def genotype_extractor():
destination = address + 'chromloc.txt'
ext_positions = np.genfromtxt(destination)
ext_chromosomes = [{'z': z, 'I': 1, 'r': 0.25} for z in ext_positions]
ext_genotype = gen.chrom2geno(ext_chromosomes)
loop_number = len(ext_genotype)
return ext_genotype
def bestRealisticize(self):
self.order(
) # Maybe unnecessary but I'm too lazy to check if it's redundant
chromosomes = self.individuals[0].chromosomes
mill_precision = myconst.mill_precision
wire_width = myconst.wire_width
wall_width = myconst.wall_width
max_stack = myconst.max_stack
r_min = myconst.r_min
self.realistic_chromosomes = gen.chromRealisticize(
chromosomes, mill_precision, wire_width, wall_width, max_stack,
r_min)
self.realistic_genotype = gen.chrom2geno(self.realistic_chromosomes)
self.realistic_fitness = mag.fitness_function(self.realistic_genotype,
None)
def genotype_update(self):
"""
Takes chromosomes and converts to genotype.
"""
#self.chromosomes = gen.chromRealisticize(self.chromosomes, Coil.wire_width, self.mill_precision)
self.genotype = gen.chrom2geno(self.chromosomes)
class Coil:
"""
Coil object. Contains coil's genotype and fitness.
Constructed so that the chromosomes define the behaviour of all update
functions.
##FIXME: All perfect coils should have loops at std_radius. Otherwise stack at r_min.
"""
### Instance Attributes:
## Evolutionary traits:
genotype = [] # All values
chromosomes = [] # Just positive values
field = []
ppm = []
fitness = None
### Class Attributes:
## Mutation Scheme
MutationScheme = myconst.MutationScheme
## Range of coil:
z_min = myconst.z_min
z_max = myconst.z_max
## Range of current:
I_min = myconst.I_min
I_max = myconst.I_max
## Range of radii:
std_radius = myconst.r_0
r_min = myconst.r_min
r_max = myconst.r_max
## Realism Parameters:
div_width = myconst.div_width
gap_precision = myconst.gap_precision
mill_precision = myconst.mill_precision # The
wire_width = myconst.wire_width
wall_width = myconst.wall_width
## Range of Fitness Calculation:
calc_z_min = myconst.calc_z_min
calc_z_max = myconst.calc_z_max
calc_points = myconst.calc_points
zlist = np.linspace(calc_z_min, calc_z_max,
calc_points) # Calculation points
field_points = zlist
walk_limit = myconst.walk_limit
div_width = myconst.div_width
## Initial values
loop_number = myconst.loop_number
radius = myconst.r_0
epsilon = myconst.epsilon
I_epsilon = myconst.I_epsilon
r_epsilon = myconst.r_epsilon
# wire_width = myconst.wire_width
gap_precision = myconst.gap_precision
chromosomes = gen.random_ChromGen(loop_number, z_min, z_max, I_min, I_max,
r_min, r_max)
genotype = gen.chrom2geno(chromosomes)
# gen.lw_ChromGen(genotype, radius)
# gen.sol_ChromGen(genotype, loop_z_max, radius)
# gen.lwb_ChromGen(genoptype, radius)
# gen.hh_ChromGen(genotype, radius)
# gen.gap_ChromGen(genotype, precision, radius)
## Standards:
# Building Solenoid:
sol_chromosomes = np.array(gen.sol_ChromGen(genotype, z_max, std_radius))
sol_genotype = np.array(gen.chrom2geno(sol_chromosomes))
sol_homogeneity = mag.fitness_function(sol_genotype, field_points)
# Building Lee-Whiting:
lw_chromosomes = np.array(gen.lw_ChromGen(genotype, std_radius))
lw_genotype = np.array(gen.chrom2geno(lw_chromosomes))
lw_homogeneity = mag.fitness_function(lw_genotype, field_points)
# Building 9/4 Lee-Whiting:
lwb_chromosomes = np.array(gen.lwb_ChromGen(genotype, std_radius))
lwb_genotype = np.array(gen.chrom2geno(lwb_chromosomes))
lwb_homogeneity = mag.fitness_function(lwb_genotype, field_points)
# Building Helmholtz:
hh_chromosomes = np.array(gen.hh_ChromGen(genotype, std_radius))
hh_genotype = np.array(gen.chrom2geno(hh_chromosomes))
hh_homogeneity = mag.fitness_function(hh_genotype, field_points)
# Building Gapped Solenoid:
gap_chromosomes = np.array(
gen.gap_ChromGen(genotype, std_radius, z_max, mill_precision))
gap_genotype = np.array(gen.chrom2geno(gap_chromosomes))
gap_homogeneity = mag.fitness_function(gap_genotype, field_points)
def __init__(self):
"""Coil initialization. Creates random genotype and sets fitness to 0."""
self.chromosomes_init()
self.genotype_update()
self.fitness_update()
self.field_update()
def manual_chromosomes_update(self, chromosomes):
"""Manually sets the chromosomes for an individual."""
self.chromosomes = chromosomes
self.genotype_update()
self.fitness_update()
self.field_update()
def chromosomes_init(self):
"""
Genotype initialization. Randomly chooses loop positions along z-axis.
