Update nodes doc from PR: 93

docs/nodes/INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT/SERIAL_SINGLE_MEASUREMENT.md

@@ -0,0 +1,50 @@
+
+[//]: # (Custom component imports)
+
+import DocString from '@site/src/components/DocString';
+import PythonCode from '@site/src/components/PythonCode';
+import Parameters from '@site/src/components/Parameters';
+import AppDisplay from '@site/src/components/AppDisplay';
+import SectionBreak from '@site/src/components/SectionBreak';
+import AppendixSection from '@site/src/components/AppendixSection';
+
+[//]: # (Docstring)
+
+import DocstringSource from '!!raw-loader!./a1-[autogen]/docstring.txt';
+import PythonSource from '!!raw-loader!./a1-[autogen]/python_code.txt';
+import ParametersSource from '!!raw-loader!./a1-[autogen]/parameters.yaml';
+
+<DocString>{DocstringSource}</DocString>
+<PythonCode GLink='bin/flojoy-io/docs/docs/./INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT/SERIAL_SINGLE_MEASUREMENT.py'>{PythonSource}</PythonCode>
+<Parameters>{ParametersSource}</Parameters>
+
+<SectionBreak />
+
+
+
+[//]: # (Examples)
+
+## Examples
+
+<AppDisplay 
+  GLink='bin/flojoy-io/docs/docs/./INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT'
+  nodeLabel='SERIAL_SINGLE_MEASUREMENT'>
+</AppDisplay>
+
+<SectionBreak />
+
+
+
+[//]: # (Appendix)
+
+import Notes from '!!raw-loader!./appendix/notes.md';
+import Hardware from '!!raw-loader!./appendix/hardware.md';
+import Media from '!!raw-loader!./appendix/media.md';
+
+## Appendix
+
+<AppendixSection index={0} folderPath='nodes/nodes/bin/flojoy-io/docs/docs/nodes/./INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT/appendix/'>{Notes}</AppendixSection>
+<AppendixSection index={1} folderPath='nodes/nodes/bin/flojoy-io/docs/docs/nodes/./INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT/appendix/'>{Hardware}</AppendixSection>
+<AppendixSection index={2} folderPath='nodes/nodes/bin/flojoy-io/docs/docs/nodes/./INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT/appendix/'>{Media}</AppendixSection>
+
+

docs/nodes/INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT/a1-[autogen]/docstring.txt

@@ -0,0 +1,28 @@
+
+    Node to take a single reading of data from an Ardunio,
+    or a similar serial device.
+    For example you can record temperature following this tutorial:
+
+    https://learn.adafruit.com/thermistor/using-a-thermistor
+
+    with Serial.println(steinhart) as the only line printing.
+
+    It is important that the last line Arduino is returning is the
+    data with a new line at the end (i.e. println()).
+
+    The other lines must be returned with print()
+    with print(",") between each line.
+
+    For example:
+
+    print(reading0)
+    print(",")
+    println(reading1)
+
+    If there is more than one column, the SELECT_ARRAY node must be
+    used after this node.
+
+    params:
+    BAUD_RATE: Baud rate for the serial device.
+    com_port: COM port of the serial device
+

docs/nodes/INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT/a1-[autogen]/parameters.yaml

@@ -0,0 +1,6 @@
+baudrate:
+  default: 9600
+  type: float
+comport:
+  default: /dev/ttyUSB0
+  type: string

docs/nodes/INSTRUMENTS/Serial/SERIAL_SINGLE_MEASUREMENT/a1-[autogen]/python_code.txt

@@ -0,0 +1,42 @@
+from flojoy import flojoy, DataContainer
+from time import sleep
+import serial
+import numpy as np
+from datetime import datetime
+import plotly.graph_objects as go
+
+
+@flojoy
+def SERIAL_SINGLE_MEASUREMENT(dc_inputs, params):
+
+    print("parameters passed to SERIAL_TIMESERIES: ", params)
+    COM_PORT = params["comport"]
+    BAUD = int(params["baudrate"])
+
+    ser = serial.Serial(COM_PORT, timeout=1, baudrate=BAUD)
+    # The first reading is commonly empty.
+    s = ser.readline().decode()
+
+    # Some readings may be empty. Try a second time if so.
+    if s != "":
+        reading = s[:-2].split(",")
+    else:
+        s = ser.readline().decode()
+        reading = s[:-2].split(",")
+
+    reading = np.array(reading)
+    reading = reading.astype("float64")
+
+    data = go.Line(x=[0], y=[0], mode="markers")
+    fig = go.Figure(data=data)
+    return DataContainer(type="plotly", fig=fig, x=[0], y=reading)
+
+
+@flojoy
+def SERIAL_SINGLE_MEASUREMENT_MOCK(dc, params):
+    print("Running mock version of Serial")
+
+    x = np.linspace(0, 100, 100)
+    y = np.linspace(0, 100, 100)
+
+    return DataContainer(x=x, y=y)

