def __calculate_area_pixels(self):
xc = 0
yc = 0
z = 0
xs, ys, zs = self.spacing
proj = Project()
orig_orien = proj.original_orientation
xy = (xs, ys)
yz = (ys, zs)
xz = (xs, zs)
if (orig_orien == const.SAGITAL):
orientation_based_spacing = {"SAGITAL" : xy,
"AXIAL" : yz,
"CORONAL" : xz}
elif(orig_orien == const.CORONAL):
orientation_based_spacing = {"CORONAL" : xy,
"AXIAL" : xz,
"SAGITAL" : yz}
else:
orientation_based_spacing = {"AXIAL" : xy,
"SAGITAL" : yz,
"CORONAL" : xz}
xs, ys = orientation_based_spacing[self.orientation]
self.pixel_list = []
for i in utils.frange(yc - self.y_length/2, yc + self.y_length/2, ys):
for k in utils.frange(xc - self.x_length/2, xc + self.x_length/2, xs):
self.pixel_list.append((k, i))
def draw(self, a, b, cell, cam, shadow):
building = cell.building
if building:
camera(cam.c.x - a * self.cell_size, cam.c.y - b * self.cell_size)
if shadow:
for i in frange(0, building.height / 2, 4):
t = Vec2(building.s.x, building.s.y)
t._mul(i * 0.015)
t._add(building.pos)
rectfill(t.x - building.w, t.y - building.h,
t.x + building.w, t.y + building.h, 5)
else:
for i in frange(building.height / 2, building.height - 1, 4):
t = Vec2(building.s.x, building.s.y)
t._mul(i * 0.015)
t._add(building.pos)
rectfill(t.x - building.w, t.y - building.h,
t.x + building.w, t.y + building.h, 5)
s = building.s.mul(building.height * 0.015)
s._add(building.pos)
rectfill(s.x - building.w, s.y - building.h,
s.x + building.w, s.y + building.h,
building.color)
def __init__(self):
self.names = ['fl', 'sax', 'vla', 'vc', 'tbn', 'gtr']
self.fl = fl =Piccolo()
self.sax = sax = SopranoSaxophone()
self.vla = vla = Viola()
self.vc = vc =Violoncello()
self.tbn = tbn = Trombone()
self.gtr = gtr = ElectricGuitar()
self.l = [fl, sax, vla, vc, tbn, gtr]
self.d = {}
for name, inst in zip(self.names, self.l):
inst.nickname = name
self.d[name] = inst
# lowest, highest notes
ranges = [
('D5', 'C7'), # Piccolo
('C4', 'C6'), # Soprano Sax
('C3', 'E5'), # Viola
('C2', 'E4'), # Cello
('E2', 'B-4'), # Trombone
('E2', 'A5') # Guitar
]
for r, i in zip(ranges, self.l):
i.lowest_note = Pitch(r[0])
i.highest_note = Pitch(r[1])
i.all_notes = list(frange(i.lowest_note.ps, i.highest_note.ps + 1))
i.all_notes_24 = list(frange(i.lowest_note.ps, i.highest_note.ps + 1, 0.5))
self.piece_range = list(frange(Pitch('E2').ps, Pitch('C7').ps + 1))
self.piece_range_at_least_two_instruments = list(frange(Pitch('E2').ps, Pitch('C6').ps + 1))
def CreateBBGrid(xMin,
xMax,
yMin,
yMax,
cellSize,
fixes,
intervals,
searchArea=None,
progressor=None):
"""Build a brownian bridge grid by dividing the extents into
square cells of size cellSize. The grid is a list of rows. Each
row is a list of cell value. Each row is built left to right, and the
rows are built top to bottom. See the EvaluateGridPoint() for details
on the remaining parameters."""
if progressor is not None:
rowCount = 1 + int((yMax - yMin) / cellSize)
if progressor == True:
rowIndex = 0
print "Start Building Grid", rowCount
else:
progressor.SetProgressor("step", "Building Grid...", 0, rowCount,
1)
if searchArea is not None:
point = arcpy.Point()
grid = []
#build the grid from the top down
for y in utils.frange(yMax, yMin, -cellSize):
row = []
for x in utils.frange(xMin, xMax, cellSize):
if searchArea is None:
cell = EvaluateGridPoint(x, y, fixes, intervals)
#cell = 1
else:
point.X, point.Y = x, y
if searchArea.contains(point):
cell = EvaluateGridPoint(x, y, fixes, intervals)
#cell = 1
else:
cell = 0
row.append(cell)
grid.append(row)
if progressor is not None:
if progressor == True:
rowIndex += 1
print "Finished row", rowIndex, "of", rowCount
else:
progressor.SetProgressorPosition()
return grid
def __init__(self):
self.names = [
'fl',
'ob',
'cl',
'sax',
'tpt',
'vln',
'vib',
'bs'
]
self.fl = fl = Flute()
self.ob = ob = Oboe()
self.cl = cl = Clarinet()
self.sax = sax = AltoSaxophone()
self.tpt = tpt = Trumpet()
self.vln = vln = Violin()
self.vib = vib = Vibraphone()
self.bs = bs = Contrabass()
self.l = [
fl,
ob,
cl,
sax,
tpt,
vln,
vib,
bs
]
self.d = {}
for name, inst in zip(self.names, self.l):
inst.nickname = name
self.d[name] = inst
# lowest, highest notes
ranges = [
('C4', 'C7'), # Flute 60 96
('B-3', 'G#6'), # Oboe 58 92
('D3', 'G6'), # Clarinet 50 91
('D-3', 'A-5'), # Sax 49 80
('E3', 'B-5'), # Trumpet 52 82
('G3', 'B6'), # Violin
('F3', 'F6'), # Vibraphone
('E1', 'G3') # Bass
]
for r, i in zip(ranges, self.l):
i.lowest_note = Pitch(r[0])
i.highest_note = Pitch(r[1])
i.all_notes = list(frange(i.lowest_note.ps, i.highest_note.ps + 1))
i.all_notes_24 = list(frange(i.lowest_note.ps, i.highest_note.ps + 1, 0.5))
def run_experiment1(args):
"""
Main entry for executing experiment1 and executing yielded
files one by one
"""
threads = []
tcp_agents = OrderedDict({})
tcp_agents['Tahoe'] = 'Agent/TCP'
tcp_agents['Reno'] = 'Agent/TCP/Reno'
tcp_agents['NewReno'] = 'Agent/TCP/Newreno'
tcp_agents['Vegas'] = 'Agent/TCP/Vegas'
cbr_rates = frange(1.00, 10.00, args.granularity)
for agent_name, agent in tcp_agents.items():
for cbr_rate in cbr_rates:
out_file = format_trace_file_name(args.out, agent_name, cbr_rate)
nsargs = [
agent, cbr_rate, out_file, args.cbr_start, args.cbr_stop,
args.tcp_start, args.tcp_stop, args.duration
]
rc = ns('../ns2/experiment1.tcl', nsargs)
nsargs.append(str(rc))
nsargs[0] = agent_name
print("experiment1, tcp_agent: %s, cbr_rate: %s, " +
"out_to: %s, cbr_start: %s, cbr_stop: %s, " +
"tcp_start: %s, tcp_stop: %s, duration: %s, " +
"return code: %s") % tuple(map(lambda x: str(x), nsargs))
kwargs = {
'cbr_rate': str(cbr_rate),
'agent_name': agent_name,
}
t = post_process(args.which, out_file, **kwargs)
threads.append(t)
# waits for all thread finish once get out of the loop
wait_for(threads)
def manipulate_latent(model, data, args):
print('-' * 30 + 'Begin: manipulate' + '-' * 30)
x_test, y_test = data
index = np.argmax(y_test, 1) == args.digit
number = np.random.randint(low=0, high=sum(index) - 1)
x, y = x_test[index][number], y_test[index][number]
x, y = np.expand_dims(x, 0), np.expand_dims(y, 0)
noise = np.zeros([1, conf.NUM_CLASSES, 16])
x_recons = []
for dim in range(16):
# for r in [-0.25, -0.2, -0.15, -0.1, -0.05, 0, 0.05, 0.1, 0.15, 0.2, 0.25]:
for r in utils.frange(-0.25, 0.25, 0.05):
tmp = np.copy(noise)
tmp[:, :, dim] = r
x_recon = model.predict([x, y, tmp])
x_recons.append(x_recon)
x_recons = np.concatenate(x_recons)
img = utils.combine_images(x_recons, height=16)
image = img * 255
Image.fromarray(image.astype(
np.uint8)).save(args.save_dir + '/manipulate-%d.png' % args.digit)
print('manipulated result saved to %s/manipulate-%d.png' %
(args.save_dir, args.digit))
print('-' * 30 + 'End: manipulate' + '-' * 30)
def create_iter_elems(param, start_only):
"""
Creates the elements corresponding to an iteration element.
