def get_coolers(self, table, res=1000000):
names = table['lib_name'].values
cool_dict = defaultdict(list)
for name in names:
if name not in self.metadata['lib_name'].values:
print(f'Name: {name} not found in metadata. Skipping')
continue
cool_dict['lib_name'].append(name)
flag = True
for cpath in self.cooler_paths:
if f'{name}.hg38.mapq_30.1000.mcool' in os.listdir(cpath):
flag = False
cool = Cooler(
cpath +
f'{name}.hg38.mapq_30.1000.mcool::/resolutions/{res}')
cool_dict[f'cooler_{res}'].append(cool)
if flag:
print(
f'Cooler not found matching {name}. Appending np.nan to appropriate row'
)
cool_dict[f'cooler_{res}'].append(np.nan)
df = pd.DataFrame(cool_dict)
df = table.copy(deep=True).merge(df, on='lib_name', how='outer')
return df
def matrix_balance(cool_uri,
nproc=1,
chunksize=int(1e7),
mad_max=5,
min_nnz=10,
min_count=0,
ignore_diags=1,
tol=1e-5,
max_iters=1000):
'''
Perform separate matrix balancing for regions with different copy numbers
and output the bias vector in the "sweight" column.
'''
cool_path, group_path = util.parse_cooler_uri(cool_uri)
# Overwrite the existing sweight column
with h5py.File(cool_path, 'r+') as h5:
grp = h5[group_path]
if 'sweight' in grp['bins']:
del grp['bins']['sweight']
clr = Cooler(cool_uri)
try:
if nproc > 1:
pool = balance.Pool(nproc)
map_ = pool.imap_unordered
else:
map_ = map
bias, stats = iterative_correction(clr,
chunksize=chunksize,
tol=tol,
min_nnz=min_nnz,
min_count=min_count,
mad_max=mad_max,
max_iters=max_iters,
ignore_diags=ignore_diags,
rescale_marginals=True,
use_lock=False,
map=map_)
finally:
if nproc > 1:
pool.close()
if not stats['converged']:
logger.error('Iteration limit reached without convergence')
logger.error('Storing final result. Check log to assess convergence.')
with h5py.File(cool_path, 'r+') as h5:
grp = h5[group_path]
# add the bias column to the file
h5opts = dict(compression='gzip', compression_opts=6)
grp['bins'].create_dataset('sweight', data=bias, **h5opts)
grp['bins']['sweight'].attrs.update(stats)
def correlate(x_mcool, y_mcool, output_prefix, resolution):
from pore_c.analyses.matrix import correlate
from cooler import Cooler
file_paths = catalogs.MatrixCorrelationCatalog.generate_paths(
output_prefix)
x_cool = Cooler(str(x_mcool) + f"::/resolutions/{resolution}")
y_cool = Cooler(str(y_mcool) + f"::/resolutions/{resolution}")
x_chrom_names = set(x_cool.chromnames)
y_chrom_names = set(y_cool.chromnames)
if x_chrom_names != y_chrom_names:
x_not_y = x_chrom_names - y_chrom_names
y_not_x = y_chrom_names - x_chrom_names
if x_not_y and y_not_x:
raise ValueError(
f"Chromosomes are not sub/supersets x:{x_not_y}, y:{y_not_x}")
elif x_not_y:
logger.warning(
f"Extra chromosomes in x, will not be included in calculations: {x_not_y}"
)
else:
logger.warning(
f"Extra chromosomes in y, will not be included in calculations: {y_not_x}"
)
metadata = correlate(x_cool,
y_cool,
xy_path=file_paths["xy"],
coefficients_path=file_paths["coefficients"],
resolution=resolution)
metadata["resolution"] = resolution
metadata["x"]["path"] = str(x_mcool)
metadata["y"]["path"] = str(y_mcool)
matrix_cat = catalogs.MatrixCorrelationCatalog.create(
file_paths, metadata, {})
logger.info(str(matrix_cat))
def __init__(self, fan_pin, peltier_pin, step_pin, thermometer_pin):
self.cooler = Cooler(Pin(fan_pin, Pin.OUT), Pin(peltier_pin, Pin.OUT))
self.cooler.fanOn()
self.cooler.coolerHigh()
self.pid = Pid(17, 1, 0.02, 0,
0.995) #(temperature, P, I, D, memoryFactor)
self.thermometer = Thermometer(thermometer_pin)
self.pump = PWMPump(Pin(step_pin, Pin.OUT))
