diff --git a/navipy/database/__init__.py b/navipy/database/__init__.py
index 814069643f410a072f5c0a98f0de6ccd7f41a4b8..bef05641d49792b26df16014a7cf02f0e7b5df79 100644
--- a/navipy/database/__init__.py
+++ b/navipy/database/__init__.py
@@ -84,12 +84,15 @@ import pandas as pd
import sqlite3
import io
import warnings
+import navipy.processing.tools as tools
def adapt_array(arr):
"""
http://stackoverflow.com/a/31312102/190597 (SoulNibbler)
"""
+ if array is None:
+ raise ValueError('array must not be None')
out = io.BytesIO()
np.save(out, arr)
out.seek(0)
@@ -97,6 +100,8 @@ def adapt_array(arr):
def convert_array(text):
+ if text is None:
+ raise ValueError('text must not be None')
out = io.BytesIO(text)
out.seek(0)
return np.load(out)
@@ -118,8 +123,11 @@ It creates three sql table on initialisation.
"""Initialisation of the database """
if not isinstance(filename, str):
raise TypeError('filename should be a string')
- if not isinstance(channels, list):
- raise TypeError('nb_channel should be an integer')
+ if (not isinstance(channels, list) or not isinstance(channels,np.array)):
+ 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)')"""
self.filename = filename
self.channels = channels
self.normalisation_columns = list()
@@ -150,9 +158,9 @@ It creates three sql table on initialisation.
timeout=10)
self.db_cursor = self.db.cursor()
for tablename, _ in self.tablecolumns.items():
- assert self.table_exist(tablename),\
- '{} does not contain a table named {}'.format(
- filename, tablename)
+ if not self.table_exist(tablename):
+ raise Exception('{} does not contain a table named {}'.format(
+ filename, tablename))
elif self.create:
# Create database
self.db = sqlite3.connect(
@@ -177,7 +185,8 @@ It creates three sql table on initialisation.
self.viewing_directions[..., 1] = ma
def table_exist(self, tablename):
- assert isinstance(tablename, str), 'tablename should be a string'
+ if not isinstance(tablename, str):
+ raise TypeError('tablename should be a string')
self.db_cursor.execute(
"""
SELECT count(*)
@@ -187,6 +196,12 @@ It creates three sql table on initialisation.
return bool(self.db_cursor.fetchone())
def check_data_validity(self, rowid):
+ 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')
self.db_cursor.execute(
"""
SELECT count(*)
@@ -210,9 +225,28 @@ It creates three sql table on initialisation.
valid = valid and bool(self.db_cursor.fetchone()[0])
return valid
- def posid(self, posorient):
- assert isinstance(posorient, pd.Series),\
- 'posorient should be a pandas Series'
+ def get_posid(self, posorient):
+ if no 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')
+ if posorient.empty:
+ raise Exception('position must not be empty')
+ if 'x' not in posorient.index:
+ raise ValueError('missing index x')
+ if 'y' not in posorient.index:
+ raise ValueError('missing index y')
+ if 'z' not in posorient.index:
+ raise ValueError('missing index z')
+ if 'alpha_0' not in posorient.index:
+ raise ValueError('missing index alpha_0')
+ if 'alpha_1' not in posorient.index:
+ raise ValueError('missing index alpha_1')
+ if 'alpha_2' not in posorient.index:
+ raise ValueError('missing index alpha_2')
+ if not ~np.any(pd.isnull(posorient)):
+ raise ValueError('posorient must not contain nan')
where = """x>=? and x<=?"""
where += """and y>=? and y<=?"""
where += """and z>=? and z<=?"""
