Implemented stimulators for trains of spindles

portiloop/notebooks/tests.ipynb

@@ -2,52 +2,23 @@
  "cells": [
   {
    "cell_type": "code",
-   "execution_count": 1,
+   "execution_count": null,
    "id": "16651843",
    "metadata": {
     "scrolled": false
    },
-   "outputs": [
-    {
-     "data": {
-      "application/vnd.jupyter.widget-view+json": {
-       "model_id": "f46843d136af4c79a73841b997fa3284",
-       "version_major": 2,
-       "version_minor": 0
-      },
-      "text/plain": [
-       "VBox(children=(Accordion(children=(GridBox(children=(Label(value='CH2'), Label(value='CH3'), Label(value='CH4'…"
-      ]
-     },
-     "metadata": {},
-     "output_type": "display_data"
-    },
-    {
-     "name": "stderr",
-     "output_type": "stream",
-     "text": [
-      "Exception in thread Thread-3:\n",
-      "Traceback (most recent call last):\n",
-      "  File \"C:\\Users\\milos\\AppData\\Local\\Programs\\Python\\Python37\\lib\\threading.py\", line 917, in _bootstrap_inner\n",
-      "    self.run()\n",
-      "  File \"C:\\Users\\milos\\AppData\\Local\\Programs\\Python\\Python37\\lib\\threading.py\", line 865, in run\n",
-      "    self._target(*self._args, **self._kwargs)\n",
-      "  File \"c:\\users\\milos\\documents\\github\\portiloop-software\\portiloop\\src\\capture.py\", line 927, in start_capture\n",
-      "    detector = detector_cls(threshold, channel=channel) if detector_cls is not None else None\n",
-      "  File \"c:\\users\\milos\\documents\\github\\portiloop-software\\portiloop\\src\\detection.py\", line 56, in __init__\n",
-      "    self.interpreters.append(edgetpu.make_interpreter(model_path))\n",
-      "NameError: name 'edgetpu' is not defined\n",
-      "\n"
-     ]
-    }
-   ],
+   "outputs": [],
    "source": [
     "from portiloop.src.capture import Capture\n",
     "from portiloop.src.detection import SleepSpindleRealTimeDetector\n",
-    "from portiloop.src.stimulation import SleepSpindleRealTimeStimulator\n",
+    "from portiloop.src.stimulation import (SleepSpindleRealTimeStimulator,\n",
+    "                                       SpindleTrainRealTimeStimulator,\n",
+    "                                       IsolatedSpindleRealTimeStimulator)\n",
     "\n",
     "my_detector_class = SleepSpindleRealTimeDetector  # you may want to implement yours\n",
-    "my_stimulator_class = SleepSpindleRealTimeStimulator  # you may also want to implement yours\n",
+    "my_stimulator_class = SleepSpindleRealTimeStimulator  # all spindles\n",
+    "# my_stimulator_class = SpindleTrainRealTimeStimulator  # uncomment for spindle trains only\n",
+    "# my_stimulator_class = IsolatedSpindleRealTimeStimulator  # uncomment for isolated spindles only\n",
     "\n",
     "cap = Capture(detector_cls=my_detector_class, stimulator_cls=my_stimulator_class)"
    ]
@@ -55,7 +26,7 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "Python 3.7.0b2 ('venv': venv)",
+   "display_name": "Python 3",
    "language": "python",
    "name": "python3"
   },
@@ -69,7 +40,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.7.0b2"
+   "version": "3.7.3"
   },
   "vscode": {
    "interpreter": {

portiloop/src/capture.py

@@ -1013,8 +1013,11 @@ class Capture:
                 with self._lock_msg_out:
                     if self._msg_out == "STOP":
                         break
-
-                index, raw_point, off_filtered_point, past_stimulation, lacourse_stimulation = file_reader.get_point()
+                
+                file_point = file_reader.get_point()
+                if file_point is None:
+                    break
+                index, raw_point, off_filtered_point, past_stimulation, lacourse_stimulation = file_point
                 n_array_raw = np.array([0, raw_point, 0, 0, 0, 0, 0, 0])
                 n_array_raw = np.reshape(n_array_raw, (1, 8))
             

portiloop/src/detection.py

@@ -14,14 +14,12 @@ import numpy as np
 
 class Detector(ABC):
     
-    def __init__(self, threshold=None):
+    def __init__(self, threshold=None, channel=None):
         """
-        If implementing __init__() in your subclass, it must take threshold as a keyword argument.
-        This is the value of the threshold that the user can set in the Portiloop GUI.
-        Caution: even if you don't need this manual threshold in your application,
-        your implementation of __init__() still needs to have this keyword argument.
+        Mandatory arguments are from the in the Portiloop GUI.
         """
         self.threshold = threshold
+        self.channel = channel
 
