# -*- coding:utf-8 -*-
# Copyright (c) 2017, System Engineering Software Society
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are met:
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above copyright
# notice, this list of conditions and the following disclaimer in the
# documentation and/or other materials provided with the distribution.
# * Neither the name of the System Engineering Software Society nor the
# names of its contributors may be used to endorse or promote products
# derived from this software without specific prior written permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
# AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
# IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
# ARE DISCLAIMED.
# IN NO EVENT SHALL SYSTEM ENGINEERING SOFTWARE SOCIETY BE LIABLE FOR ANY
# DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES
# (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES;
# LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND
# ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
# SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
from __future__ import (print_function, division, unicode_literals,
absolute_import)
import itertools
import collections
import six
import numpy as np
from six.moves import range as range_
from sympathy.api import node as synode
from sympathy.api.nodeconfig import Port, Ports, Tag, Tags, adjust
from sympathy.api.exceptions import SyConfigurationError
class IHeatMapAccumulator(object):
def __init__(self):
self._value = None
def add_data(self, data):
raise NotImplementedError
def value(self):
return self._value
class CountAccumulator(IHeatMapAccumulator):
def add_data(self, data):
if not self._value:
self._value = 0
self._value += data.size
class SumAccumulator(IHeatMapAccumulator):
def add_data(self, data):
if not self._value:
self._value = 0
self._value += data.sum()
class MinAccumulator(IHeatMapAccumulator):
def add_data(self, data):
if not data.size:
return
if self._value is None:
self._value = data.min()
else:
self._value = min(self._value, data.min())
class MaxAccumulator(IHeatMapAccumulator):
def add_data(self, data):
if not data.size:
return
if self._value is None:
self._value = data.max()
else:
self._value = max(self._value, data.max())
class MeanAccumulator(IHeatMapAccumulator):
def __init__(self):
self._sum = 0
self._count = 0
def add_data(self, data):
self._sum += data.sum()
self._count += data.size
def value(self):
if self._count:
return self._sum / self._count
else:
return None
class MedianAccumulator(IHeatMapAccumulator):
def __init__(self):
self._values = []
def add_data(self, data):
self._values.append(data)
def value(self):
if self._values:
return np.ma.median(np.vstack(self._values))
else:
return None
REDUCTION_FUNCTIONS = collections.OrderedDict([
('Count (histogram)', CountAccumulator),
('Sum', SumAccumulator),
('Min', MinAccumulator),
('Max', MaxAccumulator),
('Mean', MeanAccumulator),
('Median', MedianAccumulator)])
[docs]class HeatmapCalculation(synode.Node):
"""
This node calculates a 2D histogram or other heatmap of a given signal.
The output consists of bin edges and bin values and can for instance be
used in a heatmap plot in the node :ref:`Figure from Table`.
This node ignores any rows in the input where one or more of the selected
columns are masked.
"""
author = 'Magnus Sandén <magnus.sanden@combine.se'
copyright = "(C) 2016 System Engineering Software Society"
version = '0.1'
icon = 'heatmap_calculation.svg'
name = 'Heatmap calculation'
description = ('Calculate a 2d histogram or other heatmap of a given'
'signal.')
nodeid = 'org.sysess.sympathy.dataanalysis.heatmapcalc'
tags = Tags(Tag.Analysis.Statistic)
parameters = synode.parameters()
combo_editor = synode.Util.combo_editor().value()
reduction_editor = synode.Util.combo_editor(
options=list(REDUCTION_FUNCTIONS.keys())).value()
parameters.set_string('x_data_column', label="X data column:",
editor=combo_editor,
description='Select X axis data')
parameters.set_string('y_data_column', label="Y data column:",
editor=combo_editor,
description='Select Y axis data')
parameters.set_string('z_data_column', label="Z data column:",
description='The data points of the z data are '
'placed in bins according to the '
'cooresponding values of x and y. They '
'are then reduced to a single bin value '
'using the selected reduction function. '
'For "{}" no z data column is needed.'
