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gridgen.py
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gridgen.py
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# -*- coding: utf-8 -*-
"""
Created on Tue May 24 00:59:12 2016
@author: chgi7364
"""
import numpy as np
import os
import coronasim as sim
import matplotlib.pyplot as plt
from mpl_toolkits.mplot3d import Axes3D
from scipy import io
from scipy import interpolate as interp
import sys
zero = 1e-8
#Defines the Grid on which to simulate
class generator:
rstar = 1
params = None
backflag1 = True
backflag2 = True
def __iter__(self):
return self
def back(self):
self.currS -= self.step
def incStep(self, mult):
if self.step < self.maxStep:
self.step = min(self.step * mult, self.maxStep)
def set2minStep(self):
self.step = self.minStep
def set2midStep(self):
self.step = self.midStep
def set2maxStep(self):
self.step = self.maxStep
def setMinStep(self, step):
self.minStep = step
def setMaxStep(self, step):
self.maxStep = step
def setStep(self, step):
self.step = step
def setEnvInd(self, index):
self.envInd = index
def decStep(self, mult):
if self.step > self.minStep:
self.step = max(self.step / mult, self.minStep)
def sph2cart(self, sph):
#Change coordinate systems
rho, theta, phi = sph[:]
x = np.array(rho)*np.sin(np.array(theta))*np.cos(np.array(phi))
y = np.array(rho)*np.sin(np.array(theta))*np.sin(np.array(phi))
z = np.array(rho)*np.cos(np.array(theta))
return [x, y, z]
def cart2sph(self, cart):
#Change coordinate systems
x,y,z = cart[:]
if x == 0: x = 1e-8
if y == 0: y = 1e-8
rho = np.sqrt(x**2 + y**2 + z**2)
theta = np.arccos(z/rho)
phi = np.arctan2(y, x)
return [rho, theta, phi]
def plotSphere(self, ax, scale = True):
#Plot a sphere
u = np.linspace(0, 2 * np.pi, 100)
v = np.linspace(0, np.pi, 100)
diameter = generator.rstar
x = diameter * np.outer(np.cos(u), np.sin(v))
y = diameter * np.outer(np.sin(u), np.sin(v))
z = diameter * np.outer(np.ones(np.size(u)), np.cos(v))
ax.plot_surface(x, y, z, rstride=4, cstride=4, color='y', alpha = 0.75)
ax.set_xlabel("X axis")
ax.set_ylabel("Y axis")
ax.set_zlabel("Z axis")
if scale:
axscale = 1.5*diameter
ax.auto_scale_xyz([-axscale, axscale],
[-axscale, axscale], [-axscale, axscale])
def quadAx(self, quad = True):
fig = plt.figure("CoronaSim")
dataAxis = plt.subplot2grid((2,4), (0,2), colspan=2, rowspan = 2)
aspect = 'auto'
if quad:
ax1 = plt.subplot2grid((2,4), (0,0), projection = '3d', aspect=aspect)
ax1.view_init(elev=0., azim=0.)
ax2 = plt.subplot2grid((2,4), (0,1), projection = '3d', aspect=aspect)
ax2.view_init(elev=90, azim=0.)
ax3 = plt.subplot2grid((2,4), (1,0), projection = '3d', aspect=aspect)
ax3.view_init(elev=0, azim=90)
ax4 = plt.subplot2grid((2,4), (1,1), projection = '3d', aspect=aspect)
quadAxis = [ax1, ax2, ax3, ax4]
else:
ax1 = plt.subplot2grid((2,4), (0,0), colspan=2, rowspan = 2, projection = '3d', aspect = 'equal')
quadAxis = [ax1]
return fig, dataAxis, quadAxis
def quadAxOnly(self):
fig = plt.figure("CoronaSim")
aspect = 'equal'
ax1 = plt.subplot2grid((2,2), (0,0), projection = '3d', aspect=aspect)
ax1.view_init(elev=0., azim=0.)
ax2 = plt.subplot2grid((2,2), (0,1), projection = '3d', aspect=aspect)
ax2.view_init(elev=90, azim=0.)