     @abstractmethod
     def detect(self, datapoints):
@@ -47,10 +45,16 @@ DEFAULT_MODEL_PATH = str(Path(__file__).parent.parent / "models/portiloop_model_
 # print(DEFAULT_MODEL_PATH)
 
 class SleepSpindleRealTimeDetector(Detector):
-    def __init__(self, threshold=0.5, num_models_parallel=8, window_size=54, seq_stride=42, model_path=None, verbose=False, channel=2):
+    def __init__(self,
+                 threshold=0.5,
+                 num_models_parallel=8,
+                 window_size=54,
+                 seq_stride=42,
+                 model_path=None,
+                 verbose=False,
+                 channel=2):
         model_path = DEFAULT_MODEL_PATH if model_path is None else model_path
         self.verbose = verbose
-        self.channel = channel
         self.num_models_parallel = num_models_parallel
         
         self.interpreters = []
@@ -78,12 +82,15 @@ class SleepSpindleRealTimeDetector(Detector):
             
         self.current_stride_counter = self.stride_counters[0] - 1
         
-        super().__init__(threshold)
+        super().__init__(threshold, channel)
 
     def detect(self, datapoints):
         """
         Takes datapoints as input and outputs a detection signal.
         datapoints is a list of lists of n channels: may contain several datapoints.
+        
+        The output signal is a list of tuples (is_spindle, is_train_of_spindles).
+        
         """
         res = []
         for inp in datapoints:

portiloop/src/stimulation.py

@@ -17,8 +17,6 @@ from scipy.signal import find_peaks
 import numpy as np
 import matplotlib.pyplot as plt
 
-import alsaaudio
-import pylsl
 
 
 # Abstract interface for developers:
@@ -153,6 +151,55 @@ class SleepSpindleRealTimeStimulator(Stimulator):
         self.delayer = delayer
         self.delayer.stimulate = lambda: self.send_stimulation("DELAY_STIM", True)
 
+
+class SpindleTrainRealTimeStimulator(SleepSpindleRealTimeStimulator):
+    def __init__(self):
+        self.max_spindle_train_t = 6.0
+        super().__init__()
+        
+    def stimulate(self, detection_signal):
+        for sig in detection_signal:
+            # We detect a stimulation
+            if sig:
+                # Record time of stimulation
+                ts = time.time()
+                
+                # Check if time since last stimulation is long enough
+                elapsed = ts - self.last_detected_ts
+                if self.wait_t < elapsed < self.max_spindle_train_t:
+                    if self.delayer is not None:
+                        # If we have a delayer, notify it
+                        self.delayer.detected()
+                        # Send the LSL marer for the fast stimulation 
+                        self.send_stimulation("FAST_STIM", False)
+                    else:
+                        self.send_stimulation("STIM", True)
+
+                self.last_detected_ts = ts
+
+
+class IsolatedSpindleRealTimeStimulator(SpindleTrainRealTimeStimulator):
+    def stimulate(self, detection_signal):
+        for sig in detection_signal:
+            # We detect a stimulation
+            if sig:
+                # Record time of stimulation
+                ts = time.time()
+                
+                # Check if time since last stimulation is long enough
+                elapsed = ts - self.last_detected_ts
+                if self.max_spindle_train_t < elapsed:
+                    if self.delayer is not None:
+                        # If we have a delayer, notify it
+                        self.delayer.detected()
+                        # Send the LSL marer for the fast stimulation 
+                        self.send_stimulation("FAST_STIM", False)
+                    else:
+                        self.send_stimulation("STIM", True)
+
+                self.last_detected_ts = ts
+
+
 # Class that delays stimulation to always stimulate peak or through
 class UpStateDelayer:
     def __init__(self, sample_freq, peak, time_to_buffer, stimulate=None): 

portiloop/src/utils.py

@@ -118,9 +118,12 @@ class FileReader:
         """
         Returns the next point in the file
         """
-        point = next(self.csv_reader)
-        self.index += 1
-        while time.time() - self.last_time < self.wait_time:
-            continue
-        self.last_time = time.time()
-        return self.index, float(point[0]), float(point[1]), point[2] == '1', point[3] == '1'
+        try:
+            point = next(self.csv_reader)
+            self.index += 1
+            while time.time() - self.last_time < self.wait_time:
+                continue
+            self.last_time = time.time()
+            return self.index, float(point[0]), float(point[1]), point[2] == '1', point[3] == '1'
+        except StopIteration:
+            return None

setup.py

@@ -1,27 +1,39 @@
 from setuptools import setup, find_packages
+import io
+
+
+def is_coral():
+    try:
+        with io.open('/sys/firmware/devicetree/base/model', 'r') as m:
+            if 'phanbell' in m.read().lower(): return True
+    except Exception: pass
+    return False
+
+requirements_list = ['wheel',
+                     'EDFlib-Python',
+                     'numpy',
+                     'portilooplot',
+                     'ipywidgets',
+                     'python-periphery',
+                     'scipy',
+                     'matplotlib']
+
+if is_coral():
+    requirements_list += ['pycoral',
+                          'spidev',
+                          'pylsl-coral',
+                          'pyalsaaudio']
+else:
+    requirements_list += ['gradio',
+                          'tensorflow',
+                          'pyxdf',
+                          'wonambi']
+
 
 setup(
     name='portiloop',
     version='0.0.1',
     packages=[package for package in find_packages()],
     description='Portiloop software library',
-    install_requires=['wheel',
-                      'EDFlib-Python',
-                      'numpy',
-                      'portilooplot',
-                      'ipywidgets',
-                      'python-periphery',
-                      'scipy',
-                      'matplotlib',
-                     ],
-    extras_require={
-        'Portiloop': ['pycoral', 
-                'spidev', 
-                'pylsl-coral', 
-                'pyalsaaudio'],
-        'PC': ['gradio',
-               'tensorflow',
-               'pyxdf',
-               'wonambi']
-    },
+    install_requires=requirements_list,
 )