def __init__(self, parent=None):
super().__init__(parent=parent)
self.nextEnabled = False
title = QLabel("Programming SmartDrive Bluetooth")
self.progressBar = ProgressBar()
self.startButton = QPushButton("Start")
self.startButton.clicked.connect(self.onStart)
self.startButton.show()
self.stopButton = QPushButton("Stop")
self.stopButton.clicked.connect(self.onStop)
self.stopButton.hide()
label = QLabel("Will now automatically program SmartDrive Bluetooth.")
label.setWordWrap(True)
self.sn = QLabel("S/N: ")
self.lk = QLabel("License: ")
self.addr = QLabel("Address: ")
self.labels = [
title, label, self.sn, self.lk, self.addr, self.progressBar,
self.startButton, self.stopButton
]
self.layout.addWidget(title)
self.layout.addWidget(label)
self.layout.addWidget(self.sn)
self.layout.addWidget(self.lk)
self.layout.addWidget(self.addr)
self.layout.addWidget(self.progressBar)
self.layout.addWidget(self.startButton)
self.layout.addWidget(self.stopButton)
def partial_plot(clf,
X_,
x_name,
labels,
n_points=100,
lims=None,
n_samp=1000,
categorical=False):
X = X_.copy()
N = len(X)
if lims == None:
x_min = X[x_name].min()
x_max = X[x_name].max()
else:
x_min = lims[0]
x_max = lims[1]
if categorical:
x = np.array([x_min, x_max] * int(n_points / 2.))
else:
x = np.linspace(x_min, x_max, n_points)
p = []
pb = ProgressBar()
for i, x_i in enumerate(x):
X[x_name] = [x_i] * N
_idx = np.random.randint(
N, size=n_samp) #sub sample to reduce time to evaluate
p.append(
clf.predict_proba(X.values[_idx], labels=labels[_idx])[1].mean(0))
pb.update_progress(i / n_points)
return x, np.array(p)
def run_burnin(sampler,startPos,nSteps,storechain=False):
iStep = 0
bar = ProgressBar()
for pos, prob, state in sampler.sample(startPos,iterations=nSteps,storechain=storechain):
bar.render(int(100*iStep/nSteps),'running Burn In')
iStep += 1
return pos, prob, state
def __init__(self, parent=None):
super().__init__(parent=parent)
self.nextEnabled = False
title = QLabel("Programming Bootloader")
switchesLabel = QLabel(
"Set the MX2+ DIP switches for bootloader programming as shown below.\nThen power-cycle the SmartDrive."
)
switchesLabel.setWordWrap(True)
self.pixMap = QtGui.QPixmap(
resource.path('images/bootloaderProgramming.jpg'))
self.progressBar = ProgressBar()
self.startButton = QPushButton("Start")
self.startButton.clicked.connect(self.onStart)
self.startButton.show()
self.stopButton = QPushButton("Stop")
self.stopButton.clicked.connect(self.onStop)
self.stopButton.hide()
self.labels = [
title, switchesLabel, self.progressBar, self.startButton,
self.stopButton
]
self.picture = QLabel(self)
self.picture.setPixmap(
self.pixMap.scaled(self.getPictureSize(), Qt.KeepAspectRatio))
self.layout.addWidget(title)
self.layout.addWidget(switchesLabel)
self.layout.addWidget(self.picture)
self.layout.addWidget(self.progressBar)
self.layout.addWidget(self.startButton)
self.layout.addWidget(self.stopButton)
def colormap(hm, gradient, smoothness):
width, height = hm.size
img = Image.new('RGBA', (width, height), color=(0, 0, 0, 0))
colorlist = []
for g in range(len(gradient) - 1):
(start, color) = gradient[g]
(nextStart, nextColor) = gradient[g + 1]
begin = start * smoothness
end = (nextStart - start) * smoothness
sublist = list(Color(color).range_to(Color(nextColor), end))
colorlist += sublist
prog = ProgressBar(height)
print("\nColor Map:")
for y in range(0, height):
prog.show(y)
for x in range(0, width):
value = hm.getpixel((x, y))
if value != -2147483648:
setpixel(x, y, value, colorlist, img)
return img
def render(self, scene):
""" Render image from stuff inside scene """
width = scene.width
height = scene.height
ar = width / height
camera = scene.camera
im = Image(width, height)
xmin = -1
xmax = 1
ymax = xmax / ar
ymin = -ymax
dx = (xmax - xmin) / (width - 1)
dy = (ymax - ymin) / (height - 1)
pb = ProgressBar(height * width)
for j in range(height):
y = ymin + dy * j
for i in range(width):
x = xmin + dx * i
ray = Ray(camera, Vector(x, y, 0) - camera)
c = self.ray_trace(ray, scene)
im.set_pixel(j, i, c)
pb.update(1)
return im
def gen_var_result_scores(clf, X_train, X_test, y_train=None,
n_rounds=100, verbose=False, fit=True):
"""
Given classifier and training data, return variable importances on the
test data on a per-sample basis. UPDATED.
Result scores represent the difference between the observed score and
the mean score obtained if the specific variable is resampled from the
training data randomly.
"""
if fit:
if verbose:
print 'Training model...'
sys.stdout.flush()
t0 = time.time()
clf.fit(X_train, y_train)
if verbose:
t1 = time.time()
print 'Training took %.2f seconds' % (t1 - t0)
real_scores = clf.predict_proba(X_test)[:, 1]
result_scores = np.zeros(X_test.shape)
if verbose:
pb = ProgressBar()
progress = 0
for var in range(X_train.shape[1]):
single_var_scores = np.zeros([X_test.shape[0], n_rounds])
X_test_mod = np.copy(X_test)
for j in range(n_rounds):
if verbose:
progress += 1
pb.update_progress(progress / float(n_rounds * X_train.shape[1]))
X_test_mod[:, var] = np.random.choice(X_train[:, var], X_test.shape[0], replace=True)
single_var_scores[:, j] = clf.predict_proba(X_test_mod)[:, 1]
result_scores[:, var] = np.abs(real_scores - np.mean(single_var_scores, axis=1))
return result_scores
def cal_rows(self, css, scene, h, dh):
width = scene.width
height = scene.height
ar = width / height
camera = scene.camera
xmin = -1
xmax = 1
ymax = xmax / ar
ymin = -ymax
dx = (xmax - xmin) / (width - 1)
dy = (ymax - ymin) / (height - 1)
cs = [] # 3 * width * (dh)
pb = ProgressBar((dh) * width)
for j in range(h, h + dh):
y = ymin + dy * j
for i in range(width):
x = xmin + dx * i
ray = Ray(camera, Vector(x, y, 0) - camera)
c = self.ray_trace(ray, scene)
cs.append(c.x)
cs.append(c.y)
cs.append(c.z)
pb.update(1)
a = h * width * 3
b = (h + dh) * width * 3
css[a:b] = cs
def font_file_cracker():
try:
file = request.files.get('font_file')
type_ = request.form.get('type')
except Exception as _e:
return jsonify({'code': 400, 'msg': f'lose args,{_e}', 'res': {}})
filename = re.sub('[（(）) ]', '', file.filename)
if not os.path.exists('./font_collection'):
os.mkdir('./font_collection')
file.save('./font_collection/' + filename)
if config.is_online and not check_file('./font_collection/' + filename):
