def write(gmeasure, name):
# do the sampling
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(
po2group)
smpl, fluxes = detailedo2.sampleVessels(
po2group, gvessels, gtumor, sample_length)
#cons = dataman.detailedPO2_consumption(po2group, gtumor)
cons = dataman.obtain_data('detailedPO2_consumption', po2group,
gtumor)
# get the raw data, just for the consumption flux
po2vessels, ld, po2field, parameters = dataman.obtain_data(
'detailedPO2', po2group)
avgCons = np.asarray(myutils.largeDatasetAverage(cons),
dtype=np.float64)
fluxes['Jout_cons'] = avgCons * np.product(
cons.shape) * (ld.scale * 1.e-4)**3
del po2vessels, po2field, ld
gmeasure = gmeasure.create_group(name)
for k, v in smpl.iteritems():
gmeasure.create_dataset('smpl_' + k,
data=v,
compression=9,
dtype=np.float32)
for k, v in fluxes.iteritems():
gmeasure.create_dataset('flux_' + k,
data=v) # scalar dataset
def GenerateSingleCapillarySamples(dataman,
po2group,
cachelocation,
properties=['po2', 'sat', 'extpo2']):
vesselgroup, _ = detailedo2.OpenVesselAndTumorGroups(po2group)
smpl = dict(
weight=dataman.obtain_data('basic_vessel_samples', 'weight',
vesselgroup, sample_length),
pos=dataman.obtain_data('basic_vessel_samples', 'position',
vesselgroup, sample_length),
)
for prop in properties:
smpl[prop] = dataman.obtain_data('detailedPO2_samples', prop, po2group,
sample_length, 1, cachelocation)
# sort by x-position
x = smpl['pos'][:, 0]
ordering = np.argsort(x)
pos = smpl['pos'][ordering, ...]
x0 = 0
dv = (pos[-1] - x0)
dv /= np.linalg.norm(dv)
x = np.asarray(map(lambda x_: np.dot(dv, x_ - x0), pos))
for k, v in smpl.items():
smpl[k] = v[ordering]
smpl['x'] = x
return smpl
def write(gmeasure, name):
samplelocation = MakeSampleLocation(po2group)
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(
po2group)
smpl = dataman.obtain_data('detailedPO2_peff_samples',
po2group, sample_length, None,
samplelocation)
data, = analyzeGeneral.GenerateRadialDistributions(
dataman, gvessels, gtumor, sample_length, bins_spec,
distance_distribution_name, None,
[(smpl, analyzeGeneral.radialAvgPerVessels)])
data.write(gmeasure, name)
def read(gmeasure, name):
gmeasure = gmeasure[name]
if dataname == 'detailedPO2_samples':
if prop == 'gtv':
parameters = dataman.obtain_data(
'detailedPO2Parameters', po2group)
#po2 = dataman.obtain_data('detailedPO2_samples','po2', *args[1:])
#extpo2 = dataman.obtain_data('detailedPO2_samples','extpo2', *args[1:])
#return (po2-extpo2)/(parameters['grid_lattice_const']*parameters.get('transvascular_ring_size',0.5))
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(
po2group)
jtv = dataman.obtain_data('detailedPO2_samples', 'jtv',
*args[1:])
#radius = dataman.obtain_data('basic_vessel_samples', 'radius', gvessels, sample_length)
#radius = radius * (60.e-4*math.pi*2.* parameters['kD_tissue']*parameters['alpha_t'])
radius = (
60.e-4 *
parameters.get('D_tissue',
parameters.get('kD_tissue', None)) *
parameters.get('solubility_tissue',
parameters.get('alpha_t', None)))
gtv = jtv / radius
return gtv
elif prop == 'sat':
po2 = dataman.obtain_data('detailedPO2_samples', 'po2',
*args[1:])
parameters = dataman.obtain_data(
'detailedPO2Parameters', po2group)
return detailedo2.PO2ToSaturation(po2, parameters)
else:
ds = gmeasure['smpl_' + prop]
ds = ds[...] if every is None else ds[::every]
return ds
else:
