def test_saveload_interval():
"""Test pickling for saving and loading 'Interval'"""
m = Interval('test1', float, (-Inf, 1))
s = Interval('a_singleton', float, 0.4)
saveObjects([m, s], 'temp_objects.pkl', True)
objs_ivals = loadObjects('temp_objects.pkl')
assert objs_ivals[0].get(1) == 1
# Try loading partial list from a larger file
objs_part = loadObjects('temp_objects.pkl', ['a_singleton'])
assert objs_part[0] == s
os.remove('temp_objects.pkl')
def test_saveload_interval():
"""Test pickling for saving and loading 'Interval'"""
m = Interval('test1', float, (-Inf, 1))
s = Interval('a_singleton', float, 0.4)
saveObjects([m, s], 'temp_objects.pkl', True)
objs_ivals = loadObjects('temp_objects.pkl')
assert objs_ivals[0].get(1) == 1
# Try loading partial list from a larger file
objs_part = loadObjects('temp_objects.pkl', ['a_singleton'])
assert objs_part[0] == s
os.remove('temp_objects.pkl')
def test_saveload_implicitfngen():
"""Test pickling for saving and loading 'ImplicitFnGen'"""
argsi = {
'varspecs': {
"y": "t*t+y*y-r*r",
"x": "t"
},
'algparams': {'solvemethod': 'newton', 'atol': 1e-4},
'xdomain': {'y': [-2, 2]},
'ics': {'y': 0.75},
'tdomain': [-2, 0],
'pars': {'r': 2},
'vars': ['y'],
'checklevel': 2,
'name': 'imptest',
}
testimp = ImplicitFnGen(argsi)
traj1 = testimp.compute('traj1')
saveObjects([testimp, traj1], 'temp_objects.pkl', True)
objs_imp = loadObjects('temp_objects.pkl')
assert objs_imp[0].xdomain['y'] == [-2, 2]
assert traj1(-0.4) == objs_imp[1](-0.4)
os.remove('temp_objects.pkl')
def test_saveload_implicitfngen():
"""Test pickling for saving and loading 'ImplicitFnGen'"""
argsi = {
'varspecs': {
"y": "t*t+y*y-r*r",
"x": "t"
},
'algparams': {
'solvemethod': 'newton',
'atol': 1e-4
},
'xdomain': {
'y': [-2, 2]
},
'ics': {
'y': 0.75
},
'tdomain': [-2, 0],
'pars': {
'r': 2
},
'vars': ['y'],
'checklevel': 2,
'name': 'imptest',
}
testimp = ImplicitFnGen(argsi)
traj1 = testimp.compute('traj1')
saveObjects([testimp, traj1], 'temp_objects.pkl', True)
objs_imp = loadObjects('temp_objects.pkl')
assert objs_imp[0].xdomain['y'] == [-2, 2]
assert traj1(-0.4) == objs_imp[1](-0.4)
os.remove('temp_objects.pkl')
def test_saveload_point_and_pointset():
"""Test pickling for saving and loading 'Point' and 'Pointset'"""
x = Point(
coorddict={
'x0': [1.123456789],
'x1': [-0.4],
'x2': [4000]
},
coordtype=float64
)
v = Pointset(
coorddict={
'x0': 0.2,
'x1': -1.2
},
indepvardict={'t': 0.01},
coordtype=float,
indepvartype=float
)
saveObjects([x, v], 'temp_objects.pkl', True)
objs_pts = loadObjects('temp_objects.pkl')
assert objs_pts[0] == x
assert objs_pts[1] == v
os.remove('temp_objects.pkl')
def test_saveload_explicitfngen():
"""Test pickling for saving and loading 'ExplicitFnGen'"""
args = {
'tdomain': [-50, 50],
'pars': {
'speed': 1
},
'xdomain': {
's': [-1., 1.]
