.gitignore

@@ -1,3 +1,2 @@
 __pycache__
 .ipynb_checkpoints
-testing

MANIFEST.in

@@ -1,2 +0,0 @@
-include regina/package-data/*
-include regina/sql/*.sql

bspc_rule.sh

@@ -1 +0,0 @@
-bspc rule -a matplotlib desktop=^1 state=pseudo_tiled focus=off

k-teng/k_teng_interactive.py

@@ -1,6 +1,6 @@
 """
 run this before using this library:
-ipython -i m_teng_interactive.py
+ipython -i k_teng_interactive.py
 
 always records iv-t curves
     i-data -> smua.nvbuffer1
@@ -17,56 +17,22 @@ from time import sleep
 from os import path, makedirs
 import pickle as pkl
 import json
-import atexit
-
-import argparse
-
 
 if __name__ == "__main__":
-    import sys
     if __package__ is None:
         # make relative imports work as described here: https://peps.python.org/pep-0366/#proposed-change
-        __package__ = "m_teng"
+        __package__ = "k-teng"
+        import sys
         from os import path
         filepath = path.realpath(path.abspath(__file__))
         sys.path.insert(0, path.dirname(path.dirname(filepath)))
-    parser = argparse.ArgumentParser(
-        prog="m-teng",
-        description="measure triboelectric nanogenerator output using a Keithley SMU or an Arduino",
-    )
-    backend_group = parser.add_mutually_exclusive_group(required=True)
-    backend_group.add_argument("-k", "--keithley", action="store_true")
-    backend_group.add_argument("-a", "--arduino", action="store_true")
-    backend_group.add_argument("-t", "--testing", action='store_true')
-    parser.add_argument("-c", "--config", action="store", help="alternate path to config file")
-    args = vars(parser.parse_args())
-
-    i = 1
-    while i < len(sys.argv):
-        if args["keithley"]:
-            import m_teng.backends.keithley.keithley as _backend
-            import m_teng.backends.keithley.measure as _measure
-        elif args["arduino"]:
-            import m_teng.backends.arduino.arduino as _backend
-            import m_teng.backends.arduino.measure as _measure
-        elif args["testing"]:
-            import m_teng.backends.testing.testing as _backend
-            import m_teng.backends.testing.measure as _measure
-        elif sys.argv[i] in ["-c", "--config"]:
-            if i+1 < len(sys.argv):
-                config_path = sys.argv[i+1]
-            else:
-                print("-c requires an extra argument: path of config file")
-            i += 1
-        i += 1
 
 
-from m_teng.utility import data as _data
-from m_teng.utility.data import load_dataframe
-from m_teng.utility import file_io
-from m_teng.update_funcs import _Monitor, _ModelPredict, _update_print
-
-config_path = path.expanduser("~/.config/k-teng.json")
+from .keithley import keithley as _keithley
+from .keithley.measure import measure_count as _measure_count, measure as _measure
+from .utility import data as _data
+from .utility.data import load_dataframe
+from .utility import file_io
 
 _runtime_vars = {
     "last-measurement": ""
@@ -78,35 +44,66 @@ settings = {
     "interval":     0.02,
     "beep":         True,
 }
+config_path = path.expanduser("~/.config/k-teng.json")
 
 test = False
 
-# global variable for the instrument/client returned by pyvisa/bleak
-dev = None
+# global variable for the instrument returned by pyvisa
+k = None
 
 
-def monitor_predict(model_dir: str, count=5000, interval=settings["interval"], max_points_shown=160):
+
+def _update_print(i, ival, vval):
+    print(f"n = {i:5d}, I = {ival: .12f} A, U = {vval: .5f} V" + " "*10, end='\r')
+
+class _Monitor:
     """
-    Take <count> measurements in <interval> and predict with a machine learning model
+    Monitor v and i data
     """
-    model_predict = _ModelPredict(dev, model_dir)
-    plt_monitor = _Monitor(max_points_shown, use_print=False)
-    skip_n = 0
-    def update(i, ival, vval):
-        plt_monitor.update(i, ival, vval)
-        if skip_n % 10 == 0:
-            model_predict.update(i, ival, vval)
-        skip_n += 1
+    def __init__(self, max_points_shown=None, use_print=False):
+        self.max_points_shown = max_points_shown
+        self.use_print = use_print
+        self.index = []
+        self.vdata = []
+        self.idata = []
+
+        plt.ion()
+        self.fig1, (self.vax, self.iax) = plt.subplots(2, 1, figsize=(8, 5))
+
+        self.vline,  = self.vax.plot(self.index, self.vdata, color="g")
+        self.vax.set_ylabel("Voltage [V]")
+        self.vax.grid(True)
+
+        self.iline,  = self.iax.plot(self.index, self.idata, color="m")
+        self.iax.set_ylabel("Current [A]")
+        self.iax.grid(True)
+
+    def update(self, i, ival, vval):
+        if self.use_print:
+            _update_print(i, ival, vval)
+        self.index.append(i)
+        self.idata.append(ival)
+        self.vdata.append(vval)
+        # update data
+        self.iline.set_xdata(self.index)
+        self.iline.set_ydata(self.idata)
+        self.vline.set_xdata(self.index)
+        self.vline.set_ydata(self.vdata)
+        # recalculate limits and set them for the view
+        self.iax.relim()
+        self.vax.relim()
+        if self.max_points_shown and i > self.max_points_shown:
+            self.iax.set_xlim(i - self.max_points_shown, i)
+            self.vax.set_xlim(i - self.max_points_shown, i)
+        self.iax.autoscale_view()
+        self.vax.autoscale_view()
+        # update plot
+        self.fig1.canvas.draw()
+        self.fig1.canvas.flush_events()
+
+    def __del__(self):
+        plt.close(self.fig1)
 
-    print(f"Starting measurement with:\n\tinterval = {interval}s\nSave the data using 'save_csv()' afterwards.")
-    try:
-        _measure.measure_count(dev, count=count, interval=interval, beep_done=False, verbose=False, update_func=update, update_interval=0.1)
-    except KeyboardInterrupt:
-        if args["keithley"]:
-            dev.write(f"smua.source.output = smua.OUTPUT_OFF")
-        print("Monitoring cancelled, measurement might still continue" + " "*50)
-    else:
-        print("Measurement finished" + " "*50)
 
 def monitor_count(count=5000, interval=settings["interval"], max_points_shown=160):
     """
@@ -126,10 +123,10 @@ def monitor_count(count=5000, interval=settings["interval"], max_points_shown=16
 
     print(f"Starting measurement with:\n\tinterval = {interval}s\nSave the data using 'save_csv()' afterwards.")
     try:
-        _measure.measure_count(dev, count=count, interval=interval, beep_done=False, verbose=False, update_func=update_func, update_interval=0.05)
+        _measure_count(k, V=True, I=True, count=count, interval=interval, beep_done=False, verbose=False, update_func=update_func, update_interval=0.05, testing=test)
     except KeyboardInterrupt:
-        if args["keithley"]:
-            dev.write(f"smua.source.output = smua.OUTPUT_OFF")
+        if not test:
+            k.write(f"smua.source.output = smua.OUTPUT_OFF")
         print("Monitoring cancelled, measurement might still continue" + " "*50)
     else:
         print("Measurement finished" + " "*50)
@@ -150,10 +147,10 @@ def measure_count(count=5000, interval=settings["interval"]):
 