ax3 = plt.subplot2grid((2,2), (1,0), projection = '3d', aspect=aspect)
ax3.view_init(elev=0, azim=90)
ax4 = plt.subplot2grid((2,2), (1,1), projection = '3d', aspect=aspect)
quadAxis = [ax1, ax2, ax3, ax4]
dataAxis = []
return fig, dataAxis, quadAxis
def plot(self, iL = 1, show = False, axes = None):
#Plot the quadGrid with a sphere for the sun
if axes is None: fig, dataAxis, quadAxis = self.quadAx()
else: fig, dataAxis, quadAxis = axes
n = 0
if type(self) is sightline:
thisGrid = self.cGrid(N = 25, iL = iL)
fig.suptitle('Sightline at Position = ({:0.2f}, {:0.2f}, {:0.2f}), \
Target = ({:0.2f}, {:0.2f}, {:0.2f})'.format(*(self.cPos + self.cTarg)))
elif type(self) is plane:
thisGrid = self.cGrid(N = 10, iL = iL)
fig.suptitle('Plane with Normal = ({:0.2f}, {:0.2f}, {:0.2f}),\
Offset = ({:0.2f}, {:0.2f}, {:0.2f})'.format(*(self.normal.tolist() + self.offset)))
nax = 1
for ax in quadAxis:
for pos in thisGrid:
if n < 2: colr = 'red'
else: colr = 'blue'
ax.scatter(*pos, color = colr)
n += 1
ax.set_xlim([-1.5*iL, 1.5*iL])
ax.set_ylim([-1.5*iL, 1.5*iL])
ax.set_zlim([-1.5*iL, 1.5*iL])
#self.ax.set_title()
self.plotSphere(ax)
if nax < 4:
for tl in ax.get_xticklabels() + ax.get_yticklabels() + ax.get_zticklabels():
tl.set_visible(False)
n = 0
nax += 1
if show:
maximizePlot()
plt.show()
return fig, dataAxis
def show(self):
#Print all porperties and values
myVars = vars(self)
print("\nGenerator Properties")
for ii in sorted(myVars.keys()):
print(ii, " : ", myVars[ii])
def loadParams(self, params=None):
if params is None:
params = sim.runParameters()
self.params = params
self.setN()
def loadParams_env(self, env):
self.params = env.params
self.setN()
def setN(self, N=None):
if N is None:
self.N = self.params._N_line
else:
self.N = N
#A line of points between two given points
class sightline(generator):
default_N = 1000
exact = None
def __init__(self, position, target, coords='Cart', N='auto', envInd=0, params=None, env=None):
self.coords = coords
self.N = N
self.look(position, target, coords)
self.envInd = envInd
self.returnC()
if params is not None:
self.loadParams(params)
elif env is not None:
self.loadParams_env(env)
def look(self, position, target, coords='Cart'):
"""Initialize the sight line between two points"""
if coords.lower() == 'cart':
self.cPos = position
self.cTarg = target
self.pPos = self.cart2sph(position)
self.pTarg = self.cart2sph(target)
else:
self.cPos = self.sph2cart(position)
self.cTarg = self.sph2cart(target)
self.pPos = position
self.pTarg = target
#Find the direction the line is pointing
self.gradient = list(np.array(self.cTarg) - np.array(self.cPos))
self.gradArr = np.asarray(self.gradient).astype(float)
self.norm = np.linalg.norm(self.gradArr)
self.ngrad = self.gradArr / self.norm
self.normCm = self.norm * 695.5 * 1e8 # in cm
def returnC(self):
self.give = self.cPoint
def returnP(self):
self.give = self.pPoint
def cPoint(self, s):
"""Return the coordinates of a point along the line"""
return (np.array(self.cPos) + self.gradArr*s).tolist()
def pPoint(self, s):
"""Return the polar coordinates of a point along the line"""
return self.cart2sph(self.cPoint(s))
def set_exact(self, points):
outPoints = np.asarray(points).T
nPts = len(points)
sArray = np.ones(nPts)*1/nPts
