From 48b1436025aaa164c9bedf031c7e0343e355359e Mon Sep 17 00:00:00 2001
From: "Olivier J.N. Bertrand" <olivier.bertrand@uni-bielefeld.de>
Date: Wed, 20 Jun 2018 09:43:04 +0200
Subject: [PATCH] Fix error due to the merge
---
navipy/database/__init__.py | 2 +-
navipy/errorprop/test.py | 2 +-
navipy/moving/test_agent.py | 28 +++++++++++++++++++++-----
navipy/trajectories/__init__.py | 10 ++++-----
navipy/trajectories/plot.py | 2 +-
navipy/trajectories/random.py | 4 ++--
navipy/trajectories/test_markers.py | 6 +++---
navipy/trajectories/test_trajectory.py | 4 ++--
navipy/trajectories/test_triangle.py | 2 +-
navipy/trajectories/transformations.py | 4 ++--
10 files changed, 41 insertions(+), 23 deletions(-)
diff --git a/navipy/database/__init__.py b/navipy/database/__init__.py
index 0b8fd19..fc671ea 100644
--- a/navipy/database/__init__.py
+++ b/navipy/database/__init__.py
@@ -514,7 +514,7 @@ class DataBaseLoad(DataBase):
if 'rotconv_id' in posorient.columns:
rotconv = posorient.loc[:, 'rotconv_id']
if np.all(rotconv == rotconv.iloc[0]):
- self.__convention = rotconv
+ self.__convention = rotconv.iloc[0]
else:
self._logger.warning(
'More than one convention have been found in database')
diff --git a/navipy/errorprop/test.py b/navipy/errorprop/test.py
index d65beb0..caa509d 100644
--- a/navipy/errorprop/test.py
+++ b/navipy/errorprop/test.py
@@ -1,6 +1,6 @@
import unittest
import numpy as np
-from tra3dpy.errorprop import propagate_error, estimate_jacobian
+from navipy.errorprop import propagate_error, estimate_jacobian
def sincosine(x):
diff --git a/navipy/moving/test_agent.py b/navipy/moving/test_agent.py
index 46c46ff..2f97910 100644
--- a/navipy/moving/test_agent.py
+++ b/navipy/moving/test_agent.py
@@ -89,7 +89,7 @@ class TestNavipyMovingAgent(unittest.TestCase):
# GridAgent
#
def test_move_gridagent(self):
- agent = naviagent.GridAgent(self.brain, self.convention)
+ agent = naviagent.GridAgent(self.brain)
initposorient = None
with warnings.catch_warnings(record=True):
initposorient = self.brain.posorients.loc[13, :]
@@ -146,9 +146,13 @@ class TestNavipyMovingAgent(unittest.TestCase):
#
def test_init_graphagent(self):
+ mode_of_motion = dict()
+ mode_of_motion['mode'] = 'on_cubic_grid'
+ mode_of_motion['param'] = dict()
+ mode_of_motion['param']['grid_spacing'] = 0.5
agent = None
with warnings.catch_warnings(record=True):
- agent = naviagent.GraphAgent(self.brain)
+ agent = naviagent.GraphAgent(self.brain, mode_of_motion)
if version < 2:
graph_nodes = list(agent.graph.nodes())
else:
@@ -158,9 +162,13 @@ class TestNavipyMovingAgent(unittest.TestCase):
'Init of graph failed. Node missmatch')
def test_graph_setter(self):
+ mode_of_motion = dict()
+ mode_of_motion['mode'] = 'on_cubic_grid'
+ mode_of_motion['param'] = dict()
+ mode_of_motion['param']['grid_spacing'] = 0.5
agent = None
with warnings.catch_warnings(record=True):
- agent = naviagent.GraphAgent(self.brain)
+ agent = naviagent.GraphAgent(self.brain, mode_of_motion)
if version < 2:
graph_nodes = list(agent.graph.nodes())
else:
@@ -188,9 +196,13 @@ class TestNavipyMovingAgent(unittest.TestCase):
3 Two loops attractors
"""
# Test all node to first
+ mode_of_motion = dict()
+ mode_of_motion['mode'] = 'on_cubic_grid'
+ mode_of_motion['param'] = dict()
+ mode_of_motion['param']['grid_spacing'] = 0.5
agent = None
with warnings.catch_warnings(record=True):
- agent = naviagent.GraphAgent(self.brain)
+ agent = naviagent.GraphAgent(self.brain, mode_of_motion)
if version < 2:
graph_nodes = list(agent.graph.nodes())
@@ -255,9 +267,15 @@ class TestNavipyMovingAgent(unittest.TestCase):
2. Saddle points
3. Local minima
"""
+ # Init the agent
+ mode_of_motion = dict()
+ mode_of_motion['mode'] = 'on_cubic_grid'
+ mode_of_motion['param'] = dict()
+ mode_of_motion['param']['grid_spacing'] = 0.5
agent = None
with warnings.catch_warnings(record=True):
- agent = naviagent.GraphAgent(self.brain)
+ agent = naviagent.GraphAgent(self.brain, mode_of_motion)
+
# Local maxima
if version < 2:
graph_nodes = list(agent.graph.nodes())
diff --git a/navipy/trajectories/__init__.py b/navipy/trajectories/__init__.py
index c9851b3..677c0d8 100644
--- a/navipy/trajectories/__init__.py