     print(f"Starting measurement with:\n\tinterval = {interval}s\nSave the data using 'save_csv()' afterwards.")
     try:
-        _measure.measure_count(dev, count=count, interval=interval, beep_done=False, verbose=False, update_func=update_func, update_interval=0.05)
+        _measure_count(k, V=True, I=True, count=count, interval=interval, beep_done=False, verbose=False, update_func=update_func, update_interval=0.05, testing=test)
     except KeyboardInterrupt:
-        if args["keithley"]:
-            dev.write(f"smua.source.output = smua.OUTPUT_OFF")
+        if not test:
+            k.write(f"smua.source.output = smua.OUTPUT_OFF")
         print("Monitoring cancelled, measurement might still continue" + " "*50)
     else:
         print("Measurement finished" + " "*50)
@@ -179,7 +176,7 @@ def monitor(interval=settings["interval"], max_measurements=None, max_points_sho
     print(f"Starting measurement with:\n\tinterval = {interval}s\nUse <C-c> to stop. Save the data using 'save_csv()' afterwards.")
     plt_monitor = _Monitor(use_print=True, max_points_shown=max_points_shown)
     update_func = plt_monitor.update
-    _measure.measure(dev, interval=interval, max_measurements=max_measurements, update_func=update_func)
+    _measure(k, interval=interval, max_measurements=max_measurements, update_func=update_func, testing=test)
 
 
 def measure(interval=settings["interval"], max_measurements=None):
@@ -198,7 +195,7 @@ def measure(interval=settings["interval"], max_measurements=None):
     _runtime_vars["last_measurement"] = dtime.now().isoformat()
     print(f"Starting measurement with:\n\tinterval = {interval}s\nUse <C-c> to stop. Save the data using 'save_csv()' afterwards.")
     update_func = _update_print
-    _measure.measure(dev, interval=interval, max_measurements=max_measurements, update_func=update_func)
+    _measure(k, interval=interval, max_measurements=max_measurements, update_func=update_func, testing=test)
 
 
 def repeat(measure_func: callable, count: int, repeat_delay=0):
@@ -224,7 +221,7 @@ def repeat(measure_func: callable, count: int, repeat_delay=0):
             sleep(repeat_delay)
     except KeyboardInterrupt:
         pass
-    if settings["beep"]: _backend.beep()
+    if settings["beep"]: k.write("beeper.beep(0.3, 1000)")
 
 
 def get_dataframe():
@@ -232,14 +229,21 @@ def get_dataframe():
     Get a pandas dataframe from the data in smua.nvbuffer1 and smua.nvbuffer2
     """
     global k, settings, _runtime_vars
-    ibuffer = _backend.collect_buffer(dev, 1)
-    vbuffer = _backend.collect_buffer(dev, 2)
+    if test:
+        timestamps = np.arange(0, 50, 0.01)
+        ydata = np.array([testing.testcurve(t, amplitude=15, peak_width=2) for t in timestamps])
+        ibuffer = np.vstack((timestamps, ydata)).T
+
+        ydata = np.array([-testing.testcurve(t, amplitude=5e-8, peak_width=1) for t in timestamps])
+        vbuffer = np.vstack((timestamps, ydata)).T
+    else:
+        ibuffer = _keithley.collect_buffer(k, 1)
+        vbuffer = _keithley.collect_buffer(k, 2)
     df = _data.buffers2dataframe(ibuffer, vbuffer)
     df.basename = file_io.get_next_filename(settings["name"], settings["datadir"])
     df.name = f"{df.basename} @ {_runtime_vars['last-measurement']}"
     return df
 
-
 def save_csv():
     """
     Saves the contents of nvbuffer1 as .csv
@@ -263,7 +267,6 @@ def save_pickle():
     df.to_pickle(filename)
     print(f"Saved as '{filename}'")
 
-
 def run_script(script_path):
     """
     Run a lua script on the Keithley device
@@ -273,7 +276,7 @@ def run_script(script_path):
     if test:
         print("run_script: Test mode enabled, ignoring call to run_script")
     else:
-        _keithley.run_lua(dev, script_path=script_path)
+        _keithley.run_lua(k, script_path=script_path)
 
 
 def set(setting, value):
@@ -302,16 +305,16 @@ def help(topic=None):
     if topic == None:
         print("""
 Functions:
-    measure         [kat] - take measurements
-    monitor         [kat] - take measurements with live monitoring in a matplotlib window
-    measure_count   [kat] - take a fixed number of measurements
-    monitor_count   [kat] - take a fixed number of measurements with live monitoring in a matplotlib window
-    repeat          [kat] - measure and save to csv multiple times
-    get_dataframe   [kat] - return device internal buffer as pandas dataframe
-    save_csv        [kat] - save the last measurement as csv file
-    save_pickle     [kat] - save the last measurement as pickled pandas dataframe
-    load_dataframe  [kat] - load a pandas dataframe from csv or pickle
-    run_script      [k  ] - run a lua script on the Keithely device
+    measure         - take measurements
+    monitor         - take measurements with live monitoring in a matplotlib window
+    measure_count   - take a fixed number of measurements
+    monitor_count   - take a fixed number of measurements with live monitoring in a matplotlib window
+    repeat          - measure and save to csv multiple times
+    get_dataframe   - return smua.nvbuffer 1 and 2 as pandas dataframe
+    save_csv        - save the last measurement as csv file
+    save_pickle     - save the last measurement as pickled pandas dataframe
+    load_dataframe  - load a pandas dataframe from csv or pickle
+    run_script      - run a lua script on the Keithely device
 Run 'help(function)' to see more information on a function
 
 Available topics:
@@ -330,13 +333,13 @@ Run 'help("topic")' to see more information on a topic""")
 Functions:
     name("<name>")         - short for set("name", "<name>")
     set("setting", value)  - set a setting to a value
-    save_settings()        - store the settings as "m-teng.json" in the working directory
+    save_settings()        - store the settings as "k-teng.conf" in the working directory
     load_settings()        - load settings from a file
     The global variable 'config_path' determines the path used by save/load_settings. Use -c '<path>' to set another path.
     The serach path is:
-        <working-dir>/m-teng.json
-        $XDG_CONFIG_HOME/m-teng.json
-        ~/.config/m-teng.json
+        <working-dir>/k-teng.json
+        $XDG_CONFIG_HOME/k-teng.json
+        ~/.config/k-teng.json
               """)
     elif topic == "imports":
         print("""Imports:
@@ -346,37 +349,45 @@ Functions:
     os.path """)
     elif topic == "device":
         print("""Device:
-    keithley backend:
-        The opened pyvisa resource (deveithley device) is the global variable 'dev'.
-        You can interact using pyvisa functions, such as
-        k.write("command"), k.query("command") etc. to interact with the device.
-    arduino backend:
-        The Arduino will be avaiable as BleakClient using the global variable 'dev'.  """)
+    The opened pyvisa resource (Keithley device) is the global variable 'k'.
+    You can interact using pyvisa functions, such as
+    k.write("command"), k.query("command") etc. to interact with the device.""")
     else:
         print(topic.__doc__)
 