return jsonify({'code': 300, 'msg': 'Please use example file(*^_^*)'})
ProgressBar.init()
res = ocr_processor('./font_collection/' + filename)
if type_ == 'html':
font_dict = {}
for foo in res:
font_dict[foo['name']] = foo['ocr_result']
return jsonify({
'code': 200,
'html': render_template('images.html', result=res),
'font_dict': font_dict
})
else:
return jsonify({'code': 200, 'msg': 'success', 'res': res})
def resample_lts( lts, out_lts, new_rate = 5000, cutoff = 2000 ): """ Resample a LabeledTimeseries to an output LabeledTimeseries. Returns a LabeledTimeseries containing the new resampled data. Keyword Arguments: lts -- An input LabeledTimeseries to resample out_lts -- A LabeledTimeseries to output the resampled data to. If this is a string, create a new sibling LabeledTimeseries with this name. new_rate -- The sampling rate to resample to. (Default: 5000 samples per sec) cutoff -- The cutoff value for the FIR low-pass filter. Ensure this is set considerably *below* the nyquist of 'new_rate'. (Default: 2000 Hz) """ from h5eeg import LabeledTimeseries # Create the new LabeledTimeseries if necessary if isinstance( out_lts, basestring ): parent_group = lts.dataset.parent new_length = int( len( lts ) * ( float( new_rate ) / float( lts.get_rate() ) ) ) out_lts = LabeledTimeseries.create( parent_group, new_length, lts.get_labels(), new_rate, name = out_lts ) # Resample lts data channel by channel pbar = ProgressBar( len( lts.get_labels() ) ) for idx, ch_name in enumerate( lts.get_labels() ): print 'Resampling Channel: %s...' % ch_name ch_data = resample( lts[ :, ch_name ], lts.get_rate(), new_rate, cutoff ) convert_length = min( len( ch_data ), len( out_lts ) ) out_lts[ 0:convert_length, ch_name ] = ch_data[ 0:convert_length ] pbar.animate( idx ) # lts.dataset.file.flush() # This takes forever. Don't bother. return out_lts
def run_mcmc_save(sampler, startPos, nSteps, rState, file, **kwargs):
'''runs and MCMC chain with emcee, and saves steps to a file'''
#open chain save file
if file:
f = open(file, "w")
f.close()
iStep = 0
bar = ProgressBar()
for pos, prob, state in sampler.sample(startPos,
iterations=nSteps,
rstate0=rState,
storechain=True,
**kwargs):
if file:
f = open(file, "a")
bar.render(int(100 * iStep / nSteps), 'running MCMC')
iStep += 1
for k in range(pos.shape[0]):
# loop over all walkers and append to file
thisPos = pos[k]
thisProb = prob[k]
if file:
f.write("{0:4d} {1:s} {2:f}\n".format(
k, " ".join(map(str, thisPos)), thisProb))
if file:
f.close()
return sampler
def run_ptmcmc_save(sampler, startPos, nSteps, file, **kwargs):
'''runs PT MCMC and saves zero temperature chain to file'''
if not os.path.exists(file):
f = open(file, "w")
f.close()
iStep = 0
bar = ProgressBar()
for pos, prob, like in sampler.sample(startPos,
iterations=nSteps,
storechain=True,
**kwargs):
bar.render(int(100 * iStep / nSteps), 'running MCMC')
iStep += 1
f = open(file, "a")
# pos is shape (ntemps, nwalkers, npars)
# prob is shape (ntemps, nwalkers)
# loop over all walkers for zero temp and append to file
zpos = pos[0, ...]
zprob = prob[0, ...]
for k in range(zpos.shape[0]):
thisPos = zpos[k]
thisProb = zprob[k]
f.write("{0:4d} {1:s} {2:f}\n".format(k,
" ".join(map(str, thisPos)),
thisProb))
f.close()
return sampler
def lightmap(nm, cm, light, ambient):
width, height = nm.size
cwidth, cheight = cm.size
if cwidth != width or cheight != height:
print("Resolutions do not match.")
exit()
shaded = Image.new('RGBA', (width, height), color=(0, 0, 0, 0))
prog = ProgressBar(height)
print("\nLight Map:")
for y in range(0, height):
prog.show(y)
for x in range(0, width):
(cr, cg, cb, ca) = cm.getpixel((x, y))
(r, g, b, a) = nm.getpixel((x, y))
if a != 0:
normal = vmath.Vector3(\
(r/255 - 0.5) * 2,
(g/255 - 0.5) * 2,
(b/255 - 0.5) * 2)
angle = normal.angle(light, 'deg')
illumination = 1 - (angle / 180)
illumination = ambient + (1 - ambient) * illumination
cr = int(illumination * cr)
cg = int(illumination * cg)
cb = int(illumination * cb)
shaded.putpixel((x, y), (cr, cg, cb, ca))
return shaded
def spfilt( dataset, filt, io_blocksize = 1024, progress_bar = False ): """ Perform a spatial filter on an input two dimensional dataset. Returns dataset Keyword Arguments: dataset -- ndarray of size samples x channels filt -- ndarray spatial filter of channels x channels io_blocksize -- Number of samples to operate on at a time (Default: 1024) progress_bar -- If set to true, show a progress bar. (Default: False) TODO: Implement Parallelism """ start = 0 nsamp = len( dataset ) if progress_bar: from progress import ProgressBar pbar = ProgressBar( nsamp ) while True: end_block = start + io_blocksize end = min( end_block, nsamp - 1 ) dataset[ start:end, : ] = np.dot( dataset[ start:end, : ], filt ) start = end if progress_bar: pbar.animate( start ) if end_block >= nsamp: break return dataset
def learn(self, samples, epochs=25000, noise=0, test_samples=None, show_progress=True):
''' Learn given distribution using n data
List of sample sets
Number of epochs to be ran for each sample set
'''
# Check if samples is a list
if type(samples) not in [tuple,list]:
samples = (samples,)
epochs = (epochs,)
n = 0 # total number of epochs to be ran
for j in range(len(samples)):
n += epochs[j]
self.entropy = []
self.distortion = []
if show_progress:
bar = ProgressBar(widgets=[Percentage(), Bar()], maxval=n).start()
index = 0
for j in range(len(samples)):
self.samples = samples[j]
I = np.random.randint(0,self.samples.shape[0],n)
for i in range(epochs[j]):
# Set sigma and learning rate via time
t = index/float(n)
lrate = self.lrate_i*(self.lrate_f/self.lrate_i)**t
sigma = self.sigma_i*(self.sigma_f/self.sigma_i)**t
C = self.adj.copy()
# Learn something
S = self.samples[I[i]] + noise*(2*np.random.random(len(self.samples[I[i]]))-1)
S = np.minimum(np.maximum(S,0),1)
self.learn_data(S,lrate,sigma)
#self.learn_data(self.samples[I[i]],lrate,sigma)
if i%100 == 0:
self.entropy.append(((self.adj-C)**2).sum())
if test_samples is not None:
distortion = self.compute_distortion(test_samples)
else:
distortion = self.compute_distortion(self.samples)
self.distortion.append(distortion)
if show_progress:
bar.update(index+1)
index = index+1
