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Updates code to work with latest dependencies. (#140)
* Use Octave interp1 instead of deprecated interp1q. * oct2py >= 4.0 requires an nout kwarg for multiple outputs. * Accommodate Octave 3 and 4. * Round the indice count so that the numpy array is not indexed by a float. * Arrays seemingly copied, moved to simpler verbose code to avoid copies. * Setup Travis CI to use Conda and old/new testing. - Travis CI script uses miniconda for installs. - Two matrix entries to test against oldest support and newest. - Build the docs on Travis.
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-31
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‎.travis.yml

+40-14
Original file line numberDiff line numberDiff line change
@@ -1,17 +1,43 @@
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language: python
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python:
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- "2.7"
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virtualenv:
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system_site_packages: true
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language: generic
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os:
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- linux
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env:
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matrix:
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- DEP_VERSIONS="oldest"
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- DEP_VERSIONS="latest"
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before_install:
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- pip uninstall -y numpy
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- sudo apt-add-repository -y ppa:octave/stable
9+
- if [[ $DEP_VERSIONS == "oldest" ]]; then
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sudo apt-get install -y -qq python-pip python-setuptools python-numpy python-scipy python-matplotlib python-tables python-nose python-coverage python-pandas python-sphinx python-mock python-numpydoc python-yaml;
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sudo pip install --no-deps oct2py==2.4.2 DynamicistToolKit==0.4.0;
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elif [[ $DEP_VERSIONS == "latest" ]]; then
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MINICONDA_URL="https://repo.continuum.io/miniconda";
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MINICONDA_FILE="Miniconda3-latest-Linux-x86_64.sh";
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curl -L -O "${MINICONDA_URL}/${MINICONDA_FILE}";
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bash $MINICONDA_FILE -b;
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source ~/miniconda3/bin/activate root;
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conda config --set always_yes yes;
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conda update -q conda;
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conda env create -f env-dev-latest.yml;
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source activate gaitanalysis-dev-latest;
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sudo apt-add-repository -y ppa:octave/stable;
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fi
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- sudo apt-get update
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- sudo apt-get install -y -qq python-setuptools python-numpy python-scipy python-matplotlib python-tables python-nose python-coverage octave
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- pip install pandas==0.12.0 pyyaml oct2py==1.2.0 DynamicistToolKit==0.4.0
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- pip freeze
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- octave --version
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- sudo apt-get install -y -qq octave
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install:
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- python setup.py install
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script: nosetests -v --with-coverage --cover-package=gaitanalysis
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after_success: coveralls
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- if [[ $DEP_VERSIONS == "oldest" ]]; then
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sudo pip install --no-deps -e .;
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elif [[ $DEP_VERSIONS == "latest" ]]; then
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python setup.py install;
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fi
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before_script:
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- octave --version
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- if [[ $DEP_VERSIONS == "oldest" ]]; then
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pip freeze;
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elif [[ $DEP_VERSIONS == "latest" ]]; then
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conda info;
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conda list;
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fi
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script:
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- nosetests -v --with-coverage --cover-package=gaitanalysis
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- cd docs
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- make html

‎RELEASE.txt

+1-1
Original file line numberDiff line numberDiff line change
@@ -2,6 +2,6 @@
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2. Bump the version in gaitanalysis/version.py, for example 0.1.0dev to 0.1.0.
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3. Commit changes.
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4. git tag -a vX.X.X -m "Version X.X.X"
5-
5. python setup.py regsiter sdist upload
5+
5. python setup.py register sdist upload
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6. Make sure the latest version is available on readthedocs.org
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7. Bump the version in the git repo to one with "dev" appended.

‎env-dev-latest.yml

+18
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,18 @@
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name: gaitanalysis-dev-latest
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channels:
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- conda-forge
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dependencies:
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- python =2.7.*
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- numpy
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- scipy
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- matplotlib
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- pytables
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- pandas
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- pyyaml
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- dynamicisttoolkit
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- oct2py
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- nose
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- sphinx
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- coverage
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- mock
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- numpydoc

‎env-dev-oldest.yml

+20
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,20 @@
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name: gaitanalysis-dev-oldest
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channels:
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- defaults
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- moorepants
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dependencies:
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- python =2.7.*
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- numpy =1.9.1
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- scipy =0.14.0
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- matplotlib =1.4.2
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- pytables =3.1.1
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- pandas =0.15.1
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- pyyaml =3.11
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- nose
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- sphinx
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- coverage
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- mock
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- numpydoc
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- pip:
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- dynamicisttoolkit==0.3.5
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- oct2py==2.4.2

‎gaitanalysis/gait.py

+11-4
Original file line numberDiff line numberDiff line change
@@ -5,11 +5,13 @@
55
import os
66

77
# external libraries
8+
from pkg_resources import parse_version
89
import numpy as np
910
from scipy.integrate import simps
1011
import matplotlib.pyplot as plt
1112
import pandas
1213
from dtk import process
14+
import oct2py
1315
from oct2py import octave
1416

1517
# local
@@ -65,7 +67,7 @@ def find_constant_speed(time, speed, plot=False, filter_cutoff=1.0):
6567

6668
additional_samples = sample_rate * 0.65
6769

68-
new_indice = indice - additional_samples
70+
new_indice = indice - int(round(additional_samples))
6971