 
 def init():
-    global dev, settings, config_path
-    print(r"""              ______________________ _______     ________
-  _____       \__    ___/\_   _____/ \      \   /  _____/
- /     \  ______|    |    |    __)_  /   |   \ /   \  ___
-|  Y Y  \/_____/|    |    |        \/    |    \\    \_\  \
-|__|_|  /       |____|   /_______  /\____|__  / \______  /
-      \/                         \/         \/         \/   1.2
+    global k, settings, test, config_path
+    print(r""" ____  __.         ______________________ _______     ________
+|    |/ _|         \__    ___/\_   _____/ \      \   /  _____/
+|      <    ______   |    |    |    __)_  /   |   \ /   \  ___
+|    |  \  /_____/   |    |    |        \/    |    \\    \_\  \
+|____|__ \           |____|   /_______  /\____|__  / \______  /
+        \/                            \/         \/         \/      1.1
 Interactive Shell for TENG measurements with Keithley 2600B
 ---
 Enter 'help()' for a list of commands""")
     from os import environ
-    if path.isfile("m-teng.json"):
-        config_path = "m-teng.json"
+    if path.isfile("k-teng.json"):
+        config_path = "k-teng.json"
     elif 'XDG_CONFIG_HOME' in environ.keys():
-        # and path.isfile(environ["XDG_CONFIG_HOME"] + "/m-teng.json"):
-        config_path = environ["XDG_CONFIG_HOME"] + "/m-teng.json"
+        # and path.isfile(environ["XDG_CONFIG_HOME"] + "/k-teng.json"):
+        config_path = environ["XDG_CONFIG_HOME"] + "/k-teng.json"
     else:
-        config_path = path.expanduser("~/.config/m-teng.json")
-    if args["config"]:
-        config_path = args["config"]
+        config_path = path.expanduser("~/.config/k-teng.json")
+
+    from sys import argv
+    i = 1
+    while i < len(argv):
+        if argv[i] in ["-t", "--test"]:
+            test = True
+        elif argv[i] in ["-c", "--config"]:
+            if i+1 < len(argv):
+                config_path = argv[i+1]
+            else:
+                print("-c requires an extra argument: path of config file")
+            i += 1
+        i += 1
 
 
     if not path.isdir(path.dirname(config_path)):
@@ -388,12 +399,15 @@ Enter 'help()' for a list of commands""")
     if not path.isdir(settings["datadir"]):
         makedirs(settings["datadir"])
 
-    try:
-        dev = _backend.init(beep_success=settings["beep"])
-    except Exception as e:
-        print(e)
-        exit(1)
-    atexit.register(_backend.exit, dev)
+    if not test:
+        from .keithley.keithley import init_keithley
+        try:
+            k = init_keithley(beep_success=settings["beep"])
+        except Exception as e:
+            print(e)
+            exit()
+    else:
+        print("Running in test mode, device will not be connected.")
 
 
 if __name__ == "__main__":

k-teng/keithley/keithley.py

@@ -1,19 +1,20 @@
 import pyvisa
 import numpy as np
-import pkg_resources
 
 
 """
 Utility
 """
-
+script_dir = "../scripts/"
 scripts = {
-    "buffer_reset": pkg_resources.resource_filename("m_teng", "keithley_scripts/buffer_reset.lua"),
-    "smua_reset":   pkg_resources.resource_filename("m_teng", "keithley_scripts/smua_reset.lua"),
+    "buffer_reset":     "buffer_reset.lua",
+    "smua_reset":       "smua_reset.lua",
 }
+for key,val in scripts.items():
+    scripts[key] = script_dir + scripts[key]
 
 
-def init(beep_success=True):
+def init_keithley(beep_success=True):
     rm = pyvisa.ResourceManager('@py')
     resources = rm.list_resources()
     if len(resources) < 1:
@@ -31,11 +32,6 @@ def init(beep_success=True):
         return keithley
 
 
-def exit(instr):
-    instr.close()
-
-
-
 def run_lua(instr, script_path, verbose=False):
     """
     Run a lua script from the host on the instrument
@@ -56,15 +52,6 @@ def reset(instr, verbose=False):
     run_lua(instr, scripts["smua_reset"], verbose=verbose)
     run_lua(instr, scripts["buffer_reset"], verbose=verbose)
 
-def get_buffer_name(buffer_nr: int):
-    if buffer_nr == 2: return "smua.nvbuffer2"
-    elif buffer_nr == 1:  return "smua.nvbuffer1"
-    raise ValueError(f"Invalid buffer_nr: {buffer_nr}")
-
-def get_buffer_size(instr, buffer_nr=1):
-    n = instr.query(f"print({get_buffer_name(buffer_nr)}.n)").strip("\n")
-    return int(float(n))
-
 
 def collect_buffer(instr, buffer_nr=1, verbose=False):
     """
@@ -76,7 +63,8 @@ def collect_buffer(instr, buffer_nr=1, verbose=False):
             0: timestamps
             1: readings
     """
-    buffername = get_buffer_name(buffer_nr)
+    if buffer_nr == 2: buffername = "smua.nvbuffer2"
+    else: buffername = "smua.nvbuffer1"
     # instr.write("format.data = format.DREAL\nformat.byteorder = format.LITTLEENDIAN")
     # buffer = instr.query_binary_values(f"printbuffer(1, {buffername}.n, {buffername})", datatype='d', container=np.array)
     instr.write("format.data = format.ASCII\nformat.asciiprecision = 7")
@@ -87,30 +75,3 @@ def collect_buffer(instr, buffer_nr=1, verbose=False):
     buffer = np.vstack((timestamps, readings)).T
     return buffer
 
