Merge remote-tracking branch 'origin/master' into dev

JensBlack · JensBlack · commit 8db430a4f64a · 2020-11-20T14:58:24.000+01:00
# Conflicts:
#	DeepLabStream.py
#	settings.ini
#	utils/configloader.py
diff --git a/DeepLabStream.py b/DeepLabStream.py
@@ -18,7 +18,7 @@
 import click
 
 from utils.configloader import RESOLUTION, FRAMERATE, OUT_DIR, MODEL,  MULTI_CAM, STACK_FRAMES, \
-    ANIMALS_NUMBER, STREAMS, VIDEO, IPWEBCAM
+    ANIMALS_NUMBER, STREAMS, STREAMING_SOURCE
 from utils.poser import load_deeplabcut, get_pose, find_local_peaks_new, calculate_skeletons,\
     get_ma_pose, calculate_ma_skeletons, calculate_skeletons_dlc_live
 from utils.plotter import plot_bodyparts, plot_metadata_frame
@@ -128,18 +128,17 @@ def set_camera_manager():
         :return: the chosen camera manager
         """
 
-        if VIDEO:
+        if STREAMING_SOURCE.lower() == 'video':
             from utils.generic import VideoManager
             manager = VideoManager()
             return manager
 
-        elif IPWEBCAM:
+        elif STREAMING_SOURCE.lower() == 'ipwebcam':
             from utils.generic import WebCamManager
             manager = WebCamManager()
             return manager
 
-
-        else:
+        elif STREAMING_SOURCE.lower() == 'camera':
             manager_list = []
             # loading realsense manager, if installed
             realsense = find_spec("pyrealsense2") is not None
@@ -175,6 +174,9 @@ def check_for_cameras(camera_manager):
                 from utils.generic import GenericManager
                 generic_manager = GenericManager()
                 return generic_manager
+        else:
+            raise ValueError(f'Streaming source {STREAMING_SOURCE} is not a valid option. \n'
+                             f'Please choose from "video", "camera" or "ipwebcam".')
 
     @property
     def cameras(self):
diff --git a/experiments/base/experiments.py b/experiments/base/experiments.py
@@ -289,7 +289,7 @@ def __init__(self):
 
         #loading settings
         self._exp_parameter_dict = dict(TRIGGER ='str',
-                                        INTERSTIM_TIME = 'int',
+                                        INTERTRIAL_TIME = 'int',
                                         MAX_STIM_TIME = 'int',
                                         MIN_STIM_TIME='int',
                                         MAX_TOTAL_STIM_TIME = 'int',
diff --git a/experiments/custom/experiments.py b/experiments/custom/experiments.py
@@ -11,7 +11,7 @@
 from functools import partial
 from collections import Counter
 from experiments.custom.stimulus_process import ClassicProtocolProcess, SimpleProtocolProcess,Timer, ExampleProtocolProcess
-from experiments.custom.triggers import ScreenTrigger, RegionTrigger, OutsideTrigger, DirectionTrigger
+from experiments.custom.triggers import ScreenTrigger, RegionTrigger, OutsideTrigger, DirectionTrigger, SpeedTrigger
 from utils.plotter import plot_triggers_response
 from utils.analysis import angle_between_vectors
 from experiments.custom.stimulation import show_visual_stim_img,laser_switch
@@ -137,6 +137,80 @@ def get_trial(self):
 EXP_COMPLETION = 10
 
