diff --git a/navipy/database/__init__.py b/navipy/database/__init__.py
index e94a6d7cc684f0ace9aa548748b8250a22fd5a1f..ea54ebb5e4cc98615997468b9466ba4e97c2cf2c 100644
--- a/navipy/database/__init__.py
+++ b/navipy/database/__init__.py
@@ -9,6 +9,8 @@ import sqlite3
import io
import warnings
from navipy.scene import is_numeric_array, check_scene
+import navipy.maths.constants as mconst
+from navipy.tools.trajectory import Trajectory
def adapt_array(arr):
@@ -98,7 +100,7 @@ class DataBase():
for col in self.normalisation_columns:
self.tablecolumns['normalisation'][col] = 'real'
- if os.path.exists(filename):
+ if (os.path.exists(filename)) and (self.create is False):
# Check database
self.db = sqlite3.connect(
'file:' + filename + '?cache=shared', uri=True,
@@ -220,62 +222,58 @@ class DataBase():
"""
if not isinstance(posorient, pd.Series):
raise TypeError('posorient should be a pandas Series')
- if posorient is not None:
- if not isinstance(posorient, pd.Series):
- raise TypeError('posorient should be a pandas Series')
- if posorient.empty:
- raise Exception('position must not be empty')
- found_convention = False
- index = posorient.index
- convention = index.get_level_values(0)[-1]
- if convention == 'rxyz':
- found_convention = True
- elif convention == 'ryzx':
- found_convention = True
- elif convention == 'rxzy':
- found_convention = True
- elif convention == 'ryxz':
- found_convention = True
- elif convention == 'rzxy':
- found_convention = True
- elif convention == 'rzyx':
- found_convention = True
- elif convention == 'quaternion':
- found_convention = True
- if not found_convention:
- raise ValueError("your convention is not supported")
- if convention != 'quaternion':
- if 'x' not in posorient.index.get_level_values(1):
- raise ValueError('missing index x')
- if 'y' not in posorient.index.get_level_values(1):
- raise ValueError('missing index y')
- if 'z' not in posorient.index.get_level_values(1):
- raise ValueError('missing index z')
- if 'alpha_0' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_0')
- if 'alpha_1' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_1')
- if 'alpha_2' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- elif convention == 'quaternion':
- if 'x' not in posorient.index.get_level_values(1):
- raise ValueError('missing index x')
- if 'y' not in posorient.index.get_level_values(1):
- raise ValueError('missing index y')
- if 'z' not in posorient.index.get_level_values(1):
- raise ValueError('missing index z')
- if 'q_0' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_0')
- if 'q_1' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_1')
- if 'q_2' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- if 'q_3' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- if np.any(pd.isnull(posorient)):
- raise ValueError('posorient must not contain nan')
+ if posorient.empty:
+ raise Exception('position must not be empty')
+ found_convention = False
index = posorient.index
- convention = index.get_level_values(0)[-1]
+ convention = index.levels[0][-1]
+ if (convention in mconst._AXES2TUPLE.keys()) or \
+ convention == 'quaternion':
+ found_convention = True
+ if not found_convention:
+ msg = 'convention for rotation {} is not suppored\n'
+ msg += msg.format(convention)
+ msg += 'the following convention are supported\n:'
+ for rconv in mconst._AXES2TUPLE.keys():
+ msg += '{}\n'.format(rconv)
+ msg += 'quaternion\n'
+ raise KeyError(msg)
+ index_2ndlevel = posorient.index.get_level_values(1)
+ # Check that the posorient contains valid columns
+ # The user may be using alpha_ or q_
+ # and we therefore want to be able to handle both type
+ for val in ['x', 'y', 'z']:
+ if val not in index_2ndlevel:
+ raise ValueError('missing index {}'.format(val))
+ naming_map = list()
+ for ii in range(3):
+ if ('alpha_{}'.format(ii) not in index_2ndlevel) and \
+ ('q_{}'.format(ii) not in index_2ndlevel):
+ raise ValueError(
+ 'missing index alpha_{0:} or q_{0:}'.format(ii))
+ elif ('alpha_{}'.format(ii) in index_2ndlevel) and \
+ ('q_{}'.format(ii) in index_2ndlevel):
+ raise ValueError(
+ 'posorient should contains either alphas or qs')
+ elif ('alpha_{}'.format(ii) in index_2ndlevel):
+ naming_map.append('alpha_{}'.format(ii))
+ else:
+ naming_map.append('q_{}'.format(ii))
+ if convention == 'quaternion':
+ if 'q_3' not in index_2ndlevel:
+ raise ValueError('missing index q_3')
+ else:
+ naming_map.append('q_{}'.format(3))
+ else:
+ # q_3 is unnecessary for convention
+ # different than quaternion. The value
+ # should be set to nan, and wil therefore block during check of
+ # any nan. We drop it now.