-
-
-def collect_buffer_range(instr, range_=(1, -1), buffer_nr=1, verbose=False):
-    """
-    Get the buffer as 2D - np.array
-    @param instr : pyvisa instrument
-    @param buffer_nr : 1 or 2, for smua.nvbuffer1 or 2
-    @returns 2D numpy array:
-        i - ith reading:
-            0: timestamps
-            1: readings
-    """
-    buffername = get_buffer_name(buffer_nr)
-    # instr.write("format.data = format.DREAL\nformat.byteorder = format.LITTLEENDIAN")
-    # buffer = instr.query_binary_values(f"printbuffer(1, {buffername}.n, {buffername})", datatype='d', container=np.array)
-    if range_[1] == -1:
-        range_ = (range_[0], f"{buffername}.n")
-    instr.write("format.data = format.ASCII\nformat.asciiprecision = 7")
-    timestamps = instr.query_ascii_values(f"printbuffer({range_[0]}, {range_[1]}, {buffername}.timestamps)", container=np.array)
-    readings = instr.query_ascii_values(f"printbuffer({range_[0]}, {range_[1]}, {buffername}.readings)", container=np.array)
-    if verbose:
-        print(f"readings from {buffername}: {readings}, \ntimestamps: {timestamps}")
-    buffer = np.vstack((timestamps, readings)).T
-    return buffer
-
-
-

k-teng/keithley/measure.py

@@ -0,0 +1,107 @@
+from time import sleep
+import numpy as np
+from matplotlib import pyplot as plt
+import pyvisa
+
+from .keithley import reset
+from ..utility import testing as _testing
+
+def measure_count(instr, V=True, I=True, count=100, interval=0.05, update_func=None, update_interval=0.5, beep_done=True, verbose=True, testing=False):
+    """
+    Take <count> measurements with <interval> inbetween
+
+    @details
+        Uses the devices overlappedY function to make the measurements asynchronosly
+        The update_func is optional and only used when I == True and V == True
+        The update_func does not necessarily get all the values that are measured. To obtain the whole measurement, get them from the device buffers (smua.nvbufferX)
+    @param instr: pyvisa instrument
+    @param update_func: Callable that processes the measurements: (index, ival, vval) -> None
+    @param update_interval: interval at which the update_func is called
+    """
+    f_meas = None
+    if V and I:
+        f_meas = "smua.measure.overlappediv(smua.nvbuffer1, smua.nvbuffer2)"
+    elif V:
+        f_meas = "smua.measure.overlappedv(smua.nvbuffer1)"
+    elif I:
+        f_meas = "smua.measure.overlappedi(smua.nvbuffer1)"
+    else:
+        print("I and/or V needs to be set to True")
+        return
+
+    i = 0
+    if not testing:
+        reset(instr, verbose=verbose)
+        instr.write(f"smua.measure.count = {count}")
+        instr.write(f"smua.measure.interval = {interval}")
+
+        # start measurement
+        instr.write(f"smua.source.output = smua.OUTPUT_ON")
+        instr.write(f_meas)
+
+        condition = lambda: float(instr.query("print(status.operation.measuring.condition)").strip("\n ")) != 0
+    else:
+        condition = lambda: i < int(float(count) * interval / update_interval)
+
+    sleep(update_interval)
+    # for live viewing
+
+    query = """if smua.nvbufferX.n > 0 then print(smua.nvbufferX.readings[smua.nvbufferX.n]) else print(0) end"""
+    # will return 2.0 while measruing
+    while condition():
+        if update_func and V and I:
+            try:
+                if not testing:
+                    ival = float(instr.query(query.replace("X", "1")).strip("\n"))
+                    vval = float(instr.query(query.replace("X", "2")).strip("\n"))
+                else:
+                    ival = _testing.testcurve(i, peak_width=1, amplitude=5e-8)
+                    vval = -_testing.testcurve(i, peak_width=2, amplitude=15)
+                update_func(i, ival, vval)
+            except ValueError:
+                pass
+        sleep(update_interval)
+        i += 1
+
+    if not testing:
+        instr.write(f"smua.source.output = smua.OUTPUT_OFF")
+
+        if beep_done:
+            instr.write("beeper.beep(0.3, 1000)")
+
+
+def measure(instr, interval, update_func=None, max_measurements=None, testing=False):
+    """
+    @details:
+        - Resets the buffers
+        - Until KeyboardInterrupt:
+            - Take measurement
+            - Call update_func
+            - Wait interval
+        Uses python's time.sleep() for waiting the interval, which is not very precise. Use measure_count for better precision
+        You can take the data from the buffer afterwards, using save_csv
+    @param instr: pyvisa instrument
+    @param update_func: Callable that processes the measurements: (index, ival, vval) -> None
+    @param max_measurements : maximum number of measurements. None means infinite
+    """
+    if not testing:
+        reset(instr, verbose=True)
+        instr.write("smua.source.output = smua.OUTPUT_ON")
+        instr.write("format.data = format.ASCII\nformat.asciiprecision = 12")
+    try:
+        i = 0
+        while max_measurements is None or i < max_measurements:
+            if testing:
+                ival = _testing.testcurve(i, peak_width=1, amplitude=5e-8)
+                vval = -_testing.testcurve(i, peak_width=2, amplitude=15)
+            else:
+                ival, vval = tuple(float(v) for v in instr.query("print(smua.measure.iv(smua.nvbuffer1, smua.nvbuffer2))").strip('\n').split('\t'))
+            if update_func:
+                update_func(i, ival, vval)
+            sleep(interval)
+            i += 1
+    except KeyboardInterrupt:
+        pass
+    if not testing:
+        instr.write("smua.source.output = smua.OUTPUT_OFF")
+    print("Measurement stopped" + " "*50)

k-teng/materials

@@ -0,0 +1,4 @@
+pdms
+kapton
+plastic
+

k-teng/test.py

@@ -0,0 +1,49 @@
+readings = [
+  4.974127e-10, -1.418591e-12, -1.573563e-12, -1.728535e-12, -1.704693e-12,
+ -1.847744e-12, -1.931190e-12, -1.788139e-12, -1.871586e-12, -2.169609e-12,
+ -2.074242e-12, -1.895428e-12, -1.895428e-12, -1.776218e-12, -1.990795e-12,
+ -1.788139e-12, -1.811981e-12, -1.657009e-12, -1.573563e-12, -2.396107e-12,
+ -2.515316e-12, -2.765656e-12, -2.825260e-12, -3.147125e-12, -2.300739e-12,
+ -2.825260e-12, -3.278255e-12, -5.257130e-12, -6.818771e-12, -8.916855e-12,
+ -7.712841e-12,  6.437302e-12, -1.142025e-11, -1.206398e-11, -4.649043e-10,
+ -3.427613e-09, -2.460408e-09, -2.340376e-09, -1.306653e-10,  1.496077e-11,
+  2.933741e-11,  1.953280e-09,  8.579970e-10,  9.226799e-12, -1.095533e-11,
+ -2.508163e-11, -2.776039e-09, -8.686423e-09,  4.935264e-12,  1.246929e-11,
+  3.225744e-09,  2.814472e-09,  1.877034e-09,  2.229273e-09,  1.713574e-09,
+  8.355618e-10, -4.332781e-10,  5.896091e-11,  5.762577e-11,  8.129537e-09,
+  4.044378e-09,  1.771629e-09,  7.849216e-10,  4.098892e-10,  3.390551e-10,
+  2.956390e-10,  3.033876e-10,  1.716256e-10,  1.463890e-11, -5.078316e-12,
+ -6.949902e-12, -8.106232e-12, -6.473065e-12, -4.506111e-12,  4.919767e-11,
+  3.052297e-08,  1.161162e-08, -9.892106e-09, -3.613818e-09, -5.004287e-09,
+ -2.015829e-11, -4.183054e-11, -1.810908e-10, -2.042532e-10, -3.516316e-10,
+  5.099773e-11,  1.921976e-08, -1.256589e-08, -4.242897e-10, -1.358986e-12,
+ -3.445148e-12, -3.838539e-12, -4.184246e-12, -7.402897e-12, -2.840877e-10,
+ -2.872229e-10, -2.730966e-10, -1.134396e-10, -4.376173e-11, -3.576279e-14
+]
+timestamps = [
+ 0.      , 0.05    , 0.1     , 0.15,     0.2,      0.25,     0.3,      0.35,
+ 0.4     , 0.45    , 0.5     , 0.55,     0.6,      0.65,     0.7,      0.75,
+ 0.8     , 0.85    , 0.9     , 0.95,     1. ,      1.05,     1.1,      1.15,
+ 1.2     , 1.25    , 1.3     , 1.35,     1.4,      1.45,     1.5,      1.55,
+ 1.6     , 1.690891, 1.710923, 1.75,     1.8,      1.85,     1.9,      1.95,
+ 2.      , 2.05    , 2.1     , 2.15,     2.2,      2.25,     2.3,      2.35,
+ 2.420332, 2.45    , 2.5     , 2.55,     2.6,      2.65,     2.7,      2.75,
+ 2.820553, 2.890843, 2.910875, 2.95,     3. ,      3.05,     3.1,      3.15,
+ 3.2     , 3.25    , 3.3     , 3.35,     3.4,      3.45,     3.5,      3.55,
+ 3.6     , 3.65    , 3.7     , 3.75,     3.8,      3.85,     3.9,      3.95,
+ 4.      , 4.05    , 4.1     , 4.15,     4.2,      4.25,     4.3,      4.35,
+ 4.4     , 4.45    , 4.5     , 4.55,     4.6,      4.65,     4.7,      4.75,
+ 4.8     , 4.85    , 4.9     , 4.95,    ]
+
+import pandas as pd
+import numpy as np
+import scipy as sp
+import matplotlib.pyplot as plt
+df = pd.DataFrame(np.vstack((timestamps, readings)).T)
+df.columns = ["Time [s]", "Voltage [V]"]
+print(df)
+df.to_csv("test.csv", sep=",", header=True, index=False)
+
+df.plot(x='Time [s]', y="Voltage [V]")
+plt.show()
+