keys = filter(lambda k: k.startswith('flux_'),
gmeasure.keys())
fluxes = dict(map(lambda k: (k[5:], gmeasure[k][()]),
keys))
fluxes['e1'] = abs(
100. * (fluxes['Jin_root'] - fluxes['Jout_root'] -
fluxes['Jout_tv']) / fluxes['Jin_root'])
fluxes['e2'] = abs(
100. *
(fluxes['Jin_root'] - fluxes['Jout_root'] -
fluxes['Jout_cons'] - fluxes.get('tv_cons', 0.)) /
fluxes['Jin_root'])
fluxes['e3'] = abs(
100. * (fluxes['Jout_tv'] - fluxes['Jout_cons'] -
fluxes.get('tv_cons', 0.)) / fluxes['Jout_tv'])
return fluxes
def write(gmeasure, name):
samplelocation = MakeSampleLocation(po2group)
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(
po2group)
peff = dataman.obtain_data('detailedPO2_peff_samples',
po2group, sample_length, None,
samplelocation)
rad = dataman.obtain_data('basic_vessel_samples', 'radius',
gvessels, sample_length)
peff = peff * math.pi * 2. * rad
data, = analyzeGeneral.GenerateRadialDistributions(
dataman, gvessels, gtumor, sample_length, bins_spec,
distance_distribution_name, None,
[(peff, analyzeGeneral.radialAvgPerVolume)])
data.write(gmeasure, name)
def write(gmeasure, groupname):
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(po2group)
parameters = dataman.obtain_data('detailedPO2Parameters', po2group)
vessels = dataman.obtain_data(
'vessel_graph', gvessels,
['flow', 'pressure', 'position', 'flags', 'hematocrit'])
pos = vessels['position']
press = vessels['pressure']
flow = vessels['flow']
flags = vessels['flags']
hema = vessels['hematocrit']
po2vessels = np.asarray(po2group['po2vessels'])
hema = np.column_stack((hema, hema))
conc = detailedo2.PO2ToConcentration(po2vessels, hema, parameters)
#sat = detailedo2.PO2ToSaturation(po2vessels, parameters)
conc_diff = np.abs(conc[:, 1] - conc[:, 0])
conc = np.average(conc, axis=1)
flow_diff = 0.5 * flow * conc_diff
flow = flow * conc
roots = set(gvessels['nodes/roots'][...])
del hema
del conc
del conc_diff
del po2vessels
if gtumor:
ldtumor = dataman.obtain_data('ld', gtumor.file)
dist = dataman.obtain_data('fieldvariable', gtumor.file,
'theta_tumor', gtumor.name)
dist = krebsutils.sample_field(pos,
dist,
ldtumor,
linear_interpolation=True)
dist = dist - 0.5 # is greater 0 inside the tumor?!
total_flow_in, total_flow_out = 0., 0.
flow_in, flow_out = 0., 0.
flow_in_err, flow_out_err, total_flow_in_err, total_flow_out_err = 0., 0., 0., 0.
for i, (a, b) in enumerate(vessels.edgelist):
if not (flags[i] & krebsutils.CIRCULATED): continue
if gtumor and dist[a] < 0 and dist[b] > 0: # b is in the tumor
if press[a] < press[b]:
flow_out += flow[i]
flow_out_err += flow_diff[i]
else:
flow_in += flow[i]
#print 'tumor inflow of sat', sat[i]
flow_in_err += flow_diff[i]
elif gtumor and dist[a] > 0 and dist[b] < 0: # a is in the tumor
if press[a] > press[b]:
flow_out += flow[i]
flow_out_err += flow_diff[i]
else:
flow_in += flow[i]
#print 'tumor inflow of sat', sat[i]
flow_in_err += flow_diff[i]
if (a in roots or b in roots):
if flags[i] & krebsutils.ARTERY:
#print 'total inflow of sat', sat[i]
total_flow_in += flow[i]
total_flow_in_err += flow_diff[i]
elif flags[i] & krebsutils.VEIN:
#print 'total inflow of sat', sat[i]
total_flow_out += flow[i]
total_flow_out_err += flow_diff[i]
Err = lambda a, b, da, db: abs(1.0 / a - (a - b) / a / a) * da + abs(
1.0 / a) * db
res = dict(tumor_o2_in=flow_in,
tumor_o2_out=flow_out,
total_o2_out=total_flow_out,
