Skip to content
Snippets Groups Projects
Commit 86d05f04 authored by Luise Odenthal's avatar Luise Odenthal
Browse files

flake8 test database init

parent 5ca49f90
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
navipy/database/__init__.py
+ 41
− 32
View file @ 86d05f04
......@@ -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
......
navipy/database/__init__.py~
+ 158
− 26
View file @ 86d05f04
......@@ -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
#
......
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment