def finish_up_diffusion(n=1):
import utils; utils.DEFAULT_H5_FILE = "diffusion.h5"
import specs, models
for i, spec in enumerate(specs.Spec.all()):
num_results = len(list(models.Result.table.raw.where("spec_uuid=='{0}'".format(spec.uuid))))
print i, num_results
if num_results < n:
models.compute_probabilistic(spec).save()
def make_diffusion_data():
import utils; utils.DEFAULT_H5_FILE = "new_diffusion.h5"
import specs, models, analysis
builder = specs.SpecBuilder()
builder.add("boundary_layer", 10)
builder.add("stop_on_no_growth", 300)
builder.add("stop_on_time", 20000)
builder.add("stop_on_mass", 2000)
builder.add("light_penetration", 0, 8, 16)
builder.add("diffusion_constant", *np.linspace(0.01, 1.0, 20))
builder.add("uptake_rate", *np.linspace(0.01, 1.0, 20))
builder.add("height", 40)
builder.add("initial_cell_spacing", 2, 16)
print builder.num_specs
builder.build()
for i, spec in enumerate(specs.Spec.all()):
print i
for j in range(1):
print j,
result = models.compute_probabilistic(spec)
result.save()
print "Done!"
def make_coverage_data2():
import utils; utils.DEFAULT_H5_FILE = "new2_coverages.h5"
import specs, models, analysis
builder = specs.SpecBuilder()
builder.add("boundary_layer", 10)
builder.add("stop_on_no_growth", 300)
builder.add("stop_on_time", 20000)
builder.add("stop_on_mass", 1000, 2000)
builder.add("light_penetration", 0, 8, 16)
builder.add("diffusion_constant", 0.4)
builder.add("uptake_rate", 0.7)
builder.add("height", 40)
builder.add("initial_cell_spacing", 2, 4, 6, 8, 10, 16, 24, 32, 64)
print builder.num_specs
builder.build()
for i, spec in enumerate(specs.Spec.all()):
print i
for j in range(10):
print j,
result = models.compute_probabilistic(spec)
result.save()
analysis.coverages.compute_by_spec(spec)
print "Done!"
def make_diffusion_line():
import utils; utils.DEFAULT_H5_FILE = "diffusion_line.h5"
import specs, models, analysis
builder = specs.SpecBuilder()
builder.add("boundary_layer", 10)
builder.add("stop_on_no_growth", 300)
builder.add("stop_on_time", 20000)
builder.add("stop_on_mass", 2000)
builder.add("light_penetration", 0)
builder.add("diffusion_constant", *np.linspace(0.001, 0.25, 30))
builder.add("uptake_rate", 0.5)
builder.add("height", 40)
builder.add("initial_cell_spacing", 16)
print builder.num_specs
builder.build()
for i, spec in enumerate(specs.Spec.all()):
print i
models.compute_probabilistic(spec).save()
analysis.heights.compute_by_spec(spec)
print "Done!"
def make_biomass_vs_light_data():
import utils; utils.DEFAULT_H5_FILE = "new_growth_data.h5"
import specs, models, analysis
builder = specs.SpecBuilder()
builder.add("boundary_layer", 10)
builder.add("stop_on_no_growth", 1000)
builder.add("stop_on_time", 300000)
builder.add("light_penetration", 0, 8)
builder.add("diffusion_constant", 0.4)
builder.add("uptake_rate", 0.7)
builder.add("stop_on_mass", *np.linspace(500, 3500, 200))
builder.build()
for i, spec in enumerate(specs.Spec.all()):
print i
result = models.compute_probabilistic(spec)
result.save()
analysis.light_exposure.compute_by_spec(spec)
analysis.mass.compute_by_spec(spec)
print "Done!"