:param param:
:param start_only:
:return:
"""
name_attr = param['@name']
from_attr = float(param['@from'])
to_attr = float(param['@to'])
by_attr = float(param['@by'])
# Sanity check (positive steps only), no more than 10 steps
# If this test fails, the parameter is replaced by its starting point
if not start_only:
if from_attr < to_attr and by_attr > 0 and (to_attr - from_attr) / 10 <= 10:
logging.info("Parameter iteration found. Adding metrics for range: ")
param_range = frange(from_attr, to_attr+by_attr, by_attr)
else:
logging.warn("Illegal parameter iteration specified: from %f, to %f, by %f",
from_attr, to_attr, by_attr)
param_range = [from_attr]
else:
logging.warn("Extra iteration parameters replaced with start point %s")
param_range = [from_attr]
iter_elems = [{'@name': name_attr, '#text': param_value} for param_value in param_range]
return iter_elems
def getisosweights_gauss(weights,age,metallicity,isos,sigma):
""" same as getisoweights, but adds Gaussian scatter """
w=[0.]*len(isos)
for m,a,feh in zip(weights,age,metallicity):
for x in utils.frange(feh-4,feh+4,0.1):
w[getn(x,a,isos)]+=m*utils.gauss(x,feh,sigma)
return w
def getisosweights_gauss(weights, age, metallicity, isos, sigma):
""" same as getisoweights, but adds Gaussian scatter """
w = [0.] * len(isos)
for m, a, feh in zip(weights, age, metallicity):
for x in utils.frange(feh - 4, feh + 4, 0.1):
w[getn(x, a, isos)] += m * utils.gauss(x, feh, sigma)
return w
def choose_melody_pitches(self, notes, register, harmonies):
print 'Choosing pitches'
for h in harmonies:
h['pitch_classes'] = [p % 12 for p in h['pitch']]
set_start_end(notes)
set_start_end(harmonies)
previous_note_index = random.choice(range(int(len(register) * .4)))
prev = register[previous_note_index]
for note in notes:
beats = list(
frange(note['start'], note['start'] + note['duration'], .25))
note_harmonies = []
for b in beats:
h = get_at(b, harmonies)
h = h['pitch_classes']
if h not in note_harmonies:
note_harmonies.append(h)
print 'note_harmonies', note_harmonies
if len(note_harmonies) == 1:
pitch_options = self.get_pitch_options(note_harmonies[0], prev)
else:
pitch_options = []
c = Counter()
for h in note_harmonies:
for p in h:
c[p] += 1
common = []
for p, count in c.most_common():
if count == len(note_harmonies):
common.append(p)
if len(common) > 0:
pitch_options = self.get_pitch_options(common, prev)
if len(pitch_options) == 0:
ranked = [p for p, _ in c.most_common() if p not in common]
for p in ranked:
pitch_options = self.get_pitch_options([p], prev)
if len(pitch_options) > 0:
break
if len(pitch_options) == 0:
pitch_options = [prev - 2, prev - 1, prev + 1, prev + 2]
note['pitch'] = random.choice(pitch_options)
print note['pitch'] % 12
print
prev = note['pitch']
self.add_ornament(note, prev, note_harmonies)
def obtener_resultado(self, min, max=None, interval=None, velocidad=None):
if max == None:
max = min
min = 0
tiempo_aproximado = None
tiempo_real = None
for tiempo in utils.frange(min, max, interval):
self.velocidad_anterior.append(
self.obtener_velocidad_aproximada(tiempo))
self.velocidad_anterior_real.append(self.obtener_velocidad(tiempo))
self.tiempo_anterior.append(tiempo)
if utils.isclose(self.obtener_velocidad_aproximada(tiempo),
velocidad,
rel_tol=0.001) and tiempo_aproximado is None:
tiempo_aproximado = tiempo
if utils.isclose(self.obtener_velocidad(tiempo),
velocidad,
rel_tol=0.001) and tiempo_real is None:
tiempo_real = tiempo
if tiempo_real is not None and tiempo_aproximado is not None:
return [tiempo_aproximado, tiempo_real]
def update(self, x, y, cell, cam, cells, blobs):
building = cell.building
if building:
cellp = Vec2(cam.pos.x % self.cell_size - x * self.cell_size,
cam.pos.y % self.cell_size - y * self.cell_size)
building.s = building.pos.sub(
cellp.add(self.config.perspective_offset))
s1 = max(building.w, building.h)
s2 = min(building.w, building.h)
for i in frange(-s1 + s2 / 2, s1 - s2 / 2, s2):
p1 = Vec2((cells.pos.x + x) * self.cell_size,
(cells.pos.y + y) * self.cell_size).add(building.pos)
if s1 == building.w:
p1.x += i
else:
p1.y += i
blobs.add_blob(p1, s2)
p2 = Vec2((cells.pos.x + x) * self.cell_size,
(cells.pos.y + y) * self.cell_size).add(building.pos)
if s1 == building.w:
p2.x += s1 - s2 / 2
else:
p2.y += s1 - s2 / 2
if p2.dist(p1) > 2:
blobs.add_blob(p2, s2)
def run_experiment1(args):
"""
Main entry for executing experiment1 and executing yielded
files one by one
"""
threads = []
tcp_agents = OrderedDict({})
tcp_agents['Tahoe'] = 'Agent/TCP'
tcp_agents['Reno'] = 'Agent/TCP/Reno'
tcp_agents['NewReno'] = 'Agent/TCP/Newreno'
tcp_agents['Vegas'] = 'Agent/TCP/Vegas'
cbr_rates = frange(1.00, 10.00, args.granularity)
for agent_name, agent in tcp_agents.items():
for cbr_rate in cbr_rates:
out_file = format_trace_file_name(args.out, agent_name, cbr_rate)
nsargs = [agent, cbr_rate, out_file, args.cbr_start, args.cbr_stop,
args.tcp_start, args.tcp_stop, args.duration]
rc = ns('../ns2/experiment1.tcl', nsargs)
nsargs.append(str(rc))
nsargs[0] = agent_name
print ("experiment1, tcp_agent: %s, cbr_rate: %s, " +
"out_to: %s, cbr_start: %s, cbr_stop: %s, " +
"tcp_start: %s, tcp_stop: %s, duration: %s, " +
"return code: %s") % tuple(map(lambda x: str(x), nsargs))
kwargs = {
'cbr_rate': str(cbr_rate),
'agent_name': agent_name,
}
t = post_process(args.which, out_file, **kwargs)
threads.append(t)
# waits for all thread finish once get out of the loop
wait_for(threads)
def __calculate_area_pixels(self):
"""
Return the cursor's pixels.
This method scans the circle line by line.
Extracted equation.
http://www.mathopenref.com/chord.html
"""
xc = 0.0
yc = 0.0
z = 0.0
xs, ys, zs = self.spacing
proj = Project()
orig_orien = proj.original_orientation
xy = (xs, ys)
yz = (ys, zs)
xz = (xs, zs)
if (orig_orien == const.SAGITAL):
orientation_based_spacing = {"SAGITAL" : xy,
"AXIAL" : yz,
"CORONAL" : xz}
elif(orig_orien == const.CORONAL):
orientation_based_spacing = {"CORONAL" : xy,
"AXIAL" : xz,
"SAGITAL" : yz}
else:
orientation_based_spacing = {"AXIAL" : xy,
"SAGITAL" : yz,
"CORONAL" : xz}
xs, ys = orientation_based_spacing[self.orientation]
self.pixel_list = []
radius = self.radius
for i in utils.frange(yc - radius, yc + radius, ys):
# distance from the line to the circle's center
d = yc - i
# line size
line = sqrt(radius**2 - d**2) * 2
# line initial x
xi = xc - line/2.0
# line final
xf = line/2.0 + xc
yi = i
for k in utils.frange(xi,xf,xs):
self.pixel_list.append((k, yi))
def choose_melody_pitches(self, notes, register, harmonies):
print 'Choosing pitches'
for h in harmonies:
h['pitch_classes'] = [p % 12 for p in h['pitch']]
set_start_end(notes)
set_start_end(harmonies)
previous_note_index = random.choice(range(int(len(register) * .4)))
prev = register[previous_note_index]
for note in notes:
beats = list(frange(note['start'], note['start'] + note['duration'], .25))
note_harmonies = []
for b in beats:
h = get_at(b, harmonies)
h = h['pitch_classes']
if h not in note_harmonies:
note_harmonies.append(h)
print 'note_harmonies', note_harmonies
if len(note_harmonies) == 1:
pitch_options = self.get_pitch_options(note_harmonies[0], prev)
else:
pitch_options = []
c = Counter()
for h in note_harmonies:
for p in h:
c[p] += 1
common = []
for p, count in c.most_common():
if count == len(note_harmonies):
common.append(p)
if len(common) > 0:
pitch_options = self.get_pitch_options(common, prev)
if len(pitch_options) == 0:
ranked = [p for p, _ in c.most_common() if p not in common]
for p in ranked:
pitch_options = self.get_pitch_options([p], prev)
if len(pitch_options) > 0:
break
if len(pitch_options) == 0:
pitch_options = [prev - 2, prev - 1, prev + 1, prev + 2]
note['pitch'] = random.choice(pitch_options)
print note['pitch'] % 12
print
prev = note['pitch']
self.add_ornament(note, prev, note_harmonies)
def sumisos_gauss_slow(mass,age,metallicity,fehlist,agelist,isos,sigma):
"""slower version"""
summed_iso = 0.*isos[isos.keys()[0]]
for m,a,z in zip(mass,age,metallicity):
feh = numarray.log10(z)-numarray.log10(SOLAR)
for x in utils.frange(feh-4,feh+4,0.1):
summed_iso+= utils.gauss(x,feh,sigma)*m*getiso(x,a,fehlist,agelist,isos)
return summed_iso
def sumisos_gauss_slow(mass, age, metallicity, fehlist, agelist, isos, sigma):
"""slower version"""
summed_iso = 0. * isos[isos.keys()[0]]
for m, a, z in zip(mass, age, metallicity):
feh = numarray.log10(z) - numarray.log10(SOLAR)
for x in utils.frange(feh - 4, feh + 4, 0.1):
summed_iso += utils.gauss(x, feh, sigma) * m * getiso(
x, a, fehlist, agelist, isos)
return summed_iso
def CreateBBGrid(xMin, xMax, yMin, yMax, cellSize, fixes, intervals, searchArea=None, progressor=None):
"""Build a brownian bridge grid by dividing the extents into
square cells of size cellSize. The grid is a list of rows. Each
row is a list of cell value. Each row is built left to right, and the
rows are built top to bottom. See the EvaluateGridPoint() for details
on the remaining parameters."""
if progressor is not None:
rowCount = 1 + int((yMax - yMin) / cellSize)
if progressor == True:
rowIndex = 0
print "Start Building Grid", rowCount
else:
progressor.SetProgressor("step", "Building Grid...", 0, rowCount, 1)
if searchArea is not None:
point = arcpy.Point()
grid = []
#build the grid from the top down
for y in utils.frange(yMax, yMin, -cellSize):
row = []
for x in utils.frange(xMin, xMax, cellSize):
if searchArea is None:
cell = EvaluateGridPoint(x, y, fixes, intervals)
#cell = 1
else:
point.X, point.Y = x, y
if searchArea.contains(point):
cell = EvaluateGridPoint(x, y, fixes, intervals)
#cell = 1
else:
cell = 0
row.append(cell)
grid.append(row)
if progressor is not None:
if progressor == True:
rowIndex += 1
print "Finished row", rowIndex, "of", rowCount
else:
progressor.SetProgressorPosition()
return grid
def choose_solo_notes(self):
rest_beginning = random.choice([True, False, False, False, False])
rest_middle = random.choice([True, True, False])
rest_end = random.choice([True, True, True, False, False])
rests = [rest_beginning, rest_middle, rest_end]
num_rests = rests.count(True)
min_num_divs = 3 + num_rests
num_divs = random.randint(min_num_divs, 9)
divs = divide(16, num_divs)
notes = [{'pitch': None, 'duration': div / 4.0} for div in divs]
if rest_beginning:
notes[0]['pitch'] = 'rest'
if rest_end:
notes[-1]['pitch'] = 'rest'
if rest_middle:
if rest_beginning:
start = 2
else:
start = 1
if rest_end:
end = -2
else:
end = -1
middle_rest_index = random.choice(range(len(notes))[start:end])
notes[middle_rest_index]['pitch'] = 'rest'
for note in notes:
if note['pitch'] != 'rest':
note['pitch'] = ps = random.choice(self.soloist_shared_notes)
self.soloist_shared_notes = [p for p in frange(ps - 2, ps + 3) if p in self.all_soloists_shared_notes]
self.soloist_shared_notes = [p for p in frange(ps - 5, ps + 6) if p in self.all_soloists_shared_notes]
return notes
def getisosweights_vgauss(weights, age, metallicity, isos, sigma, dsigmadlogt):
""" same as getisoweights, but adds age-dependent Gaussian scatter """
w = [0.] * len(isos)
logt0 = numarray.log10(age[0])
for m, a, feh in zip(weights, age, metallicity):
logt = numarray.log10(a)
sig = sigma + dsigmadlogt * (logt - logt0)
for x in utils.frange(feh - 4, feh + 4, 0.1):
w[getn(x, a, isos)] += m * utils.gauss(x, feh, sig)
return w
def getisosweights_vgauss(weights,age,metallicity,isos,sigma,dsigmadlogt):
""" same as getisoweights, but adds age-dependent Gaussian scatter """
w=[0.]*len(isos)
logt0 = numarray.log10(age[0])
for m,a,feh in zip(weights,age,metallicity):
logt = numarray.log10(a)
sig = sigma+dsigmadlogt*(logt-logt0)
for x in utils.frange(feh-4,feh+4,0.1):
w[getn(x,a,isos)]+=m*utils.gauss(x,feh,sig)
return w
def range(ode_method, ode, initial_val, start, end, step_size=0.01):
values = []
old_val = initial_val
for t in frange(start, end + 0.00001, step_size):
values.append((t, old_val))
new_val = ode_method(ode, old_val, t, step_size)
old_val = new_val
return values
def __init__(self):
self.names = ['vln', 'gtr']
self.vln = vln = Violin()
self.gtr = gtr = AcousticGuitar()
self.l = [vln, gtr]
self.d = {}
for name, inst in zip(self.names, self.l):
inst.nickname = name
self.d[name] = inst
# lowest, highest notes
ranges = [
('G3', 'B6'), # Violin
('E2', 'G5') # Guitar
]
for r, i in zip(ranges, self.l):
i.lowest_note = Pitch(r[0])
i.highest_note = Pitch(r[1])
i.all_notes = list(frange(i.lowest_note.ps, i.highest_note.ps + 1))
i.all_notes_24 = list(frange(i.lowest_note.ps, i.highest_note.ps + 1, 0.5))
def __init__(self):
self.names = ['vln', 'gtr']
self.vln = vln = Violin()
self.gtr = gtr = AcousticGuitar()
self.l = [vln, gtr]
self.d = {}
for name, inst in zip(self.names, self.l):
inst.nickname = name
self.d[name] = inst
# lowest, highest notes
ranges = [
('G3', 'B6'), # Violin
('E2', 'G5') # Guitar
]
for r, i in zip(ranges, self.l):
i.lowest_note = Pitch(r[0])
i.highest_note = Pitch(r[1])
i.all_notes = list(frange(i.lowest_note.ps, i.highest_note.ps + 1))
i.all_notes_24 = list(
frange(i.lowest_note.ps, i.highest_note.ps + 1, 0.5))
def readin():
""" read in the best fit:
p,t,s,m,w,model,data,isos,isow = readin()
parameters, time, sfr, metallicity, weights, model, data, ...
