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updated user interface to support linear mixed models for differentia…
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…l data
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@paulmueller
paulmueller committed Sep 27, 2016
1 parent 195aadb commit 8977d63
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Showing 4 changed files with 286 additions and 268 deletions.
268 changes: 2 additions & 266 deletions shapeout/gui/controls.py
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@@ -1,13 +1,10 @@
#!/usr/bin/python
# -*- coding: utf-8 -*-
""" ShapeOut - control panels
"""
from __future__ import division, print_function

import numpy as np
import tempfile
import webbrowser

import wx
import wx.grid as gridlib
Expand All @@ -20,12 +17,13 @@
from ..configuration import ConfigurationFile
from .. import tlabwrap
from .. import util
from .. import lin_mix_mod

from .polygonselect import LineDrawerWindow
from . import plot_scatter
from . import plot_contour

from .controls_subpanel import SubPanel
from .controls_analysis import SubPanelAnalysis


class FlatNotebook(wx.Notebook):
Expand Down Expand Up @@ -412,268 +410,6 @@ def _onStripe(self):



class SubPanel(ScrolledPanel):
def __init__(self, parent, funcparent=None, *args, **kwargs):
"""
Notebook page dummy with methods
"""
ScrolledPanel.__init__(self, parent, *args, **kwargs)
self.SetupScrolling(scroll_y=True)
self.SetupScrolling(scroll_x=True)
self.analysis = None
self.key = None
self.funcparent = funcparent


def _box_from_cfg_read(self, analysis, key):
gen = wx.StaticBox(self, label=_(key))
hbox = wx.StaticBoxSizer(gen, wx.VERTICAL)

if analysis is not None:
items = analysis.GetCommonParameters(key).items()
items2 = analysis.GetUncommonParameters(key).items()

multiplestr = _("(multiple)")
for item in items2:
items.append((item[0], multiplestr))
items.sort()
sgen = wx.FlexGridSizer(len(items), 2)

for item in items:
a = wx.StaticText(self, label=item[0])
b = wx.StaticText(self, label=str(item[1]))
if item[1] == multiplestr:
a.Disable()
b.Disable()
sgen.Add(a, 0, wx.ALIGN_CENTER_VERTICAL)
sgen.Add(b, 0, wx.ALIGN_CENTER_VERTICAL)

sgen.Layout()
hbox.Add(sgen)

return hbox

def _create_type_wx_controls(self, analysis, key, item):
""" Create a wx control whose type is inferred by item
Returns a sizer
"""
stemp = wx.BoxSizer(wx.HORIZONTAL)
# these axes should not be displayed in the UI
ignore_axes = tlabwrap.IGNORE_AXES+analysis.GetUnusableAxes()
choices = dc_config.get_config_entry_choices(key, item[0],
ignore_axes=ignore_axes)

if len(choices) != 0:
if choices[0] in dclab.dfn.axlabels:
human_choices = [ _(dclab.dfn.axlabels[c]) for c in choices]
else:
human_choices = choices

a = wx.StaticText(self, label=_(item[0]))
# sort choices with _()?
c = wx.ComboBox(self, -1, choices=human_choices,
value=unicode(item[1]), name=item[0],
style=wx.CB_DROPDOWN|wx.CB_READONLY)
c.data = choices
if not isinstance(item[1], (str, unicode)):
# this is important for floats and ints
for ch in choices:
if float(ch) == float(item[1]):
c.SetValue(ch)
else:
# this does not work for floats and ints
idc = choices.index(item[1])
c.SetSelection(idc)
stemp.Add(a, 0, wx.ALIGN_CENTER_VERTICAL)
stemp.Add(c)

elif (dc_config.get_config_entry_dtype(key, item[0]) == bool or # @UndefinedVariable
str(item[1]).capitalize() in ["True", "False"]):
a = wx.CheckBox(self, label=_(item[0]), name=item[0])
a.SetValue(item[1])
stemp.Add(a)
else:
a = wx.StaticText(self, label=_(item[0]))
b = wx.TextCtrl(self, value=str(item[1]), name=item[0])
stemp.Add(a, 0, wx.ALIGN_CENTER_VERTICAL)
stemp.Add(b)
return stemp


def OnReset(self, e=None):
""" Reset all parameters that are defined in this panel.
It is important, that the Name for each wxWidget is set to
something available in the default configuration and that
self.key is set to a valid key, e.g. "Plotting" or "Filtering".
"""
if self.key is not None:
# Get the controls that we change
ctrls = self.GetChildren()
subkeys = list()
# identify controls via their name correspondence in the cfg
default = tlabwrap.GetDefaultConfiguration(self.key)
for c in ctrls:
subkey = c.GetName()
if subkey in default:
subkeys.append(subkey)
print(subkeys)
self.funcparent.Reset(self.key, subkeys)


def UpdatePanel(self, *args, **kwargs):
""" Overwritten by subclass """
pass


class SubPanelAnalysis(SubPanel):
def __init__(self, parent, *args, **kwargs):
SubPanel.__init__(self, parent, *args, **kwargs)
self.config = ConfigurationFile()
self.key = "Analysis"


def make_analysis_choices(self, analysis):
gen = wx.StaticBox(self, label=_("Linear mixed-effects model"))
hbox = wx.StaticBoxSizer(gen, wx.VERTICAL)

if analysis is not None:
# get common parameters
sizer_bag = wx.GridBagSizer(hgap=20, vgap=5)

sizer_bag.Add(wx.StaticText(self, label=_("Axis to analyze:")), (0,0), span=wx.GBSpan(1,1))

