Merge pull request #1 from SchwarzNeuroconLab/dev

New Feature release!

DeepLabStream.py

@@ -18,10 +18,9 @@
 import click
 
 from utils.configloader import RESOLUTION, FRAMERATE, OUT_DIR, MODEL,  MULTI_CAM, STACK_FRAMES, \
-    ANIMALS_NUMBER, STREAMS, VIDEO
+    ANIMALS_NUMBER, STREAMS, VIDEO, IPWEBCAM
 from utils.poser import load_deeplabcut, get_pose, find_local_peaks_new, calculate_skeletons
 from utils.plotter import plot_bodyparts, plot_metadata_frame
-from experiments.experiments import ExampleExperiment
 
 
 def create_video_files(directory, devices, resolution, framerate, codec):
@@ -132,6 +131,13 @@ def set_camera_manager():
             from utils.generic import VideoManager
             manager = VideoManager()
             return manager
+
+        elif IPWEBCAM:
+            from utils.generic import WebCamManager
+            manager = WebCamManager()
+            return manager
+
+
         else:
             manager_list = []
             # loading realsense manager, if installed
@@ -430,15 +436,8 @@ def calculate_fps(self, current_analysis_time):
     ##################
     @staticmethod
     def set_up_experiment():
-        import importlib
-        from utils.configloader import EXP_NAME
-        mod = importlib.import_module('experiments.experiments')
-        try:
-            experiment_class = getattr(mod, EXP_NAME)
-            experiment = experiment_class()
-        except AttributeError:
-            raise ValueError(f'Experiment: {EXP_NAME} not in experiments.py.')
-
+        from experiments.utils.exp_setup import setup_experiment
+        experiment = setup_experiment()
         return experiment
 
     def start_experiment(self):
@@ -519,9 +518,9 @@ def create_dataframes(self):
         Outputting dataframes to csv
         """
         for num, camera in enumerate(self._data_output):
+            print("Saving database for device {}".format(camera))
             df = pd.DataFrame(self._data_output[camera])
             df.index.name = 'Frame'
-            print("Saving database for device {}".format(camera))
             df.to_csv(OUT_DIR + '/DataOutput{}'.format(camera) + '-' + time.strftime('%d%m%Y-%H%M%S') + '.csv', sep=';')
             print("Database saved")
 
@@ -530,8 +529,10 @@ def create_dataframes(self):
     ######
     @staticmethod
     def greetings():
+        from utils.configloader import EXP_NAME, EXP_ORIGIN
         print("This is DeepLabStream")
         print("Developed by: Jens Schweihoff and Matvey Loshakov")
+        print(f'Initializing {EXP_ORIGIN.lower()} experiment: {EXP_NAME}...')
 
     def get_camera_manager(self):
         return self._camera_manager

Readme.md

@@ -25,13 +25,21 @@ DeepLabStreams core feature is the real-time analysis using any type of camera-b
 
  ### 2. [How to use DLStream GUI](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/How-to-use-DLStream)
 
- ### 3. [Introduction to experiments](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/Introduction)
+ ### 3. Check out our [Out-of-the-Box](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/Out-Of-The-Box:-Overview) 
 
- ### 4. [Design your first experiment](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/My-first-experiment)
+ ### 4. [Design an Out-of-the-Box Experiment](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/Out-Of-The-Box:-Design-Experiments)
 
- ### 5. [Adapting an existing experiment to your own needs](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/Adapting-an-existing-experiment-to-your-own-needs)
+### What's underneath?:
 
- #### Check out our [Out-of-the-Box](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/Out-Of-The-Box:-What-Triggers-are-available%3F) section to get a good idea, what DLStream has in stock for your own experiments!
+ ### 5. [Introduction to experiments](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/Introduction)
+
+ ### For advanced users:
+
+ ### 6. [Design your first experiment](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/My-first-experiment)
+
+ ### 7. [Adapting an existing experiment to your own needs](https://github.com/SchwarzNeuroconLab/DeepLabStream/wiki/Adapting-an-existing-experiment-to-your-own-needs)
+
+
 
 ### How to use DeepLabStream
 
@@ -52,7 +60,7 @@ To start working with DeepLabStream, press the `Start Stream` button. It will ac
 After that you can `Start Analysis` to start DeepLabCut and receive a pose estimations for each frame, or, additionally, you can `Start Recording` to record a
 video of the current feed (visible in the stream window). You will see your current video timestamp (counted in frames) and FPS after you pressed the `Start Analysis` button.
 
-![Analisys](https://user-images.githubusercontent.com/44863941/91173049-7ac34580-e6dd-11ea-80b6-ad56cb9cf22c.png)
+![Analysis](https://user-images.githubusercontent.com/44863941/91173049-7ac34580-e6dd-11ea-80b6-ad56cb9cf22c.png)
 
 As you can see, we track three points that represent three body parts of the mouse - nose, neck and tail root.
 Every single frame where the animal was tracked is outputted to the dataframe, which would create a .csv file after the analysis is finished.