"""
log_tmax = Numeric.log10(13.7e9)
data = iso.readfits(isodir + "/datarr.fits")
isos = iso.readisos(isodir)
t = utils.frange(8, log_tmax, 0.001)
p = parameters()
p.load()
m, s, w, isow, model = compute_model(t, p, isos, data)
return p, t, s, m, w, model, data, isos, isow
def readin():
""" read in the best fit:
p,t,s,m,w,model,data,isos,isow = readin()
parameters, time, sfr, metallicity, weights, model, data, ...
"""
log_tmax = Numeric.log10(13.7e9)
data=iso.readfits(isodir+"/datarr.fits")
isos = iso.readisos(isodir)
t=utils.frange(8,log_tmax,0.001)
p=parameters()
p.load()
m,s,w,isow,model = compute_model(t,p,isos,data)
return p,t,s,m,w,model,data,isos,isow
def sumisos_gauss(mass,age,metallicity,fehlist,agelist,isos,sigma):
"""Faster version."""
isoweight = {}
for k in isos.keys():
isoweight[k] = 0.
for m,a,z in zip(mass,age,metallicity):
feh = numarray.log10(z/SOLAR)
for x in utils.frange(feh-4,feh+4,0.1):
isoweight[getindices(x,a,fehlist,agelist)]+= utils.gauss(x,feh,sigma)*m
summed_iso = 0.*isos[isos.keys()[0]]
for k in isoweight.keys():
summed_iso+=isoweight[k]*isos[k]
# p(isoweight)
return summed_iso
def getisosweights_sgauss(weights,age,sfr,metallicity,isos,sigma,dsigmadlogt):
""" Same as getisoweights, but adds sfr-dependent Gaussian scatter.
**** CAUTION: not yet tested ****
"""
w=[0.]*len(isos)
logt0 = numarray.log10(age[0])
for m,a,feh,s in zip(weights,age,metallicity,sfr):
ss = numarray.maximum(sfr,1.e-5)
logs = numarray.log10(ss)
logt = numarray.log10(a)
sig = sigma+dsigmadlogs*(logs)
for x in utils.frange(feh-4,feh+4,0.1):
w[getn(x,a,isos)]+=m*utils.gauss(x,feh,sig)
return w
def getisosweights_sgauss(weights, age, sfr, metallicity, isos, sigma,
dsigmadlogt):
""" Same as getisoweights, but adds sfr-dependent Gaussian scatter.
**** CAUTION: not yet tested ****
"""
w = [0.] * len(isos)
logt0 = numarray.log10(age[0])
for m, a, feh, s in zip(weights, age, metallicity, sfr):
ss = numarray.maximum(sfr, 1.e-5)
logs = numarray.log10(ss)
logt = numarray.log10(a)
sig = sigma + dsigmadlogs * (logs)
for x in utils.frange(feh - 4, feh + 4, 0.1):
w[getn(x, a, isos)] += m * utils.gauss(x, feh, sig)
return w
def Search(func, allSquaredDistances, n, h_ref, min_percent, max_percent, step_percent):
h_min = min_percent * h_ref
h_max = max_percent * h_ref
h_step = step_percent * h_ref
h_res = h_max
minErr = func(allSquaredDistances, n, h_max)
for h_test in utils.frange(h_min, h_max, h_step):
err = func(allSquaredDistances, n, h_test)
if (err < minErr):
minErr = err
h_res = h_test
return h_res
def Search(func, allSquaredDistances, n, h_ref, min_percent, max_percent,
step_percent):
h_min = min_percent * h_ref
h_max = max_percent * h_ref
h_step = step_percent * h_ref
h_res = h_max
minErr = func(allSquaredDistances, n, h_max)
for h_test in utils.frange(h_min, h_max, h_step):
err = func(allSquaredDistances, n, h_test)
if (err < minErr):
minErr = err
h_res = h_test
return h_res
def sumisos_gauss(mass, age, metallicity, fehlist, agelist, isos, sigma):
"""Faster version."""
isoweight = {}
for k in isos.keys():
isoweight[k] = 0.
for m, a, z in zip(mass, age, metallicity):
feh = numarray.log10(z / SOLAR)
for x in utils.frange(feh - 4, feh + 4, 0.1):
isoweight[getindices(x, a, fehlist,
agelist)] += utils.gauss(x, feh, sigma) * m
summed_iso = 0. * isos[isos.keys()[0]]
for k in isoweight.keys():
summed_iso += isoweight[k] * isos[k]
# p(isoweight)
return summed_iso
def choose_pitches(self, parts):
for part in parts:
for note in part['notes']:
if note['pitch'] != 'rest':
note_opts = self.song.note_opts[part['instrument_name']]
# note_opts = self.piece.i.d[part['instrument_name']].all_notes
note['pitch'] = random.choice(note_opts)
# reset note_opts to a range within a 4th in either direction of the chosen note,
# but making sure that all notes are in all_note_opts
self.song.note_opts[part['instrument_name']] = [p for p in frange(note['pitch'] - 5, note['pitch'] + 6) if p in self.piece.i.d[part['instrument_name']].all_notes]
harmonies = get_harmonies(parts)
valid = all([validate_harmony(h) for h in harmonies])
if not valid:
self.choose_pitches(parts)
def run_experiment2(args):
"""
Main entry for executing experiment2 and executing yielded
files one by one
"""
threads = []
tcp_agent_pairs = OrderedDict({})
tcp_agent_pairs[('Reno', 'Reno')] = ('Agent/TCP/Reno', 'Agent/TCP/Reno')
tcp_agent_pairs[('NewReno', 'Reno')] = ('Agent/TCP/Newreno',
'Agent/TCP/Reno')
tcp_agent_pairs[('Vegas', 'Vegas')] = ('Agent/TCP/Vegas',
'Agent/TCP/Vegas')
tcp_agent_pairs[('NewReno', 'Vegas')] = ('Agent/TCP/Newreno',
'Agent/TCP/Vegas')
cbr_rates = frange(1.00, 10.00, args.granularity)
for pair_names, agent_pair in tcp_agent_pairs.items():
for cbr_rate in cbr_rates:
pair_name = '-'.join(pair_names)
out_file = format_trace_file_name(args.out, pair_name, cbr_rate)
nsargs = [
agent_pair[0], agent_pair[1], cbr_rate, out_file,
args.cbr_start, args.cbr_stop, args.tcp1_start, args.tcp1_stop,
args.tcp2_start, args.tcp2_stop, args.duration
]
rc = ns('../ns2/experiment2.tcl', nsargs)
nsargs.append(str(rc))
nsargs[1] = pair_name
print ("experiment2, tcp_agents: %s, cbr_rate: %s, " +
"out_to: %s, cbr_start: %s, cbr_stop: %s, " +
"tcp1_start: %s, tcp1_stop: %s, tcp2_start: %s" +
"tcp2_stop: %s, duration: %s, return code: %s") \
% tuple(map(lambda x: str(x), nsargs[1:]))
kwargs = {
'cbr_rate': str(cbr_rate),
'agent1_name': pair_names[0],
'agent2_name': pair_names[1],
}
t = post_process(args.which, out_file, **kwargs)
threads.append(t)
# waits for all thread finish once get out of the loop
wait_for(threads)
def run_experiment2(args):
"""
Main entry for executing experiment2 and executing yielded
files one by one
"""
threads = []
tcp_agent_pairs = OrderedDict({})
tcp_agent_pairs[('Reno', 'Reno')] = ('Agent/TCP/Reno',
'Agent/TCP/Reno')
tcp_agent_pairs[('NewReno', 'Reno')] = ('Agent/TCP/Newreno',
'Agent/TCP/Reno')
tcp_agent_pairs[('Vegas', 'Vegas')] = ('Agent/TCP/Vegas',
'Agent/TCP/Vegas')
tcp_agent_pairs[('NewReno', 'Vegas')] = ('Agent/TCP/Newreno',
'Agent/TCP/Vegas')
cbr_rates = frange(1.00, 10.00, args.granularity)
for pair_names, agent_pair in tcp_agent_pairs.items():
for cbr_rate in cbr_rates:
pair_name = '-'.join(pair_names)
out_file = format_trace_file_name(args.out, pair_name, cbr_rate)
nsargs = [agent_pair[0], agent_pair[1], cbr_rate, out_file,
args.cbr_start, args.cbr_stop, args.tcp1_start,
args.tcp1_stop, args.tcp2_start, args.tcp2_stop,
args.duration]
rc = ns('../ns2/experiment2.tcl', nsargs)
nsargs.append(str(rc))
nsargs[1] = pair_name
print ("experiment2, tcp_agents: %s, cbr_rate: %s, " +
"out_to: %s, cbr_start: %s, cbr_stop: %s, " +
"tcp1_start: %s, tcp1_stop: %s, tcp2_start: %s" +
"tcp2_stop: %s, duration: %s, return code: %s") \
% tuple(map(lambda x: str(x), nsargs[1:]))
kwargs = {
'cbr_rate': str(cbr_rate),
'agent1_name': pair_names[0],
'agent2_name': pair_names[1],
}
t = post_process(args.which, out_file, **kwargs)
threads.append(t)
# waits for all thread finish once get out of the loop
wait_for(threads)
def getBodies(self):
bodies = []
for r in [.3]:
for theta in frange(0, 2 * math.pi, .1):
x = 0.5 + (r + .05) * math.cos(theta)
y = 0.5 + (r + .05) * math.sin(theta)
vx = 0.4 * math.sin(theta)
vy = -0.4 * math.cos(theta)
bodies.append(
Body(mass=2,
pos=Vector(x, y),
vel=Vector(vx, vy),
rad=0.01,
value=-1))
good = random.sample(bodies, len(bodies) // 3)
for g in good:
g.color = (0, 255, 0)
g.value = 1
return bodies
def parallelizeParameters(paramFile, original):
parameters = []
if (paramFile.has_section('Parallel')):
#Open the original parameter file
with open (original, "r") as originalFile:
pFile=originalFile.read()
lists = []
replacements = []
#Read parallel section
for metrics_par in paramFile.options('Parallel'):
if metrics_par.count('#'):
value = paramFile.get('Parallel' , metrics_par)
#Parse range
if value.count('..'):
values = value.split('..')