@@ -277,6 +311,13 @@ class DataBaseLoad(DataBase):
def __init__(self, filename, channels=['R', 'G', 'B', 'D']):
"""Initialise the DataBaseLoader"""
+ if not isinstance(filename, str):
+ raise TypeError('filename should be a string')
+ if (not isinstance(channels, list) or not isinstance(channels,np.array)):
+ 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)')
DataBase.__init__(self, filename, channels=channels)
@property
@@ -315,10 +356,37 @@ database
return posorient
def read_posorient(self, posorient=None, rowid=None):
- assert (posorient is None) or (rowid is None),\
- 'posorient and rowid can not be both None'
+ if no isinstance(posorient, pd.Series):
+ ('posorient should be a pandas Series')
if posorient is not None:
- rowid = self.posid(posorient)
+ if not isinstance(posorient, pd.Series):
+ raise TypeError('posorient should be a pandas Series')
+ if posorient.empty:
+ raise Exception('position must not be empty')
+ if 'x' not in posorient.index:
+ raise ValueError('missing index x')
+ if 'y' not in posorient.index:
+ raise ValueError('missing index y')
+ if 'z' not in posorient.index:
+ raise ValueError('missing index z')
+ if 'alpha_0' not in posorient.index:
+ raise ValueError('missing index alpha_0')
+ if 'alpha_1' not in posorient.index:
+ raise ValueError('missing index alpha_1')
+ if 'alpha_2' not in posorient.index:
+ raise ValueError('missing index alpha_2')
+ if not ~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 (posorient is None) and (rowid is None):
+ Exception('posorient and rowid can not be both None')
+ if posorient is not None:
+ rowid = self.get_posid(posorient)
# Read images
tablename = 'position_orientation'
toreturn = pd.read_sql_query(
@@ -333,26 +401,9 @@ database
toreturn = toreturn.astype(float)
return toreturn
- def scene(self, posorient=None, rowid=None):
- """ Return a scene at a position orientation or given rowid \
- in a given database.
-
- :param database: a DataBaseLoad class \
- :param posorient: a pandas Series with index: \
- ['x','y','z','alpha_0,'alpha_1,'alpha_2'] (default None, i.e. not used)
- :param rowid: a row identification integer for directly reading \
- in the database (default None, i.e. not used).
- :returns: a scene [elevation, azimuth, channel, 1] or \
- [ommatidia,channel,1].
- :rtype: np.ndarray
-
- .. literalinclude:: example/database/scene.py
- :lines: 14-15
-
- .. plot:: example/database/scene.py
- """
- if (posorient is None) and (rowid is None):
- raise ValueError('posorient and rowid can not be both None')
+ def read_image(self, posorient=None, rowid=None):
+ if no 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')
@@ -372,16 +423,29 @@ database
raise ValueError('missing index alpha_2')
if not ~np.any(pd.isnull(posorient)):
raise ValueError('posorient must not contain nan')
- rowid = self.posid(posorient)
-
- if rowid is not None:
- if not isinstance(rowid, int):
- raise TypeError('rowid must be of type integer')
- if rowid <= 0:
- raise ValueError('rowid must be greater zero')
- if rowid is np.nan:
- raise ValueError('rowid must not be 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 (posorient is None) and (rowid is None):
+ raise Exception('posorient and rowid can not be both None')
+ if posorient is not None:
+ rowid = self.get_posid(posorient)
+ """Read an image at a given position-orientation or given id of row in the \
+ database.