},
'name': 'sine',
'globalt0': 0.4,
'pdomain': {
'speed': [0, 200]
},
'varspecs': {
's': "sin(globalindepvar(t)*speed)"
}
}
sin_gen = ExplicitFnGen(args)
sintraj1 = sin_gen.compute('sine1')
sin_gen.set(pars={'speed': 2})
sintraj2 = sin_gen.compute('sine2')
saveObjects([sin_gen, sintraj1, sintraj2], 'temp_objects.pkl', True)
objs_sin = loadObjects('temp_objects.pkl')
assert sintraj1(0.55) == objs_sin[1](0.55)
assert sintraj2(0.55) == objs_sin[2](0.55)
os.remove('temp_objects.pkl')
def test_2D_example():
"""
2D example: a quarter-sphere with linear constraint y = 3z,
using MINPACK's fsolve
"""
radius = 2.
fvarspecs2d = {"y": "t*t+y*y+z*z-r*r", "z": "y-3.*z", "x": "t"}
args2d = {
'varspecs': fvarspecs2d,
'algparams': {
'solvemethod': 'fsolve',
'atol': 1e-3
},
'xdomain': {
'y': [-2, 2],
'z': [-2, 2]
},
'ics': {
'y': 0.75,
'z': 0.9
},
'tdomain': [-2, 2],
'pars': {
'r': radius
},
'vars': ['y', 'z'],
'checklevel': 1,
'name': 'imptest2d'
}
testimp2d = ImplicitFnGen(args2d)
traj2 = testimp2d.compute('traj2')
p = traj2(1.5)
assert allclose(norm(p), radius)
assert allclose(p('y') - 3 * p('z'), 0)
assert traj2.dimension == 3
assert isparameterized(traj2)
# Test bounds checking
with pytest.raises(ValueError):
traj2(3.)
# Test saving and loading
fname = 'temp_implicit2D.pkl'
saveObjects([testimp2d, traj2], fname, force=True)
impgen, imptraj = loadObjects(fname)
assert impgen.xdomain['y'] == [-2, 2]
assert allclose(imptraj(-0.4)['y'], 1.85903)
impgen.set(pars={'r': 10.}, xdomain={'y': [-10, 10]})
imptraj2 = impgen.compute('test2')
with pytest.raises(PyDSTool_BoundsError):
imptraj2(-0.4)
impgen.set(xdomain={'z': [-5, 5]})
imptraj2 = impgen.compute('test2')
assert allclose(imptraj2(-0.4)['y'], 9.47924)
os.remove(fname)
def test_saveload_point_and_pointset(fname):
"""Test pickling for saving and loading 'Point' and 'Pointset'"""
x = Point(
coorddict={
'x0': [1.123456789],
'x1': [-0.4],
'x2': [4000]
},
coordtype=float64
)
v = Pointset(
coorddict={
'x0': 0.2,
'x1': -1.2
},
indepvardict={'t': 0.01},
coordtype=float,
indepvartype=float
)
saveObjects([x, v], fname, True)
objs_pts = loadObjects(fname)
assert objs_pts[0] == x
assert objs_pts[1] == v
os.remove(fname)
def test_2D_example():
"""
2D example: a quarter-sphere with linear constraint y = 3z,
using MINPACK's fsolve
"""
radius = 2.
fvarspecs2d = {
"y": "t*t+y*y+z*z-r*r",
"z": "y-3.*z",
"x": "t"
}
args2d = {
'varspecs': fvarspecs2d,
'algparams': {'solvemethod': 'fsolve', 'atol': 1e-3},
'xdomain': {
'y': [-2, 2],
'z': [-2, 2]
},
'ics': {'y': 0.75, 'z': 0.9},
'tdomain': [-2, 2],
'pars': {'r': radius},
'vars': ['y', 'z'],
'checklevel': 1,
'name': 'imptest2d'
}
testimp2d = ImplicitFnGen(args2d)
traj2 = testimp2d.compute('traj2')
p = traj2(1.5)
assert allclose(norm(p), radius)
assert allclose(p('y') - 3 * p('z'), 0)
assert traj2.dimension == 3
assert isparameterized(traj2)
# Test bounds checking
with pytest.raises(ValueError):
traj2(3.)