init = eval(values[0])
end = eval(values[1])
if len(values) > 2:
step = eval(values[2])
else:
step = 1
lists.append(u.frange(init, end, step))
#Parse list
else:
values = value.split(' ')
lists.append(values)
replacements.append('#' + metrics_par)
#Generate all combinations
combinations = list(itertools.product(*lists))
for comb in combinations:
newParams = pFile
for rep in xrange(len(replacements)):
newParams = newParams.replace(replacements[rep], str(comb[rep]))
newParParser = ConfigParser.RawConfigParser()
newParParser.optionxform=str
newParParser.readfp(StringIO.StringIO(newParams))
parameters.append(newParParser)
else:
parameters.append(paramFile)
return parameters
def ornament_bridge(a, b, n=None, prev_duration=0.75, width=2):
"""Find notes that bridge the interval between a and b"""
if n is None:
# Choose the number of notes in the ornament
if prev_duration >= 0.75:
n = weighted_choice([1, 2, 3, 4, 5, 6], [3, 3, 4, 5, 4, 3])
else:
n = weighted_choice([1, 2, 3], [3, 4, 5])
interval = b - a
direction = 0
if interval > 0:
direction = 1
if interval < 0:
direction = -1
if direction == 0:
option_groups = [range(int(a - width), int(a + width + 1))] * n
else:
offset_interval = float(interval) / n
option_groups = []
for offset in list(frange(a, b, offset_interval)):
middle = int(round(offset))
opts = range(middle - width, middle + width + 1)
option_groups.append(opts)
# Prevent the last note in the ornament from being the target note.
if b in option_groups[-1]:
option_groups[-1].remove(b)
ornaments = []
for opts in option_groups:
choice = choose(opts, ornaments)
ornaments.append(choice)
return ornaments
"""Writes all the information about the best fit to the file "protocol" """
import sys
sys.path.append("/home/ondrej/py")
import utils
import iso
from params import parameters
import fit
gauss = True
isodir = "/home/ondrej/data/isochrones/696/halo"
data = iso.readfits(isodir + "/datarr.fits")
isos = iso.readisos(isodir)
t = utils.frange(8, 10.25, 0.001)
p = parameters()
p.load()
m = fit.metallicity(t, p)
s = fit.sfr(t, p)
w = utils.calculateweights(t, s)
if gauss:
isow = iso.getisosweights_gauss(w, 10.**t, m, isos, p.sigma)
else:
isow = iso.getisosweights(w, 10.**t, m, isos)
model = iso.computeCMD(isow, isos)
#model=isos[0][2]*0.0+1.0
model = utils.normalize(model, sum(data.flat))
#model=model/sum(model.flat)
def create_videos(trainer):
"""
Create videos for visualizing. Will generate a video for each sample, so cancel when you have enough videos.
For this experiment, you need to have the images downloaded.
"""
if not trainer.args.use_cpu:
torch.cuda.synchronize()
# Switch to evaluate mode
trainer.model.eval()
len_audio = 20.48 # Only if target_spec_length = 2048
folder_name = os.path.join(trainer.args.results, 'results_video', trainer.args.name_checkpoint)
os.makedirs(folder_name, exist_ok=True)
with torch.no_grad():
for i, (image_input, audio_input, negatives, nframes, path, _) in enumerate(trainer.loaders['test']):
v_init = trainer.z[int(path[0])]
z_img = torch.FloatTensor(audio_input.size(0), v_init.shape[0])
for k in range(audio_input.size(0)):
z_img[k, :] = trainer.z[int(path[k])]
if not trainer.args.loading_image:
image_input = trainer.generator.generate_images(z_img, intervention=None)
image_input = utils.transform(image_input).detach()
# compute output
model_output = trainer.model(image_input, audio_input, [])
image_output = model_output[0]
audio_output = model_output[1]
pooling_ratio = round(audio_input.size(3) / audio_output.size(3))
nframes.div_(pooling_ratio)
fps = audio_output.size(3) / len_audio
for bs in range(image_output.size(0)):
try:
target_writer = imageio.get_writer(folder_name + f'/output_video_{path[bs]}.mp4', fps=fps)
matchmap = utils.compute_matchmap(image_output[bs],
audio_output[bs][:, :, 0:nframes[bs]]).data.cpu().numpy().copy()
wav = trainer.loaders['test'].dataset.load_audio_raw(path=path[bs])
scipy.io.wavfile.write(folder_name + f'/output_audio_{path[bs]}.mp3', 44100,
wav.astype(np.int16))
matchmap = matchmap.transpose(2, 0, 1) # l, h, w
matchmap = matchmap / matchmap.sum()
matchmap_l, matchmap_h, matchmap_w = matchmap.shape
k_ranges = utils.frange(np.max(matchmap) / 100, np.max(matchmap), np.max(matchmap) / 100)
for k in k_ranges:
binary_mask = matchmap > k
map_temp = np.multiply(matchmap, binary_mask)
if np.sum(map_temp) < 0.1:
break
smoothing_factor = 1
struct_element = [[[True]]] * smoothing_factor
binary_mask = morph.binary_dilation(binary_mask, struct_element) # Temporal smoothing
matchmap = np.multiply(matchmap, binary_mask)
matchmap = (matchmap - np.min(matchmap)) / (np.max(matchmap) - np.min(matchmap))
image = trainer.loaders['test'].dataset.load_image_raw(path=path[bs])
for t in range(matchmap_l):
mask_resize = np.array([cv2.resize(binary_mask[t, :, :].astype(float),
(image.shape[1], image.shape[0]))] * 3).transpose(1, 2, 0)
map_t = cv2.resize(matchmap[t, :, :], (image.shape[1], image.shape[0]))
map_t = 1 - map_t
map_t = 255 * map_t
map_t = map_t.astype(np.uint8)
map_t = cv2.applyColorMap(map_t, cv2.COLORMAP_JET)
im_final = np.multiply((0.3 * image + 0.7 * map_t), mask_resize) + np.multiply(image,
1 - mask_resize)
target_writer.append_data(im_final)
target_writer.close()
# -y means overwrite
os.system('ffmpeg -y -i ' +
folder_name + f'/output_video_{path[bs]}.mp4 -i ' +
folder_name + f'/output_audio_{path[bs]}.mp3 -vf scale=1200:1200 -shortest -strict -2 '
'-c:v libx264 ' +
folder_name + f'/video_{path[bs]}.mp4')
except KeyboardInterrupt as e:
print('you decided to finish!')
finally:
# Remove temporary files
try:
os.remove(folder_name + f'/output_video_{path[bs]}.mp4')
except OSError:
pass
try:
os.remove(folder_name + f'/output_audio_{path[bs]}.mp3')
except OSError:
pass
return False
def choose_melody_pitches(self, notes, register, harmonies, start_with_rest):
# print 'Choosing pitches'
for h in harmonies:
h['pitch_classes'] = [p % 12 for p in h['pitch']]
set_start_end(notes)
set_start_end(harmonies)
# Pick a random pitch from the instrument's register on which to start
previous_note_index = random.choice(range(int(len(register))))
prev = register[previous_note_index]
previous_note = {'duration': 1.0, 'pitch': prev}
pitch_history = []
first = True
# print '-'*10
for note in notes:
if first and start_with_rest:
note['pitch'] = 'rest'
first = False
continue
beats = list(frange(note['start'], note['start'] + note['duration'], .25))
note_harmonies = []
for b in beats:
h = get_at(b, harmonies)
h = h['pitch_classes']
if h not in note_harmonies:
note_harmonies.append(h)
if len(note_harmonies) == 1:
pitch_options = self.get_pitch_options(note_harmonies[0], prev)
else:
pitch_options = []
c = Counter()
for h in note_harmonies:
for p in h:
c[p] += 1
common = []
for p, count in c.most_common():
if count == len(note_harmonies):
common.append(p)
if len(common) > 0:
pitch_options = self.get_pitch_options(common, prev)
if len(pitch_options) == 0:
ranked = [p for p, _ in c.most_common() if p not in common]
for p in ranked:
pitch_options = self.get_pitch_options([p], prev)
if len(pitch_options) > 0:
break
if len(pitch_options) == 0:
pitch_options = [prev - 2, prev - 1, prev + 1, prev + 2]
note['pitch'] = random.choice(pitch_options)
self.add_ornament(note, previous_note, note_harmonies, first)
# print note
prev = note['pitch']
previous_note = note
pitch_history.append(note['pitch'])
first = False
"""Writes all the information about the best fit to the file "protocol" """
import sys
sys.path.append("/home/ondrej/py")
import utils
import iso
from params import parameters
import fit
gauss=False
isodir="/home/ondrej/data/isochrones/696/halo"
data=iso.readfits(isodir+"/datarr.fits")
isos = iso.readisos(isodir)
t=utils.frange(8,10.25,0.001)
p=parameters()
p.load()
m=fit.metallicity(t,p)
s=fit.sfr(t,p)
w=utils.calculateweights(t,s)
if gauss:
isow=iso.getisosweights_gauss(w,10.**t,m,isos,p.sigma)
else:
isow=iso.getisosweights(w,10.**t,m,isos)
model=iso.computeCMD(isow,isos)
#model=isos[0][2]*0.0+1.0
model=utils.normalize(model,sum(data.flat))
#model=model/sum(model.flat)
def plot_residuals(d,m):
def makeSquiggles(self, image):
"""
actual calculations
:param image: bitmap to squigglify
:return:
"""
noOfLines = self.parent.noOfLines.value()
height = image.height()
width = image.width()
amplitude = self.parent.strength.value()
strokeWidth = self.parent.lineWidth.value()
detail = self.parent.detail.value()
invertColors = self.parent.invertColors.checkState() == Qt.Checked
verticalSquiggles = self.parent.verticalSquiggles.checkState(
) == Qt.Checked
maxBrightness = self.parent.maxBrightness.value()
minBrightness = self.parent.minBrightness.value()
self.removeOldGraphicsItems()
group = QGraphicsItemGroup()
finalRow = False
minStepSize = self.parent.minStepSize.value()
maxStepSize = self.parent.maxStepSize.value()
