merge with backup

.gitignore

@@ -0,0 +1,4 @@
+dist/*
+*.egg-info
+__pycache__
+.ipynb_checkpoints

portiloop/capture.py

@@ -0,0 +1,487 @@
+from time import sleep
+import time
+from playsound import playsound
+import numpy as np
+import matplotlib.pyplot as plt
+import os
+from pathlib import Path
+from datetime import datetime, timedelta
+import multiprocessing as mp
+from queue import Empty
+import warnings
+import shutil
+from pyedflib import highlevel
+from datetime import datetime
+
+import matplotlib.pyplot as plt
+
+from portilooplot.jupyter_plot import ProgressPlot
+from portiloop.hardware.frontend import Frontend
+from portiloop.hardware.leds import LEDs, Color
+
+from IPython.display import clear_output, display
+import ipywidgets as widgets
+
+
+DEFAULT_FRONTEND_CONFIG = [
+    # nomenclature: name [default setting] [bits 7-0] : description
+    # Read only ID:
+    0x3E, # ID [xx] [REV_ID[2:0], 1, DEV_ID[1:0], NU_CH[1:0]] : (RO)
+    # Global Settings Across Channels:
+    0x96, # CONFIG1 [96] [1, DAISY_EN(bar), CLK_EN, 1, 0, DR[2:0]] : Datarate = 250 SPS
+    0xC0, # CONFIG2 [C0] [1, 1, 0, INT_CAL, 0, CAL_AMP0, CAL_FREQ[1:0]] : No tests
+    0x60, # CONFIG3 [60] [PD_REFBUF(bar), 1, 1, BIAS_MEAS, BIASREF_INT, PD_BIAS(bar), BIAS_LOFF_SENS, BIAS_STAT] : Power-down reference buffer, no bias
+    0x00, # LOFF [00] [COMP_TH[2:0], 0, ILEAD_OFF[1:0], FLEAD_OFF[1:0]] : No lead-off
+    # Channel-Specific Settings:
+    0x61, # CH1SET [61] [PD1, GAIN1[2:0], SRB2, MUX1[2:0]] : Channel 1 active, 24 gain, no SRB2 & input shorted
+    0x61, # CH2SET [61] [PD2, GAIN2[2:0], SRB2, MUX2[2:0]] : Channel 2 active, 24 gain, no SRB2 & input shorted
+    0x61, # CH3SET [61] [PD3, GAIN3[2:0], SRB2, MUX3[2:0]] : Channel 3 active, 24 gain, no SRB2 & input shorted
+    0x61, # CH4SET [61] [PD4, GAIN4[2:0], SRB2, MUX4[2:0]] : Channel 4 active, 24 gain, no SRB2 & input shorted
+    0x61, # CH5SET [61] [PD5, GAIN5[2:0], SRB2, MUX5[2:0]] : Channel 5 active, 24 gain, no SRB2 & input shorted
+    0x61, # CH6SET [61] [PD6, GAIN6[2:0], SRB2, MUX6[2:0]] : Channel 6 active, 24 gain, no SRB2 & input shorted
+    0x61, # CH7SET [61] [PD7, GAIN7[2:0], SRB2, MUX7[2:0]] : Channel 7 active, 24 gain, no SRB2 & input shorted
+    0x61, # CH8SET [61] [PD8, GAIN8[2:0], SRB2, MUX8[2:0]] : Channel 8 active, 24 gain, no SRB2 & input shorted
+    0x00, # BIAS_SENSP [00] [BIASP8, BIASP7, BIASP6, BIASP5, BIASP4, BIASP3, BIASP2, BIASP1] : No bias
+    0x00, # BIAS_SENSN [00] [BIASN8, BIASN7, BIASN6, BIASN5, BIASN4, BIASN3, BIASN2, BIASN1] No bias
+    0x00, # LOFF_SENSP [00] [LOFFP8, LOFFP7, LOFFP6, LOFFP5, LOFFP4, LOFFP3, LOFFP2, LOFFP1] : No lead-off
+    0x00, # LOFF_SENSN [00] [LOFFM8, LOFFM7, LOFFM6, LOFFM5, LOFFM4, LOFFM3, LOFFM2, LOFFM1] : No lead-off
+    0x00, # LOFF_FLIP [00] [LOFF_FLIP8, LOFF_FLIP7, LOFF_FLIP6, LOFF_FLIP5, LOFF_FLIP4, LOFF_FLIP3, LOFF_FLIP2, LOFF_FLIP1] : No lead-off flip
+    # Lead-Off Status Registers (Read-Only Registers):
+    0x00, # LOFF_STATP [00] [IN8P_OFF, IN7P_OFF, IN6P_OFF, IN5P_OFF, IN4P_OFF, IN3P_OFF, IN2P_OFF, IN1P_OFF] : Lead-off positive status (RO)
+    0x00, # LOFF_STATN [00] [IN8M_OFF, IN7M_OFF, IN6M_OFF, IN5M_OFF, IN4M_OFF, IN3M_OFF, IN2M_OFF, IN1M_OFF] : Laed-off negative status (RO)
+    # GPIO and OTHER Registers:
+    0x0F, # GPIO [0F] [GPIOD[4:1], GPIOC[4:1]] : All GPIOs as inputs
+    0x00, # MISC1 [00] [0, 0, SRB1, 0, 0, 0, 0, 0] : Disable SRBM
+    0x00, # MISC2 [00] [00] : Unused
+    0x00, # CONFIG4 [00] [0, 0, 0, 0, SINGLE_SHOT, 0, PD_LOFF_COMP(bar), 0] : Single-shot, lead-off comparator disabled
+]
+
+
+FRONTEND_CONFIG = [
+    0x3E, # ID (RO)
+    0x95, # CONFIG1 [95] [1, DAISY_EN(bar), CLK_EN, 1, 0, DR[2:0]] : Datarate = 500 SPS
+    0xD0, # CONFIG2 [C0] [1, 1, 0, INT_CAL, 0, CAL_AMP0, CAL_FREQ[1:0]]
+    0xE0, # CONFIG3 [E0] [PD_REFBUF(bar), 1, 1, BIAS_MEAS, BIASREF_INT, PD_BIAS(bar), BIAS_LOFF_SENS, BIAS_STAT] : Power-down reference buffer, no bias
+    0x00, # No lead-off
+    0x03, # CH1SET [60] [PD1, GAIN1[2:0], SRB2, MUX1[2:0]]
+    0x00, # CH2SET
+    0x00, # CH3SET
+    0x00, # CH4SET
+    0x00, # CH5SET voltage
+    0x00, # CH6SET voltage
+    0x00, # CH7SET test
+    0x04, # CH8SET temperature
+    0x00, # BIAS_SENSP
+    0x00, # BIAS_SENSN
+    0xFF, # LOFF_SENSP Lead-off on all positive pins?
+    0xFF, # LOFF_SENSN Lead-off on all negative pins?
+    0x00, # Normal lead-off
+    0x00, # Lead-off positive status (RO)
