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Commit 00fb285b authored by Olivier Bertrand's avatar Olivier Bertrand
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Add tutorials ipyynb

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doc/source/conf.py
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......@@ -19,9 +19,7 @@
#
import os
import sys
sys.path.insert(0, os.path.abspath('../../src/'))
sys.path.insert(0, os.path.abspath('../../src/database/'))
sys.path.insert(0, os.path.abspath('../../tutorials'))
# -- General configuration ------------------------------------------------
# If your documentation needs a minimal Sphinx version, state it here.
......
doc/source/tutorials/01-building-arena.ipynb 0 → 100644
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doc/source/tutorials/02-recording-animal-trajectory.ipynb 0 → 100644
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%% Cell type:markdown id: tags:
# Recording animal trajectory
## Conversion to navipy trajectories
### From Matlab to navipy
%% Cell type:code id: tags:
``` python
from scipy.io import loadmat
import numpy as np
import os
from navipy.tools.trajectory import Trajectory
import pkg_resources
# Use the trafile from the resources
# You can adapt this code, by changing trajfile
# with your own trajectory file
trajfile = pkg_resources.resource_filename(
'navipy',
'resources/sample_experiment/Lobecke_JEB_2018/Y101_OBFlight_0001.mat')
csvtrajfile, _ = os.path.splitext(trajfile)
csvtrajfile = csvtrajfile+'.csv'
mymat = loadmat(trajfile)
# matlab files are loaded in a dictionary
# we need to identify, under which key the trajectory has been saved
print(mymat.keys())
key = 'trajectory'
# Arrays are placed in a tupple. We need to access the level
# of the array itself.
mymat = mymat[key][0][0][0]
# The array should be a numpy array, and therefore as the .shape function
# to display the array size:
print(mymat.shape)
# In this example the array has 7661 rows and 4 columns
# the columns are: x,y,z, yaw. Therefore pitch and roll were assumed to be constant (here null)
# We can therefore init a trajectory with the convention for rotation
# often yaw-pitch-roll (i.e. 'rzyx') and with indeces the number of sampling points we have
# in the trajectory
rotconvention = 'rzyx'
indeces = np.arange(0,mymat.shape[0])
mytraj = Trajectory(rotconv = rotconvention, indeces=indeces)
# We now can assign the values
mytraj.x = mymat[:,0]
mytraj.y = mymat[:,1]
mytraj.z = mymat[:,2]
mytraj.alpha_0 = mymat[:,3]
mytraj.alpha_1 = 0
mytraj.alpha_2 = 0
# We can then save mytraj as csv file for example
mytraj.to_csv(csvtrajfile)
mytraj.head()
```
%% Output
dict_keys(['__header__', '__version__', '__globals__', 'trajectory', 'nests', 'cylinders'])
(7661, 4)
location rzyx
x y z alpha_0 alpha_1 alpha_2
0 3.056519 -214.990482 9.330593 2.79751 0 0
1 4.611665 -215.020314 8.424138 2.80863 0 0
2 4.556650 -214.593236 9.185016 2.81407 0 0
3 4.643091 -213.829769 10.542035 2.82704 0 0
4 4.647302 -214.431592 7.461187 2.82896 0 0
%% Cell type:markdown id: tags:
### From csv to navipy
Navipy can read csv files with 7 columns and a two line headers
<table>
<tr>
<td>location</td>
<td>location</td>
<td>location</td>
<td>rzyx</td>
<td>rzyx</td>
<td>rzyx</td>
</tr>
<tr>
<td>x</td>
<td>y</td>
<td>z</td>
<td>alpha_0</td>
<td>alpha_1</td>
<td>alpha_2</td>
</tr>
</table>
But you may have csv file with a different format.
Here we are going to show, how to convert your csv file format to the one required by navipy
doc/source/tutorials/03-rendering-along-trajectory.ipynb 0 → 100644
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setup.py
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......@@ -3,6 +3,8 @@
(called navipy)
"""
from setuptools import setup, find_packages
import glob
import os
excluded = []
......@@ -22,6 +24,18 @@ def create_package_list(base_package):
if not exclude_package(pkg)])
def package_data_files(base_package):
os.chdir(base_package)
filelist = glob.glob(os.path.join('resources',
'*'))
filelist.extend(glob.glob(os.path.join('resources',
'**', '*'),
recursive=True))
os.chdir('../')
print(filelist)
return filelist
setup_dict = {'name': 'navipy',
'version': '0.1',
'author': "Olivier J.N. Bertrand",
......@@ -50,10 +64,7 @@ setup_dict = {'name': 'navipy',
'Pillow',
'tables'],
'package_data': {'navipy':
['resources/*.db',
'resources/*.blend',
'resources/*.csv',
'resources/configs/*.yaml']},
package_data_files("navipy")},
'include_package_data': True,
'entry_points': {
'console_scripts': [
......
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