if show_progress: bar.finish()
def run_burnin(sampler, startPos, nSteps, storechain=False):
iStep = 0
bar = ProgressBar()
for pos, prob, state in sampler.sample(startPos,
iterations=nSteps,
storechain=storechain):
bar.render(int(100 * iStep / nSteps), 'running Burn In')
iStep += 1
return pos, prob, state
async def queue_tasks(
tasks: AsyncIterable[tuple[AuditTask, LogQueue]],
task_q: asyncio.Queue[tuple[AuditTask, LogQueue]],
progress: ProgressBar,
) -> None:
async for task, logqueue in tasks:
task.set_start_stage_cb(progress.enter_stage)
task.set_finish_stage_cb(progress.exit_stage)
await task_q.put((task, logqueue))
progress.task_enqueued()
def dropsubj_run():
pb = ProgressBar(len(PERCENT_REMOVE))
for p in PERCENT_REMOVE:
this_rand = lambda d: replace_percent_subjects(d, p)
cleaner = lambda d: remove_percent_deviant_subjects(d, p)
params = {'p': p, 'cleaner': 'devsubj'}
for row in run_experiment(this_rand, [cleaner], [params]):
yield row
pb.incr_and_errput()
def __init__(self, filename):
dfile = filename.split('.')[0] + '.pkl'
try:
dump = self.loadfile(dfile)
self.bag_of_word = dump['bag_of_word']
self.bag_of_index = dump['bag_of_index']
self.markov_matrix = np.array(dump['markov_matrix'])
except OSError as e:
self.bag_of_word = {}
self.bag_of_index = {}
self.markov_matrix = np.array([[0]])
index = 0
try:
with open(filename, 'r') as file:
print(
"log: this would show up if its a new file. A markov chain will be created and saved"
)
low = (' '.join(file.read().splitlines())).split(' ')
progress = ProgressBar(len(low) - 1, fmt=ProgressBar.FULL)
for i in range(progress.total):
progress.current += 1
progress()
if self.bag_of_word.setdefault(low[i], index) == index:
self.bag_of_index[index] = low[i]
self.markov_matrix = np.pad(self.markov_matrix,
[(0, self.max(index)),
(0, self.max(index))],
mode='constant')
index += 1
if self.bag_of_word.setdefault(low[i + 1],
index) == index:
self.bag_of_index[index] = low[i + 1]
self.markov_matrix = np.pad(self.markov_matrix,
[(0, self.max(index)),
(0, self.max(index))],
mode='constant')
index += 1
self.markov_matrix[self.bag_of_word[low[i]]][
self.bag_of_word[low[i + 1]]] += 1
progress.done()
s = np.sum(self.markov_matrix, axis=1)[:, np.newaxis]
s[s == 0] = 1
self.markov_matrix = self.markov_matrix / s
self.markov_matrix[self.markov_matrix.shape[0] - 1][0] = 1
dump = {}
dump['bag_of_word'] = self.bag_of_word
dump['bag_of_index'] = self.bag_of_index
dump['markov_matrix'] = self.markov_matrix
self.savefile(dump, dfile)
del (dump)
print("log:chain for ", filename, " is created")
except OSError as e:
print("file not found !")
exit()
def __init__(self, url, gitlab, includes=[], excludes=[], concurrency=1, in_file=None, method="http"):
self.in_file = in_file
self.method = method
self.concurrency = concurrency
self.excludes = excludes
self.includes = includes
self.url = url
self.gitlab = gitlab
self.root = Node("", root_path="", url=url)
self.disable_progress = False
self.progress = ProgressBar('* loading tree', self.disable_progress)
def minrho_run():
pb = ProgressBar(len(NUM_DROP))
sys.stderr.write("Beginning minrho eval.\n")
pb.errput()
for n in NUM_DROP:
this_rand = lambda d: replace_subjects(d, n)
cleaner = lambda d: remove_most_deviant_subjects(d, n)
params = {'n': n, 'cleaner': 'minrho'}
for row in run_experiment(this_rand, [cleaner], [params]):
yield row
pb.incr_and_errput()
def convert_bcistream( dat, h5filename = None, overwrite = False ): # If we don't have a filename for the resulting hdf5 file, we will # just make an hdf5 file from the current filename in the same directory if h5filename == None: filepath, h5filename = os.path.split( dat.filename ) h5filename = os.path.splitext( h5filename )[0] h5filename = os.path.join( filepath, h5filename + '.hdf5' ) if os.path.isfile( h5filename ) and not overwrite: print "Error: %s exists already. Not overwriting." % h5filename return None # Create the required group and set group attributes # NOTE: BCI2000 file format has no good record of experiment outfile = h5.File( h5filename, 'w' ) group = H5EEGGroup.create( outfile, subject = dat.params[ 'SubjectName' ], timestamp = dat.datestamp ) # Create the EEG, AUX, and Event datasets eeg_labels = [ str( i + 1 ) for i in range( dat.nchan ) ] if 'ChannelNames' in dat.params.keys(): eeg_labels = dat.params[ 'ChannelNames' ] eeg_offsets = dat.offsets.astype( 'int32' ) H5EEGDataset.create( group, dat.samples(), eeg_labels, eeg_offsets, dat.gains, name = 'raw', rate = dat.samplingrate(), bytes_per_sample = dat.bytesperchannel ) aux_labels = dat.statedefs.keys() H5EEGAuxDataset.create( group, dat.samples(), labels = aux_labels, rate = dat.samplingrate() ) H5EEGEvents.create( group ) # Read the data into the h5f file in blocks of 1 second each dat.seek( 0 ) eeg_dset = group.eeg().dataset aux_dset = group.aux().dataset print 'Converting %s to %s...' % ( dat.filename, h5filename ) pbar = ProgressBar( dat.samples() ) while dat.tell() != dat.samples(): samp_idx = dat.tell() read_block = int( dat.samplingrate() ) signal, states = dat.decode( nsamp = read_block, apply_gains = False ) read_block = signal.shape[1] eeg_dset[ samp_idx:( samp_idx + read_block ), : ] = signal.T for idx, label in enumerate( aux_labels ): aux_dset[ samp_idx:( samp_idx + read_block ), idx ] = np.squeeze( states[ label ] ) pbar.animate( dat.tell() ) return outfile
def zscore_run(randomizer, randomizer_name):
pb = ProgressBar(len(ZSCORES) * len(NOISES))
sys.stderr.write("Beginning zscore eval with %s randomization.\n" % randomizer_name)
pb.errput()
for percent_noise in NOISES:
this_rand = lambda d: randomizer(d, percent_noise)
cleaners = [zscore and RemoveDeviantRatings(zscore).scores or BaselineCleaner().scores
for zscore in ZSCORES]
parameters = [dict(cleaner='zscore', p=percent_noise, randomizer=randomizer_name, zscore=str(zscore))
for zscore in ZSCORES]
for row in run_experiment(this_rand, cleaners, parameters):
yield row
pb.incr_and_errput()
def cmd_dump(logger, args):
"""
Dump recorded values into a file or to stdout.
"""
if logger.is_busy():
print("Logger is currently recording.")
return 1
config = logger.configuration()
if config["count"] == 0:
print("No records available (nothing has been logged).")