total_o2_in=total_flow_in,
oef_total=(total_flow_in - total_flow_out) / total_flow_in,
oef_tumor=(flow_in - flow_out) / flow_in,
flow_in_err=flow_in_err,
flow_out_err=flow_out_err,
total_flow_in_err=total_flow_in_err,
total_flow_out_err=total_flow_out_err,
oef_total_err=Err(total_flow_in, total_flow_out,
total_flow_in_err, total_flow_out_err),
oef_err=Err(flow_in, flow_out, flow_in_err, flow_out_err))
#print 'computed oef: '
#pprint.pprint(res)
g = gmeasure.create_group(groupname)
for k, v in res.iteritems():
g.create_dataset(k, data=v)
def obtain_data(self, dataman, dataname, *args):
if dataname == 'detailedPO2_peff_samples':
po2group, sample_length, every, cachelocation = args
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(po2group)
def read(gmeasure, name):
ds = gmeasure[name]
return ds[...] if every is None else ds[::every]
def write(gmeasure, name):
samplelocation = MakeSampleLocation(po2group)
parameters = dataman.obtain_data('detailedPO2Parameters',
po2group)
rad = dataman.obtain_data('basic_vessel_samples', 'radius',
gvessels, sample_length)
hema = dataman.obtain_data('basic_vessel_samples',
'hematocrit', gvessels,
sample_length)
po2 = dataman.obtain_data('detailedPO2_samples', 'po2',
po2group, sample_length, 1,
samplelocation)
mtc = detailedo2.computeMassTransferCoefficient(
rad, parameters)
blood_solubility = parameters.get(
'solubility_plasma', parameters.get('alpha_p', None))
c_o2_total = detailedo2.PO2ToConcentration(
po2, hema, parameters)
c_o2_plasma = detailedo2.PO2ToConcentration(
po2, np.zeros_like(hema), parameters
) # to get the o2 conc. in plasma i just set the amount of RBCs to zero
c_o2_plasma *= (
1.0 - hema
) # and reduce the concentration according to the volume fraction of plasma
beta_factor = c_o2_plasma / c_o2_total
peff = (1.0 / blood_solubility) * mtc * beta_factor
# print 'po2', np.average(po2)
# print 'mtc', np.average(mtc)
# print 'hema', np.average(hema)
# print 'blood_solubility', blood_solubility
# print 'c_o2_total', np.average(c_o2_total)
# print 'c_o2_plasma', np.average(c_o2_plasma)
# print 'peff', np.average(peff)
# print 'beta_factor', np.average(beta_factor)
gmeasure.create_dataset(name, data=peff, compression=9)
version_id = myutils.checksum(sample_length, 1, getuuid_(po2group))
ret = myutils.hdf_data_caching(
read, write, cachelocation[0],
(cachelocation[1], 'samples_and_fluxes', 'Peff'),
(None, None, version_id))
return ret
elif dataname == 'detailedPO2_peff_radial':
po2group, sample_length, bins_spec, distance_distribution_name, cachelocation = args
# we assume that there is a tumor. without this measurement makes little sense
def read(gmeasure, name):
return myutils.MeanValueArray.read(gmeasure[name])
def write(gmeasure, name):
samplelocation = MakeSampleLocation(po2group)
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(
po2group)
smpl = dataman.obtain_data('detailedPO2_peff_samples',
po2group, sample_length, None,
samplelocation)
data, = analyzeGeneral.GenerateRadialDistributions(
dataman, gvessels, gtumor, sample_length, bins_spec,
distance_distribution_name, None,
[(smpl, analyzeGeneral.radialAvgPerVessels)])
data.write(gmeasure, name)
version = myutils.checksum(2, getuuid_(po2group))
ret = analyzeGeneral.HdfCacheRadialDistribution(
(read, write), 'Peff', bins_spec, distance_distribution_name,
cachelocation, version)
return ret
# IDEA: store config stuff like sample length and distance distribution as member of the data handler for less call args
# or store it in a common config instance.
# Then allow to obtain a temporary handle on data which knows its GUID for a quick accurate check if data has changed.
# The handle probably would have to obtain the GUID from disk but this is it.
elif dataname == 'detailedPO2_peffSrho_radial':
po2group, sample_length, bins_spec, distance_distribution_name, cachelocation = args
def read(gmeasure, name):
return myutils.MeanValueArray.read(gmeasure[name])
def write(gmeasure, name):
samplelocation = MakeSampleLocation(po2group)
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(
po2group)
peff = dataman.obtain_data('detailedPO2_peff_samples',
po2group, sample_length, None,
samplelocation)
rad = dataman.obtain_data('basic_vessel_samples', 'radius',
gvessels, sample_length)
peff = peff * math.pi * 2. * rad
data, = analyzeGeneral.GenerateRadialDistributions(
dataman, gvessels, gtumor, sample_length, bins_spec,
distance_distribution_name, None,
[(peff, analyzeGeneral.radialAvgPerVolume)])
data.write(gmeasure, name)
version = myutils.checksum(2, getuuid_(
po2group)) # this should actually depend on the samples
ret = analyzeGeneral.HdfCacheRadialDistribution(
(read, write), 'PeffSrho', bins_spec,
distance_distribution_name, cachelocation, version)
return ret
assert False
def write(gmeasure, name):
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(
po2group)
weight_smpl = dataman.obtain_data('basic_vessel_samples',
'weight', gvessels,
sample_length)
flags = dataman.obtain_data('basic_vessel_samples', 'flags',
gvessels, sample_length)
# get teh radial distance function (either distance from tumor border or distance from center)
dist_smpl, distmap, mask, tumor_ld = dataman.obtain_data(
'distancemap_samples', gvessels, gtumor, sample_length,
distance_distribution_name, None)
# tumor_ld might actually be a unrelated lattice
#filter uncirculated
mask = mask & myutils.bbitwise_and(flags,
krebsutils.CIRCULATED)
dist_smpl = dist_smpl[mask]
weight_smpl = weight_smpl[mask]
bins = bins_spec.arange()
gmeasure = gmeasure.create_group(name)
for name in ['po2', 'extpo2', 'jtv', 'sat', 'gtv', 'dS_dx']:
smpl = dataman.obtain_data('detailedPO2_samples', name,
po2group, sample_length, None,
samplelocation)
myutils.MeanValueArray.fromHistogram1d(
bins, dist_smpl, smpl[mask],
w=weight_smpl).write(gmeasure, name)
del smpl
_, po2ld, po2field, parameters = dataman.obtain_data(
'detailedPO2', po2group)
po2field = krebsutils.resample_field(np.asarray(po2field),
po2ld.worldBox,
tumor_ld.shape,
tumor_ld.worldBox,
order=1,
mode='nearest')
myutils.MeanValueArray.fromHistogram1d(bins, distmap.ravel(),
po2field.ravel()).write(
gmeasure,
'po2_tissue')
del po2field
uptakefield = detailedo2.computeO2Uptake(po2group, gtumor)
uptakefield = krebsutils.resample_field(uptakefield,
po2ld.worldBox,
tumor_ld.shape,
tumor_ld.worldBox,
order=1,
mode='nearest')
myutils.MeanValueArray.fromHistogram1d(
bins, distmap.ravel(),
uptakefield.ravel()).write(gmeasure, 'mro2')
del uptakefield
hema = dataman.obtain_data('basic_vessel_samples',
'hematocrit', gvessels,
sample_length)[mask]
sat = dataman.obtain_data('detailedPO2_samples', 'sat',
po2group, sample_length, None,
samplelocation)[mask]
rad = dataman.obtain_data('basic_vessel_samples', 'radius',
gvessels, sample_length)[mask]
hbvolume = weight_smpl * rad * rad * math.pi * hema
vol_per_bin = myutils.MeanValueArray.fromHistogram1d(
bins, distmap.ravel(), np.ones_like(
distmap.ravel())).cnt * (tumor_ld.scale**3)
tmp = myutils.MeanValueArray.fromHistogram1d(
bins, dist_smpl, hbvolume * sat)
tmp.cnt = vol_per_bin.copy()
tmp.write(gmeasure, 'vfhb_oxy')
tmp = myutils.MeanValueArray.fromHistogram1d(
bins, dist_smpl, hbvolume * (1. - sat))