# Test saving and loading
fname = 'temp_implicit2D.pkl'
saveObjects([testimp2d, traj2], fname, force=True)
impgen, imptraj = loadObjects(fname)
assert impgen.xdomain['y'] == [-2, 2]
assert allclose(imptraj(-0.4)['y'], 1.85903)
impgen.set(pars={'r': 10.}, xdomain={'y': [-10, 10]})
imptraj2 = impgen.compute('test2')
with pytest.raises(PyDSTool_BoundsError):
imptraj2(-0.4)
impgen.set(xdomain={'z': [-5, 5]})
imptraj2 = impgen.compute('test2')
assert allclose(imptraj2(-0.4)['y'], 9.47924)
os.remove(fname)
def test_saveload_variable():
"""Test pickling for saving and loading 'Variable'"""
var1 = Variable(Pointset(coordarray=array(range(10), float) * 0.1,
indepvararray=array(range(10), float) * 0.5),
name='v1')
saveObjects(var1, 'temp_objects.pkl', True)
obj_var = loadObjects('temp_objects.pkl')[0]
assert obj_var(1.5) == var1(1.5)
os.remove('temp_objects.pkl')
def test_saveload_interpolated_table_generator(interptable):
"""Test pickling for saving and loading 'InterpolateTable' Generator"""
itabletraj = interptable.compute('itable')
saveObjects(itabletraj, 'temp_objects.pkl', True)
obj_itab = loadObjects('temp_objects.pkl')
t = 0.1
while t < 2.1:
assert obj_itab[0](t) == itabletraj(t)
t += 0.1
os.remove('temp_objects.pkl')
def test_saveload_interpolated_table_generator(interptable):
"""Test pickling for saving and loading 'InterpolateTable' Generator"""
itabletraj = interptable.compute('itable')
saveObjects(itabletraj, 'temp_objects.pkl', True)
obj_itab = loadObjects('temp_objects.pkl')
t = 0.1
while t < 2.1:
assert obj_itab[0](t) == itabletraj(t)
t += 0.1
os.remove('temp_objects.pkl')
def test_saveload_array(fname):
"""Test pickling for saving and loading array"""
a = array([1, Inf])
b = [Inf, 0]
saveObjects([a, b], fname, True)
loadedObjs = loadObjects(fname)
assert a[0] == loadedObjs[0][0]
assert a[1] == loadedObjs[0][1]
assert b[0] == loadedObjs[1][0]
os.remove(fname)
def test_saveload_array():
"""Test pickling for saving and loading array"""
a = array([1, Inf])
b = [Inf, 0]
saveObjects([a, b], 'temp_objects.pkl', True)
loadedObjs = loadObjects('temp_objects.pkl')
assert a[0] == loadedObjs[0][0]
assert a[1] == loadedObjs[0][1]
assert b[0] == loadedObjs[1][0]
os.remove('temp_objects.pkl')
def test_saveload_array():
"""Test pickling for saving and loading array"""
a = array([1, Inf])
b = [Inf, 0]
saveObjects([a, b], 'temp_objects.pkl', True)
loadedObjs = loadObjects('temp_objects.pkl')
assert a[0] == loadedObjs[0][0]
assert a[1] == loadedObjs[0][1]
assert b[0] == loadedObjs[1][0]
os.remove('temp_objects.pkl')
def test_saveload_vode_odesystem(interptable):
"""Test pickling for saving and loading 'Vode_ODEsystem' Generator"""
# Vode object with event and external input trajectory (defined earlier)
fvarspecs = {
"w": "k*w + a*itable + sin(t) + myauxfn1(t)*myauxfn2(w)",
'aux_wdouble': 'w*2 + globalindepvar(t)',
'aux_other': 'myauxfn1(2*t) + initcond(w)'
}
fnspecs = {'myauxfn1': (['t'], '2.5*cos(3*t)'), 'myauxfn2': (['w'], 'w/2')}