k-teng/testcurve.py

@@ -0,0 +1,33 @@
+import numpy as np
+import matplotlib.pyplot as plt
+
+def testcurve(x, frequency=10, peak_width=2, amplitude=20, bias=0):
+    # want peak at n*time == frequency
+    nearest_peak = np.round(x / frequency, 0)
+    # if not peak at 0 and within peak_width
+    # print(x, nearest_peak)
+    if nearest_peak > 0 and abs((x - nearest_peak * frequency)) < peak_width:
+        # return sin that does one period within 2*peak_width
+        return amplitude * np.sin(2*np.pi * (x - nearest_peak * frequency - peak_width) / (2*peak_width)) + bias
+    else:
+        return bias
+
+    # 0 = pk - width
+    # 2pi = pk + width
+
+def baseline(data):
+    # find the value where the most values with low gradients are closest to
+    gradients = np.abs(np.gradient(data))
+    # consider the values where the absolute gradient is in the bottom 20%
+    n_gradients = len(data) // 20
+    consider_indices = np.argsort(gradients)[:n_gradients]
+    # of those, only consider values where the value 
+    consider_values = data[consider_indices]
+
+
+xdata = np.arange(0, 100, 0.01)
+ydata = np.vectorize(testcurve)(xdata)
+
+
+plt.plot(xdata, ydata)
+plt.show()

k-teng/utility/testing.py

@@ -0,0 +1,38 @@
+
+import pandas as pd
+import numpy as np
+
+def collect_buffer(instr, buffer_nr=1):
+    """
+    Get the buffer as 2D - np.array
+    @param instr : pyvisa instrument
+    @param buffer_nr : 1 or 2, for smua.nvbuffer1 or 2
+    @returns 2D numpy array:
+        i - ith reading:
+            0: timestamps
+            1: readings
+    """
+    if buffer_nr == 2: buffername = "smua.nvbuffer2"
+    else: buffername = "smua.nvbuffer1"
+    # instr.write("format.data = format.DREAL\nformat.byteorder = format.LITTLEENDIAN")
+    # buffer = instr.query_binary_values(f"printbuffer(1, {buffername}.n, {buffername})", datatype='d', container=np.array)
+    instr.write("format.data = format.ASCII\nformat.asciiprecision = 7")
+    timestamps = instr.query_ascii_values(f"printbuffer(1, {buffername}.n, {buffername}.timestamps)", container=np.array)
+    readings = instr.query_ascii_values(f"printbuffer(1, {buffername}.n, {buffername}.readings)", container=np.array)
+    print(f"readings: {readings}, \ntimestamps: {timestamps}")
+    buffer = np.vstack((timestamps, readings)).T
+    return buffer
+
+
+def testcurve(x, frequency=10, peak_width=2, amplitude=20, bias=0):
+    # want peak at n*time == frequency
+    nearest_peak = np.round(x / frequency, 0)
+    # if not peak at 0 and within peak_width
+    if nearest_peak > 0 and abs((x - nearest_peak * frequency)) < peak_width:
+        # return sin that does one period within 2*peak_width
+        return amplitude * np.sin(2*np.pi * (x - nearest_peak * frequency - peak_width) / (2*peak_width)) + bias
+    else:
+        return bias
+
+    # 0 = pk - width
+    # 2pi = pk + width