return 0
output = _open_output(args, config)
progress = None if args.no_progress else ProgressBar(config['count'])
if args.data_format:
data_format = args.data_format
else:
data_format = "%c;%d;%t"
if config["humidity"]:
data_format += ";%h"
counter = 0
for values in logger:
for value in values:
stamp, temp, hum = value
record = _format_record(data_format, counter,
stamp.strftime(args.time_format), temp,
hum if config["humidity"] else None)
print(record, file=output)
counter += 1
if progress is not None:
progress += len(values)
if progress is not None:
print()
return 0
def trim_samples(samples,nsamp,pbar=False):
weights = np.array([s.w for s in samples])
weights /= max(weights)
neff = np.sum(weights)
n = weights.size
print "effective number of samples: " , neff, "/", n
# Now trim off the ones that are too small
ntarget = sum([ w if w<1.0/n else 1 for w in weights]) + 0.0
if nsamp>0 and nsamp<ntarget:
weights *= nsamp/neff
else:
weights *= n
if pbar: progress_bar = ProgressBar(samples.size,message="trimming samples ")
else: print "trimming samples"
trimmed_samples = []
for w,s in zip(weights,samples):
if rand() < w:
s.w = max(1.0,w)
trimmed_samples.append(s)
if pbar: progress_bar()
trimmed_samples = np.array(trimmed_samples)
print "Samples trimmed from " , n, " to ", trimmed_samples.size
return trimmed_samples
def to_png(tif):
width, height = tif.size
img = Image.new('RGBA', (width, height), color=(0, 0, 0, 0))
prog = ProgressBar(height - 1)
print("\nTo PNG:")
for y in range(0, height - 1):
prog.show(y)
for x in range(0, width - 1):
value = tif.getpixel((x, y))
setpixel(x, y, value, img)
print("\n")
return img
def _align(self, Ys, X, sel=None, record=True):
pb = ProgressBar(final=len(Ys), label='align', tail_label='{i:}')
if record:
info = np.zeros((len(Ys), 11))
# set defaults
sel = sel or slice(None)
X_sel = X[:, sel]
t0 = self._calc_centroid(X_sel)
X0 = X - t0 # centre reference on origin
X0_sel = X0[:, sel]
for i, Y_ in enumerate(Ys):
pb.update()
Y_sel = Y_[:, sel]
t = self._calc_centroid(Y_sel)
Y0_ = Y_ - t # centre frame on origin
Y0_sel = Y0_[:, sel]
R = self._calc_optrot(X0_sel, Y0_sel) # get rotation matrix
Y0 = np.dot(R, Y0_.T) # rotate
Y = Y0 + t0 # centre frame on t0
Ys[i, :, :] = Y
if record:
# ref/frame comparison before alignment
info[i, 0] = self._calc_rmsd(X, Y_) # all
info[i, 2] = self._calc_rmsd(X0, Y0_) # rotational
info[i, 3] = self._calc_rmsd(X0_sel,
Y0_sel) # rotational selection
# ref/frame comparison after alignment
info[i, 4] = self._calc_rmsd(X, Y) # all
info[i, 5] = self._calc_rmsd(X0, Y0) # rotational
# aligned/unaligned frame comparisons
info[i, 6] = self._calc_rmsd(Y_, Y) # all
info[i, 7] = self._calc_rmsd(Y0, Y0_) # rotational
# ref/frame and aligned/unaligned
info[i, 8] = self._calc_rmsd(t, t0) # centre difference
# euler angles
info[i, 8:11] = self._calc_euler(R)
return (Ys, info) if record else Ys
async def task_runner(task_q: asyncio.Queue[tuple[AuditTask, LogQueue]],
result_aggr: ResultAggregator,
progress: ProgressBar) -> None:
await asyncio.sleep(
random.random()
) # Random jitter at the start so that not all requests get fired immediately
while True:
task, logqueue = await task_q.get()
progress.task_running()
progress.enter_stage(CheckStage.preprocess)
await task.audit_path.mkdir(exist_ok=True, parents=True)
progress.exit_stage(CheckStage.preprocess)
await task.run(result_aggr)
progress.enter_stage(CheckStage.postprocess)
await logqueue.flush()
progress.exit_stage(CheckStage.postprocess)
task_q.task_done()
def background_thread():
"""Example of how to send server generated events to clients."""
while True:
socketio.sleep(1)
ret = []
while not SocketQueue.res_queue.empty():
ProgressBar.now_length += 1
ret.append(SocketQueue.res_queue.get())
if ret:
socketio.emit('my_response', {
'data': ret,
'width': str(ProgressBar.calculate()) + '%'
})
socketio.emit('my_response', {
'data': ret,
'width': str(ProgressBar.calculate()) + '%'
})
def __init__(self, pdb, dmin, dmax, expand=True):
# inherit from Mixin
self.enumerate_hkl = self._enumerate_hkl_numpy
# enable access to self.F[h, k, l] with slicing support
self.F = self._make_FhklArray()
# coordinates
if expand:
pdb = pdb.get_unitcell()
uc_xyzc = np.dot(pdb.S, [pdb.x, pdb.y, pdb.z])
self.n = len(pdb)
# reflections
hkls, d = self._enumerate_hkl_numpy(dmin, dmax, S=pdb.S)
stol2 = 1.0 / (4.0 * d * d)
# Cromer-Mann scattering factors
assert os.path.isfile('cm.pkl')
with open('cm.pkl', 'rb') as _f:
_A, _B, _C = pickle.load(_f)
f0 = {
e:
_C[e] + sum(_A[e][i] * np.exp(-_B[e][i] * stol2) for i in range(4))
for e in set(pdb.e)
}
# direct summation for each summand
self.Fatoms = np.zeros((len(pdb), len(hkls)), dtype=complex)
p = ProgressBar(final=len(pdb),
label='directsum',
tail_label='{f:>10}')
for i, (xyzc, e, n, b) in enumerate(zip(uc_xyzc.T, pdb.e, pdb.n,
pdb.B)):
p.update()
hx = np.sum(hkls * xyzc, axis=1)
self.Fatoms[i, :] = n * f0[e] * np.exp(-b * stol2) * np.exp(
np.pi * 2j * hx)
# save drange
self._hkls = hkls
self._d = d
self.selection()
def font_file_cracker():
"""
接受字体文件，返回破解结果
:return:
"""
file_suffix = None
try:
file = request.files.get('font_file')
type_ = request.form.get('type')
except Exception as _e:
return jsonify({'code': 400, 'msg': f'lose args,{_e}', 'res': {}})
filename = re.sub('[（(）) ]', '', file.filename)
file.save('./font_collection/' + filename)
if config.is_online and not check_file('./font_collection/' + filename):
return jsonify({'code': 300, 'msg': 'Please use example file(*^_^*)'})
ProgressBar.init()
try:
res = ocr_processor(filename, request.remote_addr, has_pic_detail=True)
if type_ == 'html':
font_dict = {}
for idx, foo in enumerate(res):
if foo['ocr_result']:
res[idx]['ocr_result'] = foo['ocr_result'][0]['simPred']
font_dict[foo['name']] = foo['ocr_result']
else:
res[idx]['ocr_result'] = 'undefined'
font_dict[foo['name']] = 'undefined'
return jsonify({
'code': 200,
'html': render_template('images.html', result=res),
'font_dict': font_dict
})
else:
return jsonify({'code': 200, 'msg': 'success', 'res': res})
except Exception as _e:
if file_suffix:
shutil.rmtree('./fontforge_output/' + file_suffix)
return jsonify({'code': 400, 'msg': f'{_e}', 'res': {}})
def svd_run(randomizer, randomizer_name):
pb = ProgressBar((K + 1) * len(NOISES))
sys.stderr.write("Beginning SVD eval with %s randomization.\n" % randomizer_name)
pb.errput()
for percent_noise in NOISES:
this_rand = lambda d: randomizer(d, percent_noise)
parameters = [{
'cleaner': 'svd',
'p_noise': percent_noise,
'randomizer': randomizer_name,
'k': str(k)
} for k in [None] + range(1, K + 1)]
cleaners = [BaselineCleaner().scores] + [c.scores for c in create_svd_cleaners(K)]
for row in run_experiment(this_rand, cleaners, parameters):
yield row
pb.incr_and_errput()
def compute_slices(fsamples,xs,pbar=False):
if pbar: progress_bar = ProgressBar(fsamples.size,message="computing slices ")
else: print "computing slices"
slices = []
for f in fsamples:
slices.append(f(xs))
if pbar: progress_bar()
return np.array(slices).T # return transpose
def compute_kernels(slices,weights,pbar=False):
if pbar: progress_bar = ProgressBar(slices.size,message="computing kernels")
else: print "computing kernels"
kernels = []
for s in slices:
kernels.append(gaussian_kde(s,weights=weights))
if pbar: progress_bar()
return np.array(kernels)
def rebuild_random(magic, data):