 
+
+class SpeedExperiment:
+    """
+    Simple class to contain all of the experiment properties
+    Uses multiprocess to ensure the best possible performance and
+        to showcase that it is possible to work with any type of equipment, even timer-dependent
+    """
+    def __init__(self):
+        self.experiment_finished = False
+        self._threshold = 10
+        self._event = None
+        self._current_trial = None
+        self._event_count = 0
+        self._trigger = SpeedTrigger(threshold = self._threshold,bodypart= 'tailroot', timewindow_len= 5)
+        self._exp_timer = Timer(600)
+
+    def check_skeleton(self, frame, skeleton):
+        """
+        Checking each passed animal skeleton for a pre-defined set of conditions
+        Outputting the visual representation, if exist
+        Advancing trials according to inherent logic of an experiment
+        :param frame: frame, on which animal skeleton was found
+        :param skeleton: skeleton, consisting of multiple joints of an animal
+        """
+        self.check_exp_timer()  # checking if experiment is still on
+
+        if not self.experiment_finished:
+            result, response = self._trigger.check_skeleton(skeleton=skeleton)
+            plot_triggers_response(frame, response)
+            if result:
+                laser_switch(True)
+                self._event_count += 1
+                print(self._event_count)
+                print('Light on')
+
+            else:
+                laser_switch(False)
+                print('Light off')
+
+            return result, response
+
+
+    def check_exp_timer(self):
+        """
+        Checking the experiment timer
+        """
+        if not self._exp_timer.check_timer():
+            print("Experiment is finished")
+            print("Time ran out.")
+            self.stop_experiment()
+
+    def start_experiment(self):
+        """
+        Start the experiment
+        """
+        if not self.experiment_finished:
+            self._exp_timer.start()
+
+    def stop_experiment(self):
+        """
+        Stop the experiment and reset the timer
+        """
+        self.experiment_finished = True
+        print('Experiment completed!')
+        self._exp_timer.reset()
+        # don't forget to stop the laser for safety!
+        laser_switch(False)
+
+    def get_trial(self):
+        """
+        Check which trial is going on right now
+        """
+        return self._current_trial
+
 class FirstExperiment:
     def __init__(self):
         self.experiment_finished = False
diff --git a/experiments/custom/triggers.py b/experiments/custom/triggers.py
@@ -9,7 +9,8 @@
 
 from utils.analysis import angle_between_vectors, calculate_distance, EllipseROI, RectangleROI
 from utils.configloader import RESOLUTION
-
+from collections import deque
+import numpy as np
 """Single posture triggers"""
 
 class HeaddirectionROITrigger:
@@ -333,15 +334,20 @@ def check_skeleton(self, skeleton: dict):
 
 class FreezeTrigger:
     """
-    Trigger to check if animal is in freezing state
+    Trigger to check if animal is moving below a certain speed
     """
-    def __init__(self, threshold: int, debug: bool = False):
+    def __init__(self, threshold: int, bodypart: str, timewindow_len:int = 2,  debug: bool = False):
         """
         Initializing trigger with given threshold
         :param threshold: int in pixel how much of a movement does not count
-        For example threshold of 5 would mean that all movements less then 5 pixels would be ignored
+        :param bodypart: str of body part in skeleton used for speed calculation
+        For example threshold of 5 would mean that all movements more then 5 pixels in the last timewindow length frames
+        would be ignored
         """
+        self._bodypart = bodypart
         self._threshold = threshold
+        self._timewindow_len = timewindow_len
+        self._timewindow = deque(maxlen= timewindow_len)
         self._skeleton = None
         self._debug = debug  # not used in this trigger
 
@@ -354,45 +360,49 @@ def check_skeleton(self, skeleton: dict):
         """
         # choosing a point to draw near the skeleton
         org_point = skeleton[list(skeleton.keys())[0]]
-        joint_moved = []
+        joint_moved = 0
+
         if self._skeleton is None:
             result = False
-            text = 'Not freezing'
+            text = '...'
             self._skeleton = skeleton
         else:
-            for joint in skeleton:
-                joint_travel = calculate_distance(skeleton[joint], self._skeleton[joint])
-                joint_moved.append(abs(joint_travel) <= self._threshold)
-            if all(joint_moved):
+            joint_travel = calculate_distance(skeleton[self._bodypart], self._skeleton[self._bodypart])
+            self._timewindow.append(joint_travel)
+            if len(self._timewindow) == self._timewindow_len:
+                joint_moved = np.sum(self._timewindow)
+
+            if abs(joint_moved) <= self._threshold:
                 result = True
                 text = 'Freezing'
             else:
                 result = False
-                text = 'Not freezing'
-            self._skeleton = skeleton
-
+                text = 'Not Freezing'
+        self._skeleton = skeleton
         color = (0, 255, 0) if result else (0, 0, 255)
         response_body = {'plot': {'text': dict(text=text,
                                                org=org_point,
                                                color=color)}}
         response = (result, response_body)
-        return response
 