m_teng/backends/arduino/arduino.py

@@ -1,155 +0,0 @@
-import bleak as b
-import asyncio
-import numpy as np
-
-TARGET_NAME = "ArduinoTENG"
-
-# GATT service and characteristics UUIDs
-TENG_SUUID          = "00010000-9a74-4b30-9361-4a16ec09930f"
-TENG_STATUS_CUUID   = "00010001-9a74-4b30-9361-4a16ec09930f"
-TENG_COMMAND_CUUID  = "00010002-9a74-4b30-9361-4a16ec09930f"
-TENG_READING_CUUID  = "00010003-9a74-4b30-9361-4a16ec09930f"
-TENG_COUNT_CUUID    = "00010004-9a74-4b30-9361-4a16ec09930f"
-TENG_INTERVAL_CUUID = "00010005-9a74-4b30-9361-4a16ec09930f"
-
-TENG_COMMANDS = {
-    "STOP":             int(0).to_bytes(1, signed=False),
-    "MEASURE_COUNT":    int(1).to_bytes(1, signed=False),
-    "MEASURE":          int(2).to_bytes(1, signed=False),
-}
-TENG_STATUS = ["ERROR", "BUSY", "WAIT_CONNECT", "CONNECTED", "MEASURING"]
-
-# TODO save measurements on device buffer, transfer later
-
-
-# wrapper for global variable
-class Buffer:
-    def __init__(self):
-        self.data = None
-_buffer = Buffer()
-
-# class Runner:
-#     def __init__(self):
-runner = asyncio.Runner()
-
-def teng_status_callback(characteristic, data):
-    value = int.from_bytes(data, byteorder="big", signed=False)
-    if 0 <= value and value < len(TENG_STATUS):
-        print(f"Status change: {TENG_STATUS[value]}")
-    else:
-        print(f"Status change (invalid): status={value}")
-
-
-def disconnect_callback(client):
-    raise Exception(f"The Bluetooth device {client.name} was disconnected")
-
-
-async def init_arduino_async(n_tries: int=5) -> b.BleakClient:
-    n_try = 0
-    if n_tries <= 0: n_tries = "inf"
-    try:
-        target_device = None
-        while target_device is None and (n_tries == "inf" or n_try < n_tries):
-            print(f"Searching for Bluetooth device '{TARGET_NAME}' ({n_try+1}/{n_tries})", end="\r")
-            devices = await b.BleakScanner.discover(return_adv=True, timeout=1.5)
-            # print(devices)
-            for adr, (device, adv_data) in devices.items():
-                if device.name == TARGET_NAME:
-                    # print(adv_data)
-                    target_device = device
-                    break
-            n_try += 1
-        if target_device is None:
-            raise Exception(f"Could not find Bluetooth device 'ArduinoTENG'")
-        # print(f"Found target device: {target_device.name}: {target_device.metadata}, {target_device.details}")
-        # print(target_device.name, target_device.details)
-        client = b.BleakClient(target_device, disconnect_callback=disconnect_callback)
-        await client.connect()
-        print(f"Connected to Bluetooth device '{TARGET_NAME}' at [{client.address}]")
-        return client
-    except asyncio.exceptions.CancelledError:
-        raise Exception(f"Cancelled")
-
-
-def init(beep_success=True, n_tries: int=5) -> b.BleakClient:
-    """
-    Connect to the arduino
-    @returns: BleakClient
-    """
-    client = runner.run(init_arduino_async(n_tries=n_tries))
-    if beep_success: beep(client)
-    return client
-
-
-def exit(client):
-    try:
-        runner.run(stop_measurement(client))
-        runner.run(client.disconnect())
-    except Exception:
-        pass
-
-
-async def set_interval(client, interval: float):
-    """
-    Set the measurement interval
-    @param interval: interval in seconds
-    """
-    interval = int(interval * 1000)  # convert to ms for arduinos delay)
-    await client.write_gatt_char(TENG_INTERVAL_CUUID, interval.to_bytes(2, byteorder="little", signed=False))
-
-async def set_count(client, count: int):
-    """
-    Set the measurement count
-    @param count: number of measurements to take
-    """
-    await client.write_gatt_char(TENG_COUNT_CUUID, count.to_bytes(2, byteorder="little", signed=False))
-
-async def stop_measurement(client):
-    await client.write_gatt_char(TENG_COMMAND_CUUID, TENG_COMMANDS["STOP"])
-
-async def start_measure_count(client):
-    await client.write_gatt_char(TENG_COMMAND_CUUID, TENG_COMMANDS["MEASURE_COUNT"])
-
-async def start_measure(client):
-    await client.write_gatt_char(TENG_COMMAND_CUUID, TENG_COMMANDS["MEASURE"])
-
-
-# async def main():
-#             for service in client.services:
-#                 print(f"Service: {service.uuid}: {service.description}")
-#                 for c in service.characteristics:
-#                     print(f"\t{c.uuid}: {c.properties}, {c.descriptors}")
-#             teng_status     = client.services.get_characteristic(TENG_STATUS_CUUID)
-#             teng_command    = client.services.get_characteristic(TENG_COMMAND_CUUID)
-#             teng_reading    = client.services.get_characteristic(TENG_READING_CUUID)
-#             client.start_notify(teng_status, teng_status_callback)
-
-#             await client.write_gatt_char(teng_command, TENG_COMMANDS["NOOP"])
-#             await asyncio.sleep(5)
-#             await client.write_gatt_char(teng_command, TENG_COMMANDS["MEASURE_BASELINE"])
-
-#             while client.is_connected:
-#                 data = await client.read_gatt_char(teng_reading)
-
-
-#                 value = int.from_bytes(data, byteorder="little", signed=False)
-#                 print(f"Reading: {value}")
-#                 await asyncio.sleep(0.5)
-#     except KeyboardInterrupt:
-#         pass
-#     except asyncio.exceptions.CancelledError:
-#         pass
-#     print("Disconnected")
-
-
-def collect_buffer(instr, buffer_nr=1):
-    """
-    @param buffer_nr: 1 -> current, 2 -> voltage
-    """
-    assert(buffer_nr in (1, 2))
-    return np.vstack((_buffer.data[:,0], _buffer.data[:,buffer_nr])).T
-
-
-def beep(client):
-    # TODO connect beeper to arduino?
-    print("beep")

m_teng/backends/arduino/measure.py

@@ -1,75 +0,0 @@
-import bleak as b
-import numpy as np
-
-import asyncio
-import datetime
-
-from m_teng.backends.arduino.arduino import beep, set_interval, set_count, TENG_READING_CUUID, _buffer, start_measure, start_measure_count, stop_measurement, runner
-
-
-async def _measure_count_async(client, count=100, interval=0.05, update_func=None, update_interval=0.5, beep_done=True, verbose=True):
-    global _buffer
-    _buffer.data = np.zeros((count, 3))
-    i = 0
-    t_start = datetime.datetime.now()
-    async def add_reading(teng_reading_cr, reading: bytearray):
-        nonlocal i, count
-        if i >= count: return
-        _buffer.data[i][0] = float((datetime.datetime.now() - t_start).microseconds) / 1000
-        # reading = await client.read_gatt_char(TENG_READING_CUUID)
-        _buffer.data[i][2] = int.from_bytes(reading, byteorder="little", signed=False)
-        i += 1
-
-    await set_interval(client, interval)
-    await set_count(client, count)
-    # TODO check if notify works when the same value is written again
-    await client.start_notify(TENG_READING_CUUID, add_reading)
-    await start_measure_count(client)
-    while i < count:
-        await asyncio.sleep(update_interval)
-        if update_func is not None and i > 0:  # assume an update has occured
-            update_func(i-1, 0, _buffer.data[i-1, 2])
-    await client.stop_notify(TENG_READING_CUUID)
-    if beep_done: beep(client)
-
-def measure_count(client, count=100, interval=0.05, update_func=None, update_interval=0.5, beep_done=True, verbose=True):
-    runner.run(_measure_count_async(client, count=count, interval=interval, update_func=update_func, update_interval=update_interval, beep_done=beep_done, verbose=verbose))
-
-
-async def _measure_async(client, interval, update_func=None, max_measurements=None):
-    global _buffer
-    readings = []
-    timestamps = []
-    i = 0
-    t_start = datetime.datetime.now()
-
-    async def add_reading(teng_reading_cr, reading):
-        nonlocal i
-        timestamps.append(float((datetime.datetime.now() - t_start).microseconds) / 1000)
-        reading = int.from_bytes(reading, byteorder="little", signed=False)
-        readings.append(reading)
-
-        if update_func:
-            try:
-                update_func(i, 0, reading)
-            except KeyboardInterrupt:
-                raise asyncio.exceptions.CancelledError("KeyboardInterrupt in update_func")
-        i += 1
-
-    await set_interval(client, interval)
-    await client.start_notify(TENG_READING_CUUID, add_reading)
-    await start_measure(client)
-    try:
-        while max_measurements is None or i < max_measurements:
-            await asyncio.sleep(0.1)  # 
-    except asyncio.exceptions.CancelledError:
-        pass
-    except KeyboardInterrupt:
-        pass
-    await client.stop_notify(TENG_READING_CUUID)
-    await stop_measurement(client)
-    _buffer.data = np.vstack((timestamps, np.zeros(len(timestamps)), readings)).T
-    print("Measurement stopped" + " "*50)
-
-def measure(client, interval, update_func=None, max_measurements=None):
-    runner.run(_measure_async(client, interval=interval, update_func=update_func, max_measurements=max_measurements))