"""Create a random.Random() object from the data and the magic vectors
:param list[str] magic: magic vector data
:param str data: observed output from Mersenne Twister
:rtype: random.Random
"""
progress = ProgressBar()
data_vals = [ord(d) for d in data]
state = [0L for _ in xrange(N)]
def compute_masses(kernels,y,pbar=False):
if pbar: progress_bar = ProgressBar(kernels.size,message="computing masses ")
else: print "computing masses"
masses = []
for k in kernels:
masses.append( compute_pmf(y,k) ) # compute M(x,y) for each value
if pbar: progress_bar()
return np.array(masses).T # return the transpose
def download_images(uri_list, download_location, retain_original_naming=True):
num = len(uri_list)
progress = ProgressBar(num, fmt=ProgressBar.FULL)
for i, src in enumerate(uri_list):
############################### DO WORK HERE ###########################
try:
img_data = urlopen(src).read()
if len(img_data) > 0: #Read Success
filename = basename(urlsplit(src)[2]).strip()
if not retain_original_naming:
filetype = filename.split('.')[-1]
filename = str(i + 1) + '.' + filetype
output = open(os.path.join(download_location, filename), 'wb')
output.write(img_data)
output.close()
except Exception as e:
log_error(e)
############################### END OF WORK #$##########################
progress.current += 1
progress()
sleep(0.001)
progress.done()
def normalmap(hm, sobelscale):
width, height = hm.size
nm = Image.new('RGBA', (width, height), color=(0, 0, 0, 0))
prog = ProgressBar(height)
print("\nNormal Map:")
for y in range(0, height):
prog.show(y)
for x in range(0, width):
value = hm.getpixel((x, y))
if value != -2147483648:
normal = sobel(x, y, hm, sobelscale)
color = (\
int(normal.x * 255),
int(normal.y * 255),
int(normal.z * 255), 255)
nm.putpixel((x, y), color)
return nm
def run_mcmc_save(sampler,startPos,nSteps,rState,file,**kwargs):
'''runs and MCMC chain with emcee, and saves steps to a file'''
#open chain save file
if file:
f = open(file,"w")
f.close()
iStep = 0
bar = ProgressBar()
for pos, prob, state in sampler.sample(startPos,iterations=nSteps,rstate0=rState,storechain=True,**kwargs):
if file:
f = open(file,"a")
bar.render(int(100*iStep/nSteps),'running MCMC')
iStep += 1
for k in range(pos.shape[0]):
# loop over all walkers and append to file
thisPos = pos[k]
thisProb = prob[k]
if file:
f.write("{0:4d} {1:s} {2:f}\n".format(k," ".join(map(str,thisPos)),thisProb ))
if file:
f.close()
return sampler
def listen( data, rate ): """ Listen to a one-dimensional numpy array Keyword Arguments: data -- A one-dimensional numpy array rate -- The data sampling rate. This has nothing to do with the sampling rate of the audio output from your speakers. Depends on pyaudio """ import pyaudio p = pyaudio.PyAudio() stream = p.open( format = pyaudio.paFloat32, channels = 1, rate = int( rate ), output = True ) data = np.squeeze( data ) data = data / max( abs( max( data ) ), abs( min( data ) ) ) start = 0 rate = int( rate ) read_block = rate / 4 # Read in 0.25 sec increments audio_length = len( data ) / float( rate ) pbar = ProgressBar( audio_length ) print 'Listening to data (%f sec)... Interrupt (^C) to stop.' % audio_length try: while start != len( data ): end = min( len( data ), start + read_block ) pbar.animate( start / float( rate ) ) stream.write( data[ start:end ].astype( 'float32' ).tostring() ) start = end except KeyboardInterrupt: pass stream.stop_stream() stream.close() p.terminate()
def run_ptmcmc_save(sampler,startPos,nSteps,file,**kwargs):
'''runs PT MCMC and saves zero temperature chain to file'''
if not os.path.exists(file):
f = open(file,"w")
f.close()
iStep = 0
bar = ProgressBar()
for pos, prob, like in sampler.sample(startPos,iterations=nSteps,storechain=True,**kwargs):
bar.render(int(100*iStep/nSteps),'running MCMC')
iStep += 1
f = open(file,"a")
# pos is shape (ntemps, nwalkers, npars)
# prob is shape (ntemps, nwalkers)
# loop over all walkers for zero temp and append to file
zpos = pos[0,...]
zprob = prob[0,...]
for k in range(zpos.shape[0]):
thisPos = zpos[k]
thisProb = zprob[k]
f.write("{0:4d} {1:s} {2:f}\n".format(k," ".join(map(str,thisPos)),thisProb ))
f.close()
return sampler
mappings = pd.read_csv(sys.argv[1], sep="\t")
synsets = mappings.Synset[mappings.Synset.notnull()]
synsets = [y for x in synsets.map(lambda z: z.split()) for y in x]
def fetch_image_urls(synset):
data = fetch.fetch_data(MAPPING_URL % synset)
image_mappings = [y.split() for y in data.split("\r\n") if y]
return image_mappings
def fetch_hypos(synset):
data = fetch.fetch_data(HYPO_URL % synset)
return data.replace("-", "").split("\r\n")
pb = ProgressBar(len(synsets))
pb.errput()
for synset in synsets:
image_urls = fetch_image_urls(synset)
if len(image_urls) == 0:
children_synsets = fetch_hypos(synset)
children_urls = [fetch_image_urls(cs) for cs in children_synsets]
image_urls = [y for x in children_urls for y in x]
for imgid, url in image_urls:
print "%s\t%s\t%s" % (synset, imgid, url)
pb.incr_and_errput()
# Check that an IP/Hostname was sent
usage()
# Load Configuration
con = Con('ports.ini');
targetIP = sys.argv[1]
ipparse = IPParse(targetIP)
ips = ipparse.parse()
ipmatch = re.compile('(\d{1,3}\.{1}){3}\d{1,3}')
for ip in ips:
if (ipmatch.match(ip) == None):
ip = gethostbyname(ip)
# Check if the host is up first
if (is_host_up(ip) == False):
print "DOWN: %s is down" % ip
continue
print 'Starting scan on host: ', ip
p = ProgressBar(1024)
p.update_time(10)
open_ports = {}
for i in range(10, 1024):
p.update_time(i)
if(scan_port(ip, i)):
# right justify for sorting
open_ports[str(i).rjust(5, '0')] = con.get(i)
for port in sorted(open_ports.iterkeys()):
print "Port (%s): %s" % (str(int(port)).rjust(5, ' '), open_ports[port])
def spectrogram( lts, channel, events, length = None, baseline_length = None, baseline_offset = 0, nfft = 1024, shift = 10, progress_bar = False ): """ Generate a spectrogram based on a query into the dataset. Internally, this uses matplotlib.mlab.specgram, so this is a FFT-based spectrogram. <---------------------------------||||||||||||||||||||-------> data = [baseline_length][baseline_offset]| event[start_idx] |[length] <---------------------------------||||||||||||||||||||-------> Returns: ( avg_spec, f, t ) avg_spec = Average spectrogram array f = frequency labels for axis 0 of avg_spec t = time labels for axis 1 of avg_spec Keyword Arguments: lts -- LabeledTimeseries object to use as the input dataset. events -- An ndarray of event objects to generate spectrograms for. Hint: use H5EEGEvents.query_events(...) for this! channel -- The channel within lts to create the spectrogram from. length -- Length of the spectrogram in samples. This value overrides event duration and is used to define spectrogram length for flag events. (Default: None -- length defined by event duration) baseline_length -- The number of samples of 'baseline' period to collect before each event. This data segment will be transformed into a spectrogram from which a baseline distribution will be defined per-frequency bin for Z-scoring. NOTE: Set baseline_length = 0 to disable baseline referencing. (Default: None -- baseline_length = length. If length == none, use event duration) baseline_offset -- The number of samples to offset before the event start_idx before the baseline period ends. See diagram above for clarification. (Default: 0 -- No