for i in range(10):
self.pump.pwm.freq(i * 1500)
utime.sleep(0.1)
self.pump.pwm.freq(15000)
def parse_cooler(
cooler_file: str,
regions: Dict[str, np.ndarray]
) -> Tuple[Cooler, List[np.ndarray]]:
# Load cooler
c = Cooler(cooler_file)
# Fetch relevant bin_ids from the cooler file
b_ids = fetch_bins_from_cooler(cooler, regions)
# Identify unique bin_ids and isolate disjoint regions
slices = get_unique_bins(b_ids)
return c, slices
def __init__(self, source_uri, bins, chunksize, batchsize, map=map):
from cooler.api import Cooler
self._map = map
self.source_uri = source_uri
self.chunksize = chunksize
self.batchsize = batchsize
clr = Cooler(source_uri)
self._size = clr.info['nnz']
self.old_binsize = clr.binsize
self.old_chrom_offset = clr._load_dset('indexes/chrom_offset')
self.old_bin1_offset = clr._load_dset('indexes/bin1_offset')
self.gs = GenomeSegmentation(clr.chromsizes, bins)
self.new_binsize = get_binsize(bins)
assert self.new_binsize % self.old_binsize == 0
self.factor = self.new_binsize // self.old_binsize
def _aggregate(self, span):
from cooler.api import Cooler
lo, hi = span
clr = Cooler(self.source_uri)
# convert_enum=False returns chroms as raw ints
table = clr.pixels(join=True, convert_enum=False)
chunk = table[lo:hi]
# logger.info('{} {}'.format(lo, hi))
print('{} {}'.format(lo, hi))
# use the "start" point as anchor for re-binning
# XXX - alternatives: midpoint anchor, proportional re-binning
binsize = self.gs.binsize
chrom_binoffset = self.gs.chrom_binoffset
chrom_abspos = self.gs.chrom_abspos
start_abspos = self.gs.start_abspos
chrom_id1 = chunk['chrom1'].values
chrom_id2 = chunk['chrom2'].values
start1 = chunk['start1'].values
start2 = chunk['start2'].values
if binsize is None:
abs_start1 = chrom_abspos[chrom_id1] + start1
abs_start2 = chrom_abspos[chrom_id2] + start2
chunk['bin1_id'] = np.searchsorted(
start_abspos, abs_start1, side='right') - 1
chunk['bin2_id'] = np.searchsorted(
start_abspos, abs_start2, side='right') - 1
else:
rel_bin1 = np.floor(start1 / binsize).astype(int)
rel_bin2 = np.floor(start2 / binsize).astype(int)
chunk['bin1_id'] = chrom_binoffset[chrom_id1] + rel_bin1
chunk['bin2_id'] = chrom_binoffset[chrom_id2] + rel_bin2
grouped = chunk.groupby(['bin1_id', 'bin2_id'], sort=False)
return grouped['count'].sum().reset_index()
from flask import Flask, redirect, url_for, render_template, request
from cooler import Cooler
# globals
app = Flask(__name__)
cooler = Cooler(21, 20, 16)
@app.route('/', methods=('GET', 'POST'))
def index():
if request.method == 'GET':
return render_template('index.html', **cooler.__dict__)
if request.method == 'POST':
cooler.control_mode = request.form['mode']
if request.form['mode'] == 'automatic':
# TODO: check rationality if thresholds
try:
cooler.min_threshold = float(request.form['min_threshold'])
except Exception as E:
pass
try:
cooler.max_threshold = float(request.form['max_threshold'])
except Exception as E:
pass
cooler.set_speed(False)
return redirect('/update')
if request.form['mode'] == 'manual':
#!/usr/bin/env python
# encoding: utf-8
from cooler import Cooler
if __name__ == '__main__':
near_cool = Cooler()
near_cool.run()
def export_to_cooler(
contact_table,
output_prefix,
cooler_resolution,
fragment_table,
chromsizes,
query,
query_columns=None,
by_haplotype=False,
):
results = []
if query_columns:
columns = query_columns[:]
else:
columns = []
columns.extend(["align1_fragment_id", "align2_fragment_id"])
if by_haplotype:
columns.extend(["align1_haplotype", "align2_haplotype"])
contact_df = dd.read_parquet(contact_table,
