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#!/usr/bin/env python3
# Copyright (C) 2005-2007 Carabos Coop. V. All rights reserved
# Copyright (C) 2008-2024 Vicent Mas. All rights reserved
#
# This program is free software: you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation, either version 3 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
#
# Author: Vicent Mas - vmas@vitables.org
"""Several simple VLArrays."""
import pickle
import numpy as np
import tables
# Create a VLArray:
fileh = tables.open_file('vlarray_samples.h5', mode='w')
root = fileh.root
vlarray = fileh.create_vlarray(root, 'vlarray1',
tables.Int32Atom(), "ragged array of ints", filters=tables.Filters(1))
# Append some (variable length) rows:
vlarray.append(np.array([5, 6]))
vlarray.append(np.array([5, 6, 7]))
vlarray.append([5, 6, 9, 8])
# Now, do the same with native Python strings.
vlarray2 = fileh.create_vlarray(root, 'vlarray2',
tables.StringAtom(itemsize=2), "ragged array of strings",
filters=tables.Filters(1))
vlarray2.flavor = 'python'
# Append some (variable length) rows:
vlarray2.append(['5', '66'])
vlarray2.append(['5', '6', '77'])
vlarray2.append(['5', '6', '9', '88'])
# Test with lists of bidimensional vectors
vlarray3 = fileh.create_vlarray(root, 'vlarray3', tables.Int64Atom(shape=(2,)),
"Ragged array of vectors")
a = np.array([[1, 2], [1, 2]], dtype=np.int64)
vlarray3.append(a)
vlarray3.append(np.array([[1, 2], [3, 4]], dtype=np.int64))
vlarray3.append(np.zeros(dtype=np.int64, shape=(0, 2)))
vlarray3.append(np.array([[5, 6]], dtype=np.int64))
# This makes an error (shape)
#vlarray.append(array([[5], [6]], dtype=int64))
# This makes an error (type)
#vlarray.append(array([[5, 6]], dtype=uint64))
# Tests with strings
# Python flavor
vlarray5 = fileh.create_vlarray(root, 'vlarray5',
tables.StringAtom(itemsize=3), "Ragged array of strings")
vlarray5.flavor = "python"
vlarray5.append(["123", "456", "3"])
vlarray5.append(["456", "3"])
# Binary strings
vlarray6 = fileh.create_vlarray(root, 'vlarray6', tables.UInt8Atom(),
"pickled bytes")
data = pickle.dumps((["123", "456"], "3"))
vlarray6.append(np.ndarray(buffer=data, dtype=np.uint8, shape=len(data)))
# The next is a way of doing the same than before
vlarray7 = fileh.create_vlarray(root, 'vlarray7', tables.ObjectAtom(),
"pickled object")
vlarray7.append([["123", "456"], "3"])
# Boolean arrays are supported as well
vlarray8 = fileh.create_vlarray(root, 'vlarray8', tables.BoolAtom(),
"Boolean atoms")
# The next lines are equivalent...
vlarray8.append([1, 0])
vlarray8.append([1, 0, 3, 0]) # This will be converted to a boolean
# This gives a TypeError
#vlarray.append([1,0,1])
# Variable length strings
vlarray9 = fileh.create_vlarray(root, 'vlarray9', tables.VLStringAtom(),
"Variable Length String")
vlarray9.append("asd")
vlarray9.append("aaana")
# Unicode variable length strings
vlarray10 = fileh.create_vlarray(root, 'vlarray10', tables.VLUnicodeAtom(),
"Variable Length Unicode String")
vlarray10.append("aaana")
vlarray10.append("") # The empty string
vlarray10.append("asd")
vlarray10.append("para\u0140lel")
# Still more vlarrays...
N = 100
shape = (3,3)
np.random.seed(10) # For reproductible results
vlarray11 = fileh.create_vlarray(root, 'vlarray11',
tables.Float64Atom(shape=shape), "ragged array of arrays")
k = 0
for i in range(N):
vl = []
for j in range(np.random.randint(N)):
vl.append(np.random.randn(*shape))
k += 1
vlarray11.append(vl)
# Close the file.
fileh.close()
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