samples of baseline offset) nfft -- Length of fft window. Should be a power of two. Used for both baseline and spectrogram. Should be shorter than length and baseline_length. (Default: 1024) shift -- Time shift of fft windows in samples. overlap = nfft - shift. (Default: 10) progress_bar -- Show a progress bar. (Default: False) FIXME: Specify lengths in seconds, because we have a samplingrate. TODO: Parallelism """ overlap = nfft - shift if baseline_length == None: baseline_length = length # Calculate a spectrogram for every event matching the query avg_spec = None num_spectrograms = 0.0 if progress_bar: from progress import ProgressBar pbar = ProgressBar( len( events ) ) for idx, event in enumerate( events ): # Acquire information about the event name = event['name'] start_idx = event['start_idx'] duration = event['duration'] # Skip the event if we can't find a good length for it. if duration == 0: duration = length if duration == None: continue; # Acquire the data for this spectrogram and calculate the spectrogram. data = lts[ start_idx:start_idx + duration, channel ] spec, f, t = specgram( data, NFFT = nfft, Fs = lts.get_rate(), noverlap = overlap ) spec = 20.0 * np.log10( spec ) # Reference to baseline if we can if baseline_length != 0: # Acquire the baseline data if baseline_length == None: b_len = duration else: b_len = baseline_length baseline_start = start_idx - b_len - baseline_offset baseline_end = start_idx - baseline_offset baseline_data = lts[ baseline_start:baseline_end, channel ] # Calculate the baseline spectrogram and determine distribution baseline_spec, f_base, t_base = specgram( baseline_data, NFFT = nfft, Fs = lts.get_rate(), noverlap = overlap ) baseline_spec = 20.0 * np.log10( baseline_spec ) mu = np.mean( baseline_spec, axis = 1 ) sigma = np.std( baseline_spec, axis = 1 ) # Z-Score the spectrogram by the baseline distribution. def zscore( data, mu, sigma ): return np.divide( np.subtract( data, mu ), sigma ) spec = np.apply_along_axis( zscore, 0, spec, mu, sigma ) # Add the spectrogram to the list of spectrograms if avg_spec == None: avg_spec = spec else: avg_spec = np.add( avg_spec, spec ) num_spectrograms += 1.0 # Update the progress if progress_bar: pbar.animate( idx ) # Sanity Check if num_spectrograms == 0.0: raise Warning( "No spectrograms generated -- Did you forget to specify Length?" ) return None, None, None # Average the plot and return the calculated parameters np.divide( avg_spec, num_spectrograms, out = avg_spec ) return avg_spec, f, t
def frequency_feature( lts, events, length = None, band = ( 70, 110 ), smooth = 10, baseline_length = None, baseline_offset = 0, baseline_features = False, progress_bar = False, exclude_ch = [] ): """ Generate average frequency features from a LabeledTimeseries across events. <---------------------------------||||||||||||||||||||-------> data = [baseline_length][baseline_offset]| event[start_idx] |[length] <---------------------------------||||||||||||||||||||-------> Returns: ( features, obs_labels, ch_labels, t_labels ) features -- ndarray of frequency features ( obs (events) x ch x samples (time) ) obs_labels -- labels of the observation axis of features ch_labels -- labels of the ch axis of features. Equal to lts.get_labels() t_labels -- time labels in seconds. Keyword Arguments: lts -- LabeledTimeseries object to use as the input dataset. events -- An ndarray of event objects to generate features for. Hint: use H5EEGEvents.query_events(...) for this! length -- Length of the feature in seconds. This value overrides event duration and is used to define feature length for flag events. (Default: None -- length defined by event duration) band -- Frequency band in Hz defined by a tuple ( cuton, cutoff ). Data will be filtered by an FIR bandpass filter and hilbert-transformed to extract the power in that band. (Default: ( 70, 110 ) High Gamma smooth -- The power envelope is low-pass filtered to this frequency. Used to smooth feature output. Set to 0 for no additional smoothing (Default: 10 Hz) baseline_length -- The number of samples of 'baseline' period to collect before each event. This data segment will be have features extracted from which a baseline distribution will be defined per-electrode for Z-scoring. NOTE: Set baseline_length = 0 to disable baseline referencing. (Default: None -- baseline_length = length) baseline_offset -- The number of samples to offset before the event start_idx before the baseline period ends. See diagram above for clarification. (Default: 0 -- No samples of baseline offset) baseline_features -- Append features for the baseline periods rather than referencing/zscoring the features by baseline. NOTE: This will double the number of features/observations (Default: False -- Do not append baseline features) progress_bar -- Show a progress bar. (Default: False) Depends on BCPy2000 hilbert. FIXME: Remove Dependency TODO: Parallelism """ import BCPy2000.Paths from BCPy2000.SigTools.Basic import hilbert # Take sampling rate into account length = int( length * lts.get_rate() ) if baseline_length == None: baseline_length = length if baseline_length == None: baseline_length = 0 buffer_samples = int( 0.2 * lts.get_rate() ) # Calculate filter coefficients smooth = smooth / float( lts.get_rate() ) smooth_coefs = None if smooth != 0.0: smooth_coefs = firwin( 64, cutoff = smooth, window = "hamming" ) smooth_coefs = smooth_coefs / sum( smooth_coefs ) # Correct Gain # Determine channel indices def bad_ch( ch ): for q in exclude_ch: if q in ch: return True return False channels = np.array( [ ch for ch in lts.get_labels() if not bad_ch( ch ) ] ) features = [] obs_labels = [] def add_observation( name, feature ): if smooth_coefs != None: feature = filtfilt( smooth_coefs, [1.0], feature, axis = 0 ) features.append( feature.T ) obs_labels.append( name ) # Calculate features for every event matching the query if progress_bar: from progress import ProgressBar pbar = ProgressBar( len( events ) ) for idx, event in enumerate( events ): # Acquire information about the event name = event['name'] start_idx = event['start_idx'] duration = event['duration'] # Skip the event if we can't find a good length for it. # FIXME: Logic is off here. if duration == 0: duration = length if duration == None: continue; # Define start and end of feature extraction epoch end = start_idx + duration + buffer_samples start = start_idx - buffer_samples # Acquire the data for this spectrogram and calculate the spectrogram. observation = lts[ start:end, channels ] obs_features = hilbert( observation, band = band, return_dict = True, samplingfreq_hz = lts.get_rate() )[ 'amplitude' ] # Reference to baseline if we can if baseline_length != 0: # Acquire the baseline data baseline_start = start_idx - baseline_length - baseline_offset - buffer_samples baseline_end = start_idx - baseline_offset + buffer_samples baseline_data = lts[ baseline_start:baseline_end, channels ] # Calculate the baseline features and determine distribution obs_baseline = hilbert( baseline_data, band = band, return_dict = True, samplingfreq_hz = lts.get_rate() )[ 'amplitude' ] obs_baseline = obs_baseline[ buffer_samples:-buffer_samples, : ] if baseline_features == False: # Z-Score the features by the baseline distribution. # TODO: This isn't statistically sound, this assumes # independence in the time-series mu = np.mean( obs_baseline, axis = 0 ) sigma = np.std( obs_baseline, axis = 0 ) def zscore( data, mu, sigma ): return np.divide( np.subtract( data, mu ), sigma ) obs_features = np.apply_along_axis( zscore, 1, obs_features, mu, sigma ) else: add_observation( 'BASELINE_' + name, obs_baseline ) # Add the features to the list of features obs_features = obs_features[ buffer_samples:-buffer_samples, : ] add_observation( name, obs_features ) # Update the progress if progress_bar: pbar.animate( idx ) # Return the feature array features = np.array( features ) t_labels = np.arange( features.shape[-1] ) / float( lts.get_rate() ) return ( features, obs_labels, channels, t_labels )