self.exact = [outPoints, sArray]
def get_points(self, N=None, adapt=False):
"""Return the points and steps"""
if not self.exact is None:
return self.exact
N, adapt = self.params.resolution(N, adapt)
if not adapt:
# Get a straight line
if type(N) in (int, float):
self.setN(N)
else:
self.setN(1000)
return self.get_linspace()
# Find the boundaries
self.rhoCut = 15
self.rCut = 2
self.r1 = 5
self.R21 = 5
self.R32 = 5
self.setN(N)
# Create the points and output
return self.sArray_points(self.get_sArray())
def get_sArray(self):
sBounds = self.find_sBounds()
nRegions = int(len(sBounds)/2)
# Create the sArray
if nRegions == 1:
return self.oneRegion(sBounds)
elif nRegions == 2:
return self.twoRegion(sBounds)
elif nRegions == 3:
return self.threeRegion(sBounds)
def find_sBounds(self):
points, steps = self.get_linspace(10000)
x, y, z = points
rho = np.sqrt(x ** 2 + y ** 2)
r = np.sqrt(x ** 2 + y ** 2 + z**2)
check = np.zeros_like(r)
check[r <= self.rCut] += 1
check[rho <= self.rhoCut] += 1
df = np.nonzero(np.diff(check))
cumSum = np.cumsum(steps)
sBounds = cumSum[df]
sBounds = np.insert(sBounds, 0, 0)
sBounds = np.append(sBounds, 1)
# import pdb;pdb.set_trace()
return sBounds
def get_linspace(self, N=None, smin=0, smax=1):
#Return the coordinates of the sightline
if N is None:
N = self.N
self.shape = N
sArray = np.linspace(smin, smax, N)
return self.sArray_points(sArray)
def sArray_points(self, sArray):
points = np.asarray([self.give(ss) for ss in sArray]).T
stepArray = np.diff(sArray)
stepArray = np.append(stepArray, stepArray[-1])
return points, stepArray
def threeRegion(self, sBounds):
R21 = self.R21
R32 = self.R32
L1 = np.abs(sBounds[0] - sBounds[1]) * self.norm
L2 = np.abs(sBounds[1] - sBounds[2]) * self.norm
L3 = np.abs(sBounds[2] - sBounds[3]) * self.norm
L4 = np.abs(sBounds[3] - sBounds[4]) * self.norm
L5 = np.abs(sBounds[4] - sBounds[5]) * self.norm
if self.N == 'auto':
r1 = self.r1
else:
r1 = self.N / (L1 + R21*L2 + R32*R21*L3 + R21*L4 + L5)
N1 = int(np.round(r1 * L1))
N2 = int(np.round(r1 * R21 * L2))
N3 = int(np.round(r1 * R21 * R32 * L3))
N4 = int(np.round(r1 * R21 * L4))
N5 = int(np.round(r1 * L5)) + 1
R1 = N1/L1
R2 = N2/L2
R3 = N3/L3
R4 = N4/L4
R5 = N5/L5
sArray1 = np.linspace(sBounds[0], sBounds[1], N1, endpoint=False)
sArray2 = np.linspace(sBounds[1], sBounds[2], N2, endpoint=False)
sArray3 = np.linspace(sBounds[2], sBounds[3], N3, endpoint=False)
sArray4 = np.linspace(sBounds[3], sBounds[4], N4, endpoint=False)
sArray5 = np.linspace(sBounds[4], sBounds[5], N5, endpoint=True)
return np.concatenate((sArray1, sArray2, sArray3, sArray4, sArray5))
def twoRegion(self, sBounds):
R21 = self.R21
L1 = np.abs(sBounds[0] - sBounds[1]) * self.norm
L2 = np.abs(sBounds[1] - sBounds[2]) * self.norm
L3 = np.abs(sBounds[2] - sBounds[3]) * self.norm
if self.N == 'auto':
r1 = self.r1
else:
r1 = self.N / (L1 + R21 * L2 + L3)
N1 = int(np.round(r1 * L1))
N2 = int(np.round(r1 * R21 * L2))
N3 = int(np.round(r1 * L3)) + 1
R1 = N1 / L1
R2 = N2 / L2
R3 = N3 / L3
sArray1 = np.linspace(sBounds[0], sBounds[1], int(N1), endpoint=False)
sArray2 = np.linspace(sBounds[1], sBounds[2], int(N2), endpoint=False)
sArray3 = np.linspace(sBounds[2], sBounds[3], int(N3), endpoint=True)
return np.concatenate((sArray1, sArray2, sArray3))