engine=PQ_ENGINE,
version=PQ_VERSION,
columns=columns,
index=False)
if query:
contact_df = contact_df.query(query)
chrom_dict = pd.read_csv(chromsizes,
sep="\t",
header=None,
names=["chrom", "size"],
index_col=["chrom"],
squeeze=True)
# create even-widht bins using cooler
bins_df = binnify(chrom_dict, cooler_resolution)
bins_df.index.name = "bin_id"
# convert to ranges for overlap
bins = pr.PyRanges(bins_df.reset_index().rename(columns={
"start": "Start",
"end": "End",
"chrom": "Chromosome"
}))
fragment_df = dd.read_parquet(fragment_table,
engine=PQ_ENGINE,
version=PQ_VERSION).compute()
midpoint_df = pr.PyRanges(
fragment_df.reset_index()[[
"chrom", "start", "end", "fragment_id"
]].assign(start=lambda x: ((x.start + x.end) * 0.5).round(0).astype(
int)).eval("end = start + 1").rename(columns={
"chrom": "Chromosome",
"start": "Start",
"end": "End"
}))
# use a pyranges joing to assign fragments to bins
fragment_to_bin = midpoint_df.join(
bins, how="left").df[["fragment_id", "bin_id"]]
fragment_to_bin = fragment_to_bin.set_index(
"fragment_id").sort_index() # .astype(np.uint32)
nulls = fragment_to_bin["bin_id"] == -1
if nulls.any():
logger.warning(
"Some fragments did not overlap bins, removing from analysis:\n{}".
format(fragment_to_bin[nulls].join(fragment_df)))
fragment_to_bin = fragment_to_bin[~nulls]
# use a join to assign each end of a contact to a bin
binned_contacts = (contact_df.merge(
fragment_to_bin,
how="inner",
right_index=True,
left_on="align1_fragment_id").merge(
fragment_to_bin,
how="inner",
right_index=True,
left_on="align2_fragment_id",
suffixes=[None, "_2"]).rename(columns={
"bin_id": "bin1_id",
"bin_id_2": "bin2_id"
}))
if not by_haplotype:
cooler_path = output_prefix + ".cool"
# group size == number of contacts per bin_pair
pixels = binned_contacts.groupby(
["bin1_id",
"bin2_id"]).size().rename("count").astype(np.int32).reset_index()
create_cooler(cooler_path,
bins_df,
pixels,
ordered=True,
symmetric_upper=True,
ensure_sorted=True)
c = Cooler(cooler_path)
logger.info(f"Created cooler: {c.info}")
results.append(cooler_path)
else:
tmp_parquet = output_prefix + ".tmp.pq"
pixels = (
# create a key to groupy by haplotype pair, order of haplotypes doesn't matter
binned_contacts.assign(
hap_key=lambda x: x[["align1_haplotype", "align2_haplotype"]
].apply(lambda y: "{}_{}".format(*sorted(
y)).replace("-1", "nohap"),
axis=1,
meta="object")
).groupby(["hap_key", "bin1_id",
"bin2_id"]).size().rename("count").astype(
np.int32
).reset_index().astype({"hap_key": "category"}))
# save to a temporary parquet file, this might not be necessary
# but want to avoid the whole contact matrix hitting memory
pixels.to_parquet(
tmp_parquet,
write_metadata_file=True,
partition_on=["hap_key"],
write_index=False,
engine=PQ_ENGINE,
version=PQ_VERSION,
)
pixels = dd.read_parquet(tmp_parquet,
engine=PQ_ENGINE,
version=PQ_VERSION,
columns=["hap_key"],
index=False)
hap_keys = pixels["hap_key"].unique().compute()
# create a cooler for each haplotype pair
for hap_key in hap_keys:
cooler_path = f"{output_prefix}.{hap_key}.cool"
pixels = dd.read_parquet(
tmp_parquet,
filters=[("hap_key", "==", hap_key)],
index=False,
engine=PQ_ENGINE,
version=PQ_VERSION,
columns=["bin1_id", "bin2_id", "count"],
)
create_cooler(cooler_path,
bins_df,
pixels,
ordered=True,
symmetric_upper=True,
ensure_sorted=True)
c = Cooler(cooler_path)
logger.info(f"Created cooler: {c.info}")
results.append(cooler_path)
shutil.rmtree(tmp_parquet)
return results
def main():
"""Balance of plant of a boiling water nuclear reactor.
Attributes
----------
end_time: float
End of the flow time in SI unit.
time_step: float
Size of the time step between port communications in SI unit.
use_mpi: bool
If set to `True` use MPI otherwise use Python multiprocessing.
"""
# Preamble
end_time = 30.0 * unit.minute
time_step = 30.0 # seconds
show_time = (True, 5 * unit.minute)
use_mpi = False # True for MPI; False for Python multiprocessing
plot_results = True # True for enabling plotting section below
params = get_params() # parameters for BoP BWR
#*****************************************************************************
# Define Cortix system
# System top level
plant = Cortix(use_mpi=use_mpi, splash=True)
# Network
plant_net = plant.network = Network()
params['start-time'] = 0.0
params['end-time'] = end_time
params['shutdown-time'] = 999.0 * unit.hour
params['shutdown-mode'] = False
#*****************************************************************************
# Create reactor module
reactor = BWR(params)
reactor.name = 'BWR'
reactor.save = True
reactor.time_step = time_step
reactor.end_time = end_time
reactor.show_time = show_time
reactor.RCIS = True
# Add reactor module to network
plant_net.module(reactor)
#*****************************************************************************
# Create turbine high pressure module
params['turbine_inlet_pressure'] = 2
params['turbine_outlet_pressure'] = 0.5
params['high_pressure_turbine'] = True
#params_turbine = reactor.params
#params_turbine.inlet_pressure = 2
#params.turbine_outlet_pressure = 0.5
turbine_hp = Turbine(params)
turbine_hp.name = 'High Pressure Turbine'
turbine_hp.save = True
turbine_hp.time_step = time_step
turbine_hp.end_time = end_time
# Add turbine high pressure module to network
plant_net.module(turbine_hp)
#*****************************************************************************
# Create turbine low pressure module
params['turbine_inlet_pressure'] = 0.5
params['turbine_outlet_pressure'] = 0.005
params['high_pressure_turbine'] = False
params['steam flowrate'] = params['steam flowrate'] / 2
turbine_lp1 = Turbine(params)
turbine_lp1.name = 'Low Pressure Turbine 1'
turbine_lp1.save = True
turbine_lp1.time_step = time_step
turbine_lp1.end_time = end_time
plant_net.module(turbine_lp1)
#*****************************************************************************
# Create turbine low pressure module
params['turbine_inlet_pressure'] = 0.5
params['turbine_outlet_pressure'] = 0.005
params['high_pressure_turbine'] = False
turbine_lp2 = Turbine(params)
turbine_lp2.name = 'Low Pressure Turbine 2'
turbine_lp2.save = True
turbine_lp2.time_step = time_step
turbine_lp2.end_time = end_time
plant_net.module(turbine_lp2)
#*****************************************************************************
# Create condenser module
params['steam flowrate'] = params['steam flowrate'] * 2
condenser = Condenser()
condenser.name = 'Condenser'
condenser.save = True
condenser.time_step = time_step
condenser.end_time = end_time
plant_net.module(condenser)
#*****************************************************************************
params['RCIS-shutdown-time'] = 5 * unit.minute
rcis = Cooler(params)
rcis.name = 'RCIS'
rcis.save = True
rcis.time_step = time_step
rcis.end_time = end_time
plant_net.module(rcis)
#*****************************************************************************
# Create the BoP network connectivity
plant_net.connect([reactor, 'coolant-outflow'], [turbine_hp, 'inflow'])
plant_net.connect([turbine_hp, 'outflow-1'], [turbine_lp1, 'inflow'])
plant_net.connect([turbine_hp, 'outflow-2'], [turbine_lp2, 'inflow'])
plant_net.connect([turbine_lp1, 'outflow-1'], [condenser, 'inflow-1'])
plant_net.connect([turbine_lp2, 'outflow-1'], [condenser, 'inflow-2'])
plant_net.connect([condenser, 'outflow'], [reactor, 'coolant-inflow'])