+        return response
 
 class SpeedTrigger:
     """
     Trigger to check if animal is moving above a certain speed
     """
-    def __init__(self, threshold: int, bodypart: str = 'any', debug: bool = False):
+    def __init__(self, threshold: int, bodypart: str, timewindow_len:int = 2,  debug: bool = False):
         """
         Initializing trigger with given threshold
         :param threshold: int in pixel how much of a movement does not count
-        :param bodypart: str or list of str, bodypart or list of bodyparts in skeleton to use for trigger,
-         if "any" will check if any bodypart reaches treshold; default "any"
-        For example threshold of 5 would mean that all movements less then 5 pixels would be ignored
+        :param bodypart: str of body part in skeleton used for speed calculation
+        For example threshold of 5 would mean that all movements less then 5 pixels in the last timewindow length frames
+        would be ignored
         """
         self._bodypart = bodypart
         self._threshold = threshold
+        self._timewindow_len = timewindow_len
+        self._timewindow = deque(maxlen= timewindow_len)
         self._skeleton = None
         self._debug = debug  # not used in this trigger
 
@@ -405,36 +415,29 @@ def check_skeleton(self, skeleton: dict):
         """
         # choosing a point to draw near the skeleton
         org_point = skeleton[list(skeleton.keys())[0]]
-        joint_moved = []
+        joint_moved = 0
+
         if self._skeleton is None:
             result = False
-            text = 'First frame'
+            text = '...'
             self._skeleton = skeleton
         else:
-            if self._bodypart is "any":
-                for joint in skeleton:
-                    joint_travel = calculate_distance(skeleton[joint], self._skeleton[joint])
-                    joint_moved.append(abs(joint_travel) >= self._threshold)
-
-            elif isinstance(self._bodypart, list):
-                for joint in self._bodypart:
-                    joint_travel = calculate_distance(skeleton[joint], self._skeleton[joint])
-                    joint_moved.append(abs(joint_travel) >= self._threshold)
-            else:
-                joint_travel = calculate_distance(skeleton[self._bodypart], self._skeleton[self._bodypart])
-                joint_moved.append(abs(joint_travel) >= self._threshold)
+            joint_travel = calculate_distance(skeleton[self._bodypart], self._skeleton[self._bodypart])
+            self._timewindow.append(joint_travel)
+            if len(self._timewindow) == self._timewindow_len:
+                joint_moved = np.sum(self._timewindow)
 
-            if all(joint_moved):
+            if abs(joint_moved) >= self._threshold:
                 result = True
                 text = 'Running'
             else:
                 result = False
-                text = ''
-            self._skeleton = skeleton
-
+                text = 'Not Running'
+        self._skeleton = skeleton
         color = (0, 255, 0) if result else (0, 0, 255)
         response_body = {'plot': {'text': dict(text=text,
                                                org=org_point,
                                                color=color)}}
         response = (result, response_body)
+
         return response
diff --git a/settings.ini b/settings.ini
@@ -1,10 +1,12 @@
 [Streaming]
 RESOLUTION = 320, 256
 FRAMERATE = 30
-STREAMS = color, depth, infrared
 OUTPUT_DIRECTORY = /Output
-MULTIPLE_DEVICES = False
-CAMERA_SOURCE = 2
+#if you have connected multiple cameras (USB), you will need to select the number OpenCV has given them.
+#Default is "0", which takes the first available camera.
+CAMERA_SOURCE = 0
+#you can use camera, ipwebcam or video to select your input source
+STREAMING_SOURCE = camera
 
 [Pose Estimation]
 MODEL_ORIGIN = DLC
@@ -14,10 +16,17 @@ MODEL_NAME = MODEL
 ALL_BODYPARTS = bp1, bp2, bp3, bp4
 
 [Experiment]
+#Available parameters are "CUSTOM" and "BASE"
 EXP_ORIGIN = BASE/CUSTOM
+#Name of the experiment config in /experiments/configs or name of the custom experiment in /experiments/custom/experiments.py
 EXP_NAME = CONFIG_NAME
+#if you want the experiment to be recorded as a raw video set this to "True".
 RECORD_EXP = True
 