ev_args = {
'name': 'threshold',
'eventtol': 1e-4,
'eventdelay': 1e-5,
'starttime': 0,
'term': True,
}
thresh_ev = Events.makePythonStateZeroCrossEvent('w', 20, 1, ev_args)
DSargs = {
'tdomain': [0.1, 2.1],
'tdata': [0.11, 2.1],
'ics': {
'w': 3.0
},
'pars': {
'k': 2,
'a': -0.5
},
'inputs': {
'itable': interptable.variables['x1']
},
'auxvars': ['aux_wdouble', 'aux_other'],
'algparams': {
'init_step': 0.01,
'strict': False
},
'events': thresh_ev,
'checklevel': 2,
'name': 'ODEtest',
'fnspecs': fnspecs,
'varspecs': fvarspecs
}
testODE = Vode_ODEsystem(DSargs)
odetraj = testODE.compute('testode')
saveObjects([odetraj, testODE], 'temp_objects.pkl', True)
objs_ode = loadObjects('temp_objects.pkl')
objs_ode[1].diagnostics.clearWarnings()
assert len(objs_ode[1].diagnostics.warnings) == 0
odetraj2 = objs_ode[1].compute('testode2')
assert odetraj2(0.6) == odetraj(0.6)
assert len(objs_ode[1].diagnostics.warnings) == 1
os.remove('temp_objects.pkl')
def test_saveload_variable():
"""Test pickling for saving and loading 'Variable'"""
var1 = Variable(
Pointset(
coordarray=array(range(10), float) * 0.1,
indepvararray=array(range(10), float) * 0.5
),
name='v1'
)
saveObjects(var1, 'temp_objects.pkl', True)
obj_var = loadObjects('temp_objects.pkl')[0]
assert obj_var(1.5) == var1(1.5)
os.remove('temp_objects.pkl')
def test_saveload_trajectory():
"""Test pickling for saving and loading 'Trajectory'"""
var1 = Variable(Pointset(coordarray=array(range(10), float) * 0.1,
indepvararray=array(range(10), float) * 0.5),
name='v1')
var2 = Variable(Pointset(coordarray=array(range(10), float) * 0.25 + 1.0,
indepvararray=array(range(10), float) * 0.5),
name='v2')
traj = Trajectory('traj1', [var1, var2])
saveObjects(traj, 'temp_objects.pkl', True)
traj_loaded = loadObjects('temp_objects.pkl')[0]
assert traj_loaded(2.0) == traj(2.0)
os.remove('temp_objects.pkl')
def test_saveload_vode_odesystem(interptable):
"""Test pickling for saving and loading 'Vode_ODEsystem' Generator"""
# Vode object with event and external input trajectory (defined earlier)
fvarspecs = {
"w": "k*w + a*itable + sin(t) + myauxfn1(t)*myauxfn2(w)",
'aux_wdouble': 'w*2 + globalindepvar(t)',
'aux_other': 'myauxfn1(2*t) + initcond(w)'
}
fnspecs = {
'myauxfn1': (['t'], '2.5*cos(3*t)'),
'myauxfn2': (['w'], 'w/2')
}
ev_args = {
'name': 'threshold',
'eventtol': 1e-4,
'eventdelay': 1e-5,
'starttime': 0,
'term': True,
}
thresh_ev = Events.makePythonStateZeroCrossEvent('w', 20, 1, ev_args)
DSargs = {
'tdomain': [0.1, 2.1],
'tdata': [0.11, 2.1],
'ics': {'w': 3.0},
'pars': {'k': 2, 'a': -0.5},
'inputs': {'itable': interptable.variables['x1']},
'auxvars': ['aux_wdouble', 'aux_other'],
'algparams': {'init_step': 0.01, 'strict': False},
'events': thresh_ev,
'checklevel': 2,
'name': 'ODEtest',
'fnspecs': fnspecs,
'varspecs': fvarspecs
}
testODE = Vode_ODEsystem(DSargs)
odetraj = testODE.compute('testode')
saveObjects([odetraj, testODE], 'temp_objects.pkl', True)
objs_ode = loadObjects('temp_objects.pkl')
