added data prep

k-teng/k_teng_interactive.py

@@ -30,6 +30,7 @@ if __name__ == "__main__":
 
 from .keithley import keithley as _keithley
 from .utility import data as _data
+from .utility.data import load_dataframe
 from .utility import file_io
 from .utility import testing
 
@@ -155,6 +156,15 @@ def measure(max_measurements=None):
     You can take the data from the buffer afterwards, using save_csv """
     _measure(max_measurements=max_measurements, monitor=False)
 
+def automeasure(repeat, repeat_delay=0, max_measurements=None, max_points_shown=120, monitor=True):
+    """
+    Measure and save to csv multiple times
+    """
+    for i in range(repeat):
+        _measure(max_measurements=max_measurements, max_points_shown=max_points_shown, monitor=monitor)
+        save_csv()
+        sleep(repeat_delay)
+
 
 def get_dataframe():
     """
@@ -199,20 +209,6 @@ def save_pickle():
     df.to_pickle(filename)
     print(f"Saved as '{filename}'")
 
-def load_dataframe(p:str):
-    """
-    Load a dataframe from file.
-    @param p : path of the file. If it has 'csv' extension, pandas.read_csv is used, pandas.read_pickle otherwise
-    """
-    if not path.isfile(p):
-        print(f"ERROR: load_dataframe: File does not exist: {p}")
-        return None
-    if p.endswith(".csv"):
-        df = pd.read_csv(p)
-    else:
-        df = pd.read_pickle(p)
-    return df
-
 def run_script(script_path):
     """
     Run a lua script on the Keithley device
@@ -253,6 +249,7 @@ def help(topic=None):
 Functions:
     measure         - measure the voltage
     monitor         - measure the voltage with live monitoring in a matplotlib window
+    automeasure     - measure and save to csv multiple times
     get_dataframe   - return smua.nvbuffer1 as pandas dataframe
     save_csv        - save the last measurement as csv file
     save_pickle     - save the last measurement as pickled pandas dataframe

k-teng/keithley/keithley.py

@@ -14,7 +14,6 @@ for key,val in scripts.items():
     scripts[key] = script_dir + scripts[key]
 
 
-
 def init_keithley(beep_success=True):
     rm = pyvisa.ResourceManager('@py')
     resources = rm.list_resources()

k-teng/materials

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

k-teng/prepare.py

@@ -0,0 +1,151 @@
+import pandas as pd
+import numpy as np
+import scipy.signal as signal
+import matplotlib.pyplot as plt
+from time import sleep
+from random import choice as r_choice
+
+if __name__ == "__main__":
+    if __package__ is None:
+        # make relative imports work as described here: https://peps.python.org/pep-0366/#proposed-change
+        __package__ = "k-teng"
+        import sys
+        from os import path
+        filepath = path.realpath(path.abspath(__file__))
+        sys.path.insert(0, path.dirname(path.dirname(filepath)))
+from .utility.data import load_dataframe
+
+file = "/home/matth/data/gel_big_gap000.csv"
+
+class PeakInfo:
+    """
+    Helper class for "iterating" through selected peaks.
+    """
+    def __init__(self):
+        self.reset()
+
+    def reset(self):
+        self._peak_names = [ "first", "second", "last", "lowest" ]
+        self._peaks = { p: None for p in self._peak_names }
+        self._iter = 0
+
+    def current(self):
+        # return (self._peak_names[self._iter]), self._peaks[self._peak_names[self._iter]]
+        return self._peaks[self._peak_names[self._iter]]
+    def name(self):
+        return self._peak_names[self._iter]
+
+    def next(self):
+        if self._iter < len(self._peak_names) - 1: self._iter += 1
+        return self.current()
+    def prev(self):
+        if self._iter > 0: self._iter -= 1
+        return self.current()
+
+    def set(self, value):
+        """Assign a value to the crrent peak"""
+        self._peaks[self._peak_names[self._iter]] = value
+    def is_done(self):
+        for peak in self._peaks.values():
+            if peak is None: return False
+        return True
+
+    def __getitem__(self, key):
+        return self._peaks[key]
+    def __setitem__(self, key, value):
+        self._peaks[key] =  value
+    def __repr__(self):
+        return f"{self._peak_names[self._iter]} peak"
+
+
+
+def find_peaks(a):
+    peaks = signal.find_peaks(a)
+
+
+def on_click(fig, ax, peaks, event):
+    """
+    Let the user select first, second and last peak by clicking on them in this order.
+    Right click undos the last selection
+    """
+    select = None
+    if event.button == 1:  # left click
+        peaks.set((event.xdata, event.ydata))
+        print(f"{peaks}: {event.xdata} - {event.ydata}")
+        ax.set_title(f"{peaks}: {event.xdata} - {event.ydata}")
+        peaks.next()
+    elif event.button == 3:  # right click
+        ax.set_title(f"Undo {peaks.name()}")
+        if not peaks.is_done():
+            peaks.prev()
+        peaks.set(None)
+    if peaks.is_done(): message = "Close window when done"
+    else: message = f"Click on {peaks}"
+    fig.suptitle(message)
+    fig.canvas.draw()
+    # fig1.canvas.flush_events()
+
+def calc_peaks(peaks):
+    # get the peak points from the information of a Peaks object
+    # 90% distance between first and second
+    min_distance = max(1, (peaks["second"][0] - peaks["first"][0]) * 0.9)
+    min_height = peaks["lowest"][1] * 0.99
+    vpeaks = signal.find_peaks(vdata, height=min_height, distance=min_distance)
+    return vpeaks
+
+
+def normalize(a):
+    """
+    normalize so that all values are between 0 and 1
+    """
+    min_ = np.min(a)
+    a = a - min_
+    max_ = np.max(a)
+    if max_ != 0:
+        a = a / max_
+    return a
+
+if __name__ == "__main__":
+    """
+    Peak identification:
+    plot, let user choose first, second, last and lowest peak for identification
+    """
+    df = load_dataframe(file)
+    a = df.to_numpy()
+    vdata = normalize(a[:,2])
+    plt.ion()
+    # vpeaks[0] is the list of the peaks
+    vpeaks = signal.find_peaks(vdata)[0]
+    fig, ax = plt.subplots()
+    ax.plot(vdata)
+    peak_lines = ax.vlines(vpeaks, 0, 1, colors="r")
+    ax.grid(True)
+    fig.suptitle("Click on first peak")
+    peak_info = PeakInfo()
+    # handle clicks
+    fig.canvas.mpl_connect("button_press_event", lambda ev: on_click(fig, ax, peak_info, ev))
+    # run until user closes, events are handled with on_click function
+    print(vdata.size)
+    while plt.fignum_exists(fig.number):
+        plt.pause(0.01)
+        if (peak_info.is_done()):
+            vpeaks = calc_peaks(peak_info)[0]
+            x_margin = (a[-1,0] - a[0,0]) * 0.05   # allow some margin if user clicked not close enough on peak
+            vpeaks = vpeaks[(vpeaks >= peak_info["first"][0] - x_margin) & (vpeaks <= peak_info["last"][0] + x_margin)]   # remove peaks before first and after last
+            peak_lines.remove()
+            peak_lines = ax.vlines(vpeaks, 0, 1, colors="r")
+            peak_info.reset()
+    print(a[:,0], vpeaks)
+
+    # separate peaks
+    indices = np.arange(0, a[:,0].size)
+    peak_datas = []
+    for i in range(len(vpeaks) - 1):
+        # TODO: user <= or <
+        peak_datas.append(vdata[(indices >= vpeaks[i]) & (indices < vpeaks[i+1])])
+        plt.plot(peak_datas[i])
+    print(peak_datas)
+    plt.pause(20)
+
+
+

k-teng/utility/data.py

@@ -1,5 +1,6 @@
 import pandas as pd
 import numpy as np
+from os import path
 
 def buffer2dataframe(buffer):
     df = pd.DataFrame(buffer)
@@ -15,3 +16,17 @@ def buffers2dataframe(ibuffer, vbuffer):
     df = pd.DataFrame(np.vstack((ibuffer[:,0], ibuffer[:,1], vbuffer[:,1])).T)
     df.columns = ["Time [s]", "Current [A]", "Voltage [V]"]
     return df
+
+def load_dataframe(p:str):
+    """
+    Load a dataframe from file.
+    @param p : path of the file. If it has 'csv' extension, pandas.read_csv is used, pandas.read_pickle otherwise
+    """
+    if not path.isfile(p):
+        print(f"ERROR: load_dataframe: File does not exist: {p}")
+        return None
+    if p.endswith(".csv"):
+        df = pd.read_csv(p)
+    else:
+        df = pd.read_pickle(p)
+    return df