+ if 'q_3' in index_2ndlevel:
+ posorient.drop((convention, 'q_3'), inplace=True)
+ if np.any(pd.isnull(posorient)):
+ raise ValueError(
+ 'posorient must not contain nan\n {}'.format(posorient))
cursor = self.db_cursor.execute('select * from position_orientation')
names = list(map(lambda x: x[0], cursor.description))
where = ""
@@ -296,12 +294,12 @@ class DataBase():
posorient['location']['y'] + self.__float_tolerance,
posorient['location']['z'] - self.__float_tolerance,
posorient['location']['z'] + self.__float_tolerance,
- posorient[convention]['alpha_0'] - self.__float_tolerance,
- posorient[convention]['alpha_0'] + self.__float_tolerance,
- posorient[convention]['alpha_1'] - self.__float_tolerance,
- posorient[convention]['alpha_1'] + self.__float_tolerance,
- posorient[convention]['alpha_2'] - self.__float_tolerance,
- posorient[convention]['alpha_2'] + self.__float_tolerance)
+ posorient[convention][naming_map[0]] - self.__float_tolerance,
+ posorient[convention][naming_map[0]] + self.__float_tolerance,
+ posorient[convention][naming_map[1]] - self.__float_tolerance,
+ posorient[convention][naming_map[1]] + self.__float_tolerance,
+ posorient[convention][naming_map[2]] - self.__float_tolerance,
+ posorient[convention][naming_map[2]] + self.__float_tolerance)
elif convention != 'quaternion':
where += """x>=? and x<=?"""
where += """and y>=? and y<=?"""
@@ -317,12 +315,12 @@ class DataBase():
posorient['location']['y'] + self.__float_tolerance,
posorient['location']['z'] - self.__float_tolerance,
posorient['location']['z'] + self.__float_tolerance,
- posorient[convention]['alpha_0'] - self.__float_tolerance,
- posorient[convention]['alpha_0'] + self.__float_tolerance,
- posorient[convention]['alpha_1'] - self.__float_tolerance,
- posorient[convention]['alpha_1'] + self.__float_tolerance,
- posorient[convention]['alpha_2'] - self.__float_tolerance,
- posorient[convention]['alpha_2'] + self.__float_tolerance,
+ posorient[convention][naming_map[0]] - self.__float_tolerance,
+ posorient[convention][naming_map[0]] + self.__float_tolerance,
+ posorient[convention][naming_map[1]] - self.__float_tolerance,
+ posorient[convention][naming_map[1]] + self.__float_tolerance,
+ posorient[convention][naming_map[2]] - self.__float_tolerance,
+ posorient[convention][naming_map[2]] + self.__float_tolerance,
convention)
else:
where += """x>=? and x<=?"""
@@ -340,14 +338,14 @@ class DataBase():
posorient['location']['y'] + self.__float_tolerance,
posorient['location']['z'] - self.__float_tolerance,
posorient['location']['z'] + self.__float_tolerance,
- posorient[convention]['q_0'] - self.__float_tolerance,
- posorient[convention]['q_0'] + self.__float_tolerance,
- posorient[convention]['q_1'] - self.__float_tolerance,
- posorient[convention]['q_1'] + self.__float_tolerance,
- posorient[convention]['q_2'] - self.__float_tolerance,
- posorient[convention]['q_2'] + self.__float_tolerance,
- posorient[convention]['q_3'] - self.__float_tolerance,
- posorient[convention]['q_3'] + self.__float_tolerance,
+ posorient[convention][naming_map[0]] - self.__float_tolerance,
+ posorient[convention][naming_map[0]] + self.__float_tolerance,
+ posorient[convention][naming_map[1]] - self.__float_tolerance,
+ posorient[convention][naming_map[1]] + self.__float_tolerance,
+ posorient[convention][naming_map[2]] - self.__float_tolerance,
+ posorient[convention][naming_map[2]] + self.__float_tolerance,
+ posorient[convention][naming_map[3]] - self.__float_tolerance,
+ posorient[convention][naming_map[3]] + self.__float_tolerance,
convention)
self.db_cursor.execute(
"""
@@ -400,7 +398,8 @@ class DataBase():
self.db.commit()
return rowid
else:
- raise ValueError('posorient not found')
+ raise ValueError('posorient not found \n {} \n {} \n {}'.format(
+ posorient, where, params))
@property
def create(self):
@@ -458,24 +457,21 @@ class DataBaseLoad(DataBase):
posorient = pd.read_sql_query(