m_teng/backends/keithley/measure.py

@@ -1,93 +0,0 @@
-from time import sleep
-import numpy as np
-from matplotlib import pyplot as plt
-import pyvisa
-
-from m_teng.backends.keithley import reset
-from m_teng.utility import testing as _testing
-
-def measure_count(instr, count=100, interval=0.05, update_func=None, update_interval=0.5, beep_done=True, verbose=True):
-    """
-    Take <count> measurements with <interval> inbetween
-
-    @details
-        Uses the devices overlappedY function to make the measurements asynchronosly
-        The update_func is optional and only used when I == True and V == True
-        The update_func does not necessarily get all the values that are measured. To obtain the whole measurement, get them from the device buffers (smua.nvbufferX)
-    @param instr: pyvisa instrument
-    @param update_func: Callable that processes the measurements: (index, ival, vval) -> None
-    @param update_interval: interval at which the update_func is called
-    """
-    f_meas = "smua.measure.overlappediv(smua.nvbuffer1, smua.nvbuffer2)"
-    # if V and I:
-    # elif V:
-    #     f_meas = "smua.measure.overlappedv(smua.nvbuffer1)"
-    # elif I:
-    #     f_meas = "smua.measure.overlappedi(smua.nvbuffer1)"
-    # else:
-    #     print("I and/or V needs to be set to True")
-    #     return
-
-    i = 0
-    reset(instr, verbose=verbose)
-    instr.write(f"smua.measure.count = {count}")
-    instr.write(f"smua.measure.interval = {interval}")
-
-    # start measurement
-    instr.write(f"smua.source.output = smua.OUTPUT_ON")
-    instr.write(f_meas)
-
-    sleep(update_interval)
-    # for live viewing
-    query = """if smua.nvbufferX.n > 0 then print(smua.nvbufferX.readings[smua.nvbufferX.n]) else print(0) end"""
-
-    # will return 2.0 while measruing
-    while float(instr.query("print(status.operation.measuring.condition)").strip("\n ")) != 0:
-        if update_func:
-            try:
-                ival = float(instr.query(query.replace("X", "1")).strip("\n"))
-                vval = float(instr.query(query.replace("X", "2")).strip("\n"))
-                update_func(i, ival, vval)
-            except ValueError as e:
-                if i != 0:
-                    pass
-                else:
-                    print(f"measure_count: ValueError: {e}")
-        sleep(update_interval)
-        i += 1
-
-    instr.write(f"smua.source.output = smua.OUTPUT_OFF")
-
-    if beep_done:
-        instr.write("beeper.beep(0.3, 1000)")
-
-
-def measure(instr, interval, update_func=None, max_measurements=None):
-    """
-    @details:
-        - Resets the buffers
-        - Until KeyboardInterrupt:
-            - Take measurement
-            - Call update_func
-            - Wait interval
-        Uses python's time.sleep() for waiting the interval, which is not very precise. Use measure_count for better precision
-        You can take the data from the buffer afterwards, using save_csv
-    @param instr: pyvisa instrument
-    @param update_func: Callable that processes the measurements: (index, ival, vval) -> None
-    @param max_measurements : maximum number of measurements. None means infinite
-    """
-    reset(instr, verbose=True)
-    instr.write("smua.source.output = smua.OUTPUT_ON")
-    instr.write("format.data = format.ASCII\nformat.asciiprecision = 12")
-    try:
-        i = 0
-        while max_measurements is None or i < max_measurements:
-            ival, vval = tuple(float(v) for v in instr.query("print(smua.measure.iv(smua.nvbuffer1, smua.nvbuffer2))").strip('\n').split('\t'))
-            if update_func:
-                update_func(i, ival, vval)
-            sleep(interval)
-            i += 1
-    except KeyboardInterrupt:
-        pass
-    instr.write("smua.source.output = smua.OUTPUT_OFF")
-    print("Measurement stopped" + " "*50)