plant_net.connect([reactor, 'RCIS-outflow'], [rcis, 'coolant-inflow'])
plant_net.connect([rcis, 'coolant-outflow'], [reactor, 'RCIS-inflow'])
#plant_net.connect([rcis, 'signal-in'], [reactor, 'signal-out'])
plant_net.draw(engine='dot', node_shape='folder')
#*****************************************************************************
# Run network dynamics simulation
plant.run()
#*****************************************************************************
# Plot results
if plot_results and (plant.use_multiprocessing or plant.rank == 0):
# Reactor plots
reactor = plant_net.modules[0]
(quant, time_unit
) = reactor.neutron_phase.get_quantity_history('neutron-dens')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('startup-neutron-dens.png', dpi=300)
(quant, time_unit
) = reactor.neutron_phase.get_quantity_history('delayed-neutrons-cc')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('startup-delayed-neutrons-cc.png', dpi=300)
(quant, time_unit
) = reactor.coolant_outflow_phase.get_quantity_history('temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('startup-coolant-outflow-temp.png', dpi=300)
(quant,
time_unit) = reactor.reactor_phase.get_quantity_history('fuel-temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('startup-fuel-temp.png', dpi=300)
# Turbine high pressure plots
turbine_hp = plant_net.modules[1]
(quant,
time_unit) = turbine_hp.outflow_phase.get_quantity_history('power')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']',
title='High Pressure Turbine Power')
plt.grid()
plt.savefig('startup-turbine-hp-power.png', dpi=300)
(quant,
time_unit) = turbine_hp.outflow_phase.get_quantity_history('temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']',
title='High Pressure Turbine Outflow Temperature')
plt.grid()
plt.savefig('startup-turbine-hp-outflow-temp.png', dpi=300)
# Turbine low pressure graphs
turbine_lp1 = plant_net.modules[2]
(quant,
time_unit) = turbine_lp1.outflow_phase.get_quantity_history('power')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']',
title='Lower Pressure Turbine 1 Power')
plt.grid()
plt.savefig('startup-turbine-lp1-power.png', dpi=300)
(quant,
time_unit) = turbine_lp1.outflow_phase.get_quantity_history('temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']',
title='Lower Pressure Turbine 1 Outflow Temperature')
plt.grid()
plt.savefig('startup-turbine-lp1-outflow-temp.png', dpi=300)
# Condenser graphs
condenser = plant_net.modules[3]
(quant,
time_unit) = condenser.outflow_phase.get_quantity_history('temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('startup-condenser-outflow-temp.png', dpi=300)
#setup initial values for simulation
turbine1_outflow_temp = turbine_hp.outflow_phase.get_value(
'temp', end_time)
turbine1_chi = turbine_hp.outflow_phase.get_value('quality', end_time)
turbine1_power = turbine_hp.outflow_phase.get_value('power', end_time)
turbine2_outflow_temp = turbine_lp1.outflow_phase.get_value(
'temp', end_time)
turbine2_chi = turbine_lp1.outflow_phase.get_value('quality', end_time)
turbine2_power = turbine_lp1.outflow_phase.get_value('power', end_time)
condenser_runoff_temp = condenser.outflow_phase.get_value('temp', end_time)
delayed_neutron_cc = reactor.neutron_phase.get_value(
'delayed-neutrons-cc', end_time)
n_dens = reactor.neutron_phase.get_value('neutron-dens', end_time)
fuel_temp = reactor.reactor_phase.get_value('fuel-temp', end_time)
coolant_temp = reactor.coolant_outflow_phase.get_value('temp', end_time)
# Values loaded into params when they are needed (module instantiation)
# Properly shutdown simulation
plant.close()
# Now we run shutdown as a seperate simulation with starting parameters equal to the ending
# values of the startup simulation
#**************************************************************************************************
# Preamble
start_time = 0.0 * unit.minute
end_time = 60 * unit.minute
time_step = 30.0 # seconds
show_time = (True, 5 * unit.minute)
use_mpi = False # True for MPI; False for Python multiprocessing
plot_results = True # True for enabling plotting section below
params = get_params() # clear params, just to be safe
#*****************************************************************************
# Define Cortix system
# System top level
plant = Cortix(use_mpi=use_mpi, splash=True)
# Network
plant_net = plant.network = Network()
params['start-time'] = start_time
params['end-time'] = end_time
params['shutdown time'] = 0.0
params['shutdown-mode'] = True
#*****************************************************************************
# Create reactor module
params['delayed-neutron-cc'] = delayed_neutron_cc
params['n-dens'] = n_dens
params['fuel-temp'] = fuel_temp
params['coolant-temp'] = coolant_temp
params['operating-mode'] = 'shutdown'
reactor = BWR(params)
reactor.name = 'BWR'
reactor.save = True
reactor.time_step = time_step
reactor.end_time = end_time
reactor.show_time = show_time
reactor.RCIS = False
# Add reactor module to network
plant_net.module(reactor)
#*****************************************************************************
# Create turbine high pressure module
params['turbine_inlet_pressure'] = 2
params['turbine_outlet_pressure'] = 0.5
params['high_pressure_turbine'] = True
params['turbine-outflow-temp'] = turbine1_outflow_temp
params['turbine-chi'] = turbine1_chi
params['turbine-work'] = turbine1_power
params['turbine-inflow-temp'] = coolant_temp
#params_turbine = reactor.params
#params_turbine.inlet_pressure = 2
#params.turbine_outlet_pressure = 0.5
turbine_hp = Turbine(params)
turbine_hp.name = 'High Pressure Turbine'
turbine_hp.save = True
turbine_hp.time_step = time_step
turbine_hp.end_time = end_time
# Add turbine high pressure module to network
plant_net.module(turbine_hp)
#*****************************************************************************
# Create turbine low pressure 1 module
params['turbine_inlet_pressure'] = 0.5
params['turbine_outlet_pressure'] = 0.005
params['high_pressure_turbine'] = False
params['steam flowrate'] = params['steam flowrate'] / 2
params['turbine-outflow-temp'] = turbine2_outflow_temp
params['turbine-inflow-temp'] = turbine1_outflow_temp
params['turbine-chi'] = turbine2_chi
params['turbine-work'] = turbine2_power
turbine_lp1 = Turbine(params)
turbine_lp1.name = 'Low Pressure Turbine 1'
turbine_lp1.save = True
turbine_lp1.time_step = time_step
turbine_lp1.end_time = end_time
plant_net.module(turbine_lp1)
#*****************************************************************************
# Create turbine low pressure 2 module
params['turbine_inlet_pressure'] = 0.5
params['turbine_outlet_pressure'] = 0.005
params['high_pressure_turbine'] = False
turbine_lp2 = Turbine(params)
turbine_lp2.name = 'Low Pressure Turbine 2'
turbine_lp2.save = True
turbine_lp2.time_step = time_step
turbine_lp2.end_time = end_time
plant_net.module(turbine_lp2)
#*****************************************************************************
# Create condenser module
params['steam flowrate'] = params['steam flowrate'] * 2
params['condenser-runoff-temp'] = condenser_runoff_temp
condenser = Condenser()
condenser.name = 'Condenser'
condenser.save = True
condenser.time_step = time_step
condenser.end_time = end_time
plant_net.module(condenser)
#*****************************************************************************
params['RCIS-shutdown-time'] = -1 * unit.minute
rcis = Cooler(params)
rcis.name = 'RCIS'
rcis.save = True
rcis.time_step = time_step
rcis.end_time = end_time
plant_net.module(rcis)
#*****************************************************************************
# Create the BoP network connectivity
plant_net.connect([reactor, 'coolant-outflow'], [turbine_hp, 'inflow'])