"select * from position_orientation;", self.db)
posorient.set_index('id', inplace=True)
- if not isinstance(posorient.index, pd.core.index.MultiIndex):
+ if 'rotconv_id' in posorient.columns:
+ rotconv = posorient.loc[:, 'rotconv_id']
+ if np.all(rotconv == rotconv.iloc[0]):
+ posorients = Trajectory(
+ rotconv.iloc[0], indeces=posorient.index)
+ posorients.from_dataframe(posorient)
+ else:
+ posorients = posorient
+ else:
warnings.warn("you are loading a database with old\
- conventions, it will be transformed\
- automatically into the new one")
- convention = 'rxyz'
- tuples = []
- for n in posorient.columns:
- if n in ['x', 'y', 'z']:
- tuples.append(('location', n))
- else:
- tuples.append((convention, n))
- index = pd.MultiIndex.from_tuples(tuples,
- names=['position',
- 'orientation'])
- posorient.columns = index
- return posorient
-
- return posorient
+ conventions, it will be transformed\
+ automatically into the new one")
+ posorients = Trajectory(rotconv, indeces=posorient.index)
+ posorients.from_dataframe(posorient, rotconv='rxyz')
+ return posorients
@property
def normalisations(self):
@@ -490,60 +486,6 @@ class DataBaseLoad(DataBase):
return posorient
def read_posorient(self, posorient=None, rowid=None):
- if posorient is not None:
- if not isinstance(posorient, pd.Series):
- raise TypeError('posorient should be a pandas Series')
- if posorient.empty:
- raise Exception('position must not be empty')
- found_convention = False
- index = posorient.index
- convention = index.get_level_values(0)[-1]
- if convention == 'rxyz':
- found_convention = True
- elif convention == 'ryzx':
- found_convention = True
- elif convention == 'rxzy':
- found_convention = True
- elif convention == 'ryxz':
- found_convention = True
- elif convention == 'rzxy':
- found_convention = True
- elif convention == 'rzyx':
- found_convention = True
- elif convention == 'quaternion':
- found_convention = True
- if not found_convention:
- raise ValueError("your convention is not supported")
- if convention != 'quaternion':
- if 'x' not in posorient.index.get_level_values(1):
- raise ValueError('missing index x')
- if 'y' not in posorient.index.get_level_values(1):
- raise ValueError('missing index y')
- if 'z' not in posorient.index.get_level_values(1):
- raise ValueError('missing index z')
- if 'alpha_0' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_0')
- if 'alpha_1' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_1')
- if 'alpha_2' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- elif convention == 'quaternion':
- if 'x' not in posorient.index.get_level_values(1):
- raise ValueError('missing index x')
- if 'y' not in posorient.index.get_level_values(1):
- raise ValueError('missing index y')
- if 'z' not in posorient.index.get_level_values(1):
- raise ValueError('missing index z')
- if 'q_0' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_0')
- if 'q_1' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_1')
- if 'q_2' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- if 'q_3' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- if np.any(pd.isnull(posorient)):
- raise ValueError('posorient must not contain nan')
if rowid is not None:
if not isinstance(rowid, int):
raise TypeError('rowid must be an integer')
@@ -629,61 +571,6 @@ class DataBaseLoad(DataBase):
:returns: an image
:rtype: numpy.ndarray
"""
-
- if posorient is not None:
- if not isinstance(posorient, pd.Series):
- raise TypeError('posorient should be a pandas Series')
- if posorient.empty:
- raise Exception('position must not be empty')
- found_convention = False
- index = posorient.index
- convention = index.get_level_values(0)[-1]
- if convention == 'rxyz':
- found_convention = True
- elif convention == 'ryzx':
- found_convention = True
- elif convention == 'rxzy':
- found_convention = True
- elif convention == 'ryxz':
- found_convention = True
- elif convention == 'rzxy':