Positions act as individual chromosomes.
## NOTE: Currently note actually generating loops at different radii. The range is [r_min, r_min]
"""
self.chromosomes = gen.random_ChromGen(Coil.loop_number, Coil.z_min,
Coil.z_max, Coil.I_min,
Coil.I_max, Coil.r_min,
Coil.r_max)
def genotype_update(self):
"""
Takes chromosomes and converts to genotype.
"""
#self.chromosomes = gen.chromRealisticize(self.chromosomes, Coil.wire_width, self.mill_precision)
self.genotype = gen.chrom2geno(self.chromosomes)
def fitness_update(self):
"""Updates fitness of self"""
self.fitness = mag.fitness_function(self.genotype, Coil.zlist)
def field_update(self):
"""Updates the fields along the axis."""
args = [self.genotype, Coil.zlist]
self.field = mag.field_along_axis(*args)
self.ppm = mag.ppm_field(*args)
def mutate(self):
"""
Mutates chromosomes randomly with probability m.
Note: Currently mutates ALL chromosomes, maybe change later.
FIXME: Mutation probability must be handled externally.
"""
mutated_positions, mutated_currents, mutated_radii = gen.chrom_mutate(
self.chromosomes, Coil.epsilon, Coil.I_epsilon, Coil.r_epsilon)
args = [
mutated_positions, mutated_currents, mutated_radii, Coil.z_min,
Coil.z_max, Coil.I_min, Coil.I_max, Coil.r_min, Coil.r_max
]
if (Coil.MutationScheme == 'PILEUP'):
mutated_chromosomes = gen.pileupCorrect(*args)
elif (Coil.MutationScheme == 'REFLECTION'):
mutated_chromosomes = gen.reflectCorrect(*args)
elif (Coil.MutationScheme == 'REDRAW'):
mutated_chromosomes = gen.redrawCorrect(*args)
elif (Coil.MutationScheme == 'SPREADOUT'):
pass
else:
print('INVALID MUTATION SCHEME')
exit()
# Assigning changes to instance:
self.chromosomes = gen.coil_order(mutated_chromosomes)
self.genotype_update()
import Modules.genetix as gen
import Modules.magnetix as mag
import Modules.myconstants as myconst
import matplotlib.pyplot as plt
import numpy as np
show_points_number = 1000 # Number of points on +ve z axis (double this to get total)
show_points = np.linspace(0, 1.0, show_points_number)
loop_number = 378
radius = myconst.radius
# init_genotype= Population.initial_best.genotype
lw_genotype = gen.chrom2geno(gen.lw_perfectChromGen(loop_number,
radius=radius))
# init_error= mag.ppm_field(init_genotype, show_points, a=radius)
lw_error = mag.ppm_field(lw_genotype, show_points, a=radius)
lw_y = lw_error[:, 1]
x = lw_error[:, 0]
plt.plot(x, lw_y, label='Lee-Whiting')
plt.title('PPM Error Field of L-W Coils')
plt.xlabel('z [m]')
plt.ylabel('PPM Error')
plt.legend()
plt.grid()
def field_plot(address, genotype):
loop_number = len(genotype)
# loop_z_max = genotype[-1]['z']
# r_min = sorted(genotype, key=lambda k: k['r'])[0]['r']
r_0 = myconst.r_0
r_min = myconst.r_min
r_max = myconst.r_max
mill_precision = myconst.mill_precision
loop_z_max = myconst.z_max
ext_genotype = genotype
# init_genotype= Population.initial_best.genotype
# lw_genotype = gen.chrom2geno(gen.lw_ChromGen(loop_number,radius=r_min))
# lwb_genotype = gen.chrom2geno(gen.lwb_ChromGen(loop_number,radius=r_min))
# hh_genotype = gen.chrom2geno(gen.hh_ChromGen(loop_number,radius=r_min))
# sol_genotype = gen.chrom2geno(gen.sol_ChromGen(loop_number,loop_z_max=loop_z_max, radius=r_min))
# gap_genotype = gen.chrom2geno(gen.gap_ChromGen(r_min, loop_z_max, loop_number, gap_precision))
lw_genotype = gen.chrom2geno(gen.lw_ChromGen(genotype, r_0))
lwb_genotype = gen.chrom2geno(gen.lwb_ChromGen(genotype, r_0))
hh_genotype = gen.chrom2geno(gen.hh_ChromGen(genotype, r_0))
sol_genotype = gen.chrom2geno(
