From ac3ca4d04b5c16c1c51bc4075c49e42d7b4aeb48 Mon Sep 17 00:00:00 2001
From: "Olivier J.N. Bertrand" <olivier.bertrand@uni-bielefeld.de>
Date: Tue, 25 Sep 2018 11:55:44 +0200
Subject: [PATCH] Update database to save frame # as well in order to avoid
confusion in case of nans
---
doc/source/tutorials/04-optic-flow.ipynb | 38 ++++++-
navipy/database/__init__.py | 132 ++++++++++-------------
2 files changed, 89 insertions(+), 81 deletions(-)
diff --git a/doc/source/tutorials/04-optic-flow.ipynb b/doc/source/tutorials/04-optic-flow.ipynb
index 1b2bc3a..748a288 100644
--- a/doc/source/tutorials/04-optic-flow.ipynb
+++ b/doc/source/tutorials/04-optic-flow.ipynb
@@ -650,9 +650,41 @@
"cell_type": "markdown",
"metadata": {},
"source": [
- "ToDO:\n",
- "* implement obpc in optic flow\n",
- "* convert markers2bee_sh into obpc format. Need to create viewing dir for el and az, and scene from radius.\n"
+ "## Optic flow from a database\n",
+ "\n",
+ "Database of rendered views along a trajectory can be created by using the tool `blendalongtraj`. Once the database has been created, optic flow can be obtain by using the difference in the position orientation and the distance to surrounding objects (The 'D' channel)."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": null,
+ "metadata": {},
+ "outputs": [],
+ "source": [
+ "import pkg_resources\n",
+ "from navipy.database import DataBase\n",
+ "mydbfile = pkg_resources.resource_filename(\n",
+ " 'navipy', 'resources/database.db')\n",
+ "mydb = DataBase(mydbfile)\n",
+ "mytraj = mydb.posorients\n",
+ "mytrajdiff = mytraj.differentiate(periods=1)\n",
+ "mytrajvel = mytraj.join(mytrajdiff)\n",
+ "mytrajvel.dropna().head()\n",
+ "\n",
+ "my_opticflow=pd.DataFrame(index=mytrajvel.index,\n",
+ " columns=pd.MultiIndex.from_product([points_name,['rof','hof','vof']]))\n",
+ "my_opticflow=my_opticflow.swaplevel(axis=1)\n",
+ "horizontal_of = np.zeros((mytrajvel.shape[0],*mydb.viewing_directions[...,0].shape))\n",
+ "vertical_of = horizontal_of.copy()\n",
+ "\n",
+ "for ii, (frame_i, velocity) in enumerate(mytrajvel.dropna().iterrows()):\n",
+ " scene = mydb.scene(velocity)\n",
+ " distance = scene[...,3,0]\n",
+ " # Calculate the optic flow of these points\n",
+ " _,hof,vof = optic_flow(distance,mydb.viewing_directions,velocity)\n",
+ " # save the results in df\n",
+ " horizontal_of[ii,...]=hof\n",
+ " vertical_of[ii,...]=vof"
]
},
{
diff --git a/navipy/database/__init__.py b/navipy/database/__init__.py
index f7a84ab..0083324 100644
--- a/navipy/database/__init__.py
+++ b/navipy/database/__init__.py
@@ -137,6 +137,7 @@ class DataBase():
self.tablecolumns['position_orientation']['q_1'] = 'real'
self.tablecolumns['position_orientation']['q_2'] = 'real'
self.tablecolumns['position_orientation']['q_3'] = 'real'
+ self.tablecolumns['position_orientation']['frame_i'] = 'real'
self.tablecolumns['position_orientation']['rotconv_id'] = 'string'
self.tablecolumns['image'] = dict()
self.tablecolumns['image']['data'] = 'array'
@@ -292,6 +293,12 @@ class DataBase():
raise Exception(msg)
found_convention = False
index = posorient.index
+ if isinstance(posorient.name, int):
+ msg = 'posorient.name should give the frame #'
+ self._logger.exception(msg)
+ raise Exception(msg)
+ frame_i = posorient.name
+
if isinstance(index, pd.MultiIndex):
convention = index.levels[0][-1]
else:
@@ -353,79 +360,35 @@ class DataBase():
msg = 'posorient must not contain nan\n {}'.format(posorient)
self._logger.exception(msg)
raise ValueError(msg)
- cursor = self.db_cursor.execute('select * from position_orientation')
- names = list(map(lambda x: x[0], cursor.description))
where = ""
- params = None
- if 'alpha_0' in names:
- self._logger.warning("you are loading a database with an\
- old convention")
- where += """x>=? and x<=?"""
- where += """and y>=? and y<=?"""
- where += """and z>=? and z<=?"""
- where += """and alpha_0>=? and alpha_0<=?"""
- where += """and alpha_1>=? and alpha_1<=?"""
- where += """and alpha_2>=? and alpha_2<=?"""
- params = (
- posorient['location']['x'] - self.__float_tolerance,
- posorient['location']['x'] + self.__float_tolerance,
- posorient['location']['y'] - self.__float_tolerance,
- posorient['location']['y'] + self.__float_tolerance,
- posorient['location']['z'] - self.__float_tolerance,
- posorient['location']['z'] + 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<=?"""