+    0x00, # Lead-off negative status (RO)
+    0x00, # All GPIOs as output ?
+    0x20, # Enable SRB1
+]
+
+def mod_config(config, datarate):
+    possible_datarates = [(250, 0x06),
+                          (500, 0x05),
+                          (1000, 0x04),
+                          (2000, 0x03),
+                          (4000, 0x02),
+                          (8000, 0x01),
+                          (16000, 0x00)]
+    mod_dr = 0x00
+    for i, j in possible_datarates:
+        if i >= datarate:
+            mod_dr = j
+            break
+    
+    new_cf1 = config[1] & 0xF8
+    new_cf1 = new_cf1 | j
+    config[1] = new_cf1
+    print(f"DEBUG: new cf1: {hex(config[1])}")
+    return config
+
+def filter_24(value):
+    return (value * 4.5) / (2**23 - 1)  # 23 because 1 bit is lost for sign
+
+def filter_2scomplement_np(value):
+    v = np.where((value & (1 << 23)) != 0, value - (1 << 24), value)
+    return filter_24(v)
+
+class LiveDisplay():
+    def __init__(self, datapoint_dim=8, window_len=100):
+        self.datapoint_dim = datapoint_dim
+        self.queue = mp.Queue()
+        channel_names = [f"channel#{i+1}" for i in range(datapoint_dim)]
+        channel_names[0] = "voltage"
+        channel_names[7] = "temperature"
+        self.pp = ProgressPlot(plot_names=channel_names, max_window_len=window_len)
+
+    def add_datapoints(self, datapoints):
+        """
+        Adds 8 lists of datapoints to the plot
+        
+        Args:
+            datapoints: list of 8 lists of floats (or list of 8 floats)
+        """
+        disp_list = []
+        for datapoint in datapoints:
+            d = [[elt] for elt in datapoint]
+            disp_list.append(d)
+        self.pp.update_with_datapoints(disp_list)
+    
+    def add_datapoint(self, datapoint):
+        disp_list = [[elt] for elt in datapoint]
+        self.pp.update(disp_list)
+
+
+def _capture_process(q_data, q_out, q_in, duration, frequency, python_clock=True):
+    """
+    Args:
+        q_data: multiprocessing.Queue: captured datapoints are put in the queue
+        q_out: mutliprocessing.Queue: to pass messages to the parent process
+            'STOP': end of the the process
+        q_in: mutliprocessing.Queue: to pass messages from the parent process
+            'STOP': stops the process
+    """
+    if duration <= 0:
+        duration = np.inf
+    
+    sample_time = 1 / frequency
+
+    frontend = Frontend()
+    leds = LEDs()
+    leds.led2(Color.PURPLE)
+    leds.aquisition(True)
+    
+    try:
+        data = frontend.read_regs(0x00, 1)
+        assert data == [0x3E], "The communication with the ADS cannot be established."
+        leds.led2(Color.BLUE)
+        
+        config = FRONTEND_CONFIG
+        if python_clock:  # set ADS to 2 * frequency
+            config = mod_config(config, 2 * frequency)
+        else:  # set ADS to frequency
+            config = mod_config(config, frequency)
+        
+        frontend.write_regs(0x00, config)
+        data = frontend.read_regs(0x00, len(config))
+        assert data == config, f"Wrong config: {data} vs {config}"
+        frontend.start()
+        leds.led2(Color.PURPLE)
+        while not frontend.is_ready():
+            pass
+
+        # Set up of leds
+        leds.aquisition(True)
+        sleep(0.5)
+        leds.aquisition(False)
+        sleep(0.5)
+        leds.aquisition(True)
+
+        c = True
+
+        it = 0
+        t_start = time.time()
+        t_max = t_start + duration
+        t = t_start
+        
+        # first sample:
+        reading = frontend.read()
+        datapoint = reading.channels()
+        q_data.put(datapoint)
+        
+        t_next = t + sample_time
+        
+        # sampling loop:
+        while c and t < t_max:
+            t = time.time()
+            if python_clock:
+                if t <= t_next:
+                    time.sleep(t_next - t)
+                t_next += sample_time
+                reading = frontend.read()
+            else:
+                reading = frontend.wait_new_data()
+            datapoint = reading.channels()
+            q_data.put(datapoint)
+            
+
+            # Check for messages  # this takes too long :/
+#             try:
+#                 message = q_in.get_nowait()
+#                 if message == 'STOP':
+#                     c = False
+#             except Empty:
+#                 pass
+            it += 1