 [Video]
+#Full path to video that you want to use as input. Needs "STREAMING_SOURCE" set to "video"!
 VIDEO_SOURCE = PATH_TO_PRERECORDED_VIDEO
-VIDEO = False
+
+[IPWEBCAM]
+#Standard Port is 5555 if you followed the SmoothStream setup
+PORT = 5555
diff --git a/utils/advanced_settings.ini b/utils/advanced_settings.ini
@@ -0,0 +1,7 @@
+#advanced settings only change them if you know what you do!
+
+[Streaming]
+STREAMS = color, depth, infrared
+MULTIPLE_DEVICES = False
+STACK_FRAMES = False
+ANIMALS_NUMBER = 1
diff --git a/utils/configloader.py b/utils/configloader.py
@@ -13,6 +13,7 @@
 # loading DeepLabStream configuration
 # remember when it was called DSC?
 dsc_config = cfg.ConfigParser()
+adv_dsc_config = cfg.ConfigParser()
 
 
 def get_script_path():
@@ -23,14 +24,11 @@ def get_script_path():
 with open(cfg_path) as cfg_file:
     dsc_config.read_file(cfg_file)
 
-
-#poseestimation
-MODEL_ORIGIN = dsc_config['Pose Estimation'].get('MODEL_ORIGIN')
-MODEL_PATH = dsc_config['Pose Estimation'].get('MODEL_PATH')
-MODEL_NAME = dsc_config['Pose Estimation'].get('MODEL_NAME')
-ALL_BODYPARTS = tuple(part for part in dsc_config['Streaming'].get('ALL_BODYPARTS').split(','))
-
-
+adv_cfg_path = os.path.join(os.path.dirname(__file__), 'advanced_settings.ini')
+with open(adv_cfg_path) as adv_cfg_file:
+    adv_dsc_config.read_file(adv_cfg_file)
+# DeepLabCut
+deeplabcut_config = dict(dsc_config.items('DeepLabCut'))
 
 # Streaming items
 try:
@@ -39,24 +37,16 @@ def get_script_path():
     print('Incorrect resolution in config!\n'
           'Using default value "RESOLUTION = 848, 480"')
     RESOLUTION = (848, 480)
+MODEL = dsc_config['Streaming'].get('MODEL')
 FRAMERATE = dsc_config['Streaming'].getint('FRAMERATE')
 OUT_DIR = dsc_config['Streaming'].get('OUTPUT_DIRECTORY')
-STREAM = dsc_config['Streaming'].getboolean('STREAM')
-MULTI_CAM = dsc_config['Streaming'].getboolean('MULTIPLE_DEVICES')
-STACK_FRAMES = dsc_config['Streaming'].getboolean('STACK_FRAMES') if dsc_config['Streaming'].getboolean(
-    'STACK_FRAMES') is not None else False
-ANIMALS_NUMBER = dsc_config['Streaming'].getint('ANIMALS_NUMBER') if dsc_config['Streaming'].getint(
-    'ANIMALS_NUMBER') is not None else 1
-STREAMS = [str(part).strip() for part in dsc_config['Streaming'].get('STREAMS').split(',')]
 CAMERA_SOURCE = dsc_config['Streaming'].get('CAMERA_SOURCE')
-
+STREAMING_SOURCE = dsc_config['Streaming'].get('STREAMING_SOURCE')
 # Video
 VIDEO_SOURCE = dsc_config['Video'].get('VIDEO_SOURCE')
-VIDEO = dsc_config['Video'].getboolean('VIDEO')
 
 #IPWEBCAM
 PORT = dsc_config['IPWEBCAM'].get('PORT')
-IPWEBCAM = dsc_config['IPWEBCAM'].getboolean('IPWEBCAM')
 
 
 # experiment
@@ -65,4 +55,12 @@ def get_script_path():
 RECORD_EXP = dsc_config['Experiment'].getboolean('RECORD_EXP')
 
 START_TIME = time.time()
-EGG = "".join(format(ord(x), 'b') for x in "Hello there!")
+
+
+"""advanced settings"""
+STREAMS = [str(part).strip() for part in adv_dsc_config['Streaming'].get('STREAMS').split(',')]
+MULTI_CAM = adv_dsc_config['Streaming'].getboolean('MULTIPLE_DEVICES')
+STACK_FRAMES = adv_dsc_config['Streaming'].getboolean('STACK_FRAMES') if adv_dsc_config['Streaming'].getboolean(
+    'STACK_FRAMES') is not None else False
+ANIMALS_NUMBER = adv_dsc_config['Streaming'].getint('ANIMALS_NUMBER') if adv_dsc_config['Streaming'].getint(
+    'ANIMALS_NUMBER') is not None else 1
diff --git a/utils/generic.py b/utils/generic.py
diff --git a/utils/plotter.py b/utils/plotter.py