- found_convention = True
- elif convention == 'rzyx':
- found_convention = True
- elif convention == 'quaternion':
- found_convention = True
- if not found_convention:
- raise ValueError("your convention is not supported")
- if convention != 'quaternion':
- if 'x' not in posorient.index.get_level_values(1):
- raise ValueError('missing index x')
- if 'y' not in posorient.index.get_level_values(1):
- raise ValueError('missing index y')
- if 'z' not in posorient.index.get_level_values(1):
- raise ValueError('missing index z')
- if 'alpha_0' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_0')
- if 'alpha_1' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_1')
- if 'alpha_2' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- elif convention == 'quaternion':
- if 'x' not in posorient.index.get_level_values(1):
- raise ValueError('missing index x')
- if 'y' not in posorient.index.get_level_values(1):
- raise ValueError('missing index y')
- if 'z' not in posorient.index.get_level_values(1):
- raise ValueError('missing index z')
- if 'q_0' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_0')
- if 'q_1' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_1')
- if 'q_2' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- if 'q_3' not in posorient.index.get_level_values(1):
- raise ValueError('missing index alpha_2')
- if np.any(pd.isnull(posorient)):
- raise ValueError('posorient must not contain nan')
if rowid is not None:
if not isinstance(rowid, int):
raise TypeError('rowid must be an integer')
diff --git a/navipy/resources/database.db b/navipy/resources/database.db
index 450fe54728c12e42263541e1541b71d2e9e2a815..7fd82a0e02adad748ceec1126ae10d0f9744d128 100644
Binary files a/navipy/resources/database.db and b/navipy/resources/database.db differ
diff --git a/navipy/sensors/blendtest_renderer.py b/navipy/sensors/blendtest_renderer.py
index c6ce93aeea1fe892f436f05cba69cc5949e4876a..76c1ae56c9038ca0b3f3c9c441fe9062a42ec54c 100644
--- a/navipy/sensors/blendtest_renderer.py
+++ b/navipy/sensors/blendtest_renderer.py
@@ -77,23 +77,25 @@ class TestBlenderRender_renderer(unittest.TestCase):
"""
x = np.linspace(-0.5, 0.5, 5)
y = np.linspace(-0.5, 0.5, 5)
- z = [0]
- rotconv = 'rxyz'
+ z = [3]
+ alpha_0 = [np.pi/2]
+ rotconv = 'rzyx'
db_reffilename = pkg_resources.resource_filename(
'navipy', 'resources/database.db')
db_ref = DataBaseLoad(db_reffilename)
- with tempfile.NamedTemporaryFile() as tfile:
- outputfile = tfile.name
- self.renderer.render_ongrid(outputfile,
- x, y, z,
- rotconv=rotconv)
- db = DataBaseLoad(outputfile)
- posorients = db_ref.posorients
- for row_i, posorient in posorients.iterrows():
- refscene = db_ref.scene(posorient)
- try:
- scene = db.scene(posorient)
- except ValueError:
- msg = 'Scene has not been found'
- self.assertEqual(False, True, msg)
- np.testing.assert_allclose(scene, refscene)
+ tfile = tempfile.NamedTemporaryFile()
+ outputfile = tfile.name
+ self.renderer.render_ongrid(outputfile,
+ x, y, z, alpha_0,
+ rotconv=rotconv)
+ db = DataBaseLoad(outputfile)
+ posorients = db_ref.posorients
+ for row_i, posorient in posorients.iterrows():
+ refscene = db_ref.scene(posorient)
+ try:
+ scene = db.scene(posorient)
+ except ValueError:
+ msg = 'Scene has not been found {}'.format(db.posorients)
+ msg += '\n{}'.format(posorient)
+ self.assertEqual(False, True, msg)
+ np.testing.assert_allclose(scene, refscene)
diff --git a/navipy/sensors/blendunittest.py b/navipy/sensors/blendunittest.py
index 889dc2e5b8fba33d7f42c6107322ebe14692928b..4dabe5527dcaaef8744a1c0f530e8c4705f6063b 100644
--- a/navipy/sensors/blendunittest.py
+++ b/navipy/sensors/blendunittest.py
@@ -25,6 +25,11 @@ def parser_blendnavipy():
type=str,
default='navipy',
help=arghelp)
+ arghelp = 'Set pattern to look for in unittest (default: blendtest*.py)'
+ parser.add_argument('--pattern',
+ type=str,
+ default='blendtest*.py',
+ help=arghelp)
