First code commit

Basic features are present. More testing needed.

Author: davidt0x

.gitignore

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+.idea/
+.pytest_cache/
+
+*.pyc
+
+nlopt-2.4.2-dll64/
+
+example/*.dat
+example/*.log
+example/test-template.png
+example/output.txt
+
+fictrac/
+
+
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+*$py.class
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+build/
+develop-eggs/
+dist/
+downloads/
+eggs/
+.eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+wheels/
+*.egg-info/
+.installed.cfg
+*.egg
+MANIFEST
+
+# PyInstaller
+#  Usually these files are written by a python script from a template
+#  before PyInstaller builds the exe, so as to inject date/other infos into it.
+*.manifest
+*.spec
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
+.nox/
+.coverage
+.coverage.*
+.cache
+nosetests.xml
+coverage.xml
+*.cover
+.hypothesis/
+.pytest_cache/
+
+# Translations
+*.mo
+*.pot
+
+# Django stuff:
+*.log
+local_settings.py
+db.sqlite3
+
+# Flask stuff:
+instance/
+.webassets-cache
+
+# Scrapy stuff:
+.scrapy
+
+# Sphinx documentation
+docs/_build/
+
+# PyBuilder
+target/
+
+# Jupyter Notebook
+.ipynb_checkpoints
+
+# IPython
+profile_default/
+ipython_config.py
+
+# pyenv
+.python-version
+
+# celery beat schedule file
+celerybeat-schedule
+
+# SageMath parsed files
+*.sage.py
+
+# Environments
+.env
+.venv
+env/
+venv/
+ENV/
+env.bak/
+venv.bak/
+
+# Spyder project settings
+.spyderproject
+.spyproject
+
+# Rope project settings
+.ropeproject
+
+# mkdocs documentation
+/site
+
+# mypy
+.mypy_cache/
+.dmypy.json
+dmypy.json
+
+# Pyre type checker
+.pyre/

example/config.txt

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+## FicTrac config file (build Nov  2 2018)
+c2a_cnrs_yz      : { 304, 37, 293, 37, 293, 48, 304, 48 }
+c2a_r            : { -1.209684, 1.208704, 1.208508 }
+c2a_src          : c2a_cnrs_yz
+c2a_t            : { 5.318191, -13.863654, 658.317226 }
+do_display       : y
+do_socket        : y
+max_bad_frames   : -1
+opt_bound        : 0.25
+opt_do_global    : n
+opt_max_err      : -1.000000
+opt_max_evals    : 50
+opt_tol          : 0.001
+q_factor         : 9
+roi_c            : { 0.002001, 0.006799, 0.999975 }
+roi_circ         : { 82, 162, 97, 118, 131, 81, 289, 94, 324, 162 }
+roi_ignr         : { { 46, 186, 358, 192, 364, 286, 44, 284 }, { 193, 125, 205, 120, 224, 127, 234, 134, 237, 154, 229, 170, 209, 173, 189, 170, 184, 155, 181, 141 } }
+roi_r            : 0.022890
+save_debug       : n
+save_raw         : 0
+socket_port      : 5556
+src_fn           : test.mp4
+src_fps          : -1.000000
+thr_ratio        : 1.25
+thr_win_pc       : 0.25
+vfov             : 3.085
+

example/run_example.py

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+
+from pybmt.callback.threshold_callback import ThresholdCallback
+from pybmt.fictrac.driver import FicTracDriver
+
+def run_pybmt_example():
+
+    fictrac_config = "config.txt"
+    fictrac_console_out = "output.txt"
+
+    # Instantiate the callback object thats methods are invoked when new tracking state is detected.
+    callback = ThresholdCallback()
+
+    # Instantiate a FicTracDriver object to handle running of FicTrac in the background and communication
+    # of program state.
+    tracDrv = FicTracDriver(config_file=fictrac_config, console_ouput_file=fictrac_console_out,
+                            #remote_endpoint_url="localhost:5556",
+                            track_change_callback=callback, plot_on=False)
+
+    # This will start FicTrac and the
+    tracDrv.run()
+
+if __name__ == "__main__":
+    run_pybmt_example()

example/test-configImg.png

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+
+
+class PyBMTCallback:
+    """
+    FlyVRCallback is a base class that derived classes should use to implement control logic for closed loop experiments.
+    It provides developers with method entry points for injecting custom logic for processing tracking signals and
+    triggering stimuli. This class should never be instantiated directly, it provides only an abstract interface.
+    """
+
+    def setup_callback(self):
+        """
+        This method is called once and only once before any event processing is triggered. Place any one time setup
+        functionality within this function.
+
+        :return: None
+        """
+        pass
+
+    def shutdown_callback(self):
+        """
+        This method is called once and only once before exiting the programe. Place any one time shutdown
+        functionality within this function.
+
+        :return: None
+        """
+        pass
+
+    def process_callback(self, track_state):
+        """
+        This method is called each time an update is detected in the online tracking state. Code placed within this
+        method should execute as quickly and deterministically as possible.
+
+        :param tracking_update: A ctypes structure of type fictrac.SHMEMFicTracState
+        :return: bool True to keep running, False to stop running.
+        """
+        pass