+        t = time.time()
+        tot = (t - t_start) / it        
+
+        print(f"Average frequency: {1 / tot} Hz for {it} samples")
+
+        leds.aquisition(False)
+
+    finally:
+        frontend.close()
+        leds.close()
+        q_in.close()
+        q_out.put('STOP')
+
+        
+class Capture:
+    def __init__(self):
+        
+        self.filename = Path.home() / 'edf_recording' / f"recording_{now.strftime('%m_%d_%Y_%H_%M_%S')}.edf"
+        self._p_capture = None
+        self.__capture_on = False
+        self.frequency = 250
+        self.duration = 10
+        self.record = False
+        self.display = False
+        self.recording_file = None
+        self.python_clock = True
+        
+        self.binfile = None
+        self.temp_path = Path.home() / '.temp'
+        
+        # widgets
+        
+        self.b_capture = widgets.ToggleButtons(
+            options=['Stop', 'Start'],
+            description='Capture:',
+            disabled=False,
+            button_style='', # 'success', 'info', 'warning', 'danger' or ''
+            tooltips=['Stop capture', 'Start capture'],
+            # icons=['check'] * 2
+        )
+        
+        self.b_clock = widgets.ToggleButtons(
+            options=['Coral', 'ADS'],
+            description='Clock:',
+            disabled=False,
+            button_style='', # 'success', 'info', 'warning', 'danger' or ''
+            tooltips=['Use Coral clock (very precise, not very timely)',
+                      'Use ADS clock (not very precise, very timely)'],
+            # icons=['check'] * 2
+        )
+        
+        self.b_filename = widgets.Text(
+            value=self.filename,
+            description='Filename:',
+            placeholder='All files will be in the edf_recording folder'
+            disabled=False
+        )
+        
+        self.b_frequency = widgets.IntText(
+            value=250,
+            description='Freq (Hz):',
+            disabled=False
+        )
+        
+        self.b_duration = widgets.IntText(
+            value=10,
+            description='Time (s):',
+            disabled=False
+        )
+        
+        self.b_record = widgets.Checkbox(
+            value=False,
+            description='Record',
+            disabled=False,
+            indent=False
+        )
+        
+        self.b_display = widgets.Checkbox(
+            value=False,
+            description='Display',
+            disabled=False,
+            indent=False
+        )
+        
+        self.b_capture.observe(self.on_b_capture, 'value')
+        self.b_clock.observe(self.on_b_clock, 'value')
+        self.b_frequency.observe(self.on_b_frequency, 'value')
+        self.b_duration.observe(self.on_b_duration, 'value')
+        self.b_record.observe(self.on_b_record, 'value')
+        self.b_display.observe(self.on_b_display, 'value')
+        self.b_filename.observe(self.on_b_filename, 'value')
+        
+        self.display_buttons()
+
+    def __del__(self):
+        self.b_capture.close()
+    
+    def display_buttons(self):
+        display(widgets.VBox([self.b_frequency,
+                              self.b_duration,
+                              widgets.HBox([self.b_record, self.b_display]),
+                              self.b_clock,
+                              self.b_capture]))
+    
+    def on_b_capture(self, value):
+        val = value['new']
+        if val == 'Start':
+            self.start_capture(
+                record=self.record,
+                viz=self.display,
+                width=500,
+                python_clock=self.python_clock)
+        elif val == 'Stop':
+            clear_output()
+            self.display_buttons()
+        else:
+            print(f"This option is not supported: {val}.")
+    
+    def on_b_clock(self, value):
+        val = value['new']
+        if val == 'Coral':
+            self.python_clock = True
+        elif val == 'ADS':
+            self.python_clock = False
+        else:
+            print(f"This option is not supported: {val}.")
+    
+    def on_b_frequency(self, value):
+        val = value['new']
+        if val > 0:
+            self.frequency = val
+        else:
+            print(f"Unsupported frequency: {val} Hz")
+            
+    def on_b_filename(self, value):
+        val = value['new']
+        if val != '':
+            self.filename = Path.home() / 'edf_recording' / val