# TODO: too much code duplication!
path = QPainterPath()
if not verticalSquiggles:
scaledystep = max(1, height / noOfLines)
for y in frange(0, height, scaledystep):
if fabs(y - height) < 1e-3 or y >= height:
finalRow = True
x = 0
disturbance_direction = -1
prevX = 0
prevY = y
while x < width:
disturbance_direction = -disturbance_direction
grayvalue = qGray(image.pixel(x, y))
if invertColors:
grayvalue = 255 - grayvalue
stepSize = Mapping.linexp(grayvalue, 0, 255, minStepSize,
maxStepSize)
stepSize = Mapping.linlin(stepSize, 1, 10, 1, 10 / detail)
amplitudeSize = Mapping.linlin(grayvalue, 0, 255,
amplitude, 0)
if x == 0:
path = QPainterPath()
path.moveTo(x, y)
x = prevX + stepSize
newY = prevY + amplitudeSize * disturbance_direction
if minBrightness <= grayvalue <= maxBrightness:
path.quadTo((prevX + x) / 2, newY, x, prevY)
else:
path.moveTo(x, prevY)
if x >= width:
item = QGraphicsPathItem(path)
pen = QPen()
pen.setWidth(strokeWidth)
item.setPen(pen)
group.addToGroup(item)
prevX = x
prevY = y
if finalRow:
break
else:
scaledxstep = max(1, width / noOfLines)
for x in frange(0, width, scaledxstep):
if fabs(x - width) < 1e-3 or x >= width:
finalRow = True
y = 0
disturbance_direction = -1
prevX = x
prevY = 0
while y < height:
disturbance_direction = -disturbance_direction
grayvalue = qGray(image.pixel(x, y))
if invertColors:
grayvalue = 255 - grayvalue
stepSize = Mapping.linexp(grayvalue, 0, 255, minStepSize,
maxStepSize)
stepSize = Mapping.linlin(stepSize, 1, 10, 1, 10 / detail)
amplitudeSize = Mapping.linlin(grayvalue, 0, 255,
amplitude, 0)
if y == 0:
path = QPainterPath()
path.moveTo(x, y)
y = prevY + stepSize
newX = prevX + amplitudeSize * disturbance_direction
if minBrightness <= grayvalue <= maxBrightness:
path.quadTo(newX, (prevY + y) / 2, prevX, y)
else:
path.moveTo(x, prevY)
if y >= height:
item = QGraphicsPathItem(path)
pen = QPen()
pen.setWidth(strokeWidth)
item.setPen(pen)
group.addToGroup(item)
prevX = x
prevY = y
if finalRow:
break
self.addNewGraphicsItems(group)
def objective(trial, ctf):
learning_rate = trial.suggest_uniform('learning_rate', 0.0, 0.1)
gamma = trial.suggest_uniform('gamma', 0.0, 0.1)
dimensions = trial.suggest_int('dimensions', 750, 1000)
x, y = calculate_fisher_discriminant(training_images_flat,
training_labels, ctf)
local_svm = SVMTree(x.shape[1],
list(range(10)),
learning_rate,
dimensions=dimensions,
gamma=gamma)
return local_svm.train(x, y, 14)
data = []
for ctf in frange(0.0, 1.0, 0.2):
study = optuna.create_study(pruner=MedianPruner())
study.optimize(lambda trial: objective(trial, ctf), n_trials=25)
best = study.best_params
x, y = calculate_fisher_discriminant(training_images_flat,
training_labels, ctf)
svm = SVMTree(x.shape[1],
list(range(10)),
best['learning_rate'],
dimensions=best['dimensions'],
gamma=best['gamma'])
t1 = time.time()
svm.train(x, y, 14)
t2 = time.time()
adv_ex, bro_ex, grad_ex, peraccuracy = stage(test_images, test_labels,
def run(solvent_ratio):
utils.Molecule.set_params('oplsaa4.prm')
tail = utils.Molecule('hexanenitrile.arc')
solvent = utils.Molecule('methane.arc')
for a in tail.atoms:
a.x, a.z = a.z, a.x
directory = 'lammps'
os.chdir(directory)
n_steps = 1
for step in range(0,n_steps):
atoms = []
bonds = []
angles = []
dihedrals = []
S = 3.5
box_size = [20,20,20]
theta = 0; z = 0.0
print len(atoms)/len(tail.atoms)
atom_count = len(atoms)
solvent_spacing = [(max(solvent.atoms, key=lambda a:a.x).x-min(solvent.atoms, key=lambda a:a.x).x), (max(solvent.atoms, key=lambda a:a.y).y-min(solvent.atoms, key=lambda a:a.y).y), (max(solvent.atoms, key=lambda a:a.z).z-min(solvent.atoms, key=lambda a:a.z).z)]
solvent_spacing = [x+1.0 for x in solvent_spacing]
max_vdw_r = max(solvent.atoms, key=lambda a:a.type.vdw_r).type.vdw_r
solvent_spacing = [max(x,max_vdw_r) for x in solvent_spacing]
for x in utils.frange(-box_size[0]/2, box_size[0]/2-solvent_spacing[0], solvent_spacing[0]):
for y in utils.frange(-box_size[1]/2, box_size[1]/2-solvent_spacing[1], solvent_spacing[1]):
for z in utils.frange(-box_size[2]/2, box_size[2]/2-solvent_spacing[2], solvent_spacing[2]):
try:
for a in atoms[:atom_count]:
if (a.x-x)**2 + (a.y-y)**2 + (a.z-z)**2 < max_vdw_r**2:
raise Exception()
solvent.add_to(x, y, z, atoms, bonds, angles, dihedrals)
except: pass
T = 94.0
P = 1.45
print (len(atoms)-atom_count)/len(solvent.atoms)
filetypes.write_xyz('out', atoms)
run_name = 'azoto_solv__'+str(int(step))
atom_types = dict( [(t.type,True) for t in atoms] ).keys()
atom_type_numbers = dict( [(t,i+1) for i,t in enumerate(atom_types)] )
is_charged = True
lammps.write_data_file_general(atoms, bonds, angles, dihedrals, box_size, run_name, atom_types=atom_types)
os.system('cp ../'+sys.argv[0]+' '+run_name+'.py')
f = open(run_name+'.in', 'w')
f.write('units real\natom_style full #bonds, angles, dihedrals, impropers, charges\n')
if is_charged:
f.write('pair_style lj/cut/coul/long 8.0\n')
else:
f.write('pair_style lj/cut 8.0\n')
if bonds: f.write('bond_style harmonic\n')
if angles: f.write('angle_style harmonic\n')
if dihedrals: f.write('dihedral_style opls\n')
if is_charged: f.write('kspace_style pppm 1.0e-3\n')
f.write('special_bonds lj/coul 0.0 0.0 0.5\nread_data '+run_name+'.data\n')
f.write('''thermo 0
dump 1 all xyz 10000 '''+run_name+'''.xyz
thermo_style custom etotal ke temp pe ebond eangle edihed evdwl ecoul elong press lx ly lz tpcpu
thermo_modify line multi format float %14.6f
minimize 0.0 1.0e-8 1000 100000
velocity all create '''+str(T)+''' 1 rot yes dist gaussian
fix press all npt temp '''+str(T)+' '+str(T)+''' 100 aniso '''+str(P)+' '+str(P)+''' 500
timestep 4.0
neigh_modify check yes every 1 delay 0
run_style respa 4 2 2 2 inner 2 4.5 6.0 middle 3 7.0 8.0 outer 4
thermo 100
run 25000
unfix press
fix dynamics all nvt temp '''+str(T)+' '+str(T)+''' 100
thermo_style custom epair pe etotal
thermo 1
run 25000
''')
f.close()
if True: #start multiple processes
os.system('nohup ~/lammps/src/lmp_g++_no_cuda -in %s.in -log %s.log &> /dev/null &' % (run_name, run_name) )
print 'Running', run_name
else:
os.system('~/lammps/src/lmp_g++_no_cuda -in %s.in -log %s.log' % (run_name, run_name) )
sys.exit()
os.chdir('..')
def CVL(fixes, lowerBound, upperBound, step, scaleFactor):
"""Return a list (with step number of items). Each item is a tuple of
(variance, likelihood). Variances in the list are equally distributed between
lowerBound to upperBound. The likelihood is based on Equation 7 in Horne, et al
and I beleive it is a likelihood cross validation.
fixes is a list of fixes where each fix is (time, x, y, locational_variance).
fixes are assumed to be in chronological order, and time is a number. The units
of time are unimportant, as the mobility variance varies with the units chosen.
The algorithm is as follows: Assume a mobility variance, vm. For the first three fixes,
pretend that fix2 is missing, and calculate the normal distribution at the observed
location of fix2 based on the predicted (part way between fix1 and fix3) mean location of
fix2. Do this again for fixes 2,3,4 then 3,4,5 etc until the last 3 fixes. The product
of the normal distributions is the indicator of the likelihood of the assumed mobility
variance.
In Horne, et al (2007), only odd numbered fixes are considered independent.
in the adehabitat code, each group of three is considered. This code uses
the second approach."""
#print "In CVL(); len(fixes) =", len(fixes), "lowerBound =",lowerBound, "upperBound =",upperBound, "step =", step, "scaleFactor =", scaleFactor
if len(fixes) < 3:
raise ValueError, "Not enough fixes provided"
results = []
for vm in utils.frange(lowerBound, (upperBound + step), step):
#print "vm = ",vm
likelihood = 1
for i in range(1, (len(fixes) - 1)):
#times
prevTime = fixes[i-1][0]
thisTime = fixes[i][0]
nextTime = fixes[i+1][0]
#locations
prevX = fixes[i-1][1]
thisX = fixes[i][1]
nextX = fixes[i+1][1]
prevY = fixes[i-1][2]
thisY = fixes[i][2]
nextY = fixes[i+1][2]
#locational Variance
prevV = fixes[i-1][3]
nextV = fixes[i+1][3]
T = nextTime - prevTime
#a = alphai = percent of path
a = float(thisTime - prevTime) / T
# (meanX, meanY) = mui(ti) = mean predicted location at time i
meanX = prevX + a * (nextX - prevX)
meanY = prevY + a * (nextY - prevY)
# v = sigmai^2(ti) = total assumed brownian motion variance at time i
v = T * a * (1 - a) * vm + (1-a)**2 * prevV + a**2 * nextV
#distanceSquared = ((thisX - meanX)**2 + (thisY - meanY)**2)
#print "thisX =",thisX,"thisY =",thisY,"meanX =",meanX,"meanY =",meanY, "v =", v
#print "distanceSquared =",distanceSquared, "T =", T, "a =", a, "vm =", vm, "prevV =", prevV, "nextV =", nextV,
# (thisX, thisY) = Zi = location at which to get value of PDF
normal = Horne2dNormal(thisX, thisY, meanX, meanY, v)
#print "normal =",normal
# The normal is typically very small (the total area under the normal curve = 1.0)
# the scale factor keeps the product from decaying to zero with a
# large number of fixes. Since the likelihoods are relative, the
# scale factor will not alter the relative likelihood of the Vm
likelihood *= (normal * scaleFactor)
#print "likelihood =",likelihood
if likelihood == 0:
break
results.append((vm, likelihood))
return results
def CVL(fixes, lowerBound, upperBound, step, scaleFactor):
"""Return a list (with step number of items). Each item is a tuple of
(variance, likelihood). Variances in the list are equally distributed between
lowerBound to upperBound. The likelihood is based on Equation 7 in Horne, et al
and I beleive it is a likelihood cross validation.
fixes is a list of fixes where each fix is (time, x, y, locational_variance).
fixes are assumed to be in chronological order, and time is a number. The units
of time are unimportant, as the mobility variance varies with the units chosen.
The algorithm is as follows: Assume a mobility variance, vm. For the first three fixes,
pretend that fix2 is missing, and calculate the normal distribution at the observed
location of fix2 based on the predicted (part way between fix1 and fix3) mean location of
fix2. Do this again for fixes 2,3,4 then 3,4,5 etc until the last 3 fixes. The product
of the normal distributions is the indicator of the likelihood of the assumed mobility
variance.
In Horne, et al (2007), only odd numbered fixes are considered independent.
in the adehabitat code, each group of three is considered. This code uses
the second approach."""
#print "In CVL(); len(fixes) =", len(fixes), "lowerBound =",lowerBound, "upperBound =",upperBound, "step =", step, "scaleFactor =", scaleFactor
if len(fixes) < 3:
raise ValueError, "Not enough fixes provided"
results = []
for vm in utils.frange(lowerBound, (upperBound + step), step):
#print "vm = ",vm
likelihood = 1
for i in range(1, (len(fixes) - 1)):
#times
prevTime = fixes[i - 1][0]
thisTime = fixes[i][0]
nextTime = fixes[i + 1][0]
#locations
prevX = fixes[i - 1][1]
thisX = fixes[i][1]
nextX = fixes[i + 1][1]
prevY = fixes[i - 1][2]
thisY = fixes[i][2]
nextY = fixes[i + 1][2]
#locational Variance
prevV = fixes[i - 1][3]
nextV = fixes[i + 1][3]
T = nextTime - prevTime
#a = alphai = percent of path
a = float(thisTime - prevTime) / T
# (meanX, meanY) = mui(ti) = mean predicted location at time i
meanX = prevX + a * (nextX - prevX)
meanY = prevY + a * (nextY - prevY)
# v = sigmai^2(ti) = total assumed brownian motion variance at time i
v = T * a * (1 - a) * vm + (1 - a)**2 * prevV + a**2 * nextV
#distanceSquared = ((thisX - meanX)**2 + (thisY - meanY)**2)
#print "thisX =",thisX,"thisY =",thisY,"meanX =",meanX,"meanY =",meanY, "v =", v
#print "distanceSquared =",distanceSquared, "T =", T, "a =", a, "vm =", vm, "prevV =", prevV, "nextV =", nextV,
# (thisX, thisY) = Zi = location at which to get value of PDF
normal = Horne2dNormal(thisX, thisY, meanX, meanY, v)
#print "normal =",normal
# The normal is typically very small (the total area under the normal curve = 1.0)
# the scale factor keeps the product from decaying to zero with a
# large number of fixes. Since the likelihoods are relative, the
# scale factor will not alter the relative likelihood of the Vm
likelihood *= (normal * scaleFactor)
#print "likelihood =",likelihood
if likelihood == 0:
break
results.append((vm, likelihood))
return results
def readCEData(parameters, variable):
try:
fileName = parameters.get(variable, 'input_files')
field = parameters.get(variable, 'field')
popType = parameters.get(variable, 'population_type')
dims = parameters.getint(variable, 'dimensions')
if popType != 'statistical' and popType != 'spatial':
print 'ERROR: Population type ' + popType + ' for field ' + field + ' incorrect.'
if dims < 1 or dims > 4:
print 'ERROR: Number of dimensions ' + dims + ' for field ' + field + ' is incorrect. It should be from 1 up to 4.'
stat_from = ""
time_from = ""
group_from = ""
if parameters.has_option(variable, 'stat_from'):
stat_from = eval(parameters.get(variable, 'stat_from'))
stat_to = eval(parameters.get(variable, 'stat_to'))
stat_step = 1
if parameters.has_option(variable, 'stat_step'):
stat_step = eval(parameters.get(variable, 'stat_step'))
if parameters.has_option(variable, 'time_from'):
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'stat_to'))
time_step = 1
if parameters.has_option(variable, 'time_step'):
time_step = eval(parameters.get(variable, 'time_step'))
if parameters.has_option(variable, 'group_from'):
group_from = eval(parameters.get(variable, 'group_from'))
group_to = eval(parameters.get(variable, 'group_to'))
group_step = 1
if parameters.has_option(variable, 'group_step'):
group_step = eval(parameters.get(variable, 'group_step'))
#Read actual dimensions in the field
fName = fileName.replace('[P]', str(stat_from)).replace('[T]', str(time_from)).replace('[G]', str(group_from))
fileDims = getDataDims(fName, field)
dimesionsToAdd = dims - fileDims
if dims < fileDims:
print 'ERROR: Variable ' + variable + ' has more dimensions than specified.'
if dims == 1:
if popType == 'spatial':
print 'ERROR: Variable ' + variable + ' should have more than one dimension to use spatial population_type.'
if dimesionsToAdd == 0:
if popType == 'spatial':
aux_init_data = readSpatialData(fileName, field, parameters, variable)
if popType == 'statistical':
aux_init_data = readField(fileName, field)
if dimesionsToAdd == 1:
if popType == 'spatial':
if fileName.count('[T]') != 1:
print 'ERROR: Spatial population for variable ' + variable + ' must have "[T]" wildcard.'
try:
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'time_to'))
initial = True
i = 0
for index in u.frange(time_from, time_to + time_step, time_step):
fName = fileName.replace('[T]', str(index))
tmp = readSpatialData(fName, field, parameters, variable)
if initial:
aux_init_data = np.ndarray(shape=(round((time_to - time_from)/time_step + 1), len(tmp)), dtype=object)
initial = False
aux_init_data[i, :] = tmp[:]
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Spatial population must have time_from and time_to configurations.'
if popType == 'statistical':
if fileName.count('[P]') != 1:
print 'ERROR: Statistical population for variable ' + variable + ' must have "[P]" wildcard.'
try:
stat_from = eval(parameters.get(variable, 'stat_from'))
stat_to = eval(parameters.get(variable, 'stat_to'))
stat_step = 1
if parameters.has_option(variable, 'stat_step'):
stat_step = eval(parameters.get(variable, 'stat_step'))
initial = True
i = 0
for index_stat in u.frange(stat_from, stat_to + stat_step, stat_step):
fName = fileName.replace('[P]', str(index_stat))
var = readField (fName, field)
if initial:
aux_init_data = np.ndarray(shape=(var.shape + (round((stat_to - stat_from)/stat_step + 1),)), dtype='float')
initial = False
aux_init_data[..., i] = var
i = i + 1
except ValueError as e:
import traceback
print traceback.format_exc()
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Statistical population must have stat_from and stat_to configurations.'
if dimesionsToAdd == 2:
if popType == 'spatial':
if fileName.count('[T]') != 1 or fileName.count('[G]') != 1:
print 'ERROR: Spatial population for variable ' + variable + ' must have "[T]" and "[G]" wildcards.'
try:
group_from = eval(parameters.get(variable, 'group_from'))
group_to = eval(parameters.get(variable, 'group_to'))
group_step = 1
if parameters.has_option(variable, 'group_step'):
group_step = eval(parameters.get(variable, 'group_step'))
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'time_to'))
time_step = 1
if parameters.has_option(variable, 'time_step'):
time_step = eval(parameters.get(variable, 'time_step'))
initial = True
i = 0
for index_group in u.frange(group_from, group_to + group_step, group_step):
j = 0
for index_time in u.frange(time_from, time_to + time_step, time_step):
fName = fileName.replace('[T]', str(index_time)).replace('[G]', str(index_group))
tmp = readSpatialData(fName, field, parameters, variable)
if initial:
aux_init_data = np.ndarray(shape=(round((group_to - group_from)/group_step + 1), round((time_to - time_from)/time_step + 1), len(tmp)), dtype=object)
initial = False
aux_init_data[i, j, :] = tmp[:]
j = j + 1
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Spatial population must have group_from, group_to, time_from and time_to configurations.'
if popType == 'statistical':
if fileName.count('[P]') != 1 or fileName.count('[T]') != 1:
print 'ERROR: Statistical population for variable ' + variable + ' must have "[P]" and "[T]" wildcards.'
try:
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'time_to'))
time_step = 1
if parameters.has_option(variable, 'time_step'):
time_step = eval(parameters.get(variable, 'time_step'))
stat_from = eval(parameters.get(variable, 'stat_from'))
stat_to = eval(parameters.get(variable, 'stat_to'))
stat_step = 1
if parameters.has_option(variable, 'stat_step'):
stat_step = eval(parameters.get(variable, 'stat_step'))
initial = True
i = 0
for index_time in u.frange(time_from, time_to + time_step, time_step):
j = 0
for index_stat in u.frange(stat_from, stat_to + stat_step, stat_step):
fName = fileName.replace('[P]', str(index_stat)).replace('[T]', str(index_time))
var = readField (fName, field)
if initial:
aux_init_data = np.ndarray(shape=((round((time_to - time_from)/time_step + 1),) + var.shape + (round((stat_to - stat_from)/stat_step + 1),)), dtype='float')
initial = False
aux_init_data[i, ..., j] = var
j = j + 1
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Statistical population must have time_from, time_to, stat_from and stat_to configurations.'
if dimesionsToAdd == 3:
if popType == 'spatial':
print 'ERROR: Error in ', variable, '. Cannot add more than 2 extra dimensions to the spatial data provided.'
if popType == 'statistical':
if fileName.count('[P]') != 1 or fileName.count('[T]') != 1 or fileName.count('[G]') != 1:
print 'ERROR: Statistical population for variable ' + variable + ' must have "[P]", "[G]" and "[T]" wildcards.'
try:
group_from = eval(parameters.get(variable, 'group_from'))
group_to = eval(parameters.get(variable, 'group_to'))
group_step = 1
if parameters.has_option(variable, 'group_step'):
group_step = eval(parameters.get(variable, 'group_step'))
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'time_to'))
time_step = 1
if parameters.has_option(variable, 'time_step'):
time_step = eval(parameters.get(variable, 'time_step'))
stat_from = eval(parameters.get(variable, 'stat_from'))
stat_to = eval(parameters.get(variable, 'stat_to'))
stat_step = 1
if parameters.has_option(variable, 'stat_step'):
stat_step = eval(parameters.get(variable, 'stat_step'))
initial = True
i = 0
for index_group in u.frange(group_from, group_to + group_step, group_step):
j = 0
for index_time in u.frange(time_from, time_to + time_step, time_step):
k = 0
for index_stat in u.frange(stat_from, stat_to + stat_step, stat_step):
fName = fileName.replace('[P]', str(index_stat)).replace('[T]', str(index_time)).replace('[G]', str(index_group))
var = readField (fName, field)
if initial:
aux_init_data = np.ndarray(shape=((round((group_to - group_from)/group_step + 1), round((time_to - time_from)/time_step + 1),) + var.shape + (round((stat_to - stat_from)/stat_step + 1),)), dtype='float')
initial = False
aux_init_data[i, j, ..., k] = var
k = k + 1
j = j + 1
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Statistical population must have group_from, group_to, time_from, time_to, stat_from and stat_to configurations.'
return aux_init_data
except Exception as e:
print 'ERROR: ', e
def readMeshlessData(parameters, variable):
try:
fileName = parameters.get(variable, 'input_files')
field = parameters.get(variable, 'field')
popType = parameters.get(variable, 'population_type')
dims = parameters.getint(variable, 'dimensions')
if popType != 'statistical' and popType != 'spatial':
print 'ERROR: Population type ' + popType + ' for field ' + field + ' incorrect.'
if dims < 2 or dims > 4:
print 'ERROR: Number of dimensions ' + dims + ' for field ' + field + ' is incorrect. It should be 2, 3, or 4.'
if dims == 2:
if popType == 'spatial':
return np.array(readSpatialData(fileName, field, parameters, variable))
if popType == 'statistical':
if fileName.count('[P]') != 1:
print 'ERROR: Statistical population for variable ' + variable + ' must have "[P]" wildcard.'
try:
stat_from = eval(parameters.get(variable, 'stat_from'))
stat_to = eval(parameters.get(variable, 'stat_to'))
stat_step = 1
if parameters.has_option(variable, 'stat_step'):
stat_step = eval(parameters.get(variable, 'stat_step'))
initial = True
i = 0
for index_stat in u.frange(stat_from, stat_to + stat_step, stat_step):
fName = fileName.replace('[P]', str(index_stat))
var = readField (fName, field)
if initial:
aux_init_data = np.ndarray(shape=(var.shape[0], round((stat_to - stat_from)/stat_step + 1)), dtype='float')
initial = False
aux_init_data[:, i] = np.resize(var, var.size)
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Statistical population must have stat_from and stat_to configurations.'
if dims == 3:
if popType == 'spatial':
if fileName.count('[T]') != 1:
print 'ERROR: Spatial population for variable ' + variable + ' must have "[T]" wildcard.'
