diff --git a/navipy/database/__init__.py b/navipy/database/__init__.py
index bef05641d49792b26df16014a7cf02f0e7b5df79..e111ad5f7956a0fa12261cc551f262ca3e40890a 100644
--- a/navipy/database/__init__.py
+++ b/navipy/database/__init__.py
@@ -91,7 +91,7 @@ def adapt_array(arr):
"""
http://stackoverflow.com/a/31312102/190597 (SoulNibbler)
"""
- if array is None:
+ if arr is None:
raise ValueError('array must not be None')
out = io.BytesIO()
np.save(out, arr)
@@ -123,11 +123,13 @@ 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) or not isinstance(channels,np.array)):
+ 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)')"""
+ raise ValueError('channels
+ must be either R,G,B or D (Distance)')"""
self.filename = filename
self.channels = channels
self.normalisation_columns = list()
@@ -159,8 +161,8 @@ It creates three sql table on initialisation.
self.db_cursor = self.db.cursor()
for tablename, _ in self.tablecolumns.items():
if not self.table_exist(tablename):
- raise Exception('{} does not contain a table named {}'.format(
- filename, tablename))
+ raise Exception('{} does not contain a table\
+ named {}'.format(filename, tablename))
elif self.create:
# Create database
self.db = sqlite3.connect(
@@ -196,7 +198,7 @@ It creates three sql table on initialisation.
return bool(self.db_cursor.fetchone())
def check_data_validity(self, rowid):
- if not isinstance(rowid,int):
+ if not isinstance(rowid, int):
raise TypeError('rowid must be an integer')
if rowid <= 0:
raise ValueError('rowid must be greater zero')
@@ -226,8 +228,8 @@ It creates three sql table on initialisation.
return valid
def get_posid(self, posorient):
- if no isinstance(posorient, pd.Series):
- ('posorient should be a pandas Series')
+ 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')
@@ -313,11 +315,13 @@ class DataBaseLoad(DataBase):
"""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)):
+ 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)')
+ if c not in ['R', 'G', 'B', 'D']:
+ raise ValueError('channels must be either\
+ R,G,B or D (Distance)')
DataBase.__init__(self, filename, channels=channels)
@property
@@ -356,7 +360,7 @@ database
return posorient
def read_posorient(self, posorient=None, rowid=None):
- if no isinstance(posorient, pd.Series):
+ if not isinstance(posorient, pd.Series):
('posorient should be a pandas Series')
if posorient is not None:
if not isinstance(posorient, pd.Series):
@@ -375,15 +379,15 @@ database
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)):
+ if np.any(pd.isnull(posorient)):
raise ValueError('posorient must not contain nan')
- if not isinstance(rowid,int):
+ 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):
+ 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)
@@ -402,7 +406,7 @@ database
return toreturn
def read_image(self, posorient=None, rowid=None):
- if no isinstance(posorient, pd.Series):
+ if not isinstance(posorient, pd.Series):
('posorient should be a pandas Series')
if posorient is not None:
if not isinstance(posorient, pd.Series):
@@ -421,9 +425,9 @@ database
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)):
+ if np.any(pd.isnull(posorient)):
raise ValueError('posorient must not contain nan')
- if not isinstance(rowid,int):
+ if not isinstance(rowid, int):
raise TypeError('rowid must be an integer')
if rowid <= 0:
raise ValueError('rowid must be greater zero')
@@ -463,7 +467,7 @@ database
FROM {}
WHERE (rowid={})
""".format(tablename, rowid), self.db)
- if cmaxminrange.shape[0] != 1:
+ if cmaxminrange.shape[0] != 1:
raise Exception('Error while reading normalisation factors')
cmaxminrange = cmaxminrange.iloc[0, :]
cmaxminrange.name = cmaxminrange.id
@@ -475,19 +479,23 @@ database
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(
+ 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')
+ 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 str(chan_n) + '_max' not in cmaxminrange.index:
+ raise ValueError('cminmax range is missing index '
+ + str(chan_n) + '_max')
+ if str(chan_n) + '_min' not in cmaxminrange.index:
+ raise ValueError('cminmax range is missing index '
+ + str(chan_n) + '_min')
+ if str(chan_n) + '_range' not in cmaxminrange.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'])):
@@ -575,15 +583,16 @@ class DataBaseSave(DataBase):
self.db.commit()
def normalise_image(self, image, dtype=np.uint8):
- if not isinstance(image,np.ndarray):
+ 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:
+ 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):
+ if image.shape[2] != len(self.channels):
+ raise Exception('image channels number differs from\
+ given channel number')
+ if not tools.is_numeric_array(image):
raise TypeError('scene is of non numeric type')
normed_im = np.zeros(image.shape, dtype=dtype)
maxval_nim = np.iinfo(normed_im.dtype).max
diff --git a/navipy/database/__init__.py~ b/navipy/database/__init__.py~
index 5828dddd76cb670ab3418d7be26f89ef894379b9..2e0ee2bdaefcafd9fa3ed0fd56460020946432d3 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 +123,13 @@ 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 +160,9 @@ 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 +187,8 @@ 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 +198,12 @@ 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(*)
@@ -211,8 +228,27 @@ It creates three sql table on initialisation.
return valid
def get_posid(self, posorient):
- assert isinstance(posorient, pd.Series),\
- 'posorient should be a pandas Series'
+ 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')
+ 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 +313,15 @@ 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 c not in ['R', 'G', 'B', 'D']:
+ raise ValueError('channels must be either\
+ R,G,B or D (Distance)')
DataBase.__init__(self, filename, channels=channels)
@property
@@ -315,8 +360,35 @@ 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 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')
+ 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 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
@@ -334,6 +406,37 @@ database
return toreturn
def read_image(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')
+ 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 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):
+ 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.
@@ -343,8 +446,8 @@ database
:returns: an image
:rtype: numpy.ndarray
"""
- assert (posorient is None) or (rowid is None),\
- 'posorient and rowid can not be both None'
+ 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
@@ -364,8 +467,8 @@ 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')
@@ -373,13 +476,32 @@ database
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 cmaxminrange.index:
+ raise ValueError('cminmax range is missing index '
+ + str(chan_n) + '_max')
+ if str(chan_n) + '_min' not in cmaxminrange.index:
+ raise ValueError('cminmax range is missing index '
+ + str(chan_n) + '_min')
+ if str(chan_n) + '_range' not in cmaxminrange.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
#
@@ -408,7 +530,6 @@ class DataBaseSave(DataBase):
DataBase.__init__(self, filename, channels=channels)
self.arr_dtype = arr_dtype
-
def create(self):
"""use to decide weather to alter the database or not
return True because we will need
@@ -433,10 +554,10 @@ 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():
@@ -462,6 +583,17 @@ 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(image):
+ raise TypeError('scene is of non numeric type')
normed_im = np.zeros(image.shape, dtype=dtype)
maxval_nim = np.iinfo(normed_im.dtype).max
#