docs/nodes/INSTRUMENTS/Serial/Serial_timeseries/SERIAL_TIMESERIES.md

@@ -0,0 +1,50 @@
+
+[//]: # (Custom component imports)
+
+import DocString from '@site/src/components/DocString';
+import PythonCode from '@site/src/components/PythonCode';
+import Parameters from '@site/src/components/Parameters';
+import AppDisplay from '@site/src/components/AppDisplay';
+import SectionBreak from '@site/src/components/SectionBreak';
+import AppendixSection from '@site/src/components/AppendixSection';
+
+[//]: # (Docstring)
+
+import DocstringSource from '!!raw-loader!./a1-[autogen]/docstring.txt';
+import PythonSource from '!!raw-loader!./a1-[autogen]/python_code.txt';
+import ParametersSource from '!!raw-loader!./a1-[autogen]/parameters.yaml';
+
+<DocString>{DocstringSource}</DocString>
+<PythonCode GLink='bin/flojoy-io/docs/docs/./INSTRUMENTS/Serial/Serial_timeseries/SERIAL_TIMESERIES.py'>{PythonSource}</PythonCode>
+<Parameters>{ParametersSource}</Parameters>
+
+<SectionBreak />
+
+
+
+[//]: # (Examples)
+
+## Examples
+
+<AppDisplay 
+  GLink='bin/flojoy-io/docs/docs/./INSTRUMENTS/Serial/Serial_timeseries'
+  nodeLabel='SERIAL_TIMESERIES'>
+</AppDisplay>
+
+<SectionBreak />
+
+
+
+[//]: # (Appendix)
+
+import Notes from '!!raw-loader!./appendix/notes.md';
+import Hardware from '!!raw-loader!./appendix/hardware.md';
+import Media from '!!raw-loader!./appendix/media.md';
+
+## Appendix
+
+<AppendixSection index={0} folderPath='nodes/nodes/bin/flojoy-io/docs/docs/nodes/./INSTRUMENTS/Serial/Serial_timeseries/appendix/'>{Notes}</AppendixSection>
+<AppendixSection index={1} folderPath='nodes/nodes/bin/flojoy-io/docs/docs/nodes/./INSTRUMENTS/Serial/Serial_timeseries/appendix/'>{Hardware}</AppendixSection>
+<AppendixSection index={2} folderPath='nodes/nodes/bin/flojoy-io/docs/docs/nodes/./INSTRUMENTS/Serial/Serial_timeseries/appendix/'>{Media}</AppendixSection>
+
+

docs/nodes/INSTRUMENTS/Serial/Serial_timeseries/a1-[autogen]/docstring.txt

@@ -0,0 +1,32 @@
+
+    Node to take simple time dependent 1d data from an Ardunio,
+    or a similar serial device.
+    For example, you can record temperature following this tutorial:
+
+    https://learn.adafruit.com/thermistor/using-a-thermistor
+
+    with Serial.println(steinhart) as the only line printing.
+
+    It is important that the last line Arduino is returning is the
+    data with a new line at the end (i.e. println()).
+
+    The other lines must be returned with print()
+    with print(",") between each line.
+
+    For example:
+
+    print(reading0)
+    print(",")
+    println(reading1)
+
+    If there is more than one column, the SELECT_ARRAY node must be
+    used after this node.
+
+    params:
+    num_readings: Number of points to record.
+    record_period: Length between two recordings in seconds.
+    BAUD_RATE: Baud rate for the serial device.
+    com_port: COM port of the serial device
+
+    num_readings * record_period is roughly the run length in seconds.
+

docs/nodes/INSTRUMENTS/Serial/Serial_timeseries/a1-[autogen]/parameters.yaml

@@ -0,0 +1,12 @@
+baudrate:
+  default: 9600
+  type: int
+comport:
+  default: /dev/ttyACM0
+  type: string
+num_readings:
+  default: 100
+  type: int
+record_period:
+  default: 1
+  type: float

docs/nodes/INSTRUMENTS/Serial/Serial_timeseries/a1-[autogen]/python_code.txt

@@ -0,0 +1,71 @@
+from flojoy import flojoy, DataContainer
+from time import sleep
+import serial
+import numpy as np
+from datetime import datetime
+import plotly.graph_objects as go
+
+
+@flojoy
+def SERIAL_TIMESERIES(dc_inputs, params):
+
+
+    COM_PORT = params.get("com_port", "/dev/ttyUSB0")
+    BAUD = params.get("baudrate", 9600)
+    NUM = params.get("num_readings", 100)
+    RECORD_PERIOD = params.get("record_period", 1)
+
+    ser = serial.Serial(COM_PORT, timeout=1, baudrate=BAUD)
+    readings = []
+    times = []
+    # The first reading is commonly empty.
+    s = ser.readline().decode()
+
+    for i in range(NUM):
+        ts = datetime.now()
+        s = ser.readline().decode()
+        # Some readings may be empty.
+        if s != "":
+            reading = s[:-2].split(",")
+            if len(reading) == 1:
+                reading = reading[0]
+            readings.append(reading)
+
+            ts = datetime.now()
+            seconds = float(
+                ts.hour * 3600 + ts.minute * 60 + ts.second + ts.microsecond / 10**6
+            )
+
+            times.append(seconds)
+
+            if len(times) > 0:
+                time1 = seconds - times[i]
+            else:
+                # Estimate execution time.
+                time1 = 0.1
+
+            if time1 < RECORD_PERIOD:
+                sleep(RECORD_PERIOD - time1)
+
+    times = np.array(times)
+    try:
+        times -= times[0]
+    except IndexError:
+        raise IndexError("No data detected from the Arduino")
+
+    readings = np.array(readings)
+    readings = readings.astype("float64")
+    # If there are two or more columns return a Plotly figure.
+    if readings.ndim == 2:
+        data = go.Line(x=times, y=readings[:, 0], mode="markers")
+        fig = go.Figure(data=data)
+        return DataContainer(type="plotly", fig=fig, x=times, y=readings)
+    else:
+        return DataContainer(x=times, y=readings)
+
+
+@flojoy
+def SERIAL_TIMESERIES_MOCK(dc, params):
+    x = np.linspace(0, 100, 100)
+    y = np.linspace(0, 100, 100)
+    return DataContainer(x=x, y=y)