plant_net.connect([turbine_hp, 'outflow-1'], [turbine_lp1, 'inflow'])
plant_net.connect([turbine_hp, 'outflow-2'], [turbine_lp2, 'inflow'])
plant_net.connect([turbine_lp1, 'outflow-1'], [condenser, 'inflow-1'])
plant_net.connect([turbine_lp2, 'outflow-1'], [condenser, 'inflow-2'])
plant_net.connect([condenser, 'outflow'], [reactor, 'coolant-inflow'])
plant_net.connect([reactor, 'RCIS-outflow'], [rcis, 'coolant-inflow'])
plant_net.connect([rcis, 'coolant-outflow'], [reactor, 'RCIS-inflow'])
#plant_net.connect([rcis, 'signal-in'], [reactor, 'signal-out'])
plant_net.draw(engine='dot', node_shape='folder')
#*****************************************************************************
# Run network dynamics simulation
plant.run()
#*****************************************************************************
# Plot results
if plot_results and (plant.use_multiprocessing or plant.rank == 0):
# Reactor plots
reactor = plant_net.modules[0]
(quant, time_unit
) = reactor.neutron_phase.get_quantity_history('neutron-dens')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('shutdown-neutron-dens.png', dpi=300)
(quant, time_unit
) = reactor.neutron_phase.get_quantity_history('delayed-neutrons-cc')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('shutdown-delayed-neutrons-cc.png', dpi=300)
(quant, time_unit
) = reactor.coolant_outflow_phase.get_quantity_history('temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('shutdown-coolant-outflow-temp.png', dpi=300)
(quant,
time_unit) = reactor.reactor_phase.get_quantity_history('fuel-temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('shutdown-fuel-temp.png', dpi=300)
# Turbine high pressure plots
turbine_hp = plant_net.modules[1]
(quant,
time_unit) = turbine_hp.outflow_phase.get_quantity_history('power')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']',
title='High Pressure Turbine Power')
plt.grid()
plt.savefig('shutdown-turbine-hp-power.png', dpi=300)
(quant,
time_unit) = turbine_hp.outflow_phase.get_quantity_history('temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']',
title='High Pressure Turbine Outflow Temperature')
plt.grid()
plt.savefig('shutdown-turbine-hp-outflow-temp.png', dpi=300)
# Turbine low pressure graphs
turbine_lp1 = plant_net.modules[2]
(quant,
time_unit) = turbine_lp1.outflow_phase.get_quantity_history('power')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']',
title='Lower Pressure Turbine 1 Power')
plt.grid()
plt.savefig('shutdown-turbine-lp1-power.png', dpi=300)
(quant,
time_unit) = turbine_lp1.outflow_phase.get_quantity_history('temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']',
title='Lower Pressure Turbine 1 Outflow Temperature')
plt.grid()
plt.savefig('shutdown-turbine-lp1-outflow-temp.png', dpi=300)
# Condenser graphs
condenser = plant_net.modules[4]
(quant,
time_unit) = condenser.outflow_phase.get_quantity_history('temp')
quant.plot(x_scaling=1 / unit.minute,
x_label='Time [m]',
y_label=quant.latex_name + ' [' + quant.unit + ']')
plt.grid()
plt.savefig('shutdown-condenser-outflow-temp.png', dpi=300)
# Shutdown The Simulation
plant.close()
for i in range(0, len(spans), batchsize):
try:
lock.acquire()
print("right before collapse ...{} {}".format(
i, spans[i:i + batchsize]))
results = self._map(self.aggregate, spans[i:i + batchsize])
finally:
lock.release()
for df in results:
# yield {k: v.values for k, v in six.iteritems(df)}
yield df
input_uri = ""
c = Cooler(input_uri)
new_bins = binnify(c.chromsizes, 2 * c.binsize)
iterator = CoolerAggregator(input_uri, new_bins, 1000000, batchsize=1, map=map)
# # last message before it fails ...
# # INFO:cooler:17868809 17872380
# for ii in iterator:
# print(ii)
# from cooler.api import Cooler
lo, hi = 17869999, 17872300
# lo, hi = 17868809, 17872380
clr = Cooler(input_uri)