+        else:
+            now = datetime.now()
+            self.filename = Path.home() / 'edf_recording' / f"recording_{now.strftime('%m_%d_%Y_%H_%M_%S')}.edf"
+        
+    def on_b_duration(self, value):
+        val = value['new']
+        if val > 0:
+            self.duration = val
+        else:
+            print(f"Unsupported duration: {val} s")
+    
+    def on_b_record(self, value):
+        val = value['new']
+        self.record = val
+    
+    def on_b_display(self, value):
+        val = value['new']
+        self.display = val
+    
+    def open_recording_file(self):
+        print(f"Will store edf recording in {self.filename}")
+        os.mkdir(self.temp_path)
+        self.binfile = open(self.temp_path / 'data.bin', 'wb')
+    
+    def close_recording_file(self):
+        
+        print('Saving recording data...')
+        # Channel names
+        channels = ['Voltage', 'Ch2', 'Ch3', 'Ch4', 'Ch5', 'Ch6', 'Ch7', 'Temperature']
+        
+        # Read binary data
+        data = np.fromfile(self.temp_path / 'data.bin', dtype=float)
+        data = data.reshape((8, int(data.shape[0]/8)))
+        
+        # Declare and write EDF format file
+        signal_headers = highlevel.make_signal_headers(channels, sample_frequency=self.frequency)
+        header = highlevel.make_header(patientname='patient_x', gender='Female')
+        highlevel.write_edf(self.filename, data, signal_headers, header)
+        
+        # Close and delete temp binary file
+        self.binfile.close()        
+        shutil.rmtree(self.temp_path)
+        
+        print('...done')
+    
+    def add_recording_data(self, data):
+        np.array(data).tofile(self.binfile)
+
+    def start_capture(self,
+                      record=True,
+                      viz=False,
+                      width=500,
+                      python_clock=True):
+        self.q_messages_send = mp.Queue()
+        self.q_messages_recv = mp.Queue()
+        self.q_data = mp.Queue()
+
+        if self.__capture_on:
+            print("Capture is already ongoing, ignoring command.")
+            return
+        else:
+            self.__capture_on = True
+        SAMPLE_TIME = 1 / frequency
+        self._p_capture = mp.Process(target=_capture_process, args=(self.q_data,
+                                                                    self.q_messages_recv,
+                                                                    self.q_messages_send,
+                                                                    self.duration,
+                                                                    self.frequency,
+                                                                    python_clock))
+        self._p_capture.start()
+        
+        if viz:
+            live_disp = LiveDisplay(window_len=width)
+        
+        if record:
+            self.open_recording_file()
+
+        cc = True
+        while cc:
+            try:
+                mess = self.q_messages_recv.get_nowait()
+                if mess == 'STOP':
+                    cc = False
+            except Empty:
+                pass
+
+            # retrieve all data points from q_data and put them in a list of np.array:
+            res = []
+            c = True
+            while c and len(res) < 25:
+                try:
+                    point = self.q_data.get(timeout=SAMPLE_TIME)
+                    res.append(point)
+                except Empty:
+                    c = False
+            if len(res) == 0:
+                continue
+            n_array = np.array(res)
+            n_array = filter_2scomplement_np(n_array)
+            
+            to_add = n_array.tolist()
+            
+            if viz:
+                live_disp.add_datapoints(to_add)
+            if record:
+                self.add_recording_data(to_add)
+        
+        # empty q_data
+        cc = True 
+        while cc:
+            try:
+                _ = self.q_data.get_nowait()
+            except Empty:
+                cc = False
+
+        self.q_messages_recv.close()
+        self.q_data.close()
+        
+        if record:
+            self.close_recording_file()
+
+        # print("DEBUG: joining capture process...")
+        self._p_capture.join()
+        # print("DEBUG: capture process joined.")
+        self.__capture_on = False
+
+
+if __name__ == "__main__":
+    # TODO: Argparse this
+    pass