objs_ode[1].diagnostics.clearWarnings()
assert len(objs_ode[1].diagnostics.warnings) == 0
odetraj2 = objs_ode[1].compute('testode2')
assert odetraj2(0.6) == odetraj(0.6)
assert len(objs_ode[1].diagnostics.warnings) == 1
os.remove('temp_objects.pkl')
def test_saveload_explicitfngen():
"""Test pickling for saving and loading 'ExplicitFnGen'"""
args = {
'tdomain': [-50, 50],
'pars': {'speed': 1},
'xdomain': {'s': [-1., 1.]},
'name': 'sine',
'globalt0': 0.4,
'pdomain': {'speed': [0, 200]},
'varspecs': {'s': "sin(globalindepvar(t)*speed)"}
}
sin_gen = ExplicitFnGen(args)
sintraj1 = sin_gen.compute('sine1')
sin_gen.set(pars={'speed': 2})
sintraj2 = sin_gen.compute('sine2')
saveObjects([sin_gen, sintraj1, sintraj2], 'temp_objects.pkl', True)
objs_sin = loadObjects('temp_objects.pkl')
assert sintraj1(0.55) == objs_sin[1](0.55)
assert sintraj2(0.55) == objs_sin[2](0.55)
os.remove('temp_objects.pkl')
def test_saveload_trajectory():
"""Test pickling for saving and loading 'Trajectory'"""
var1 = Variable(
Pointset(
coordarray=array(range(10), float) * 0.1,
indepvararray=array(range(10), float) * 0.5
),
name='v1'
)
var2 = Variable(
Pointset(
coordarray=array(range(10), float) * 0.25 + 1.0,
indepvararray=array(range(10), float) * 0.5
),
name='v2'
)
traj = Trajectory('traj1', [var1, var2])
saveObjects(traj, 'temp_objects.pkl', True)
traj_loaded = loadObjects('temp_objects.pkl')[0]
assert traj_loaded(2.0) == traj(2.0)
os.remove('temp_objects.pkl')
def prep_boxplots(data, xlabel_str, figname='', fignum=1, do_legend=1,
means=1, xlegoff=0, ylegstep=1, ylegoff=0, spacing=None):
spacing_actual = {
'width': 0.1,
'wgapfac': 0.75,
'markersize': 12,
'off_fac': 0.7,
'x_step': 0.9, # 9 * width
'x_off': 0,
'box_to_marker': 1.1,
'notch_size': 0.2}
if spacing is not None:
spacing_actual.update(spacing)
width = spacing_actual['width']
wgapfac = spacing_actual['wgapfac']
markersize = spacing_actual['markersize']
off_fac = spacing_actual['off_fac']
x_step = spacing_actual['x_step']
x_off = spacing_actual['x_off']
box_to_marker = spacing_actual['box_to_marker']
notch_size = spacing_actual['notch_size']
n = len(data)
x_min = -width*3.8 #3.75
x_max = (n-1)*x_step+width*4.5 #3.75
if n > 1:
halfticks = arange(1,n)*x_step-x_step/2
figure(fignum)
# work out ordering of data from 'pos' key
order = {}
# `pos` position runs from 1 to n, `ns` runs from 0 to n-1
ns = []
for k, v in data.iteritems():
order[v['pos']] = k
ns.append(v['pos']-1)
ns.sort()
assert ns == range(n)
maxD = 0
max_dimval_markers = 0
labels = []
for pos in range(n):
name = order[pos+1]
pde_name = 'PD_E-'+name
if 'known_dim' in data[name]:
if n == 1:
kdx1 = x_min
kdx2 = x_max
else:
if pos == 0:
kdx1 = x_min
kdx2 = halfticks[0]
elif pos == n-1:
kdx1 = halfticks[n-2]
kdx2 = x_max
else:
kdx1 = halfticks[pos-1]
kdx2 = halfticks[pos]
plot([[kdx1], [kdx2]],
[data[name]['known_dim'],data[name]['known_dim']],
'k', linewidth=1, zorder=0)
slope_data = loadObjects(pde_name)[2]