7072
if plot is True:
7173
fig, ax = plt.subplots(2, 1)
@@ -237,9 +239,14 @@ def inverse_dynamics_2d(self, left_leg_markers, right_leg_markers,
237239
# oct2py doesn't allow multiple outputs to be stored in a tuple
238240
# like python, so you have to output each variable
239241
# independently
240-
angles, velocities, moments, forces = \
241-
octave.leg2d(time, marker_array, normalized_force_array,
242-
options)
242+
if parse_version(oct2py.__version__) >= parse_version('4.0'):
243+
angles, velocities, moments, forces = \
244+
octave.leg2d(time, marker_array, normalized_force_array,
245+
options, nout=4)
246+
else:
247+
angles, velocities, moments, forces = \
248+
octave.leg2d(time, marker_array, normalized_force_array,
249+
options)
243250

244251
dynamics = angles, velocities, moments, forces
245252

‎gaitanalysis/motek.py

+15-7
Original file line numberDiff line numberDiff line change
@@ -1209,17 +1209,25 @@ def orient_accelerometer(orientation, x_prime, y_prime, z_prime):
12091209
y_inertial = np.zeros(np.shape(y_prime))
12101210
z_inertial = np.zeros(np.shape(z_prime))
12111211

1212-
for row, world in enumerate([x_inertial, y_inertial, z_inertial]):
1213-
for col, local in enumerate([x_prime, y_prime, z_prime]):
1214-
world += orientation[row,col] * local
1212+
for col, local in enumerate([x_prime, y_prime, z_prime]):
1213+
x_inertial += orientation[0, col] * local
1214+
1215+
for col, local in enumerate([x_prime, y_prime, z_prime]):
1216+
y_inertial += orientation[1, col] * local
1217+
1218+
for col, local in enumerate([x_prime, y_prime, z_prime]):
1219+
z_inertial += orientation[2, col] * local
12151220

12161221
return x_inertial, y_inertial, z_inertial
12171222

12181223
for sensor, rot_matrix in self.meta['trial']['sensor-orientation'].iteritems():
1219-
data_frame[sensor + '_AccX'], data_frame[sensor + '_AccY'], \
1220-
data_frame[sensor + '_AccZ'] = orient_accelerometer(
1221-
np.array(rot_matrix), data_frame[sensor + '_AccX'],
1222-
data_frame[sensor + '_AccY'], data_frame[sensor + '_AccZ'])
1224+
ax, ay, az = orient_accelerometer(np.array(rot_matrix),
1225+
data_frame[sensor + '_AccX'],
1226+
data_frame[sensor + '_AccY'],
1227+
data_frame[sensor + '_AccZ'])
1228+
data_frame[sensor + '_AccX'] = ax
1229+
data_frame[sensor + '_AccY'] = ay
1230+
data_frame[sensor + '_AccZ'] = az
12231231

12241232
return data_frame
12251233

‎gaitanalysis/octave/2d_inverse_dynamics/leg2d.m

+12-3
Original file line numberDiff line numberDiff line change
@@ -37,6 +37,8 @@
3737
% - missing marker data is interpolated *after* low pass filtering
3838
% - x and y coordinates of the same marker must be either both valid or both NaN (missing)
3939

40+
oct_ver = strsplit(OCTAVE_VERSION, '.');
41+
4042
% some constants
4143
Nmarkers = 6;
4244
Ncoords = 2*Nmarkers;
@@ -91,9 +93,16 @@
9193
maxmissing = max(diff(validsamples))-1; % determine largest gap
9294
fprintf('Marker %d: %d samples are missing, longest gap is %d samples.\n', i, missing, maxmissing);
9395
[xf, xd, xdd] = myfiltfilt(validtimes, d(validsamples,:), options.freq);
94-
mocap_f(:,columns) = interp1q(validtimes, xf, times); % resample filtered signal to original time stamps
95-
mocap_d(:,columns) = interp1q(validtimes, xd, times); % resample first derivative to original time stamps
96-
mocap_dd(:,columns) = interp1q(validtimes, xdd, times); % resample second derivative to original time stamps
96+
% Octave removed interp1q in version 4.2.
97+
if ((str2num(oct_ver{1}) >= 4) && (str2num(oct_ver{2}) >= 2))
98+
mocap_f(:,columns) = interp1(validtimes, xf, times); % resample filtered signal to original time stamps
99+
mocap_d(:,columns) = interp1(validtimes, xd, times); % resample first derivative to original time stamps
100+
mocap_dd(:,columns) = interp1(validtimes, xdd, times); % resample second derivative to original time stamps
101+
else
102+
mocap_f(:,columns) = interp1q(validtimes, xf, times); % resample filtered signal to original time stamps
103+
mocap_d(:,columns) = interp1q(validtimes, xd, times); % resample first derivative to original time stamps
104+
mocap_dd(:,columns) = interp1q(validtimes, xdd, times); % resample second derivative to original time stamps
105+
end
97106
end
98107

99108
% do the low-pass filtering on the force plate data

‎gaitanalysis/tests/test_gait.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -180,8 +180,8 @@ def test_grf_landmarks(self, plot=False):
180180
min_idx = len(self.data_frame) / 3
181181
max_idx = 2*len(self.data_frame) / 3
182182

183-
min_time = self.data_frame.index.astype(float)[min_idx]
184-
max_time = self.data_frame.index.astype(float)[max_idx]
183+
min_time = self.data_frame.index.values.astype(float)[min_idx]
184+
max_time = self.data_frame.index.values.astype(float)[max_idx]
185185

186186
right_strikes, left_strikes, right_offs, left_offs = \
187187
gait_data.grf_landmarks('Right Vertical GRF',

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