{src → portiloop}/notebooks/test_capture.ipynb

@@ -1,20 +1,60 @@
 {
  "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 11,
+   "id": "199cbac1",
+   "metadata": {},
+   "outputs": [
+    {
+     "data": {
+      "application/vnd.jupyter.widget-view+json": {
+       "model_id": "69ac3694fc054d05af462214263ed101",
+       "version_major": 2,
+       "version_minor": 0
+      },
+      "text/plain": [
+       "ToggleButtons(description='Recording:', options=('Stop', 'Start'), tooltips=('Stop capture', 'Start capture'),…"
+      ]
+     },
+     "metadata": {},
+     "output_type": "display_data"
+    }
+   ],
+   "source": [
+    "import ipywidgets as widgets\n",
+    "\n",
+    "widgets.ToggleButtons(\n",
+    "    options=['Stop', 'Start'],\n",
+    "    description='Recording:',\n",
+    "    disabled=False,\n",
+    "    button_style='', # 'success', 'info', 'warning', 'danger' or ''\n",
+    "    tooltips=['Stop capture', 'Start capture'],\n",
+    "    # icons=['check'] * 2\n",
+    ")"
+   ]
+  },
   {
    "cell_type": "code",
    "execution_count": 1,
    "id": "22d798fb",
    "metadata": {},
+   "outputs": [],
+   "source": [
+    "from portilooplot.jupyter_plot import ProgressPlot\n",
+    "import random\n",
+    "import pyinstrument\n",
+    "import tracemalloc"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "b3634f53",
+   "metadata": {
+    "scrolled": false
+   },
    "outputs": [
-    {
-     "name": "stdout",
-     "output_type": "stream",
-     "text": [
-      "Configuring EEG Frontend\n",
-      "EEG Frontend configured\n",
-      "Ready for data\n"
-     ]
-    },
     {
      "data": {
       "text/html": [
@@ -9863,7 +9903,7 @@
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        "  };\n",
        "})();\n",
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+       "</script><svg id=\"b324761b-9bc3-4572-8eeb-ad443c1263e9\" class=\"learning-curve\"></svg><script>  window.setupLearningCurve({\"id\": \"b324761b-9bc3-4572-8eeb-ad443c1263e9\", \"width\": 600, \"height\": 1690, \"lineConfig\": {\"line-1\": {\"name\": \"line-1\", \"color\": \"#1f77b4\"}}, \"facetConfig\": {\"1\": {\"name\": \"1\", \"limit\": [null, null]}, \"2\": {\"name\": \"2\", \"limit\": [null, null]}, \"3\": {\"name\": \"3\", \"limit\": [null, null]}, \"4\": {\"name\": \"4\", \"limit\": [null, null]}, \"5\": {\"name\": \"5\", \"limit\": [null, null]}, \"6\": {\"name\": \"6\", \"limit\": [null, null]}, \"7\": {\"name\": \"7\", \"limit\": [null, null]}, \"8\": {\"name\": \"8\", \"limit\": [null, null]}}, \"xAxisConfig\": {\"name\": \"iteration\", \"limit\": [null, null]}, \"max_window_len\": 100});</script>"
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0.12407743368207114}, \"7\": {\"line-1\": 0.12407743368207114}, \"8\": {\"line-1\": 0.12407743368207114}}}]);"
       ],
       "text/plain": [
-       "<IPython.core.display.HTML object>"
+       "<IPython.core.display.Javascript object>"
       ]
      },
      "metadata": {},
@@ -9888,14 +9928,63 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "Saving Method is not yet implemented\n"
+      "FINISH\n",
+      "Top 10\n",
+      "/home/mendel/.local/lib/python3.7/site-packages/portilooplot/plot_learning_curve.py:186: size=32.0 MiB, count=287463, average=117 B\n",
+      "/home/mendel/.local/lib/python3.7/site-packages/portilooplot/plot_learning_curve.py:188: size=10.1 MiB, count=58586, average=180 B\n",
+      "/home/mendel/.local/lib/python3.7/site-packages/portilooplot/plot_learning_curve.py:185: size=4455 KiB, count=37997, average=120 B\n",
+      "/tmp/ipykernel_5820/4036902884.py:18: size=464 KiB, count=19605, average=24 B\n",
+      "/home/mendel/.local/lib/python3.7/site-packages/portilooplot/plot_learning_curve.py:184: size=464 KiB, count=19778, average=24 B\n",
+      "/home/mendel/.local/lib/python3.7/site-packages/portilooplot/plot_learning_curve.py:191: size=174 KiB, count=1, average=174 KiB\n",
+      "/home/mendel/.local/lib/python3.7/site-packages/IPython/core/display.py:350: size=163 KiB, count=1395, average=120 B\n",
+      "/home/mendel/.local/lib/python3.7/site-packages/IPython/core/display.py:400: size=162 KiB, count=1378, average=120 B\n",
+      "/usr/lib/python3.7/inspect.py:2882: size=131 KiB, count=800, average=168 B\n",
+      "/home/mendel/.local/lib/python3.7/site-packages/decorator.py:203: size=122 KiB, count=1201, average=104 B\n"
      ]
     }
    ],
    "source": [
-    "from capture import Capture\n",
+    "tracemalloc.start()\n",
+    "\n",
+    "channel_names = [\"1\", \"2\", \"3\", \"4\", \"5\", \"6\", \"7\", \"8\"]\n",
+    "window_len = 100\n",
+    "pp=ProgressPlot(plot_names=channel_names, max_window_len=window_len)\n",
+    "\n",
+    "# from pyinstrument import Profiler\n",
+    "# from pyinstrument.renderers import ConsoleRenderer\n",
     "\n",
-    "cap = Capture()"
+    "# pro = Profiler()\n",
+    "\n",
+    "# pro.start()\n",
+    "\n",
+    "for i in range(500):\n",
+    "    l = []\n",
+    "    nb_pts = 500 # random.randint(0, 5)\n",
+    "    for _ in range(nb_pts):\n",
+    "        l.append([[random.random()]] * 8)\n",
+    "    if i == 400:\n",
+    "            snapshot = tracemalloc.take_snapshot()\n",
+    "            top_stats= snapshot.statistics('lineno')\n",
+    "    pp.update_with_datapoints(l)\n",
+    "    \n",
+    "print(\"FINISH\")\n",
+    "\n",
+    "print(\"Top 10\")\n",
+    "for stat in top_stats[:10]:\n",
+    "    print(stat)\n",
+    "\n",
+    "# session = pro.stop()\n",
+    "\n",
+    "# cr = ConsoleRenderer(unicode=True, color=True, show_all=True)\n",
+    "# print(cr.render(session))"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2f712706",
+   "metadata": {},
+   "source": [
+    "# "
    ]
   }
  ],