arghelp = 'Command to run blender\n'
arghelp += 'If not provided, the script will try to find the command'
arghelp += " by using: shutil.which('blender')"
@@ -40,12 +45,13 @@ def parser_blendnavipy():
action='count',
default=0,
help=arghelp)
+
return parser
-def run(start_dir):
+def run(start_dir, pattern):
suite = unittest.defaultTestLoader.discover(start_dir=start_dir,
- pattern='blendtest*.py')
+ pattern=pattern)
success = unittest.TextTestRunner().run(suite).wasSuccessful()
print(success)
if not success:
@@ -69,7 +75,8 @@ def main():
tfile.write(line.encode(encoding))
tfile.write('\n\n'.encode(encoding))
tfile.write('try:\n'.encode(encoding))
- tfile.write(' run("{}")\n'.format(args.start_dir).encode(encoding))
+ tfile.write(' run("{}","{}")\n'.format(
+ args.start_dir, args.pattern).encode(encoding))
tfile.write(' sys.exit(0)\n'.encode(encoding))
tfile.write('except Exception:\n'.encode(encoding))
tfile.write(' sys.exit(1)\n'.encode(encoding))
diff --git a/navipy/sensors/renderer.py b/navipy/sensors/renderer.py
index 10b3935443de22143e3930138f88a15b743c6899..fef4b8891012f19e5aad37362b4fe9208e52dce8 100644
--- a/navipy/sensors/renderer.py
+++ b/navipy/sensors/renderer.py
@@ -207,7 +207,7 @@ class BlenderRender(AbstractRender):
"""Initialise the Cyberbee
..todo check that TemporaryDirectory is writtable and readable
"""
- super(AbstractRender).__init__()
+ super(BlenderRender, self).__init__()
# Rendering engine needs to be Cycles to support panoramic
# equirectangular camera
bpy.context.scene.render.engine = 'CYCLES'
diff --git a/navipy/tools/trajectory.py b/navipy/tools/trajectory.py
index 7c049d9a57f58ea638b094766e18defc2cbdcf4c..cc2c890768bbab3b4cf9bbb1ea7937a2fc413ab8 100644
--- a/navipy/tools/trajectory.py
+++ b/navipy/tools/trajectory.py
@@ -2,11 +2,17 @@
Trajectory in navipy
"""
import pandas as pd
+import numpy as np
import navipy.maths.constants as mconst
class Trajectory(pd.DataFrame):
def __init__(self, rotconv, indeces):
+ columns = self.__build_columns(rotconv)
+ super().__init__(index=indeces, columns=columns)
+ self.__rotconv = rotconv
+
+ def __build_columns(self, rotconv):
if rotconv == 'quaternion':
index = pd.MultiIndex.from_tuples(
[('location', 'x'), ('location', 'y'),
@@ -26,8 +32,7 @@ class Trajectory(pd.DataFrame):
msg += '{}\n'.format(rconv)
msg += 'quaternion\n'
raise KeyError(msg)
- super().__init__(index=indeces, columns=index)
- self.__rotconv = rotconv
+ return index
@property
def x(self):
@@ -137,5 +142,53 @@ class Trajectory(pd.DataFrame):
def q_3(self, q_3):
self.__set_q_i(3, q_3)
+ def from_dataframe(self, df, rotconv=None):
+ """ Assign trajectory from a dataframe
+ """
+ if 'rotconv_id' in df.columns:
+ rotconv = df.loc[:, 'rotconv_id']
+ if not np.all(rotconv == rotconv.iloc[0]):
+ raise ValueError('More than one rotconv detected')
+ rotconv = rotconv.iloc[0] # They are all the same :)
+ elif rotconv is None:
+ msg = 'When dataframe does not contains rotconv_id,'
+ msg += 'a convention should be given'
+ raise ValueError(msg)
+
+ indeces = df.index
+ columns = self.__build_columns(rotconv)
+ super().__init__(index=indeces, columns=columns)
+ self.__rotconv = rotconv
+ # Position
+ self.x = df.x
+ self.y = df.y
+ self.z = df.z
+ # Orientation
+ if self.__rotconv == 'quaternion':
+ self.q_0 = df.q_0
+ self.q_1 = df.q_1
+ self.q_2 = df.q_2
+ else:
+ if 'q_0' in df.columns:
+ self.alpha_0 = df.q_0
+ elif 'alpha_0' in df.columns:
+ self.alpha_0 = df.alpha_0
+ else:
+ raise KeyError('df should contains q_0 or alpha_0')
+
+ if 'q_1' in df.columns:
+ self.alpha_1 = df.q_1
+ elif 'alpha_1' in df.columns:
+ self.alpha_1 = df.alpha_1
+ else:
+ raise KeyError('df should contains q_1 or alpha_1')
+
+ if 'q_2' in df.columns:
+ self.alpha_2 = df.q_2
+ elif 'alpha_2' in df.columns:
+ self.alpha_2 = df.alpha_2
+ else:
+ raise KeyError('df should contains q_2 or alpha_2')
+
def lollipops(self):
raise NameError('Not implemented')