gen.sol_ChromGen(genotype, loop_z_max=loop_z_max, std_radius=r_0))
gap_genotype = gen.chrom2geno(
gen.gap_ChromGen(genotype,
r_0,
length=loop_z_max,
precision=mill_precision))
# init_field = mag.field_along_axis(init_genotype,show_points, a=radius)
ext_field = mag.field_along_axis(ext_genotype, show_points)
lw_field = mag.field_along_axis(lw_genotype, show_points)
lwb_field = mag.field_along_axis(lwb_genotype, show_points)
hh_field = mag.field_along_axis(hh_genotype, show_points)
sol_field = mag.field_along_axis(sol_genotype, show_points)
gap_field = mag.field_along_axis(gap_genotype, show_points)
ext_y = ext_field[:, 1]
lw_y = lw_field[:, 1]
lwb_y = lw_field[:, 1]
hh_y = hh_field[:, 1]
sol_y = sol_field[:, 1]
gap_y = gap_field[:, 1]
# init_y = init_field[:,1]
x = lw_field[:, 0]
plt.plot(x, lw_y, label='Lee-Whiting')
plt.plot(x, lwb_y, label='9/4 Lee-Whiting')
plt.plot(x, hh_y, label='Helmholtz')
plt.plot(x, ext_y, label='External')
plt.plot(x, sol_y, label='Solenoid')
plt.plot(x, gap_y, label='Gapped Solenoid')
# plt.plot(x, init_y, label = 'Initial')
plt.title('Magnetic Field Strengths of Competing Coils')
plt.xlabel('z [m]')
plt.ylabel('|B| [$\\mu$T]')
plt.legend()
plt.grid()
plt.savefig(address + '/Fields.png', dpi=400)
plt.show()
plt.clf()
plt.close()
return
def err_zoom_plot(address, genotype):
r_0 = myconst.r_0
mill_precision = myconst.mill_precision
loop_z_max = myconst.z_max
loop_number = len(genotype)
# loop_z_max = genotype[-1]['z']
r_min = sorted(genotype, key=lambda k: k['r'])[0]['r']
ext_genotype = genotype
# init_genotype= Population.initial_best.genotype
# lw_genotype = gen.chrom2geno(gen.lw_ChromGen(loop_number,radius=r_min))
# lwb_genotype = gen.chrom2geno(gen.lwb_ChromGen(loop_number, r_min))
# hh_genotype = gen.chrom2geno(gen.hh_ChromGen(loop_number,radius=r_min))
# sol_genotype = gen.chrom2geno(gen.sol_ChromGen(loop_number,loop_z_max=loop_z_max, radius=r_min))
# gap_genotype = gen.chrom2geno(gen.gap_ChromGen(r_min, loop_z_max, loop_number, gap_precision))
lw_genotype = gen.chrom2geno(gen.lw_ChromGen(genotype, r_0))
lwb_genotype = gen.chrom2geno(gen.lwb_ChromGen(genotype, r_0))
hh_genotype = gen.chrom2geno(gen.hh_ChromGen(genotype, r_0))
sol_genotype = gen.chrom2geno(
gen.sol_ChromGen(genotype, loop_z_max=loop_z_max, std_radius=r_0))
gap_genotype = gen.chrom2geno(
gen.gap_ChromGen(genotype,
r_0,
length=loop_z_max,
precision=mill_precision))
# init_error= mag.ppm_field(init_genotype, show_points, a=radius)
lw_error = mag.ppm_field(lw_genotype, show_points)
lwb_error = mag.ppm_field(lwb_genotype, show_points)
hh_error = mag.ppm_field(hh_genotype, show_points)
ext_error = mag.ppm_field(ext_genotype, show_points)
sol_error = mag.ppm_field(sol_genotype, show_points)
gap_error = mag.ppm_field(gap_genotype, show_points)
# init_y= init_error[:,1]
lw_y = lw_error[:, 1]
lwb_y = lwb_error[:, 1]
hh_y = hh_error[:, 1]
ext_y = ext_error[:, 1]
sol_y = sol_error[:, 1]
gap_y = gap_error[:, 1]
y_max = max(ext_y)
x_max = 0.6
x = lw_error[:, 0]
plt.plot(x, lw_y, label='Lee-Whiting')
plt.plot(x, lwb_y, label='9/4 Lee-Whiting')
plt.plot(x, hh_y, label='Helmholtz')
plt.plot(x, ext_y, label='External')
plt.plot(x, sol_y, label='Solenoid')
plt.plot(x, gap_y, label='Gapped Solenoid')
# plt.plot(x, init_y, label = 'Initial')
plt.ylim(-y_max, y_max)
plt.xlim(-x_max, x_max)
plt.title('PPM Error Fields of Competing Coils (zoomed)')
plt.xlabel('z [m]')
plt.ylabel('PPM Error')
plt.legend()
plt.grid()
plt.savefig(address + '/PPM_zoom.png', dpi=600)
plt.show()
plt.clf()
plt.close()
return