portiloop/notebooks/tests.ipynb

@@ -0,0 +1,60 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "7b2fc5da",
+   "metadata": {
+    "scrolled": false
+   },
+   "outputs": [
+    {
+     "ename": "ModuleNotFoundError",
+     "evalue": "No module named 'pyedflib'",
+     "output_type": "error",
+     "traceback": [
+      "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m                       Traceback (most recent call last)",
+      "\u001b[0;32m/tmp/ipykernel_3997/3113449869.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[0;32m----> 1\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mportiloop\u001b[0m\u001b[0;34m.\u001b[0m\u001b[0mcapture\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mCapture\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m      2\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m      3\u001b[0m \u001b[0mcap\u001b[0m \u001b[0;34m=\u001b[0m \u001b[0mCapture\u001b[0m\u001b[0;34m(\u001b[0m\u001b[0;34m)\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;32m~/capture_stream/portiloop-prog/portiloop/capture.py\u001b[0m in \u001b[0;36m<module>\u001b[0;34m\u001b[0m\n\u001b[1;32m     11\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mwarnings\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     12\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mshutil\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0;32m---> 13\u001b[0;31m \u001b[0;32mfrom\u001b[0m \u001b[0mpyedflib\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mhighlevel\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[0m\u001b[1;32m     14\u001b[0m \u001b[0;32mfrom\u001b[0m \u001b[0mdatetime\u001b[0m \u001b[0;32mimport\u001b[0m \u001b[0mdatetime\u001b[0m\u001b[0;34m\u001b[0m\u001b[0;34m\u001b[0m\u001b[0m\n\u001b[1;32m     15\u001b[0m \u001b[0;34m\u001b[0m\u001b[0m\n",
+      "\u001b[0;31mModuleNotFoundError\u001b[0m: No module named 'pyedflib'"
+     ]
+    }
+   ],
+   "source": [
+    "from portiloop.capture import Capture\n",
+    "\n",
+    "cap = Capture()"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "475b8dde",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.7.3"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

pyproject.toml

@@ -1,3 +0,0 @@
-[build-system]
-requires = ["setuptools"]
-build-backend = "setuptools.build_meta"

setup.cfg

@@ -1,16 +0,0 @@
-[metadata]
-name=portiloop
-version=0.0.1
-description="Library for portiloop"
-
-[options]
-package_dir=
-	=src
-packages=find:
-install_requires=
-	matplotlib
-	numpy
-	portilooplot
-
-[options.packages.find]
-where=src

setup.py

@@ -3,9 +3,10 @@ from setuptools import setup, find_packages
 setup(
     name='portiloop',
     version='0.0.1',
-    packages=[package for package in find_packages(where='src')],
+    packages=[package for package in find_packages()],
     description='Library for portiloop',
     install_requires=['numpy',
                      'matplotlib',
-                     'portilooplot']
+                     'portilooplot',
+                     'ipywidgets']
 )