# axes dropdown
self.axes = analysis.GetUsableAxes()
axeslist = [dclab.dfn.axlabels[a] for a in self.axes]
self.WXCB_axes = wx.ComboBox(self, -1, choices=axeslist,
value=_("None"), name="None",
style=wx.CB_DROPDOWN|wx.CB_READONLY)
# Set y-axis as default
ax = analysis.GetPlotAxes()[1]
if ax in self.axes:
axid = self.axes.index(ax)
else:
axid = 0
self.WXCB_axes.SetSelection(axid)
sizer_bag.Add(self.WXCB_axes, (0,1), span=wx.GBSpan(1,4))

# Header for table
sizer_bag.Add(wx.StaticText(self, label=_("Data set")), (1,0), span=wx.GBSpan(1,1))
sizer_bag.Add(wx.StaticText(self, label=_("Treatment")), (1,1), span=wx.GBSpan(1,1))
sizer_bag.Add(wx.StaticText(self, label=_("Repetition")), (1,2), span=wx.GBSpan(1,1))

treatments = [_("None"), _("Control")] + [_("Treatment {}").format(i) for i in range(1,5)]
repetitions = [str(i) for i in range(1,10)]

self.WXCB_treatment = []
self.WXCB_repetition = []

for ii, mm in enumerate(analysis.measurements):
# title
sizer_bag.Add(wx.StaticText(self, label=mm.title), (2+ii,0), span=wx.GBSpan(1,1))
# treatment
cbgtemp = wx.ComboBox(self, -1, choices=treatments,
name=mm.identifier,
style=wx.CB_DROPDOWN|wx.CB_READONLY)
if mm.title.lower().count("control") or ii==0:
cbgtemp.SetSelection(1)
else:
cbgtemp.SetSelection(0)
sizer_bag.Add(cbgtemp, (2+ii,1), span=wx.GBSpan(1,1))
# repetition
cbgtemp2 = wx.ComboBox(self, -1, choices=repetitions,
name=mm.identifier,
style=wx.CB_DROPDOWN|wx.CB_READONLY)
cbgtemp2.SetSelection(0)
sizer_bag.Add(cbgtemp2, (2+ii,2), span=wx.GBSpan(1,1))

self.WXCB_treatment.append(cbgtemp)
self.WXCB_repetition.append(cbgtemp2)

hbox.Add(sizer_bag)

return hbox

def OnApply(self, e=None):
"""
Perfrom LME4 computation
"""
# Get axis name
axname = self.axes[self.WXCB_axes.GetSelection()]
# Get axis property
axprop = dclab.dfn.cfgmaprev[axname]

# loop through analysis
treatment = []
timeunit = []
xs = []

for ii, mm in enumerate(self.analysis.measurements):
# get treatment (ignore 0)
if self.WXCB_treatment[ii].GetSelection() == 0:
# The user selected _("None")
continue
xs.append(getattr(mm, axprop)[mm._filter])
treatment.append(self.WXCB_treatment[ii].GetValue())
# get repetition
timeunit.append(int(self.WXCB_repetition[ii].GetValue()))

# run lme4
result = lin_mix_mod.linmixmod(xs=xs,
treatment=treatment,
timeunit=timeunit)
# display results
# write to temporary file and display with webbrowser
with tempfile.NamedTemporaryFile(mode="w", prefix="linmixmod_", suffix=".txt", delete=False) as fd:
fd.writelines(result["Full Summary"])

webbrowser.open(fd.name)

def OnReset(self, e=None):
"""
Reset everything in the analysis tab.
"""
self.UpdatePanel(self.analysis)

def UpdatePanel(self, analysis=None):
if analysis is None:
analysis = self.analysis
self.analysis = analysis

for item in self.GetChildren():
item.Hide()
self.RemoveChild(item)
item.Destroy()

sizer = wx.BoxSizer(wx.HORIZONTAL)

statbox = self.make_analysis_choices(analysis)
sizer.Add(statbox)

sizerv = wx.BoxSizer(wx.VERTICAL)
sizer.Add(sizerv)
vertsizer = wx.BoxSizer(wx.VERTICAL)

btn_apply = wx.Button(self, label=_("Apply"))
## TODO:
# write function in this class that gives ControlPanel a new
# analysis, such that OnChangeFilter becomes shorter.
self.Bind(wx.EVT_BUTTON, self.OnApply, btn_apply)
vertsizer.Add(btn_apply)

btn_reset = wx.Button(self, label=_("Reset"))
self.Bind(wx.EVT_BUTTON, self.OnReset, btn_reset)
vertsizer.Add(btn_reset)

sizer.Add(vertsizer)

self.SetSizer(sizer)
sizer.Fit(self)
self.Layout()


class SubPanelFilter(SubPanel):
def __init__(self, parent, *args, **kwargs):
SubPanel.__init__(self, parent, *args, **kwargs)
Expand Down

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