# **************************************************************************
# *
# * Authors: J.M. De la Rosa Trevin (jmdelarosa@cnb.csic.es)
# * Carlos Oscar Sorzano (info@kinestat.com)
# *
# * Unidad de Bioinformatica of Centro Nacional de Biotecnologia , CSIC
# *
# * 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 2 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, write to the Free Software
# * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
# * 02111-1307 USA
# *
# * All comments concerning this program package may be sent to the
# * e-mail address 'info@kinestat.com'
# *
# **************************************************************************
import numpy as np
from collections import OrderedDict
import tkinter as tk
import pyworkflow.object as pwobj
import pyworkflow.gui as gui
from pyworkflow.gui.widgets import HotButton
from pyworkflow.gui.tree import TreeProvider, BoundTree
from pyworkflow.gui.text import TaggedText
from pwem.viewers.plotter import EmPlotter
from pkpd.pkpd_units import PKPDUnit
[docs]class PopulationVar(pwobj.Object):
def __init__(self, **kwargs):
self.data = kwargs
for k, v in kwargs.items():
setattr(self, k, v)
[docs]class PopulationVariablesTreeProvider(TreeProvider):
def __init__(self, variables):
#self.population = population
self._variables = variables
[docs] def getColumns(self):
w = 60
return [('Name', w), ('Unit', w),
('Mean', w), ('Std', w),
('Minimum', w), ('2.5%', w), ('25%', w), ('50%', w),
('75%', w), ('97.5%', w), ('Maximum', w)]
[docs] def getObjects(self):
return self._variables
[docs] def getObjectInfo(self, obj):
key = obj.varName
p = obj.percentiles
return {'key': key, 'text': key,
'values': (obj.unitStr,
obj.mu, obj.sigma,
p[0], p[1], p[2], p[3], p[4], p[5], p[6])}
[docs]class PopulationWindow(gui.Window):
"""
"""
def __init__(self, **kwargs):
gui.Window.__init__(self, minsize=(620, 200), **kwargs)
self.population = kwargs.get('population')
self.callback = kwargs.get('callback', None)
self.plotter = None
self._variables = OrderedDict()
self._variablesDict = {}
self._loadVariables(self.population)
content = tk.Frame(self.root)
self._createContent(content)
content.grid(row=0, column=0, sticky='news')
gui.configureWeigths(content)
def _loadVariables(self, population):
self.observations = population.getAllParameters()
mu, sigma, self.R, percentiles = population.getStats(self.observations)
for i, varName in enumerate(population.modelParameters):
v = PopulationVar(index=i,
varName=varName,
unitStr=PKPDUnit.codeToString(population.modelParameterUnits[i]),
mu=mu[i], sigma=sigma[i],
percentiles=[p[i] for p in percentiles])
self._variables[varName] = v
def _createContent(self, content):
# Create top frame with the variables list
self._createTopFrame(content)
# Create button frame with Plot button
self._createButtonsFrame(content)
# Create an info frame
self._createBottomFrame(content)
def _createTopFrame(self, content):
frame = tk.Frame(content)
lfSamples = tk.LabelFrame(frame, text='Plot')
gui.configureWeigths(frame)
lfSamples.grid(row=0, column=0, sticky='news', padx=5, pady=5)
# Create tree for Population Variables
tp = PopulationVariablesTreeProvider(self._variables.values())
self.tree = BoundTree(frame, tp, height=10)
self.tree.grid(row=0, column=0, sticky='news', padx=5, pady=5)
gui.configureWeigths(frame)
frame.grid(row=0, column=0, sticky='news', padx=5, pady=(10, 5))
def _createButtonsFrame(self, content):
frame = tk.Frame(content)
self.plotButton = HotButton(frame, ' Plot ', font=self.fontBold,
command=self._onPlotClick,
tooltip='Select one or two variables to plot ')
self.plotButton.grid(row=0, column=0, sticky='se', padx=5)
frame.grid(row=1, column=0, sticky='sew', padx=5, pady=5)
gui.configureWeigths(frame)
def _createBottomFrame(self, content):
frame = tk.Frame(content)
t = TaggedText(frame, height=10)
t.grid(row=0, column=0, sticky='news', padx=5, pady=5)
t.addLine("*Correlation Matrix*")
t.addText(np.array2string(self.R))
frame.grid(row=2, column=0, sticky='sew', padx=5, pady=5)
gui.configureWeigths(frame)
def _onPlotClick(self, e=None):
selection = self.tree.selection()
n = len(selection)
if n < 1 or n > 2:
self.showError("Select one or two variables to plot.")
else:
plotter = EmPlotter(style='seaborn-whitegrid')
varX = self._variables[selection[0]]
xValues = self.observations[:, varX.index]
def _label(var):
return "%s [%s]" % (var.varName, var.unitStr)
if n == 1:
plotter.createSubPlot("Histogram", _label(varX), "Count")
plotter.plotHist(xValues, 50)
else: # n == 2
varY = self._variables[selection[1]]
yValues = self.observations[:, varY.index]
ax = plotter.createSubPlot("Scatter Plot",
_label(varX), _label(varY))
ax.plot(xValues, yValues, '.')
plotter.show()