src/capture.py

@@ -1,363 +0,0 @@
-from abc import abstractmethod
-import threading
-import time
-import logging
-import random
-from queue import Queue
-
-from hardware.frontend import Frontend
-from hardware.leds import LEDs, Color
-from portilooplot.jupyter_plot import ProgressPlot
-
-import ctypes
-import numpy as np
-import json
-
-FRONTEND_CONFIG =  [
-    0x3E, # ID (RO)
-    0x95, # CONFIG1 [95] [1, DAISY_EN(bar), CLK_EN, 1, 0, DR[2:0]] : Datarate = 500 SPS
-    0xD0, # CONFIG2 [C0] [1, 1, 0, INT_CAL, 0, CAL_AMP0, CAL_FREQ[1:0]]
-    0xE0, # CONFIG3 [E0] [PD_REFBUF(bar), 1, 1, BIAS_MEAS, BIASREF_INT, PD_BIAS(bar), BIAS_LOFF_SENS, BIAS_STAT] : Power-down reference buffer, no bias
-    0x00, # No lead-off
-    0x03, # CH1SET [60] [PD1, GAIN1[2:0], SRB2, MUX1[2:0]] test signal
-    0x00, # CH2SET
-    0x00, # CH3SET
-    0x00, # CH4SET voltage DVDD / 4
-    0x03, # CH5SET voltage 0.5 × (AVDD + AVSS)
-    0x03, # CH6SET
-    0x05, # CH7SET test
-    0x04, # CH8SET temperature
-    0x00, # BIAS_SENSP
-    0x00, # BIAS_SENSN
-    0xFF, # LOFF_SENSP Lead-off on all positive pins?
-    0xFF, # LOFF_SENSN Lead-off on all negative pins?
-    0x00, # Normal lead-off
-    0x00, # Lead-off positive status (RO)
-    0x00, # Lead-off negative status (RO)
-    0x00, # All GPIOs as output ?
-    0x20, # Enable SRB1
-]
-
-class Datapoint:
-    '''
-    Class to represent a single reading
-    '''
-    def __init__(self, raw_datapoint, temperature=[], num_channels=8):
-        # Initialize necessary data structures
-        self.num_channels = num_channels
-        self.reading = np.empty(num_channels, dtype=float)
-
-        assert len(temperature) <= len(raw_datapoint), "Temperature array length must be lesser or equal to number of channels"
-        self.temperature = temperature
-
-        self._filter_datapoint(raw_datapoint, Datapoint.filter_2scomplement)
-
-    def _filter_datapoint(self, raw_datapoint, filter):
-        # Filter one datapoint with the given filter
-        assert len(raw_datapoint) == self.num_channels, "Datapoint dimensions do not match channel number"
-        for idx, point in enumerate(raw_datapoint):
-            # If the given index is a temperature, add that filter to get correct reading
-            if idx in self.temperature:
-                filter = lambda x : Datapoint.filter_temp(filter(x))
-            self.reading[idx] = filter(point)
-
-    def get_datapoint(self):
-        '''
-        Get readings of all channels in numpy array format
-        '''
-        return self.reading
-
-    def get_channel(self, channel_idx):
-        '''
-        Reading at the channel specified by channel_idx (0-7)
-        Returns a tuple (value(float), temperature(boolean)) --> temperature is True if channel is a temperature
-        '''
-        assert 0 <= channel_idx < self.num_channels - 1, "Channel index must be in range [0 - channel_num-1]"
-        return self.reading[channel_idx], (channel_idx in self.temperature)
-
-    def get_portilooplot(self):
-        '''
-        Returns the portilooplot ready version of the Datapoint
-        '''
-        return [[point] for point in self.reading]
-
-    @staticmethod
-    def filter_2scomplement(value):
-        '''
-        Convert from binary two's complement to binary int
-        '''
-        if (value & (1 << 23)) != 0:
-            value = value - (1 << 24)
-        return Datapoint.filter_23(value)
-
-    @staticmethod
-    def filter_23(value):
-        '''
-        Convert from binary int to normal int
-        '''
-        return (value * 4.5) / (2**23 - 1)  # 23 because 1 bit is lost for sign
-
-    @staticmethod
-    def filter_temp(value):
-        '''
-        Convert from voltage reading to temperature reading in Celcius
-        '''
-        return int((value * 1000000.0 - 145300.0) / 490.0 + 25.0)
-
-
-class CaptureThread(threading.Thread):
-    '''
-    Producer thread which reads from the EEG device. Thread does not process the data
-    '''
-
-    def __init__(self, q, freq=250, timeout=None, target=None, name=None):
-        super(CaptureThread, self).__init__()
-        self.timeout = timeout
-        self.target = target
-        self.name = name
-        self.q = q
-        self.freq = freq
-        self.frontend = Frontend()
-        self.leds = LEDs()
-
-    def run(self):
-        '''
-        Run the data capture continuously or until timeout
-        '''
-        self.init_checks()
-        start_time = time.time()
-        prev_ts = time.time()
-        ts_len = 1 / self.freq
-        
-        while True:
-            if not self.q.full():
-                # Wait for frontend and for minimum time limit
-                while not self.frontend.is_ready() and not time.time() - prev_ts >= ts_len:
-                    pass
-                prev_ts = time.time()
-                
-                # Read values and add to q
-                values = self.frontend.read()
-                self.q.put(values.channels())
-                
-                # Wait until reading is fully ompleted
-                while self.frontend.is_ready():
-                    pass
-
-            # Check for timeout
-            if self.timeout is not None:
-                if time.time() - start_time > self.timeout:
-                    break
-        return
-
-    def init_checks(self):
-        '''
-        Run Initial threads to the registers to make sure we can start reading
-        '''
-        print("Configuring EEG Frontend")
-        self.frontend.write_regs(0x00, FRONTEND_CONFIG)
-        data = self.frontend.read_regs(0x00, len(FRONTEND_CONFIG))
-        assert data == FRONTEND_CONFIG, f"Wrong config: {data} vs {FRONTEND_CONFIG}"
-        self.frontend.start()
-        print("EEG Frontend configured")
-        self.leds.led2(Color.PURPLE)
-        while not self.frontend.is_ready():
-            pass
-        print("Ready for data")
-
-
-class FilterThread(threading.Thread):
