Beginning of v0.2.

Author: moorepants

README.rst

@@ -1,6 +1,6 @@
-=================
-DynamicistToolKit
-=================
+============
+DynamicistTK
+============
 
 This is a collection of python modules and tools that are helpful for a
 dynamicist. Basically a place to throw things general tools that I use in the
@@ -21,3 +21,6 @@ bicycle
 -------
 Generic tools for basic bicycle dynamics analysis. (These are not in a stable
 state yet).
+
+walk
+----

UNLICENSE.txt

@@ -0,0 +1,24 @@
+This is free and unencumbered software released into the public domain.
+
+Anyone is free to copy, modify, publish, use, compile, sell, or
+distribute this software, either in source code form or as a compiled
+binary, for any purpose, commercial or non-commercial, and by any
+means.
+
+In jurisdictions that recognize copyright laws, the author or authors
+of this software dedicate any and all copyright interest in the
+software to the public domain. We make this dedication for the benefit
+of the public at large and to the detriment of our heirs and
+successors. We intend this dedication to be an overt act of
+relinquishment in perpetuity of all present and future rights to this
+software under copyright law.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
+IN NO EVENT SHALL THE AUTHORS BE LIABLE FOR ANY CLAIM, DAMAGES OR
+OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE,
+ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
+OTHER DEALINGS IN THE SOFTWARE.
+
+For more information, please refer to <http://unlicense.org/>

dtk/walk.py

@@ -2,6 +2,7 @@
 # -*- coding: utf-8 -*-
 
 import numpy as np
+import matplotlib.pyplot as plt
 
 from dtk import process
 
@@ -55,3 +56,126 @@ def find_constant_speed(time, speed, plot=False):
         fig.show()
 
     return len(time) - (new_indice), time[len(time) - new_indice]
+
+
+def gait_landmarks_from_grf(mot_file,
+                            right_grfy_column_name='ground_force_vy',
+                            left_grfy_column_name='1_ground_force_vy',
+                            threshold=1e-5, do_plot=False, min_time=None,
+                            max_time=None):
+    """
+    Obtain gait landmarks (right and left foot strike & toe-off) from ground
+    reaction force (GRF) time series data.
+
+    Parameters
+    ----------
+    mot_file : str
+        Name of *.mot (OpenSim Storage) file containing GRF data.
+    right_grfy_column_name : str, optional
+        Name of column in `mot_file` containing the y (vertical) component
+        of GRF data for the right leg.
+    left_grfy_column_name : str, optional
+        Same as above, but for the left leg.
+    threshold : float, optional
+        Below this value, the force is considered to be zero (and the
+        corresponding foot is not touching the ground).
+    do_plot : bool, optional (default: False)
+        Create plots of the detected gait landmarks on top of the vertical
+        ground reaction forces.
+    min_time : float, optional
+        If set, only consider times greater than `min_time`.
+    max_time : float, optional
+        If set, only consider times greater than `max_time`.
+
+    Returns
+    -------
+    right_foot_strikes : np.array
+        All times at which right_grfy is non-zero and it was 0 at the
+        preceding time index.
+    left_foot_strikes : np.array
+        Same as above, but for the left foot.
+    right_toe_offs : np.array
+        All times at which left_grfy is 0 and it was non-zero at the
+        preceding time index.
+    left_toe_offs : np.array
+        Same as above, but for the left foot.
+
+    Notes
+    -----
+    Source modifed from:
+
+    https://github.com/fitze/epimysium/blob/master/epimysium/postprocessing.py
+
+    """
+    data = dataman.storage2numpy(mot_file)
+
+    time = data['time']
+    right_grfy = data[right_grfy_column_name]
+    left_grfy = data[left_grfy_column_name]
+
+    # Time range to consider.
+    if max_time == None: max_idx = len(time)
+    else: max_idx = nearest_index(time, max_time)
+
+    if min_time == None: min_idx = 1
+    else: min_idx = max(1, nearest_index(time, min_time))
+
+    index_range = range(min_idx, max_idx)
+
+    # Helper functions
+    # ----------------
+    def zero(number):
+        return abs(number) < threshold
+
+    def birth_times(ordinate):
+        births = list()
+        for i in index_range:
+            # 'Skip' first value because we're going to peak back at previous
+            # index.
+            if zero(ordinate[i - 1]) and (not zero(ordinate[i])):
+                births.append(time[i])
+        return np.array(births)
+
+    def death_times(ordinate):
+        deaths = list()
+        for i in index_range:
+            if (not zero(ordinate[i - 1])) and zero(ordinate[i]):
+                deaths.append(time[i])
+        return np.array(deaths)
+
+    right_foot_strikes = birth_times(right_grfy)
+    left_foot_strikes = birth_times(left_grfy)
+    right_toe_offs = death_times(right_grfy)
+    left_toe_offs = death_times(left_grfy)
+
+    if do_plot:
+
+        #pl.figure(figsize=(4, 8))
+        ones = np.array([1, 1])
+
+        def myplot(index, label, ordinate, foot_strikes, toe_offs):
+            ax = plt.subplot(2, 1, index)
+            plt.plot(time[min_idx:max_idx], ordinate[min_idx:max_idx], 'k')
+            plt.ylabel('vertical ground reaction force (N)')
+            plt.title('%s (%i foot strikes, %i toe-offs)' % (
+                label, len(foot_strikes), len(toe_offs)))
+
+            for i, strike in enumerate(foot_strikes):
+                if i == 0: kwargs = {'label': 'foot strikes'}
+                else: kwargs = dict()
+                plt.plot(strike * ones, ax.get_ylim(), 'r', **kwargs)
+
+            for i, off in enumerate(toe_offs):
+                if i == 0: kwargs = {'label': 'toe-offs'}
+                else: kwargs = dict()
+                plt.plot(off * ones, ax.get_ylim(), 'b', **kwargs)
+
+
+        myplot(1, 'left foot', left_grfy, left_foot_strikes, left_toe_offs)
+        plt.legend(loc='best')
+
+        myplot(2, 'right foot', right_grfy, right_foot_strikes, right_toe_offs)
+
+        plt.xlabel('time (s)')
+
+    return right_foot_strikes, left_foot_strikes, right_toe_offs, left_toe_offs

setup.py

@@ -1,10 +1,22 @@
-from setuptools import setup
+from setuptools import setup, find_packages
 
 setup(name='DynamicistToolKit',
       author='Jason Moore',
       author_email='moorepants@gmail.com',
       version='0.1.0',
-      packages=['dtk'],
-      license='Creative Commons Attribution-Noncommercial-Share Alike license',
+      url="http://github.com/moorepants/DynamicistToolKit",
+      description='Various tool kits for theorectical and experimental dynamics.',
+      license='UNLICENSE.txt',
+      packages=find_packages(),
+      install_requires=['numpy', 'scipy', 'matplotlib'],
+      tests_require=['nose'],
+      test_suite='nose.collector',
       long_description=open('README.rst').read(),
+      classifiers=[
+                   'Development Status :: 4 - Beta',
+                   'Intended Audience :: Science/Research',
+                   'Operating System :: OS Independent',
+                   'Programming Language :: Python :: 2.7',
+                   'Topic :: Scientific/Engineering :: Physics',
+                  ],
       )