diff --git a/navipy/database/__init__.py b/navipy/database/__init__.py
index e48e7fc04a2f54d7fd69910070984e6899b5b1b6..2affba62d28d0be496b54ff925335cd1c2bfd494 100644
--- a/navipy/database/__init__.py
+++ b/navipy/database/__init__.py
@@ -110,10 +110,16 @@ It creates three sql table on initialisation.
raise TypeError('filename should be a string')
if not isinstance(channels, list):
raise TypeError('nb_channel should be a list or np array')
- """for c in channels:
- if not c in ['R','G','B','D']:
- raise ValueError('channels
- must be either R,G,B or D (Distance)')"""
+ for c in channels:
+ if c is None:
+ raise ValueError('channels\
+ must not be None')
+ if c is np.nan:
+ raise ValueError('channels\
+ must not be of nan value')
+ if isinstance(c, list) or isinstance(c, np.ndarray):
+ raise ValueError('channels\
+ must be single value')
self.filename = filename
self.channels = channels
self.normalisation_columns = list()
@@ -343,8 +349,6 @@ database
return posorient
def read_posorient(self, posorient=None, rowid=None):
- if not isinstance(posorient, pd.Series):
- ('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')
@@ -364,16 +368,17 @@ database
raise ValueError('missing index alpha_2')
if np.any(pd.isnull(posorient)):
raise ValueError('posorient must not contain nan')
- if not isinstance(rowid, int):
- raise TypeError('rowid must be an integer')
- if rowid <= 0:
- raise ValueError('rowid must be greater zero')
- if rowid is np.nan:
- raise ValueError('rowid must not be nan')
+ if rowid is not None:
+ if not isinstance(rowid, int):
+ raise TypeError('rowid must be an integer')
+ if rowid <= 0:
+ raise ValueError('rowid must be greater zero')
+ if rowid is np.nan:
+ raise ValueError('rowid must not be nan')
if (posorient is None) and (rowid is None):
- Exception('posorient and rowid can not be both None')
+ raise Exception('posorient and rowid can not be both None')
if posorient is not None:
- rowid = self.get_posid(posorient)
+ rowid = self.get_posid(posorient)
# Read images
tablename = 'position_orientation'
toreturn = pd.read_sql_query(
@@ -399,8 +404,6 @@ database
:rtype: numpy.ndarray
"""
- if not isinstance(posorient, pd.Series):
- ('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')
@@ -463,6 +466,8 @@ database
return toreturn
def denormalise_image(self, image, cmaxminrange):
+ if not isinstance(image, np.ndarray):
+ raise TypeError('image must be np.array')
if len(image.shape) != 3:
raise Exception('image should be 3D array')
if image.shape[2] != len(self.channels):
@@ -470,7 +475,7 @@ database
number of channels {}'.format(
len(self.channels)))
if not isinstance(cmaxminrange, pd.Series):
- raise Exception('cmaxminrange should be a pandas Series')
+ raise TypeError('cmaxminrange should be a pandas Series')
if cmaxminrange.empty:
raise Exception('cmaxminrange must not be empty')
for chan_n in self.channels:
@@ -517,6 +522,7 @@ class DataBaseSave(DataBase):
DataBase.__init__(self, filename, channels=channels)
self.arr_dtype = arr_dtype
+ @property
def create(self):
"""use to decide weather to alter the database or not
return True because we will need
@@ -542,9 +548,9 @@ class DataBaseSave(DataBase):
def insert_replace(self, tablename, params):
if not isinstance(tablename, str):
- raise ValueError('table are named by string')
+ raise TypeError('table are named by string')
if not isinstance(params, dict):
- raise ValueError('params should be dictionary columns:val')
+ raise TypeError('params should be dictionary columns:val')
params_list = list()
columns_str = ''
for key, val in params.items():
diff --git a/navipy/moving/agent.py b/navipy/moving/agent.py
index 3a13cc2eb3dac580baa1c90ff26bcb667a34ba9a..6b0225e42c4512fa54fe9eca664435310fe27791 100644
--- a/navipy/moving/agent.py
+++ b/navipy/moving/agent.py
@@ -10,6 +10,8 @@ import inspect
from navipy.database import DataBaseLoad
import navipy.moving.maths as navimomath
+version = float(nx.__version__)
+
def defaultcallback(*args, **kwargs):
"""default call back"""
@@ -309,7 +311,11 @@ class GraphAgent():
results_edges = []
posorients_queue = JoinableQueue()
results_queue = Queue()
- for node in self._graph.nodes:
+ if version < 2:
+ graph_nodes = list(self._graph.nodes())
+ else:
+ graph_nodes = list(self._graph.nodes)
+ for node in graph_nodes:
posorients_queue.put(self._graph.nodes[node]['posorient'])
# Start ndatabase loader
@@ -341,7 +347,11 @@ class GraphAgent():
self.check_single_target()
def check_single_target(self):
- for node in self._graph.nodes:
+ if version < 2:
+ graph_nodes = list(self._graph.nodes())
+ else:
+ graph_nodes = list(self._graph.nodes)
+ for node in graph_nodes:
# not connected -> loop not ran
for count, _ in enumerate(self._graph.neighbors(node)):
# count == 0 -> connected to one node
diff --git a/navipy/moving/test_agent.py b/navipy/moving/test_agent.py
index 65f2df4aceccb4a63e83b335fe5a542f89c44fc8..0247b407359794581950d17b79712943844394a7 100644
--- a/navipy/moving/test_agent.py
+++ b/navipy/moving/test_agent.py
@@ -10,6 +10,8 @@ import pkg_resources
import unittest
+version = float(nx.__version__)
+
class TestNavipyMovingAgent(unittest.TestCase):
@@ -89,13 +91,20 @@ class TestNavipyMovingAgent(unittest.TestCase):
def test_init_graphagent(self):
agent = naviagent.GraphAgent(self.mydb_filename)
- self.assertEqual(sorted(agent.graph.nodes),
+ if version < 2:
+ graph_nodes = list(agent.graph.nodes())
+ else:
+ graph_nodes = list(agent.graph.nodes)
+ self.assertEqual(sorted(graph_nodes),
sorted(list(self.mydb.posorients.index)),
'Init of graph failed. Node missmatch')
def test_graph_setter(self):
agent = naviagent.GraphAgent(self.mydb_filename)
- graph_nodes = list(agent.graph.nodes)
+ if version < 2:
+ graph_nodes = list(agent.graph.nodes())
+ else:
+ graph_nodes = list(agent.graph.nodes)
graph_edges = list()
for gnode in graph_nodes[1:]:
graph_edges.append((gnode, graph_nodes[0]))
@@ -121,7 +130,10 @@ class TestNavipyMovingAgent(unittest.TestCase):
# Test all node to first
agent = naviagent.GraphAgent(self.mydb_filename)
- graph_nodes = list(agent.graph.nodes)
+ if version < 2:
+ graph_nodes = list(agent.graph.nodes())
+ else:
+ graph_nodes = list(agent.graph.nodes)
graph_edges = list()
for gnode in graph_nodes[1:]:
graph_edges.append((gnode, graph_nodes[0]))
@@ -183,7 +195,10 @@ class TestNavipyMovingAgent(unittest.TestCase):
"""
agent = naviagent.GraphAgent(self.mydb_filename)
# Local maxima
- graph_nodes = list(agent.graph.nodes)
+ if version < 2:
+ graph_nodes = list(agent.graph.nodes())
+ else:
+ graph_nodes = list(agent.graph.nodes)
graph_edges = list()
graph_edges.append((graph_nodes[0],
graph_nodes[1]))
diff --git a/todo b/todo
index 51df4e6d00379601db1e82052674e9e2d9fe3b91..ac8b3a852f9689eab6fd57b47e0fca83053c1fa2 100644
--- a/todo
+++ b/todo
@@ -16,28 +16,19 @@ should be replaced by
def posorients(self)
Need to propagate the changes through all the code (see rendering / processing / moving )
-------------------------------------------------------
-0004: Change every assert by a if () raise TypeError/IOError/KeyError/...
-- present in processing
-- present in database
+
+Should be done, but maybe I missed something?
------------------------------------------------------
0005: Write test function for raise Error
- for every raise error create a test function, checking that the error is correctly thrown (see moving/test_agent for inspiration)
-------------------------------------------------------
-0006: Improve comparing/__init__.py
-- Change comment in simple_image_diff
-- call simple_image_diff in imagediff. you can then remove all the assert (that should be raise Error at that point) from imagediff
-- Add comment to diff_optic_flow / add reference to article.
-- rename capitalised variable A,ATA, and b as longer variable name [future PEP8 will forbid this]
+also should be done. But I did not add any more checks to the moving part, shall I check for additional possible checks?
-------------------------------------------------------
-0007: Improve cyber_bee so that every getter and setter are properties
-0008: Improve bee_sampling so that every getter and setter are properties
--------------------------------------------------------------------
0009: can the last dimension (4) of the place-code be greater 1? (should be 1)
Yes it can, see apcv a [1x1x1x3] array
0010: what is the image in the database? must it be transformed to a a scene?
The image is an image, and distance the distance. I added scene as a join image+distance array
+ now we do not have a read_image function in database anymore, is it supposed to be like this?