tmp.cnt = vol_per_bin.copy()
tmp.write(gmeasure, 'vfhb_deoxy')
del tmp, hbvolume, vol_per_bin
def write(gmeasure, measurename):
assert prop == measurename
gvessels, gtumor = detailedo2.OpenVesselAndTumorGroups(
po2group)
if prop in ['po2', 'sat', 'gtv', 'jtv']:
w = dataman.obtain_data('basic_vessel_samples', 'weight',
gvessels, sample_length)
d = dataman.obtain_data('detailedPO2_samples', prop,
po2group, sample_length, 1,
samplelocation)
gmeasure.create_dataset(prop,
data=myutils.WeightedAverageStd(
d, weights=w))
elif prop in ['sat_vein', 'sat_capi', 'sat_art']:
w = dataman.obtain_data('basic_vessel_samples', 'weight',
gvessels, sample_length)
d = dataman.obtain_data('detailedPO2_samples', 'sat',
po2group, sample_length, 1,
samplelocation)
f = dataman.obtain_data('basic_vessel_samples', 'flags',
gvessels, sample_length)
mask = ~myutils.bbitwise_and(
f, krebsutils.WITHIN_TUMOR) & myutils.bbitwise_and(
f, krebsutils.CIRCULATED)
m = {
'sat_vein': krebsutils.VEIN,
'sat_capi': krebsutils.CAPILLARY,
'sat_art': krebsutils.ARTERY
}
mask &= myutils.bbitwise_and(f, m[prop])
d, w = d[mask], w[mask]
gmeasure.create_dataset(prop,
data=myutils.WeightedAverageStd(
d, weights=w))
elif prop in [
'e1', 'e2', 'e3', 'Jin_root', 'Jout_root', 'Jout_tv',
'tv_cons', 'Jout_cons'
]:
d = dataman.obtain_data('detailedPO2_total_fluxes', prop,
po2group, sample_length, 1,
samplelocation)
gmeasure.create_dataset(prop, data=[d[prop], 0])
elif prop == 'po2_tissue':
_, po2ld, po2field, parameters = dataman.obtain_data(
'detailedPO2', po2group)
d = myutils.largeDatasetAverageAndStd(po2field)
gmeasure.create_dataset(prop, data=d)
elif prop == 'mro2':
uptakefield = detailedo2.computeO2Uptake(po2group, gtumor)
d = myutils.largeDatasetAverageAndStd(uptakefield)
gmeasure.create_dataset(prop, data=d)
elif prop in ('sat_via_hb_ratio', 'vfhb_oxy', 'vfhb_deoxy',
'vfhb'):
weight = dataman.obtain_data('basic_vessel_samples',
'weight', gvessels,
sample_length)
flags = dataman.obtain_data('basic_vessel_samples',
'flags', gvessels,
sample_length)
mask = myutils.bbitwise_and(flags, krebsutils.CIRCULATED)
hema = dataman.obtain_data('basic_vessel_samples',
'hematocrit', gvessels,
sample_length)[mask]
sat = dataman.obtain_data('detailedPO2_samples', 'sat',
po2group, sample_length, None,
samplelocation)[mask]
rad = dataman.obtain_data('basic_vessel_samples', 'radius',
gvessels, sample_length)[mask]
weight = weight[mask]
hbvolume = weight * rad * rad * math.pi * hema
ld = krebsutils.read_lattice_data_from_hdf(
po2group['field_ld'])
volume = np.product(ld.GetWorldSize())
if prop == 'sat_via_hb_ratio':
result = np.sum(hbvolume * sat) / np.sum(hbvolume)
elif prop == 'vfhb_oxy':
result = np.sum(hbvolume * sat) / volume
elif prop == 'vfhb_deoxy':
result = np.sum(hbvolume * (1. - sat)) / volume
elif prop == 'vfhb':
result = np.sum(hbvolume) / volume
gmeasure.create_dataset(prop, data=[result, 0.])
elif prop in ('chb_oxy', 'chb_deoxy', 'chb'):
m = {
'chb_oxy': 'vfhb_oxy',
'chb_deoxy': 'vfhb_deoxy',
'chb': 'vfhb'
}
result = dataman.obtain_data('detailedPO2_global', m[prop],
po2group, sample_length,
cachelocation)
result = result * detailedo2.chb_of_rbcs
gmeasure.create_dataset(prop, data=[result, 0.])
elif prop == 'mro2_by_j':
fluxes = dataman.obtain_data('detailedPO2_total_fluxes',
prop, po2group, sample_length,
1)
ld = krebsutils.read_lattice_data_from_hdf(
po2group['field_ld'])
worldbb = ld.worldBox
result = fluxes['Jout_tv'] / np.prod(worldbb[1] -
worldbb[0]) * 1.e12
gmeasure.create_dataset(prop, data=[result, 0.])
elif prop == 'oef':
fluxes = dataman.obtain_data('detailedPO2_total_fluxes',
prop, po2group, sample_length,
1, samplelocation)
result = (fluxes['Jin_root'] -
fluxes['Jout_root']) / fluxes['Jin_root']
gmeasure.create_dataset(prop, data=[result, 0.])
else:
assert False