try:
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'time_to'))
time_step = 1
if parameters.has_option(variable, 'time_step'):
time_step = eval(parameters.get(variable, 'time_step'))
initial = True
i = 0
for index in u.frange(time_from, time_to + time_step, time_step):
fName = fileName.replace('[T]', str(index))
tmp = readSpatialData(fName, field, parameters, variable)
if initial:
aux_init_data = np.ndarray(shape=(round((time_to - time_from)/time_step + 1), len(tmp)), dtype=object)
initial = False
aux_init_data[i, :] = tmp[:]
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Spatial population must have time_from and time_to configurations.'
if popType == 'statistical':
if fileName.count('[P]') != 1 or fileName.count('[T]') != 1:
print 'ERROR: Statistical population for variable ' + variable + ' must have "[P]" and "[T]" wildcard.'
try:
stat_from = eval(parameters.get(variable, 'stat_from'))
stat_to = eval(parameters.get(variable, 'stat_to'))
stat_step = 1
if parameters.has_option(variable, 'stat_step'):
stat_step = eval(parameters.get(variable, 'stat_step'))
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'time_to'))
time_step = 1
if parameters.has_option(variable, 'time_step'):
time_step = eval(parameters.get(variable, 'time_step'))
initial = True
i = 0
for index_time in u.frange(time_from, time_to + time_step, time_step):
j = 0
for index_stat in u.frange(stat_from, stat_to + stat_step, stat_step):
fName = fileName.replace('[P]', str(index_stat)).replace('[T]', str(index_time))
var = readField (fName, field)
if initial:
aux_init_data = np.ndarray(shape=(round((time_to - time_from)/time_step + 1), var.shape[0], round((stat_to - stat_from)/stat_step + 1)), dtype='float')
initial = False
aux_init_data[i, :, j] = np.resize(var, var.size)
j = j + 1
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Statistical population must have time_from, time_to, stat_from and stat_to configurations.'
if dims == 4:
if popType == 'spatial':
if fileName.count('[T]') != 1 or fileName.count('[G]') != 1:
print 'ERROR: Spatial population for variable ' + variable + ' must have "[T]" and "[G]" wildcard.'
try:
group_from = eval(parameters.get(variable, 'group_from'))
group_to = eval(parameters.get(variable, 'group_to'))
group_step = 1
if parameters.has_option(variable, 'group_step'):
group_step = eval(parameters.get(variable, 'group_step'))
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'time_to'))
time_step = 1
if parameters.has_option(variable, 'time_step'):
time_step = eval(parameters.get(variable, 'time_step'))
initial = True
i = 0
for index_group in u.frange(group_from, group_to + group_step, group_step):
j = 0
for index_time in u.frange(time_from, time_to + time_step, time_step):
fName = fileName.replace('[T]', str(index_time)).replace('[G]', str(index_group))
tmp = readSpatialData(fName, field, parameters, variable)
if initial:
aux_init_data = np.ndarray(shape=(round((group_to - group_from)/group_step + 1), round((time_to - time_from)/time_step + 1), len(tmp)), dtype=object)
initial = False
aux_init_data[i, j, :] = tmp[:]
j = j + 1
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Spatial population must have group_from, group_to, time_from and time_to configurations.'
if popType == 'statistical':
if fileName.count('[P]') != 1 or fileName.count('[T]') != 1 or fileName.count('[G]') != 1:
print 'ERROR: Statistical population for variable ' + variable + ' must have "[P]", "[G]" and "[T]" wildcard.'
try:
group_from = eval(parameters.get(variable, 'group_from'))
group_to = eval(parameters.get(variable, 'group_to'))
group_step = 1
if parameters.has_option(variable, 'group_step'):
group_step = eval(parameters.get(variable, 'group_step'))
stat_from = eval(parameters.get(variable, 'stat_from'))
stat_to = eval(parameters.get(variable, 'stat_to'))
stat_step = 1
if parameters.has_option(variable, 'stat_step'):
stat_step = eval(parameters.get(variable, 'stat_step'))
time_from = eval(parameters.get(variable, 'time_from'))
time_to = eval(parameters.get(variable, 'time_to'))
time_step = 1
if parameters.has_option(variable, 'time_step'):
time_step = eval(parameters.get(variable, 'time_step'))
initial = True
i = 0
for index_group in u.frange(group_from, group_to + group_step, group_step):
j = 0
for index_time in u.frange(time_from, time_to + time_step, time_step):
k = 0
for index_stat in u.frange(stat_from, stat_to + stat_step, stat_step):
fName = fileName.replace('[P]', str(index_stat)).replace('[T]', str(index_time)).replace('[G]', str(index_group))
var = readField (fName, field)
if initial:
aux_init_data = np.ndarray(shape=(round((group_to - group_from)/group_step + 1), round((time_to - time_from)/time_step + 1), var.shape[0], round((stat_to - stat_from)/stat_step + 1)), dtype='float')
initial = False
aux_init_data[i, j, :, k] = np.resize(var, var.size)
k = k + 1
j = j + 1
i = i + 1
except ValueError as e:
print 'ERROR: ', e
except ConfigParser.NoOptionError:
print 'ERROR: Error in ', variable, '. Statistical population must have stat_from and stat_to configurations.'
return aux_init_data
except Exception as e:
print 'ERROR: ', e
def raycast(self, screen, numrays=5, angle=45):
self.rays = []
for curangle in utils.frange(-angle, angle, angle / 2, inclusive=True):
r, c = utils.ray(screen, self.pos, self.rot + utils.rad(curangle))
self.rays.append(Ray(r, c, self.pos))
self.running = False
self.ticks -= self.STEADY_STATE_THRESHOLD # hack to make run() return the right val
self.print("Controller reached steady state in {} ticks".format(self.ticks))
else:
self.steady_state_ticks = 0
output = error * self.PROPORTIONAL_GAIN
self.temperature_delta = output
if __name__ == "__main__":
# sim = PController(0.01)
# sim.run()
results = {}
start = 0.001
step = 0.01
stop = 0.999
for gain in frange(start, stop, step):
sim = PController(gain, verbose=False)
results[gain] = sim.run()
print("{:<10}|{:>8}".format("Gain", "Ticks"))
for gain, ticks in sorted(results.items(), key=operator.itemgetter(0)):
print("{:<10f}|{:>8}".format(gain, ticks))
gain, ticks = min(results.items(), key=operator.itemgetter(1))
print("Winner: {:f} at {} ticks".format(gain, ticks))
def readGraphData(parameters, variable):
try:
fieldType = parameters.get(variable, "field_type")
fileName = parameters.get(variable, "input_files")
field = parameters.get(variable, "field")
popType = parameters.get(variable, "population_type")
dims = parameters.getint(variable, "dimensions")
if popType != "statistical" and popType != "spatial":
print "ERROR: Population type " + popType + " for field " + field + " incorrect."
if fieldType != "edge" and fieldType != "node":
print "ERROR: Field type" + fieldType + " for field " + field + " incorrect."
if dims < 2 or dims > 4:
print "ERROR: Number of dimensions " + dims + " for field " + field + " is incorrect. It should be 2, 3, or 4."
if dims == 2:
if popType == "spatial":
if fieldType == "edge":
print "ERROR: Edge, " + field + ", population cannot be spatial."
aux_init_data = readGraphFieldSpatial(fileName, field)
if popType == "statistical":
if fileName.count("[P]") != 1:
print "ERROR: Statistical population for bidimensional variable " + variable + ' must have "[P]" wildcard. E.g: ./output_[P]/result.dot'
try:
stat_from = eval(parameters.get(variable, "stat_from"))
stat_to = eval(parameters.get(variable, "stat_to"))
stat_step = 1
if parameters.has_option(variable, "stat_step"):
stat_step = eval(parameters.get(variable, "stat_step"))
initial = True
i = 0
for index in u.frange(stat_from, stat_to + stat_step, stat_step):
print stat_from, index
fName = fileName.replace("[P]", str(index))
g = readGraphField(fName, field, fieldType)
if initial:
aux_init_data = np.ndarray(
shape=(len(g), round((stat_to - stat_from) / stat_step + 1)), dtype="float"
)
initial = False
aux_init_data[:, i] = g[:]
i = i + 1
except ValueError as e:
print "ERROR: ", e
except ConfigParser.NoOptionError:
print "ERROR: Error in ", variable, ". Bidimensional statistical population must have stat_from and stat_to configurations."
if dims == 3:
if popType == "spatial":
if fileName.count("[T]") != 1:
print "ERROR: Spatial population for tridimensional variable " + variable + ' must have "[T]" wildcard. E.g: ./output_[T]/result.dot'
aux_init_data = []
if fieldType == "edge":
print "ERROR: Edge, " + field + ", population cannot be spatial."
try:
time_from = eval(parameters.get(variable, "time_from"))
time_to = eval(parameters.get(variable, "time_to"))
time_step = 1
if parameters.has_option(variable, "time_step"):
time_step = eval(parameters.get(variable, "time_step"))
initial = True
i = 0
for index in u.frange(time_from, time_to + time_step, time_step):
fName = fileName.replace("[T]", str(index))
tmp = readGraphFieldSpatial(fName, field)
if initial:
aux_init_data = np.ndarray(
shape=(round((time_to - time_from) / time_step + 1), len(tmp)), dtype=object
)
initial = False
aux_init_data[i, :] = tmp[:]
i = i + 1
except ValueError as e:
print "ERROR: ", e
except ConfigParser.NoOptionError:
print "ERROR: Error in ", variable, ". Tridimensional spatial population must have time_from and time_to configurations."
if popType == "statistical":
if fileName.count("[P]") != 1 or fileName.count("[T]") != 1:
print "ERROR: Statistical population for tridimensional variable " + variable + ' must have "[P]" and "[T]" wildcards. E.g: ./output_[P]/result[T].dot'
try:
stat_from = eval(parameters.get(variable, "stat_from"))
stat_to = eval(parameters.get(variable, "stat_to"))
stat_step = 1
if parameters.has_option(variable, "stat_step"):
stat_step = eval(parameters.get(variable, "stat_step"))
time_from = eval(parameters.get(variable, "time_from"))
time_to = eval(parameters.get(variable, "time_to"))
time_step = 1
if parameters.has_option(variable, "time_step"):
time_step = eval(parameters.get(variable, "time_step"))
initial = True
i = 0
for index_t in u.frange(time_from, time_to + time_step, time_step):
j = 0
for index_s in u.frange(stat_from, stat_to + stat_step, stat_step):
fName = fileName.replace("[P]", str(index_s)).replace("[T]", str(index_t))
g = readGraphField(fName, field, fieldType)
if initial:
aux_init_data = np.ndarray(
shape=(
round((time_to - time_from) / time_step + 1),
len(g),
round((stat_to - stat_from) / stat_step + 1),
),
dtype="float",
)
initial = False
aux_init_data[i, :, j] = g[:]
j = j + 1
i = i + 1
except ValueError as e:
print "ERROR: ", e
except ConfigParser.NoOptionError:
print "ERROR: Error in ", variable, ". Tridimensional statistical population must have time_from, time_to, stat_from and stat_to configurations."
if dims == 4:
if popType == "spatial":
if fileName.count("[T]") != 1 or fileName.count("[G]") != 1:
print "ERROR: Spatial population for 4-dimensional variable " + variable + ' must have "[T]" and "[G]" wildcards. E.g: ./output_[T]_[G]/result.dot'
aux_init_data = []
if fieldType == "edge":
print "ERROR: Edge, " + field + ", population cannot be spatial."