example/test.mp4

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+from pybmt.callback.callback import PyBMTCallback
+from collections import deque
+
+from pybmt.fictrac.state import FicTracState
+
+
+class ThresholdCallback(PyBMTCallback):
+    """
+    This class implements control logic for triggering a stimulus when tracking velocity reaches a certain
+    threshold. It is just an example of how things can work in a closed loop experiment where tracking state triggers
+    stimuli response.
+    """
+
+    def __init__(self, speed_threshold=0.009, num_frames_mean=25):
+        """
+        Setup a closed loop experiment that keeps track of a running average of the ball speed and generates a stimulus
+        when the speed crosses a threshold.
+
+        :param speed_threshold: The speed threshold that must be reached to generate a stimulus.
+        :param num_frames_mean: The number frames to use in computing the average.
+        """
+
+        # Call the base class constructor
+        super(ThresholdCallback, self).__init__()
+
+        self.speed_threshold = speed_threshold
+        self.num_frames_mean = num_frames_mean
+
+    def setup_callback(self):
+        """
+        We don't need to do much here.
+
+        :return:
+        """
+
+        # Our buffer of past speeds
+        self.speed_history = deque(maxlen=self.num_frames_mean)
+
+        self.is_signal_on = False
+
+
+    def process_callback(self, track_state: FicTracState):
+        """
+        This function is called with each update of fictrac's tracking state.
+        A closed loop experiment that keeps track of a running average of the ball speed and generates a stimulus
+        when the speed crosses a threshold.
+
+        :param track_state:
+        :return:
+        """
+
+        # Get the current ball speed
+        speed = track_state.speed
+
+        # Add the speed to our history
+        self.speed_history.append(speed)
+
+        # Get the running average speed
+        avg_speed = sum(self.speed_history)/len(self.speed_history)
+
+        if avg_speed > self.speed_threshold and not self.is_signal_on:
+            print("Stimulus ON!")
+            self.is_signal_on = True
+
+        if avg_speed < self.speed_threshold and self.is_signal_on:
+            print("Stimulus OFF!")
+            self.is_signal_on = False
+
+        return True
+
+    def shutdown_callback(self):
+        """
+        We don't need to do anything special during shutdown.
+
+        :return:
+        """
+        pass

pybmt/__init__.py

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+def which(program):
+    """
+    Locate an executable's path that is on the PATH
+
+    :param program: The name of the executable.
+    :return: The full path to the executable
+    """
+    import os
+    def is_exe(fpath):
+        return os.path.isfile(fpath) and os.access(fpath, os.X_OK)
+
+    fpath, fname = os.path.split(program)
+    if fpath:
+        if is_exe(program):
+            return program
+    else:
+        for path in os.environ["PATH"].split(os.pathsep):
+            path = path.strip('"')
+
+            exe_file = os.path.join(path, program)
+            if is_exe(exe_file):
+                return exe_file
+
+    return None
+
+def get_flyvr_git_hash():
+
+    hash = None
+    try:
+
+        # Find the directory location of the script, the actual repo directory is the parent of this directory
+        # because we are in common.
+        import os
+        repo_dir = os.path.dirname(os.path.realpath(__file__))
+
+        import subprocess
+        hash = subprocess.check_output(['git', '--git-dir={}\\..\\.git'.format(repo_dir), 'rev-parse', 'HEAD'])
+
+    except:
+        print("Warning: Problem getting git hash for current fly-vr repo. Won't log in experiment output.")
+
+    return hash

pybmt/callback/__init__.py

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+numpy
+pyzmq
+matplotlib

pybmt/callback/callback.py

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+from setuptools import setup
+
+setup(
+    name='pybmt',
+    version='0.1',
+    python_requires='>3.6',
+    description='Python Ball Motion Tracking (pymbt): A python interface for closed loop fictrac (https://github.com/rjdmoore/fictrac)',
+    author='David Turner',
+    author_email='[email protected]',
+    license='Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License',
+    keywords='fictive, tracking, animal tracking, webcamera, sphere, closed loop',
+    url="https://github.com/murthylab/pybmt",
+    packages=['pybmt'],
+    install_requires=[
+        'pyzmq',
+        'numpy',
+        'matplotlib',
+        'pytest'],
+    zip_safe=False
+)