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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
#
# This script is based on a set of scripts by Francesc Alted.
"""Several simple Tables."""
import numpy as np
import tables
class Particle(tables.IsDescription):
"""Description of a table record.
"""
name = tables.StringCol(16, pos=1) # 16-character String
lati = tables.Int32Col(pos=2) # integer
longi = tables.Int32Col(pos=3) # integer
pressure = tables.Float32Col(pos=4) # float (single-precision)
temperature = tables.Float64Col(pos=5) # double (double-precision)
# Open a file in "w"rite mode
fileh = tables.open_file("table_samples.h5", mode = "w")
root = fileh.root
# Create a new group
group = fileh.create_group(root, "newgroup")
# Create a new table in newgroup group
table = fileh.create_table(group, 'table', Particle, "A table",
tables.Filters(1))
particle = table.row
# Fill the table with 10 particles
for i in range(10):
# First, assign the values to the Particle record
particle['name'] = 'Particle: %6d' % (i)
particle['lati'] = i
particle['longi'] = 10 - i
particle['pressure'] = float(i*i)
particle['temperature'] = float(i**2)
# This injects the row values.
particle.append()
# We need to flush the buffers in table in order to get an
# accurate number of records on it.
table.flush()
# Add a couple of user attrs
table.attrs.user_attr1 = 1.023
table.attrs.user_attr2 = "This is the second user attr"
# Append several rows in only one call
table.append([("Particle: 10", 10, 0, 10*10, 10**2),
("Particle: 11", 11, -1, 11*11, 11**2),
("Particle: 12", 12, -2, 12*12, 12**2)])
table.flush()
class Particle2(tables.IsDescription):
"""Description of a table record.
"""
name = tables.StringCol(16, pos=1) # 16-character String
lati = tables.ComplexCol(itemsize=16, pos=2)
longi = tables.ComplexCol(itemsize=8, pos=3)
vector = tables.ComplexCol(itemsize=8, shape=(2,), pos=4)
matrix2D = tables.ComplexCol(itemsize=16, shape=(2, 2), pos=5)
# Open a file in "w"rite mode
table1 = fileh.create_table(root, 'table1', Particle2, "A table")
# Append several rows in only one call
table1.append([("Particle: 10", 10j, 0, (10*9+1j, 1), [[10**2j, 11*3]]*2),
("Particle: 11", 11j, -1, (11*10+2j, 2), [[11**2j, 10*3]]*2),
("Particle: 12", 12j, -2, (12*11+3j, 3), [[12**2j, 9*3]]*2),
("Particle: 13", 13j, -3, (13*11+4j, 4), [[13**2j, 8*3]]*2),
("Particle: 14", 14j, -4, (14*11+5j, 5), [[14**2j, 7*3]]*2)])
table1.flush()
######
class Particle3(tables.IsDescription):
ADCcount = tables.Int16Col() # signed short integer
TDCcount = tables.UInt8Col() # unsigned byte
grid_i = tables.Int32Col() # integer
grid_j = tables.Int32Col() # integer
idnumber = tables.Int64Col() # signed long long
name = tables.StringCol(16, dflt="") # 16-character String
pressure = tables.Float32Col(shape=2) # float (single-precision)
temperature = tables.Float64Col() # double (double-precision)
Particle4 = {
# You can also use any of the atom factories, i.e. the one which
# accepts a PyTables type.
"ADCcount" : tables.Col.from_type("int16"), # signed short integer
"TDCcount" : tables.Col.from_type("uint8"), # unsigned byte
"grid_i" : tables.Col.from_type("int32"), # integer
"grid_j" : tables.Col.from_type("int32"), # integer
"idnumber" : tables.Col.from_type("int64"), # signed long long
"name" : tables.Col.from_kind("string", 16), # 16-character String
"pressure" : tables.Col.from_type("float32", (2,)), # float (single-precision)
"temperature" : tables.Col.from_type("float64"), # double (double-precision)
}
# Create a new group under "/" (root)
group = fileh.create_group("/", 'detector')
# Create one table on it
#table = h5file.create_table(group, 'table', Particle, "Title example")
# You can choose creating a Table from a description dictionary if you wish
table2 = fileh.create_table(group, 'table', Particle4, "Title example")
# Create a shortcut to the table record object
particle = table2.row
# Fill the table with 10 particles
for i in range(10):
# First, assign the values to the Particle record
particle['name'] = 'Particle: %6d' % (i)
particle['TDCcount'] = i % 256
particle['ADCcount'] = (i * 256) % (1 << 16)
particle['grid_i'] = i
particle['grid_j'] = 10 - i
particle['pressure'] = [float(i*i), float(i*2)]
particle['temperature'] = float(i**2)
particle['idnumber'] = i * (2 ** 34) # This exceeds integer range
# This injects the Record values.
particle.append()
# Flush the buffers for table
table2.flush()
# Create a new group to hold new arrays
gcolumns = fileh.create_group("/", "columns")
pressure = [ p['pressure'] for p in table2.iterrows() ]
# Create an array with this info under '/columns' having a 'list' flavor
fileh.create_array(gcolumns, 'pressure', pressure,
"Pressure column")
# Do the same with TDCcount, but with a numpy object
TDC = [ p['TDCcount'] for p in table2.iterrows() ]
fileh.create_array('/columns', 'TDC', np.array(TDC), "TDCcount column")
# Do the same with name column
names = [ p['name'] for p in table2.iterrows() ]
fileh.create_array('/columns', 'name', names, "Name column")
# Save a recarray object under detector
r = np.rec.array("a"*300, formats='f4,3i4,a5,i2', shape=3)
recarrt = fileh.create_table("/detector", 'recarray', r, "RecArray example")
r2 = r[0:3:2]
# Change the byteorder property
recarrt = fileh.create_table("/detector", 'recarray2', r2,
"Non-contiguous recarray")
# Finally, append some new records to table
table3 = fileh.root.detector.table
# Append 5 new particles to table (yes, tables can be enlarged!)
particle = table3.row
for i in range(10, 15):
# First, assign the values to the Particle record
particle['name'] = 'Particle: %6d' % (i)
particle['TDCcount'] = i % 256
particle['ADCcount'] = (i * 256) % (1 << 16)
particle['grid_i'] = i
particle['grid_j'] = 10 - i
particle['pressure'] = [float(i*i), float(i*2)]
particle['temperature'] = float(i**2)
particle['idnumber'] = i * (2 ** 34) # This exceeds integer range
# This injects the Row values.
particle.append()
# Flush this table
table3.flush()
# Finally, close the file
fileh.close()
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