-    def __init__(self, q, target=None, name=None, temperature=[], num_channels=8):
-        '''
-        Consume raw datapoint from the Capture points, filter them, put resulting datapoint objects into all queues in list
-        '''
-        super(FilterThread, self).__init__()
-        self.target = target
-        self.name = name
-
-        # Initialize thread safe datastructures for both consuming and producing
-        self.raw_q = q
-        self.qs = []
-
-        # Initilialize settings for the filtering
-        self.temperature = temperature
-        self.num_channels = num_channels
-
-        return
-
-    def run(self):
-        while True:
-            raw_data = None
-            # Get an item from CaptureThread
-            if not self.raw_q.empty():
-                raw_data = self.raw_q.get()
-#             assert raw_data is not None, "Got a None item from CaptureThread in FilterThread"
-            if raw_data is None:
-                continue
-            datapoint = Datapoint(raw_data, )
-
-            # Put Item to all ConsumerThreads
-            for q in self.qs:
-                if not q.full():
-                    q.put(datapoint)
-        return
-
-    def add_q(self, q):
-        '''
-        Add a Queue to the list of queues where filtered values get added
-        '''
-        self.qs.append(q)
-
-    def remove_q(self, q):
-        '''
-        Remove a queue from the list
-        '''
-        self.qs.remove(q)
-
-    def update_settings(self, temperature=None, num_channels=None):
-        '''
-        Update Settings on the go
-        '''
-        if self.temperatures is not None:
-            self.temperature = temperature
-        if num_channels is not None:
-            self.num_channels = num_channels
-
-
-class ConsumerThread(threading.Thread):
-    def __init__(self, q, target=None, name=None):
-        '''
-        Implemetns basic consumer logic, needs _consume_item() to be implemented 
-        '''
-        super(ConsumerThread,self).__init__()
-        self.target = target
-        self.name = name
-        self.q = q
-
-    def run(self):
-        try:
-            while True:
-                item = None
-                if not self.q.empty():
-                    item = self.q.get()
-
-                assert item is not None, "Got a None value from FilterThread in ConsumerThread"
-                self._consume_item(item)
-        except Exception:
-            self._on_exit()
-
-    def get_id(self):
- 
-        # returns id of the respective thread
-        if hasattr(self, '_thread_id'):
-            return self._thread_id
-        for id, thread in threading._active.items():
-            if thread is self:
-                return id
-  
-    def raise_exception(self):
-        thread_id = self.get_id()
-        res = ctypes.pythonapi.PyThreadState_SetAsyncExc(thread_id,
-              ctypes.py_object(SystemExit))
-        if res > 1:
-            ctypes.pythonapi.PyThreadState_SetAsyncExc(thread_id, 0)
-            print('Exception raise failure')
-
-    @abstractmethod
-    def _consume_item(self, item):
-        raise NotImplementedError("_consume_item needs to be implemented in Subclass of ConsumerThread")
-
-    @abstractmethod
-    def _on_exit(self):
-        raise NotImplementedError("_on_exit needs to be implemented in Subclass of ConsumerThread")
-
-
-class DisplayThread(ConsumerThread):
-    def __init__(self, q, max_window_len=100, num_channel=8, target=None, name=None):
-        super().__init__(q, target, name)
-        self.pp = ProgressPlot(plot_names=[f"channel#{i+1}" for i in range(num_channel)], max_window_len=max_window_len)
-
-    def _consume_item(self, item):
-        self.pp.update(item.get_portilooplot())
-
-    def _on_exit(self):
-        self.pp.finalize()
-
-
-class SaveThread(ConsumerThread):
-    def __init__(self, q, default_loc='', target=None, name=None):
-        super().__init__(q, target, name)
-        self.save = []
-        self.default_loc = default_loc
-
-    def to_disk(self, destination):
-        print('Saving Method is not yet implemented')
-        pass
-
-    def _consume_item(self, item):
-        self.save.append(item.get_datapoint().to_list())
-
-    def _on_exit(self):
-        self.to_disk(self.default_loc)
-
-
-class Capture:
-    def __init__(self, viz=True, record=True):
-        self.viz = viz
-        self.record = record
-
-        # Initialize data structures for capture and filtering
-        raw_q = Queue()
-        self.capture_thread = CaptureThread(raw_q, name='CapThread')
-        self.filter_thread = FilterThread(raw_q, name='FilterThread')
-
-        # Declare data structures for viz and record functionality
-        self.viz_q = None
-        self.record_q = None
-        self.viz_thread = None
-        self.record_thread = None
-
-        self.capture_thread.start()
-        self.filter_thread.start()
-
-        if viz:
-            self.start_viz()
-        
-        if record:
-            self.start_record()
-
-    def start_viz(self):
-        self.viz_q = Queue()
-        self.viz_thread = DisplayThread(self.viz_q, name='VizThread')
-        self.filter_thread.add_q(self.viz_q)
-        self.viz_thread.start()
-
-    def stop_viz(self):
-        self.filter_thread.remove_q(self.viz_q)
-        self.viz_q = None
-        self.viz_thread.raise_exception()
-
-    def start_record(self):
-        self.record_q = Queue()
-        self.record_thread = SaveThread(self.record_q, name='RecThread')
-        self.filter_thread.add_q(self.record_q)
-        self.record_thread.start()
-
-    def stop_record(self):
-        self.filter_thread.remove_q(self.viz_q)
-        self.viz_q = None
-        self.record_thread.raise_exception()
-
-    def save(self, destination=None):
-        if destination is not None:
-            self.record_thread.save(destination)
-        else:
-            self.record_thread.save()
-
-  
-
-
-
-if __name__ == "__main__":
-    # TODO: Argparse this
-    pass