+
+ :param posorient: a pandas Series with index \
+ ['x','y','z','alpha_0','alpha_1','alpha_2']
+ :param rowid: an integer
+ :returns: an image
+ :rtype: numpy.ndarray
+ """
+ if (posorient is None) and (rowid is None):
+ Exception('posorient and rowid can not be both None')
+ if posorient is not None:
+ rowid = self.get_posid(posorient)
# Read images
tablename = 'image'
self.db_cursor.execute(
@@ -399,24 +463,37 @@ database
FROM {}
WHERE (rowid={})
""".format(tablename, rowid), self.db)
- assert cmaxminrange.shape[0] == 1,\
- 'Error while reading normalisation factors'
+ if cmaxminrange.shape[0] != 1:
+ raise Exception('Error while reading normalisation factors')
cmaxminrange = cmaxminrange.iloc[0, :]
cmaxminrange.name = cmaxminrange.id
cmaxminrange.drop('id')
cmaxminrange = cmaxminrange.astype(float)
- scene = self.denormalise_image(image, cmaxminrange)
- scene = scene[..., np.newaxis]
- return scene
+ return self.denormalise_image(image, cmaxminrange)
def denormalise_image(self, image, cmaxminrange):
- assert len(image.shape) == 3,\
- 'image should be 3D array'
- assert image.shape[2] == len(self.channels),\
- 'image does not have the required number of channels {}'.format(
- len(self.channels))
- assert isinstance(cmaxminrange, pd.Series),\
- 'cmaxminrange should be a pandas Series'
+ if len(image.shape) != 3:
+ raise Exception('image should be 3D array')
+ if image.shape[2] != len(self.channels):
+ raise Exception('image does not have the required number of channels {}'.format(
+ len(self.channels)))
+ if not isinstance(cmaxminrange, pd.Series):
+ raise Exception('cmaxminrange should be a pandas Series')
+ if cmaxminrange.empty:
+ raise Exception('cmaxminrange must not be empty')
+ for chan_n in self.channels:
+ if str(chan_n) + '_max' not in posorient.index:
+ raise ValueError('cminmax range is missing index '+str(chan_n) + '_max')
+ if str(chan_n) + '_min' not in posorient.index:
+ raise ValueError('cminmax range is missing index '+str(chan_n) + '_min')
+ if str(chan_n) + '_range' not in posorient.index:
+ raise ValueError('cminmax range is missing index '+str(chan_n) + '_range')
+ if any(np.isnan(cmaxminrange.loc[str(chan_n) + '_max'])):
+ raise ValueError('cmaxminrange contains nans')
+ if any(np.isnan(cmaxminrange.loc[str(chan_n) + '_min'])):
+ raise ValueError('cmaxminrange contains nans')
+ if any(np.isnan(cmaxminrange.loc[str(chan_n) + '_range'])):
+ raise ValueError('cmaxminrange contains nans')
denormed_im = np.zeros(image.shape, dtype=np.float)
maxval_nim = np.iinfo(image.dtype).max
#
@@ -453,7 +530,7 @@ class DataBaseSave(DataBase):
def write_image(self, posorient, image):
normed_im, cmaxminrange = self.normalise_image(image, self.arr_dtype)
- rowid = self.posid(posorient)
+ rowid = self.get_posid(posorient)
# Write image
tablename = 'image'
params = dict()
@@ -469,10 +546,10 @@ class DataBaseSave(DataBase):
self.insert_replace(tablename, params)
def insert_replace(self, tablename, params):
- assert isinstance(tablename, str),\
- 'table are named by string'
- assert isinstance(params, dict),\
- 'params should be dictionary columns:val'
+ if not isinstance(tablename, str):
+ raise ValueError('table are named by string')
+ if not isinstance(params, dict):
+ raise ValueError('params should be dictionary columns:val')
params_list = list()
columns_str = ''
for key, val in params.items():
@@ -498,6 +575,16 @@ class DataBaseSave(DataBase):
self.db.commit()
def normalise_image(self, image, dtype=np.uint8):
+ if not isinstance(image,np.ndarray):
+ raise TypeError('image must be np.array')
+ if any(np.isnan(image)):
+ raise ValueError('image must not contain nan values')
+ if image.shape[0]<=0 or image.shape[1]<=0:
+ raise Exception('image dimensions incorrect')
+ if image.shape[2]!=len(self.channels):
+ raise Exception('image channels number differs from given channel number')
+ if not tools.is_numeric_array(scene):
+ raise TypeError('scene is of non numeric type')
normed_im = np.zeros(image.shape, dtype=dtype)
maxval_nim = np.iinfo(normed_im.dtype).max
#