+++ b/navipy/trajectories/__init__.py
@@ -7,7 +7,7 @@ import navipy.maths.constants as mconst
import navipy.maths.quaternion as htq
import navipy.maths.euler as hte
from navipy.errorprop import propagate_error
-import navipy.trajectories.transformations as mtf
+from transformations import markers2translate, markers2euler
def _markers2position(x, kwargs):
@@ -16,8 +16,8 @@ def _markers2position(x, kwargs):
mark2 = pd.Series(x[6:], index=['x', 'y', 'z'])
triangle_mode = kwargs['triangle_mode']
euler_axes = kwargs['euler_axes']
- return mtf.markers2translate(mark0, mark1, mark2,
- triangle_mode, euler_axes)
+ return markers2translate(mark0, mark1, mark2,
+ triangle_mode, euler_axes)
def _markers2angles(x, kwargs):
@@ -26,8 +26,8 @@ def _markers2angles(x, kwargs):
mark2 = pd.Series(x[6:], index=['x', 'y', 'z'])
triangle_mode = kwargs['triangle_mode']
euler_axes = kwargs['euler_axes']
- return mtf.markers2euler(mark0, mark1, mark2,
- triangle_mode, euler_axes)
+ return markers2euler(mark0, mark1, mark2,
+ triangle_mode, euler_axes)
class Trajectory(pd.DataFrame):
diff --git a/navipy/trajectories/plot.py b/navipy/trajectories/plot.py
index bb96ca6..c2f141d 100644
--- a/navipy/trajectories/plot.py
+++ b/navipy/trajectories/plot.py
@@ -3,7 +3,7 @@
import matplotlib.pyplot as plt
import numpy as np
import pandas as pd
-from tra3dpy.trajectory.transform import agent_facing_vector, world2body
+from navipy.trajectories.transform import agent_facing_vector, world2body
def get_color_frame_dataframe(frame_range=[0, 100], cmap=plt.get_cmap('jet')):
diff --git a/navipy/trajectories/random.py b/navipy/trajectories/random.py
index cf1631e..76a7440 100644
--- a/navipy/trajectories/random.py
+++ b/navipy/trajectories/random.py
@@ -21,11 +21,11 @@ having for columns:
"""
-from tra3dpy.maths.euler import matrix
+from navipy.maths.euler import matrix
from scipy.stats import norm
import numpy as np
import pandas as pd
-from tra3dpy.trajectory import Trajectory
+from navipy.trajectories import Trajectory
def yawpitchroll(yaw, pitch, roll):
diff --git a/navipy/trajectories/test_markers.py b/navipy/trajectories/test_markers.py
index 6ccc2a3..811bd68 100644
--- a/navipy/trajectories/test_markers.py
+++ b/navipy/trajectories/test_markers.py
@@ -1,9 +1,9 @@
import unittest
import numpy as np
import pandas as pd
-from tra3dpy.maths.homogeneous_transformations import compose_matrix
-import tra3dpy.markers.transformations as mtf
-from tra3dpy.markers.triangle import Triangle
+from navipy.maths.homogeneous_transformations import compose_matrix
+import navipy.trajectories.transformations as mtf
+from navipy.trajectories.triangle import Triangle
class TestMarkersTransform(unittest.TestCase):
diff --git a/navipy/trajectories/test_trajectory.py b/navipy/trajectories/test_trajectory.py
index 755c012..57ffa76 100644
--- a/navipy/trajectories/test_trajectory.py
+++ b/navipy/trajectories/test_trajectory.py
@@ -1,8 +1,8 @@
import unittest
import numpy as np
import pandas as pd
-import tra3dpy.maths.constants as htconst
-from tra3dpy.trajectory import Trajectory
+import navipy.maths.constants as htconst
+from navipy.trajectories import Trajectory
class TestTrajectoryTransform(unittest.TestCase):
diff --git a/navipy/trajectories/test_triangle.py b/navipy/trajectories/test_triangle.py
index 76a06b9..b76cc92 100644
--- a/navipy/trajectories/test_triangle.py
+++ b/navipy/trajectories/test_triangle.py
@@ -3,7 +3,7 @@
import unittest
import numpy as np
import pandas as pd
-from tra3dpy.markers.triangle import Triangle
+from navipy.trajectories.triangle import Triangle
class TestTriangle(unittest.TestCase):
diff --git a/navipy/trajectories/transformations.py b/navipy/trajectories/transformations.py
index 4b61734..bd59423 100644
--- a/navipy/trajectories/transformations.py
+++ b/navipy/trajectories/transformations.py
@@ -1,8 +1,8 @@
"""
"""
import numpy as np
-from tra3dpy.markers.triangle import Triangle
-import tra3dpy.maths.homogeneous_transformations as ht
+from navipy.trajectories.triangle import Triangle
+import navipy.maths.homogeneous_transformations as ht
from scipy.optimize import minimize
_modes = []
--
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