m_teng/update_funcs.py

@@ -1,123 +0,0 @@
-import matplotlib.pyplot as plt
-import numpy as np
-
-import torch
-
-from teng_ml.util import model_io as mio
-from teng_ml.util.settings import MLSettings
-from teng_ml.util.split import DataSplitter
-
-from m_teng.backends.keithley import keithley
-
-def _update_print(i, ival, vval):
-    print(f"n = {i:5d}, I = {ival: .12f} A, U = {vval: .5f} V" + " "*10, end='\r')
-
-class _Monitor:
-    """
-    Monitor v and i data
-    """
-    def __init__(self, max_points_shown=None, use_print=False):
-        self.max_points_shown = max_points_shown
-        self.use_print = use_print
-        self.index = []
-        self.vdata = []
-        self.idata = []
-
-        plt.ion()
-        self.fig1, (self.vax, self.iax) = plt.subplots(2, 1, figsize=(8, 5))
-
-        self.vline, = self.vax.plot(self.index, self.vdata, color="g")
-        self.vax.set_ylabel("Voltage [V]")
-        self.vax.grid(True)
-
-        self.iline, = self.iax.plot(self.index, self.idata, color="m")
-        self.iax.set_ylabel("Current [A]")
-        self.iax.grid(True)
-
-    def update(self, i, ival, vval):
-        if self.use_print:
-            _update_print(i, ival, vval)
-        self.index.append(i)
-        self.idata.append(ival)
-        self.vdata.append(vval)
-        # update data
-        self.iline.set_xdata(self.index)
-        self.iline.set_ydata(self.idata)
-        self.vline.set_xdata(self.index)
-        self.vline.set_ydata(self.vdata)
-        # recalculate limits and set them for the view
-        self.iax.relim()
-        self.vax.relim()
-        if self.max_points_shown and i > self.max_points_shown:
-            self.iax.set_xlim(i - self.max_points_shown, i)
-            self.vax.set_xlim(i - self.max_points_shown, i)
-        self.iax.autoscale_view()
-        self.vax.autoscale_view()
-        # update plot
-        self.fig1.canvas.draw()
-        self.fig1.canvas.flush_events()
-
-    def __del__(self):
-        plt.close(self.fig1)
-
-
-class _ModelPredict:
-    colors = ["red", "green", "purple", "blue", "orange", "grey", "cyan"]
-    def __init__(self, instr, model_dir):
-        """
-        @param model_dir: directory where model.plk and settings.pkl are stored
-
-        Predict the values that are currently being recorded
-        @details:
-            Load the model and model settings from model dir
-            Wait until the number of recoreded points is >= the size of the models DataSplitter
-            Collect the data from the keithley, apply the transforms and predict the label with the model
-            Shows the prediction with a bar plot
-        """
-        self.instr = instr
-        self.model = mio.load_model(model_dir)
-        self.model_settings: MLSettings = mio.load_settings(model_dir)
-        if type(self.model_settings.splitter) == DataSplitter:
-            self.data_length = self.model_settings.splitter.split_size
-        else:
-            self.data_length = 200
-
-        plt.ion()
-        self.fig1, (self.ax) = plt.subplots(1, 1, figsize=(8, 5))
-
-        self.bar_cont = self.ax.bar(self.model_settings.labels.get_labels(), [ 1 for _ in range(len(self.model_settings.labels))])
-        self.ax.set_ylabel("Prediction")
-        self.ax.grid(True)
-
-    def update(self, i, ival, vval):
-        buffer_size = keithley.get_buffer_size(self.instr, buffer_nr=1)
-        if buffer_size <= self.data_length:
-            print(f"ModelPredict.update: buffer_size={buffer_size} < {self.data_length}")
-            return
-        else:
-            ibuffer = keithley.collect_buffer_range(self.instr, (buffer_size-self.data_length, buffer_size), buffer_nr=1)
-            vbuffer = keithley.collect_buffer_range(self.instr, (buffer_size-self.data_length, buffer_size), buffer_nr=2)
-        if self.model_settings.num_features == 1:  # model uses only voltage
-            data = np.vstack((ibuffer[:,0], ibuffer[:,1], vbuffer[:,1])).T
-            # print(f"data.shape:", data.shape)
-        else:
-            raise NotImplementedError(f"Cant handle models with num_features != 1 yet")
-        for t in self.model_settings.transforms:
-            data = t(data)
-        data = np.reshape(data[:,2], (1, -1, 1))  # batch_size, seq, features
-        with torch.no_grad():
-            x = torch.FloatTensor(data)   # select voltage data, without timestamps
-            # print(x.shape)
-
-            prediction = self.model(x)  # (batch_size, label-predictions)
-            prediction = torch.nn.functional.softmax(prediction)  # TODO remove when softmax is already applied by model
-            predicted = torch.argmax(prediction, dim=1, keepdim=False)  # -> [ label_indices ]
-            # print(f"raw={prediction[0]}, predicted_index={predicted[0}")
-            label = self.model_settings.labels[predicted[0]]
-            # print(f"-> label={label}")
-
-        self.bar_cont.remove()
-        self.bar_cont = self.ax.bar(self.model_settings.labels.get_labels(), prediction[0], color=_ModelPredict.colors[:len(self.model_settings.labels)])
-        # update plot
-        self.fig1.canvas.draw()
-        self.fig1.canvas.flush_events()

m_teng/utility/testing.py

@@ -1,17 +0,0 @@
-import numpy as np
-
-def testcurve(x, frequency=10, peak_width=2, amplitude=20, bias=0):
-    # 0 = pk - width
-    # 2pi = pk + width
-    # want peak at n*time == frequency
-    nearest_peak = np.round(x / frequency, 0)
-    # if not peak at 0 and within peak_width
-    if nearest_peak > 0 and np.abs((x - nearest_peak * frequency)) < peak_width:
-        # return sin that does one period within 2*peak_width
-        return amplitude * np.sin(2*np.pi * (x - nearest_peak * frequency - peak_width) / (2*peak_width)) + bias
-    else:
-        return bias
-
-def get_testcurve(frequency=10, peak_width=2, amplitude=20, bias=0):
-    return np.vectorize(lambda x: testcurve(x, frequency=frequency, peak_width=peak_width, amplitude=amplitude, bias=bias))
-

pyproject.toml

@@ -1,35 +0,0 @@
-[build-system]
-requires = ["setuptools"]
-
-[project]
-name = "k_teng"
-version = "1.0.0"
-description = "Interactive utility for I-V measurements with a Keitley 2600 SMU"
-requires-python = ">=3.10"
-readme = "readme.md"
-license = {file = "LICENSE"}
-authors = [
-    { name = "Matthias Quintern", email = "matthias@quintern.xyz" }
-]
-classifiers = [
-    "Operating System :: POSIX :: Linux",
-    "Environment :: Console",
-    "Programming Language :: Python :: 3",
-    "License :: OSI Approved :: GNU General Public License v3 (GPLv3)",
-]
-dependencies = [
-    "matplotlib>=3.6",
-    "numpy",
-    "pyvisa",
-    "pyvisa-py"
-]
-
-[project.urls]
-repository = "https://git.quintern.xyz/MatthiasQuintern/k-teng"
-
-
-[tool.setuptools.packages.find]
-where = ["."]
-
-[project.scripts]
-k-teng = "k_teng.k_teng_interactive:main"

readme.md

@@ -1,39 +1,23 @@
-# m-TENG
-Helper scripts and shell for measuring **T**ribo**e**lectric **N**ano**g**enerator-based sensor output with a Keithley 2611B SMU or an Arduino
+# K-TENG
+Helper scripts and shell for measuring **T**ribo**e**lectric **N**ano**g**enerator-based sensor output with a Keithley 2611B SMU using pyvisa
 
 ## Features
-
+### Useful functions for scripts
+- Measure Voltage and/or Current
+- Transfer buffer from device to host
+- Save/load as csv
+- Run lua script on device
+- Auto-filenames
 ### Interactive (shell) mode
 - Live view
 - Press button to stop
 - Save and load settings (default interval, data directory...)
 - Easily run arbitrary command on device
 
-
-### Useful functions for scripts
-- Measure voltage and/or current
-- Transfer buffer from measurement device to host
-- Save/load as csv
-- Run lua script on Keithley SMU
-- Auto-filenames
-
-## Available backends
-### keithley
-    Use a Keithley 2611B Source-Measure-Unit via *pyvisa*. This backend allows measuring both voltage and current simultaneously.
-
-### arduino
-    Use a Bluetooth capable Arduino with [https://git.quintern.xyz/MatthiasQuintern/teng-arduino](this software on the arduino).
-    This backend only allows measuring voltage using an Arduinos analog input pin (0 - 3.3 V, 12 bit resolution).
-
-### testing
-    Use the shell without measuring TENG output. When starting a measurement, sample data will be generated.
-
-
 ## Shell mode
-It is recommended to run the shell with ipython:
+Start with:
 ```shell
-ipython -i k_teng_interactive.py -- -*X*
+ipython -i k_teng_interactive.py
 ```
-Substitute *X* for `-k` for keithley backend, `-a` for arduino backend or `-t` for testing backend.
 
-In the shell, run `help()` to get a list of available commands
+Use `help()` to get a list of available commands