ds_mins = array(slope_data[:,0])#,shape=(len(slope_data),1))
ds_mins.shape=(len(slope_data),1)
ds_maxs = array(slope_data[:,1])#,shape=(len(slope_data),1))
ds_maxs.shape=(len(slope_data),1)
max_ds = max([max(ds_mins[:,0]),max(ds_maxs[:,0])])
if max_ds > maxD:
maxD = max_ds
# limits args are ineffective here
boxplot(ds_mins,positions=[pos*x_step-width*wgapfac+x_off],whis=100,
means=means,monochrome=True,notch=2,notchsize=notch_size,
limits=(),widths=width,fill=1)
boxplot(ds_maxs,positions=[pos*x_step+width*wgapfac+x_off],whis=100,
means=means,monochrome=True,notch=2,notchsize=notch_size,
limits=(),widths=width,fill=1)
if pos == 0:
fa = figure(fignum).axes[0]
fa.hold(True)
if means:
ds_all_mean = (mean(ds_mins[:,0])+mean(ds_maxs[:,0]))/2
plot([pos*x_step+x_off], [ds_all_mean], 'k^',
markersize=markersize-2)
pca_x = pos*x_step-width*(wgapfac+box_to_marker)+x_off
isomap_x = pos*x_step+width*(wgapfac+box_to_marker)+x_off
pca_ds = {}
isomap_ds = {}
try:
pca_data = data[name]['pca']
except KeyError:
pca_data = []
pca_ds, max_dimval_pca, pca_used = plot_markers(pca_data,
pca_x, 'PCA',
symbol_map['pca'], -1,
width, off_fac, markersize)
if max_dimval_pca > maxD:
maxD = max_dimval_pca
if max_dimval_pca > max_dimval_markers:
max_dimval_markers = max_dimval_pca
try:
isomap_data = data[name]['isomap']
except KeyError:
isomap_data = []
isomap_ds, max_dimval_iso, isomap_used = plot_markers(isomap_data,
isomap_x, 'Isomap',
symbol_map['isomap'], 1,
width, off_fac, markersize)
if max_dimval_iso > maxD:
maxD = max_dimval_iso
if max_dimval_iso > max_dimval_markers:
max_dimval_markers = max_dimval_iso
labels.append(data[name]['label'])
## legend
if do_legend:
font = FontProperties()
font.set_family('sans-serif')
font.set_size(11)
x_legend = x_min + 3*width/4 + xlegoff
y_legend = maxD+ylegoff
# pca legend
for k, s in pca_used:
plot_markers([(k,s,y_legend)], x_legend, 'Legend', symbol_map['pca'],
1, width, off_fac, markersize)
if k == 'var':
legstr = "%s=%d%%"%(k,s)
else:
legstr = "%s=%d"%(k,s)
text(x_legend+3*width/4, y_legend-width*2., legstr,
fontproperties=font)
y_legend -= ylegstep
# isomap legend
isomap_leg_data = []
for k, s in isomap_used:
if y_legend-width*2. <= max_dimval_markers + 2:
y_legend = maxD+ylegoff
x_legend += x_step #-width*.75
plot_markers([(k,s,y_legend)], x_legend, 'Legend', symbol_map['isomap'],
1, width, off_fac, markersize)
## if k == 'eps':
## kstr = '\\epsilon'
## else:
## kstr = k
text(x_legend+3*width/4, y_legend-width*2., "%s=%d"%(k,s),
fontproperties=font)
y_legend -= ylegstep
## tidy up axes, etc.
fa.set_xticks(arange(n)*x_step)
if n>1:
for h in range(n-1):
plot([halfticks[h], halfticks[h]], [0,maxD+1+ylegoff], 'k:')
fa.set_xticklabels(labels)
fa.set_position([0.07, 0.11, 0.9, 0.85])
fa.set_xlim(x_min,x_max)
fa.set_ylim(0,maxD+1+ylegoff)
if xlabel_str != '':
xlabel(r'$\rm{'+xlabel_str+r'}$',args(fontsize=20,fontname='Times'))
ylabel(r'$\rm{Dimension}$',args(fontsize=20,fontname='Times'))
draw()
if figname != '':
save_fig(fignum, figname)