from progress import ProgressBar
from time import sleep
from random import random
my_list = range(20)
print 'TEST: Using a default ProgressBar'
sleep(1.0)
pb = ProgressBar(len(my_list), 20)
pb.start()
for i in my_list:
sleep(0.3)
pb.tick()
pb.finish()
print 'TEST: Using a custom design'
sleep(1.0)
pb = ProgressBar(len(my_list), 20, bookends='<{}>',
bar_char='/', empty_char='-')
pb.start()
for i in my_list:
sleep(0.3)
pb.tick()
pb.finish()
print 'TEST: Using a minimal design'
sleep(1.0)
pb = ProgressBar(len(my_list), 20, bookends='',
bar_char='-', empty_char=' ', show_percent=True, show_iter=False,
show_time=False)
pb.start()
v = np.random.uniform(low=0, high=1, size=N//2)
theta = 2*np.pi*u
phi = np.arccos(2*v-1)
spheres[:N//2,0] = rho*np.cos(theta)*np.sin(phi)+.5
spheres[:N//2,1] = rho*np.sin(theta)*np.sin(phi)+.0
spheres[:N//2,2] = rho*np.cos(phi)+.5
spheres[N//2:,0] = rho*np.cos(theta)*np.sin(phi)+.5
spheres[N//2:,1] = rho*np.sin(theta)*np.sin(phi)+1.0
spheres[N//2:,2] = rho*np.cos(phi)+.5
samples = sphere
np.random.seed(123)
net = DSOM((n,n,3), elasticity=1.0, init_method='fixed')
I = np.random.randint(0,samples.shape[0], epochs)
bar = ProgressBar(widgets=[Percentage(), Bar()], maxval=epochs).start()
plotfile = '/tmp/plot.txt'
datafile = '/tmp/data.txt'
rot_x, rot_z = 65,225
for i in range(epochs):
if i == (epochs//2):
samples = spheres
I = np.random.randint(0,samples.shape[0], epochs)
if i%5 == 0:
rot_x = 20+(1+np.cos(i/float(epochs)*4*np.pi))*45
rot_z = (rot_z+1) % 360
filename = '/tmp/image-%05d' % i
file = open(plotfile, 'w')
print "parsing file '%s'" % sopts.inputfile
neighbor = ""
lc = 0
# open input+output file
fh = open(sopts.inputfile, 'r')
fhout = open(sopts.outputfile, 'w') # rewrite
fhout.write("timestamp,neighbor,capabilities,mrr_T,mrr_t,mrr_P,rate,throughput,ewma_prob,this_prob,this_succ,this_attempt,success,attempts\n")
linebuffer = []
headers = False
t0 = time()
print "getting length of file... ",
numlines = get_num_lines(sopts.inputfile)
if (numlines > -1):
print "%d lines" % numlines
progress = ProgressBar(50)
progress.show(0)
else:
print "failed"
while (main_loop):
try:
filepos = fh.tell() # remember position before reading
line = fh.readline()
if ((not "\n" in line) and (line != '')):
fh.seek(filepos)
else:
if (line != ''):
lc += 1
if (lc % 10000 == 0 and numlines > -1):
duration = (time() - t0)
def main(plistpath, dest, options=None):
if options:
flat = options.flat
delete = options.delete
pretend = options.pretend
plist = open(plistpath)
srcset = set()
destset = set()
p.message("Parsing playlist.", 1)
playlistpaths = []
for line in plist:
if line[0] == '#':
continue
if line[-1] == '\n':
path = line[:-1] # strip the new line
else:
path = line
playlistpaths.append(path)
if len(playlistpaths) == 0:
p.message("Playlist is empty!", 1)
sys.exit()
p.message("Loading metadata from playlist files.", 1)
if p.level > 1 and p.level < 4:
bar = ProgressBar(len(playlistpaths),"numbers")
bar.draw()
i = 0
totalbytes=0
for path in playlistpaths:
try:
song = getMetaData(path)
totalbytes += os.path.getsize(path)
srcset.add(song)
except (OSError, IOError) as e:
p.message("\nError loading {0}: {1}".format(path, e.strerror), 2)
i += 1
if p.level > 1 and p.level < 4:
bar.update(i)
p.message("{0} files, {1} MB".format(len(playlistpaths), totalbytes/(1024.0*1024.0)), 2)
p.message("Loading existing files", 1)
existingFilePaths = []
for dirpath, dirnames, filenames in os.walk(dest):
for path in filenames:
if path[-3:] == 'mp3':
fullpath = os.path.join(dirpath, path)
existingFilePaths.append(fullpath)
if len(existingFilePaths) > 0:
p.message("Loading metadata from existing files.", 2)
if p.level > 1 and p.level < 4:
bar = ProgressBar(len(existingFilePaths),"numbers")
bar.draw()
i = 0
for path in existingFilePaths:
try:
song = getMetaData(path)
destset.add(song)
except HeaderNotFoundError:
# This is when the mp3 file in place is malformed, like when it is
# only a partial file
os.remove(path)
except IOError:
# Something wierd happened
p.message("File not found" + path, 2)
i += 1
if p.level > 1 and p.level < 4:
bar.update(i)
else:
p.message("No existing files", 3)
toAdd = srcset - destset
toDel = destset - srcset
# we can't just take the intersection, because we need the version from
# dest
toCheck = set()
for song in destset:
if song in srcset:
toCheck.add(song)
# Delete songs that shouldn't be there (if we should delete things)
if delete and len(toDel) > 0 and not pretend:
p.message("Deleting songs", 1)
for song in toDel:
os.remove(song.mp3path)
else:
p.message("Not deleting: delete flag={0}, pretend={1} len(toDel)={2}".format(delete,pretend,len(toDel)),5)
# Move songs around that are already there, but possibly not in the right
# place
first = False
if len(toCheck) > 0:
for song in toCheck:
data = song.data(root=dest)
data['artist'] = sanitize(data['artist'])
data['album'] = sanitize(data['album'])
data['title'] = sanitize(data['title'])
newFile = ""
if flat == False:
artistDir = u"{0[root]}/{0[artist]}".format(data)
albumDir = artistDir + u"/{0[album]}".format(data)
newFile = albumDir + u"/{0[track]:0>2} {0[title]}.mp3".format(data)
if not os.path.exists(artistDir):
os.mkdir(artistDir)
if not os.path.exists(albumDir):
os.mkdir(albumDir)
else:
newFile = u"{0[root]}/{0[artist]} - {0[album]} - {0[track]:0>2} {0[title]}.mp3".format(data)
if not song.mp3path == newFile:
if first:
first = False
p.message("Organizing old songs", 1)
if not pretend:
shutil.move(song.mp3path, newFile)
# Copy new songs
if len(toAdd) > 0:
p.message("Copying songs", 1)
if p.level > 1 and p.level < 4:
bar = ProgressBar(len(toAdd),"numbers")
bar.draw()
i = 0
for song in toAdd:
data = song.data(root=dest)
data['artist'] = sanitize(data['artist'])
data['album'] = sanitize(data['album'])
data['title'] = sanitize(data['title'])
newPath = ""
if flat == False:
artistDir = u"{0[root]}/{0[artist]}".format(data)
albumDir = artistDir + u"/{0[album]}".format(data)
newPath = albumDir + u"/{0[track]:0>2} {0[title]}.mp3".format(data)
if not os.path.exists(artistDir) and not pretend:
os.mkdir(artistDir)
if not os.path.exists(albumDir) and not pretend:
os.mkdir(albumDir)
else:
newPath = u"{0[root]}/{0[artist]} - {0[album]} - {0[track]:0>2} {0[title]}.mp3".format(data)
p.message("Copying {0}".format(newPath), 4)
if not pretend:
try:
shutil.copyfile(song.mp3path, newPath)
except IOError as e:
p.message("Error copying {0}: {1}".format(newPath, e.strerror), 3)
i += 1
if p.level > 1 and p.level < 4:
bar.update(i)
else:
p.message("All songs already there!", 1)
p.message("\nDone.", 1)
def parse_crux_search_txt(filename):
"""Iterate over records in a search.{target,decoy}.txt.