design_experiment.py

@@ -0,0 +1,118 @@
+from experiments.utils.exp_setup import DlStreamConfigWriter
+import click
+
+@click.command()
+@click.option('--default', 'default', is_flag=True)
+def design_experiment(default):
+    config = DlStreamConfigWriter()
+    input_dict = dict(EXPERIMENT = None,
+                      TRIGGER = None,
+                      PROCESS = None,
+                      STIMULATION = None)
+
+    def get_input(input_name):
+        click.echo(f'Choosing {input_name}... \n Available {input_name}s are: ' + ', '.join(config.get_available_module_names(input_name)))
+        input_value = click.prompt(f'Enter a base {input_name} module',type=str)
+        while not config.check_if_default_exists(input_value,input_name):
+            click.echo(f'{input_name} {input_value} does not exists.')
+            input_value = click.prompt(f'Enter a base {input_name} module',type=str)
+        return input_value
+    """Experiment"""
+
+    input_value = get_input('EXPERIMENT')
+    input_dict['EXPERIMENT'] = input_value
+    if input_value == 'BaseOptogeneticExperiment':
+        input_dict['STIMULATION'] = 'BaseStimulation'
+        input_dict['PROCESS'] = 'BaseProtocolProcess'
+
+    elif input_value == 'BaseTrialExperiment':
+        click.echo(f'Available Triggers are: ' + ', '.join(config.get_available_module_names('TRIGGER')))
+        click.echo('Note, that you cannot select the same Trigger as selected in TRIGGER.')
+
+        input_value = click.prompt(f'Enter TRIAL_TRIGGER for BaseTrialExperiment', type=str)
+        while not config.check_if_default_exists(input_value, 'TRIGGER'):
+            click.echo(f'TRIGGER {input_value} does not exists.')
+            input_value = click.prompt(f'Enter a base TRIGGER module', type=str)
+
+        input_dict['TRIAL_TRIGGER'] = input_value
+        click.echo(f'TRIAL_TRIGGER for BaseTrialExperiment set to {input_value}.')
+
+    """TRIGGER"""
+
+    input_value = get_input('TRIGGER')
+    input_dict['TRIGGER'] = input_value
+
+
+    """Process"""
+
+    if input_dict['PROCESS'] is None:
+        input_value = get_input('PROCESS')
+        input_dict['PROCESS'] = input_value
+
+    """STIMULATION"""
+    if input_dict['STIMULATION'] is None:
+        input_value = get_input('STIMULATION')
+        input_dict['STIMULATION'] = input_value
+
+    """Setting Process Type"""
+
+    if input_dict['EXPERIMENT'] == 'BaseTrialExperiment':
+        input_dict['PROCESS_TYPE'] = 'trial'
+    elif input_dict['STIMULATION'] == 'BaseStimulation':
+        input_dict['PROCESS_TYPE'] = 'switch'
+    elif input_dict['STIMULATION'] == 'ScreenStimulation' or input_dict['STIMULATION'] == 'RewardDispenser':
+        input_dict['PROCESS_TYPE'] = 'supply'
+
+
+    if input_dict['EXPERIMENT'] == 'BaseTrialExperiment':
+        config.import_default(experiment_name=input_dict['EXPERIMENT'], trigger_name=input_dict['TRIGGER'],
+                                  process_name=input_dict['PROCESS'], stimulation_name=input_dict['STIMULATION'],
+                              trial_trigger_name=input_dict['TRIAL_TRIGGER'])
+
+    else:
+        config.import_default(experiment_name=input_dict['EXPERIMENT'], trigger_name=input_dict['TRIGGER'],
+                                  process_name=input_dict['PROCESS'], stimulation_name=input_dict['STIMULATION'])
+
+    if 'PROCESS_TYPE' in input_dict.keys():
+        config._change_parameter(module_name=input_dict['PROCESS'],parameter_name='TYPE',
+                                 parameter_value=input_dict['PROCESS_TYPE'])
+
+
+    if click.confirm('Do you want to set parameters as well (Not recommended)? \n Note, that you can change them in the created file later.'):
+        current_config = config.get_current_config()
+        ignore_list = ['EXPERIMENT', 'BaseProtocolProcess']
+        inner_ignore_list = ['EXPERIMENTER', 'PROCESS', 'STIMULATION', 'TRIGGER', 'DEBUG']
+        try:
+            for module in current_config.keys():
+                parameter_dict = config.get_parameters(module)
+                if module not in ignore_list:
+                    for input_key in parameter_dict.keys():
+                        if input_key not in inner_ignore_list:
+                            click.echo(f'Default {input_key} is: ' + str(parameter_dict[input_key]))
+                            input_value = click.prompt(f'Enter new value: ',type=str)
+                            config._change_parameter(module_name=module,parameter_name=input_key,
+                                                     parameter_value=input_value)
+        except:
+            click.echo('Failed to set individual parameters. Please change them later in the config file...')
+    else:
+        click.echo('Skipping parameters. Experiment config will be created with default values...')
+    """Finish up"""
+    # Name of experimentor
+    experimenter = click.prompt('Enter an experimenter name',type=str)
+    click.echo(f'Experimenter set to {experimenter}.')
+    config.set_experimenter(experimenter)
+
+    click.echo('Current modules are:\n BaseExperiment: {}\n Trigger: {}\n Process: {} \n Stimulation: {}'.format(
+        input_dict['EXPERIMENT'],
+        input_dict['TRIGGER'],
+        input_dict['PROCESS'],
+        input_dict['STIMULATION']))
+
+
+    if click.confirm('Do you want to continue?'):
+        config.write_ini()
+        click.echo('Config was created. It can be found in experiments/configs')
+
+
+if __name__ == '__main__':
+    design_experiment()