''.format(
list(REDUCTION_FUNCTIONS.keys())[0]),
editor=combo_editor)
parameters.set_string('reduction', label="Reduction function:",
value=list(REDUCTION_FUNCTIONS.keys())[0],
description='A function used on all the z data '
'points in a bin. For "{}" no z data '
'column is needed.'.format(
list(REDUCTION_FUNCTIONS.keys())[0]),
editor=reduction_editor)
parameters.set_integer('x_bins', label="X Bins:", value=10,
description='Number of bins on the x axis')
parameters.set_integer('y_bins', label="Y Bins:", value=10,
description='Number of bins on the y axis')
parameters.set_boolean('auto_range', label="Auto range", value=True,
description=('When checked, use data range as '
'histogram range'))
parameters.set_float(
'x_min', label="X min:", value=0.0, description='Set minimum X value')
parameters.set_float(
'x_max', label="X max:", value=1.0, description='Set maximum X value')
parameters.set_float(
'y_min', label="Y min:", value=0.0, description='Set minimum Y value')
parameters.set_float(
'y_max', label="Y max:", value=1.0, description='Set maximum Y value')
controllers = (synode.controller(
when=synode.field('auto_range', 'checked'),
action=(synode.field('x_min', 'disabled'),
synode.field('x_max', 'disabled'),
synode.field('y_min', 'disabled'),
synode.field('y_max', 'disabled'))),
synode.controller(
when=synode.field(
'reduction', 'value', list(REDUCTION_FUNCTIONS.keys())[0]),
action=synode.field('z_data_column', 'disabled')))
inputs = Ports([Port.Table('Input data', name='in')])
outputs = Ports([Port.Table('Heatmap data', name='out')])
def adjust_parameters(self, node_context):
adjust(node_context.parameters['x_data_column'],
node_context.input['in'])
adjust(node_context.parameters['y_data_column'],
node_context.input['in'])
adjust(node_context.parameters['z_data_column'],
node_context.input['in'])
def execute(self, node_context):
parameters = node_context.parameters
x_bins = parameters['x_bins'].value
y_bins = parameters['y_bins'].value
x_data_column = parameters['x_data_column'].value
y_data_column = parameters['y_data_column'].value
z_data_column = parameters['z_data_column'].value
auto_range = parameters['auto_range'].value
if x_data_column is None or y_data_column is None or (
z_data_column is None and
list(REDUCTION_FUNCTIONS.keys())[0] !=
parameters['reduction'].value):
raise SyConfigurationError('Please choose a data column.')
x_data = node_context.input['in'].get_column_to_array(x_data_column)
y_data = node_context.input['in'].get_column_to_array(y_data_column)
if (list(REDUCTION_FUNCTIONS.keys())[0] ==
parameters['reduction'].value):
z_data = np.zeros_like(x_data)
else:
z_data = node_context.input['in'].get_column_to_array(
z_data_column)
# Handle masked arrays
mask = np.zeros(x_data.shape, dtype=bool)
if isinstance(x_data, np.ma.MaskedArray):
mask |= x_data.mask
if isinstance(y_data, np.ma.MaskedArray):
mask |= y_data.mask
if isinstance(z_data, np.ma.MaskedArray):
mask |= z_data.mask
if np.any(mask):
mask = np.logical_not(mask)
x_data = x_data[mask]
y_data = y_data[mask]
z_data = z_data[mask]
if auto_range:
x_min = min(x_data)
x_max = max(x_data)
y_min = min(y_data)
y_max = max(y_data)
else:
x_min = parameters['x_min'].value
x_max = parameters['x_max'].value
y_min = parameters['y_min'].value
y_max = parameters['y_max'].value
x_bin_edges = np.linspace(x_min, x_max, x_bins + 1)
y_bin_edges = np.linspace(y_min, y_max, y_bins + 1)
Accumulator = REDUCTION_FUNCTIONS[parameters['reduction'].value] # noqa
values_buffer = np.empty((x_bins, y_bins), dtype=object)
x_bin_indices = np.digitize(x_data, x_bin_edges)
y_bin_indices = np.digitize(y_data, y_bin_edges)
# Digitize puts values on bin edges in the right bin, but for the
# rightmost bin this is not what we want. We want the rightmost bin to
# be a closed interval.
on_x_edge = x_data == x_bin_edges[-1]
on_y_edge = y_data == y_bin_edges[-1]
x_bin_indices[on_x_edge] -= 1
y_bin_indices[on_y_edge] -= 1
# Build the values buffer. The values buffer holds a list of z
# values for each bin.
for x_bin_index, y_bin_index, z in six.moves.zip(
x_bin_indices, y_bin_indices, z_data):
if 0 < x_bin_index <= x_bins and 0 < y_bin_index <= y_bins:
xi = x_bin_index - 1
yi = y_bin_index - 1
else:
# print("bin doesn't exist: ({}, {})".format(
# x_bin_index, y_bin_index))
continue
if values_buffer[xi, yi] is None:
values_buffer[xi, yi] = Accumulator()
values_buffer[xi, yi].add_data(z)
# Now go through the values buffer and reduce each list into the real z
# data for that bin.
bin_values = np.ma.masked_all((x_bins, y_bins), dtype=float)
for xi, yi in itertools.product(range_(x_bins), range_(y_bins)):
z_values = values_buffer[xi, yi]
if z_values is not None:
bin_values[xi, yi] = z_values.value()
x_output = np.array([x_bin_edges[:-1]] * y_bins).reshape(-1, order='F')
y_output = np.array([y_bin_edges[:-1]] * x_bins).reshape(-1, order='C')
node_context.output['out'].set_column_from_array(
"X bin edges", x_output)
node_context.output['out'].set_column_from_array(
"Y bin edges", y_output)
node_context.output['out'].set_column_from_array(
"Bin values", bin_values.flatten())