- where += """and z>=? and z<=?"""
- where += """and q_0>=? and q_0<=?"""
- where += """and q_1>=? and q_1<=?"""
- where += """and q_2>=? and q_2<=?"""
- where += """and rotconv_id =?"""
- params = (
- posorient['location']['x'] - self.__float_tolerance,
- posorient['location']['x'] + self.__float_tolerance,
- posorient['location']['y'] - self.__float_tolerance,
- posorient['location']['y'] + self.__float_tolerance,
- posorient['location']['z'] - self.__float_tolerance,
- posorient['location']['z'] + 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<=?"""
- where += """and y>=? and y<=?"""
- where += """and z>=? and z<=?"""
- where += """and q_0>=? and q_0<=?"""
- where += """and q_1>=? and q_1<=?"""
- where += """and q_2>=? and q_2<=?"""
+ where += """x>=? and x<=?"""
+ where += """and y>=? and y<=?"""
+ where += """and z>=? and z<=?"""
+ where += """and q_0>=? and q_0<=?"""
+ where += """and q_1>=? and q_1<=?"""
+ where += """and q_2>=? and q_2<=?"""
+ where += """and rotconv_id =?"""
+ where += """and frame_i = ?"""
+ params = (
+ posorient['location']['x'] - self.__float_tolerance,
+ posorient['location']['x'] + self.__float_tolerance,
+ posorient['location']['y'] - self.__float_tolerance,
+ posorient['location']['y'] + self.__float_tolerance,
+ posorient['location']['z'] - self.__float_tolerance,
+ posorient['location']['z'] + 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,
+ frame_i)
+ if convention == 'quaternion':
where += """and q_3>=? and q_3<=?"""
- where += """and rotconv_id =?"""
- params = (
- posorient['location']['x'] - self.__float_tolerance,
- posorient['location']['x'] + self.__float_tolerance,
- posorient['location']['y'] - self.__float_tolerance,
- posorient['location']['y'] + self.__float_tolerance,
- posorient['location']['z'] - self.__float_tolerance,
- posorient['location']['z'] + 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,
+ params = params + (
posorient[convention][naming_map[3]] - self.__float_tolerance,
- posorient[convention][naming_map[3]] + self.__float_tolerance,
- convention)
+ posorient[convention][naming_map[3]] + self.__float_tolerance)
self.db_cursor.execute(
"""
SELECT count(*)
@@ -445,8 +408,8 @@ class DataBase():
self.db_cursor.execute(
"""
INSERT
- INTO position_orientation(x,y,z,q_0,q_1,q_2,q_3,rotconv_id)
- VALUES (?,?,?,?,?,?,?,?)
+ INTO position_orientation(x,y,z,q_0,q_1,q_2,q_3,rotconv_id,frame_i)
+ VALUES (?,?,?,?,?,?,?,?,?)
""", (
posorient['location']['x'],
posorient['location']['y'],
@@ -455,13 +418,13 @@ class DataBase():
posorient[convention]['alpha_1'],
posorient[convention]['alpha_2'],
np.nan,
- convention))
+ convention, frame_i))
else:
self.db_cursor.execute(
"""
INSERT
- INTO position_orientation(x,y,z,q_0,q_1,q_2,rotconv_id)
- VALUES (?,?,?,?,?,?,?,?)
+ INTO position_orientation(x,y,z,q_0,q_1,q_2,rotconv_id,frame_i)
+ VALUES (?,?,?,?,?,?,?,?,?)
""", (
posorient['location']['x'],
posorient['location']['y'],
@@ -470,7 +433,7 @@ class DataBase():
posorient[convention]['q_1'],
posorient[convention]['q_2'],
posorient[convention]['q_3'],
- convention))
+ convention, frame_i))
rowid = self.db_cursor.lastrowid
self.db.commit()
return rowid
@@ -532,15 +495,20 @@ class DataBase():
return self.__convention
@property
- def posorients(self):
+ def posorients(self, indexby='frame_i'):
"""Return the position orientations of all points in the \
database
+ :params indexby: index posorients by 'frame_i' (default) or 'id'
:returns: all position orientations
:rtype: list of pd.Series
"""
posorient = pd.read_sql_query(
"select * from position_orientation;", self.db)
- posorient.set_index('id', inplace=True)
+ if indexby in posorient.columns:
+ posorient.set_index('frame_i', inplace=True)
+ else: # Handle older db version
+ print('Could not index by {}'.format(indexby))
+ posorient.set_index('id', inplace=True)
if self.rotation_convention is not None:
posorients = Trajectory()
posorients.from_dataframe(posorient, rotconv=self.__convention)
@@ -562,6 +530,14 @@ class DataBase():
# Read from database
#
def read_posorient(self, posorient=None, rowid=None):
+ """Read posorient with a given posorient or rowid
+
+ :param posorient: pd.Series with MuliIndex
+ :param rowid: integer, rowid of the database
+ :returns: return posorient
+ :rtype: pd.Series
+
+ """
if rowid is not None:
if not isinstance(rowid, int):
msg = 'rowid must be an integer'
--
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