [i for i in 'ABCDEFGHRISJTUVWKL']
+
+root = tk.Tk()
+root.wm_title('TeraHz Demo')
+
+fig = Figure(figsize=(5, 4), dpi=100)
+plot = fig.add_subplot(111)
+canvas = FigureCanvasTkAgg(fig, master=root)