try:
time_from = eval(parameters.get(variable, "time_from"))
time_to = eval(parameters.get(variable, "time_to"))
time_step = 1
if parameters.has_option(variable, "time_step"):
time_step = eval(parameters.get(variable, "time_step"))
group_from = eval(parameters.get(variable, "group_from"))
group_to = eval(parameters.get(variable, "group_to"))
group_step = 1
if parameters.has_option(variable, "group_step"):
group_step = eval(parameters.get(variable, "group_step"))
initial = True
i = 0
for index_g in u.frange(group_from, group_to + group_step, group_step):
j = 0
for index_t in u.frange(time_from, time_to + time_step, time_step):
fName = fileName.replace("[T]", str(index_t)).replace("[G]", str(index_g))
tmp = readGraphFieldSpatial(fName, field)
if initial:
aux_init_data = np.ndarray(
shape=(
round((group_to - group_from) / group_step + 1),
round((time_to - time_from) / time_step + 1),
len(tmp),
),
dtype=object,
)
initial = False
aux_init_data[i, j, :] = tmp[:]
j = j + 1
i = i + 1
except ValueError as e:
print "ERROR: ", e
except ConfigParser.NoOptionError:
print "ERROR: Error in ", variable, ". 4-dimensional spatial population must have group_from, group_to, time_from and time_to configurations."
if popType == "statistical":
if fileName.count("[P]") != 1 or fileName.count("[T]") != 1 or fileName.count("[G]") != 1:
print "ERROR: Statistical population for 4-dimensional variable " + variable + ' must have "[P]" and "[T]" and "[G]" wildcards. E.g: ./output_[P]_[G]/result[T].dot'
try:
stat_from = eval(parameters.get(variable, "stat_from"))
stat_to = eval(parameters.get(variable, "stat_to"))
stat_step = 1
if parameters.has_option(variable, "stat_step"):
stat_step = eval(parameters.get(variable, "stat_step"))
time_from = eval(parameters.get(variable, "time_from"))
time_to = eval(parameters.get(variable, "time_to"))
time_step = 1
if parameters.has_option(variable, "time_step"):
time_step = eval(parameters.get(variable, "time_step"))
group_from = eval(parameters.get(variable, "group_from"))
group_to = eval(parameters.get(variable, "group_to"))
group_step = 1
if parameters.has_option(variable, "group_step"):
group_step = eval(parameters.get(variable, "group_step"))
initial = True
i = 0
for index_g in u.frange(group_from, group_to + group_step, group_step):
j = 0
for index_t in u.frange(time_from, time_to + time_step, time_step):
k = 0
for index_s in u.frange(stat_from, stat_to + stat_step, stat_step):
fName = (
fileName.replace("[P]", str(index_s))
.replace("[T]", str(index_t))
.replace("[G]", str(index_g))
)
g = readGraphField(fName, field, fieldType)
if initial:
aux_init_data = np.ndarray(
shape=(
round((group_to - group_from) / group_step + 1),
round((time_to - time_from) / time_step + 1),
var.shape[0],
round((stat_to - stat_from) / stat_step + 1),
),
dtype="float",
)
initial = False
aux_init_data[i, j, :, k] = g[:]
k = k + 1
j = j + 1
i = i + 1
except ValueError as e:
print "ERROR: ", e
except ConfigParser.NoOptionError:
print "ERROR: Error in ", variable, ". Tridimensional statistical population must have group_from, group_to, time_from, time_to, stat_from and stat_to configurations."
return aux_init_data
except Exception as e:
print "ERROR: ", e
def test1():
for f in utils.frange(1, 2, 0.16):
print f
for f in utils.frange(3, 2, -0.16):
print f
if __name__ == "__main__":
# sim = PIController(0.01, 0.01)
# sim.run()
results = defaultdict(dict)
pg_args = (0.0, 1.0, 0.05)
ig_args = (-1.0, 1.0, 0.1)
total_sims = ((pg_args[1] - pg_args[0]) / pg_args[2]) * (
(ig_args[1] - ig_args[0]) / ig_args[2])
print("Doing {} simulations...".format(total_sims))
sims = 0
for proportional_gain in frange(*pg_args):
for integral_gain in frange(*ig_args):
sim = PIController(proportional_gain, integral_gain, verbose=False)
results[proportional_gain][integral_gain] = sim.run()
sims += 1
if sims % 100 == 0:
print("Done {} of {} ({} %)".format(
sims, total_sims, round(100 * sims / total_sims, 0)))
min_ticks = 1E6
min_pg = 0
min_ig = 0
for proportional_gain in results:
for integral_gain in results[proportional_gain]:
ticks = results[proportional_gain][integral_gain]
if ticks < min_ticks:
def simul(isodir):
""" Read in parameters, data and isochrones. Create callback functions
for the optimization routine, one of which will return the log(likelihood)
and the other of which will print the best-fit parameter values. Having
done this, call the optimization routine to minimize log(L).
"""
log_tmax = math.log10(13.7e9)
params=parameters()
eps=0.01
#feh
params.set("m0y" ,1.0, 0,2.5,True)
params.set("m0cphi",-0.001, -pi/2+eps,0,True)
params.set("m0cr" ,0.01, 0,2,True)
params.set("m1y" ,-2.5, -2.5,0.9,True)
params.set("m1cphi",1.67, pi/2+eps,pi,True)
params.set("m1cr" ,1.06, 0,2,True)
params.set("sigma" ,0.2, 0,1, True)
params.set("dsigmadlogt" ,0.2, -1,1, True)
#sfr
params.set("s0x" ,8.0, 8.0,9.0,True)
params.set("s0y" ,0.5, 0.0,1,True)
params.set("s0tx" ,0.1, 0.,1.,True)
params.set("s0ty" ,0.1, 0,1,True)
params.set("s1tx" ,0.1, 0.,1.,True)
params.set("s1ty" ,0.1, -1,1,True)
params.set("s1x" ,0.5, 0,1,True)
params.set("s1y" ,1.0, 0.0,1.0,False)
params.set("s2x" ,log_tmax, 9.5,10.25,True)
params.set("s2y" ,0.1, 0,1.0,True)
params.set("s2tx" ,0.1, 0.,1.,True)
params.set("s2ty" ,0.1, 0.,1.,True)
if len(sys.argv) == 2:
if sys.argv[1] == "start": #run with a param to start from the beginning
params.save()
params.load()
if not params.pars.has_key('dsigmadlogt'):
params.set('dsigmadlogt',0.,0,False)
if not params.pars.has_key('dsigmadlogs'): # Hook for SFR-depenedent spread; not fully implemented
params.set('dsigmadlogs',0.,0,False)
if len(sys.argv) == 2:
if sys.argv[1] == "nudge": #Tweak the values near their limits
print "Nudging parameters near the limits"
p1 = params.getl()
utils.nudge(params)
p2 = params.getl()
for pp1,pp2 in zip(p1,p2):
if pp1[1] != pp2[1]:
print "%s %.8f -> %.8f" % (pp1[0],pp1[1],pp2[1])
data=iso.readfits(isodir+"/datarr.fits")
isos = iso.readisos(isodir)
t=utils.frange(8,log_tmax,0.001)
def f(par):
params.setvalues(par)
p = params
w=utils.calculateweights(t,sfr(t,params))
# isow=iso.getisosweights(w,10.**t,metallicity(t,params),isos)
if p.sigma > 0.:
if p.dsigmadlogt == 0.:
isow=iso.getisosweights_gauss(w,10.**t,metallicity(t,p),isos,p.sigma)
if p.dsigmadlogt != 0.:
# print "Gaussian sigma, ds/dlogt ",p.sigma,p.dsigmadlogt
isow=iso.getisosweights_vgauss(w,10.**t,metallicity(t,p),isos,p.sigma,p.dsigmadlogt)
if p.dsigmadlogs != 0.: # Hook for SFR-depenedent spread; not fully implemented
isow=iso.getisosweights_sgauss(w,10.**t,sfr(t,params),metallicity(t,p),
isos,p.sigma,p.dsigmadlogs)
else:
isow=iso.getisosweights(w,10.**t,metallicity(t,p),isos)
m=iso.computeCMD(isow,isos)
m=utils.normalize(m,sum(data.flat))
return utils.loglikelihood(m,data)
d = numarray.maximum(data,1e-20)
llhC=sum( (d*numarray.log(d)).flat )
def b(par,value,iter):
params.setvalues(par)
params.save()
print "henry:",value,"tom:",2.0*(value+llhC),"iter:",iter,time.ctime()
sys.stdout.flush()
optimization.minmax(optimization.fmin_simplex,f,
params.getvalues(),params.min(),params.max(),b)
def buildMappedMultidimEPD( samples, sig_pvals, bkg_pvals, nbins = 30, nbins1D = 40, cuts = None, name='NDimEPD' ):
from ROOT import TObjArray
from ROOT import Array2D
from ROOT import Array1D
treeList = TObjArray( len( samples ) )
infoList = TObjArray( len( samples ) )
binning = Array2D( len(bkg_pvals), Array1D(nbins,0) )
varListString = ''
sigme = '+'.join( ['%s'%(me) for me in sig_pvals] )
alpha = { }
for ipval, pval in enumerate( bkg_pvals ):
nonill = '(' + '&&'.join( ['(%s>0)'%(me) for me in sig_pvals ] ) + '&& (%s>0)'%(pval) + ')'
samples.draw( 'alpha:'+pval, '', 'log((%s)/(%s))/log(10)'%(sigme,pval), 1000, utils.frange(-100,100,ndiv=1000), cuts = nonill )
hSumBkg = None
for ismpl, smpl in enumerate( samples ):
if smpl.get_stype() != 'bkg':
continue
if hSumBkg==None: hSumBkg = smpl['alpha:'+pval]( 'SumBkgAlpha' )
else: hSumBkg += smpl['alpha:'+pval]
il, ir = -1, -1
for ib in xrange( 1, hSumBkg.GetNbinsX() + 2 ):
if il < 0 and hSumBkg.GetBinContent(ib) > 0:
il = ib
if il > 0 and hSumBkg.GetBinContent(ib) > 0:
ir = ib
xlow, xhigh = hSumBkg.GetBinLowEdge(il-1), hSumBkg.GetBinLowEdge(ir+1)
print xlow, xhigh
formString = 'log( (%s) / (%s) )/log(10)'%( sigme, pval ) ## @FIXME what about nil p-values ??
for ibin in xrange( nbins + 1 ):
binning[ipval][ibin] = ( (xhigh-xlow) / nbins * ibin + xlow )
hSumBkg.Delete()
if len( varListString ) == '': varListString = formString
else: varListString = ':'.join( (varListString, formString) )
if cuts == None or len(cuts) == 0:
cuts = '0<1'
for ismpl, smpl in enumerate( samples ):
treeList.AddLast( smpl.get_tree() )
struct = ROOT.TSampleStruct( )
struct.Variable = varListString
struct.Name = smpl.get_name()
struct.Weight = '(%s * %0.5g * %0.5g)'%( smpl.get_weights(),
smpl.get_scale(),
abs(smpl.get_lumi()) )
struct.Selection = '( %s ) && ( %s )'%( cuts, smpl.get_cuts() )
struct.Type = smpl.get_stype()
infoList.AddLast( struct )
mappedNDList = ROOT.getMappedNDim( treeList, infoList, binning, "ND" )
hists1D = []
for ismpl, smpl in enumerate( samples ):
hists1D += [ ROOT.get1DMapped( mappedNDList[ismpl], len(varListString.split(':')), nbins, nbins1D ) ]
smpl[name+'Mapped'] = histogram.pyhist1F( hists1D[-1] )
smpl.set_style()
return mappedNDList
def test1():
for f in utils.frange(1,2,0.16):
print f
for f in utils.frange(3,2,-0.16):
print f