Crux txt format files are tab-delimited with 30 fields*, described
in the online documentation [1]. This function returns an iterator
which yields a dictionary with the fields and their values.
* 'decoy q-value (p-value)' is not output by Crux, at least as of v1.33.
[1] http://noble.gs.washington.edu/proj/crux/txt-format.html
Arguments:
filename: Name of the crux search-for-matches output.
Returns:
Dictionary that maps field names to values. Only fields that
are non-empty in the input exist in the returned dictionary.
Many of the fields are not usually set in the output of crux
search-for-matches, and will not be available.
"""
fields = ['scan', # int
'charge', # int
'spectrum precursor m/z', # float
'spectrum neutral mass', # float
'peptide mass', # float
'delta_cn', # float
'sp score', # float
'sp rank', # float
'xcorr score', # float
'xcorr rank', # int
'p-value', # float
'Weibull est. q-value', # float
'decoy q-value (xcorr)', # float
'percolator score', # float
'percolator rank', # int
'percolator q-value', # float
'q-ranker score', # float
'q-ranker q-value', # float
'b/y ions matched', # int
'b/y ions total', # int
'matches/spectrum', # int
'sequence', # string
'cleavage type', # string
'protein id', # string
'flanking aa', # string
'unshuffled sequence', # string
'eta', # float
'beta', # float
'shift', # float
'corr'] # float
casts = [ int, int, float, float, float, float, float, float, float, int,
float, float, float, float, int, float, float, float, int, int,
int, str, str, str, str, str, float, float, float, float ]
assert(len(fields) == len(casts))
_mandatories = [ 'scan', 'charge', 'spectrum precursor m/z',
'spectrum neutral mass', 'xcorr score',
'xcorr rank', 'sequence' ]
def conv(f, value):
value = value.strip()
if len(value):
return f(value)
def validate(record):
return all(record.has_key(m) for m in _mandatories)
widgets = [ Percentage(), Bar(), ETA() ]
progress = ProgressBar(widgets = widgets,
maxval = os.path.getsize(filename)).start()
with open(filename) as f:
reader = csv.reader(f, delimiter='\t')
# Header
row = reader.next()
if row != fields:
raise ParseError('Header: ', filename, 1, ' '.join(row))
# Body
for row in reader:
progress.update(f.tell())
if len(row) != len(fields):
raise ParseError('Line: ', filename, reader.line_num,
' '.join(row))
r = dict((k, conv(f,x)) for k, f, x in zip(fields, casts, row))
if r:
if not validate(r):
raise ParseError('Missing: ', filename, reader.line_num,
' '.join(row))
yield r
progress.finish()
sys.stdout.write('\n')
#!/usr/bin/env python2
# -*- coding: utf-8 -*-
from progress import ProgressBar
from animation import *
from time import sleep
p = ProgressBar(" Doing the 1st thing:", max_value=20, width=20)
for i in range(21):
p.update(i)
sleep(.25)
p.finish("Success")
a = Animation("Waiting for the 2nd thing:")
for i in range(21):
a.next()
sleep(.25)
a.finish("Success")
a = Animation("Waiting for the 3rd thing:", animation=ANIMATE_VGROW)
for i in range(21):
a.next()
sleep(.25)
a.finish("Success")
a = Animation("Waiting for the 4th thing:", animation=ANIMATE_HGROW)
for i in range(21):
a.next()
sleep(.25)
a.finish("Success")
a = Animation("Waiting for the 5th thing:", animation=ANIMATE_COUNT)
# white dwarf temp
twdVals = np.random.normal(loc=args.twd,scale=args.e_twd,size=chainLength)*units.K
# period
pVals = np.random.normal(loc=args.p,scale=args.e_p,size=chainLength)*units.d
# loop over the MCMC chain, calculating system parameters as we go
# table for results
results = Table(names=('q','Mw','Rw','Mr','Rr','a','Kw','Kr','incl'))
# need to be a little careful about astropy versions here, since only
# versions >=1.0 allow quantities in tables
# function below extracts value from quantity and floats alike
getval = lambda el: getattr(el,'value',el)
psolve = partial(solve,baseDir=baseDir)
data = zip(qVals,dphiVals,rwVals,twdVals,pVals)
solvedParams = PB.map(psolve,data,multiprocess=True)
print 'Writing out results...'
# loop over these results and put all the solutions in our results table
iStep = 0
bar = ProgressBar()
for thisResult in solvedParams:
bar.render(int(100*iStep/(len(solvedParams))),'Combining data')
iStep += 1
if thisResult is not None:
results.add_row(thisResult)
print 'Found solutions for %d percent of samples in MCMC chain' % (100*float(len(results))/float(chainLength))
results.write('physicalparams.log',format='ascii.commented_header')
from noisify import *
from progress import ProgressBar
REPEATS = 100
heads, mods, whole, assoc = load_data()
concatted = pd.concat([heads, mods], ignore_index=True)
agg_concat_orig = combine_measures(aggregate_ratings(concatted))['mean']
agg_whole_orig = aggregate_ratings(whole)['mean']
output = []
NUM_DROP = range(1, 26)
pb = ProgressBar(len(NUM_DROP) * REPEATS)
pb.errput()
for n in NUM_DROP:
this_row = {}
for i in xrange(REPEATS):
noisy_concat = replace_subjects(concatted, n)
noisy_whole = replace_subjects(whole, n)
clean_concat = remove_most_deviant_subjects(noisy_concat, n)
clean_whole = remove_most_deviant_subjects(noisy_whole, n)
agg_concat = combine_measures(aggregate_ratings(noisy_concat))['mean']
agg_whole = aggregate_ratings(noisy_whole)['mean']
agg_cl_concat = combine_measures(aggregate_ratings(clean_concat))['mean']
agg_cl_whole = aggregate_ratings(clean_whole)['mean']
zfile.extractall('tmp')
extract_files('tmp')
#cleaning up
shutil.rmtree('tmp')
try:
url = obj["url"][1:][:-1]
name = obj["url"][1:][:-1].split('/')[-1]
filename = os.path.join(DOWNLOADS_FOLDER, name)
name, ext = os.path.splitext(filename)
bar = ProgressBar(title="Downloading Started : Downloading %s V. %s " % (name, obj["version"]))
if(ext not in [".app",".zip",".pkg",".dmg"]):
bar.update(0, message="Can't handle files of type %s" % ext)
time.sleep(2)
raise
os.chdir(DOWNLOADS_FOLDER)
def prg(count, blockSize, totalSize):
percent = int(count * blockSize * 100 / totalSize)
bar.update(percent,message="(%s%%) Downloading %s " % (percent,url))