def oneRegion(self, sBounds):
if self.N == 'auto':
L1 = np.abs(sBounds[0] - sBounds[1]) * self.norm
r1 = self.r1
self.N = int(np.round(r1 * L1))
return np.linspace(sBounds[0], sBounds[1], self.N, endpoint=True)
#A plane normal to a given vector
class plane(generator):
#TODO Make plane adaptive
default_N = 20
norm = 1 #THIS IS WRONG
def __init__(self, normal = [1,0,0], offset = [0,3,-3], iL = 6, rotAxis = [-1,1,1], ncoords = 'Cart', findT = False, absolute = False, envInd = 0, params=None):
#print("Initializing Plane, normal = {}, offset = {}".format(normal, offset))
self.absolute = absolute
self.findT = findT
self.iL = iL
self.envInd = envInd
self.rotArray = np.asarray(rotAxis)
if ncoords.lower() == 'cart':
self.normal = np.asarray(normal).astype(float)
self.offset = offset
else:
self.normal = np.asarray(self.sph2cart(normal)).astype(float)
if len(offset) == 3:
self.offset = offset
elif len(offset) == 2:
self.offset = [normal[0], offset[0], offset[1]]
self.findGrads()
self.loadParams(params)
def __next__(self):
if not self.defGrid:
raise StopIteration
return (self.defGrid.pop(0), 1/self.N)
def setN(self, N=None):
self.defGrid = self.cGrid(N = N, iL = self.iL)
def findCoords(self):
hind = -1
vind = -1
vdiff, hdiff = 0,0
for ii in np.arange(3):
vert = [self.baseA[ii], self.baseB[ii]]
newvdiff = np.abs(vert[1]-vert[0])
if newvdiff > vdiff:
vdiff = newvdiff
vind = ii
horiz = [self.crossA[ii], self.crossB[ii]]
newhdiff = np.abs(horiz[1]-horiz[0])
if newhdiff > hdiff:
hdiff = newhdiff
hind = ii
horiz = [self.crossA[hind], self.crossB[hind]]
vert = [self.baseB[vind], self.baseA[vind]]
return horiz + vert, hind, vind #[hmin, hmax, vmin, vmax], hlabel, vlabel
def findGrads(self):
#Determine the eigenvectors of the plane
grad1 = np.cross(self.normal, self.rotArray)
grad2 = np.cross(self.normal, grad1)
self.ngrad1 = grad1 / np.linalg.norm(grad1)
self.ngrad2 = grad2 / np.linalg.norm(grad2)
self.ngrad = self.ngrad2
self.nnormal = self.normal / np.linalg.norm(self.normal)
if self.absolute:
self.noffset = self.offset
else:
self.noffset = self.nnormal*self.offset[0] + self.ngrad1*self.offset[1] + self.ngrad2*self.offset[2]
self.normCm = self.norm * 695.5 * 1e8 # in cm
def cGrid(self, N = None, iL = 1, N2 = None, iL2 = None):
#Return a list of points in the plane
if N is None: self.N = self.params.resolution()[0]
else: self.N = N
if N2 is None: self.N2 = self.N
else: self.N2 = N2
if iL2 is None: iL2 = iL
L1 = self.rstar*iL
L2 = self.rstar*iL2
sGrad1 = self.ngrad1*L1
sGrad2 = self.ngrad2*L2
self.baseA = sGrad1 + self.noffset
self.baseB = -sGrad1 + self.noffset
self.crossA = self.baseA +sGrad2
self.crossB = self.baseA -sGrad2
baseLine = sightline(self.baseA, self.baseB, params=self.params).get_points(self.N)[0]
pos0 = baseLine[:,0]
self.nx = len(baseLine[0,:])
llll = sightline(pos0+sGrad2, pos0-sGrad2, params=self.params)
self.ny = len(llll.get_points(self.N2)[0][0,:])
self.shape = [self.nx, self.ny]
self.Npoints = self.nx * self.ny
thisPlane = []
for pos in baseLine.T:
thisPlane.extend(sightline(pos+sGrad2, pos-sGrad2, params=self.params).get_points(self.N2)[0].T)
# print(pos)
# import pdb; pdb.set_trace()
self.thisPlane = thisPlane
# import pdb; pdb.set_trace()
return thisPlane
def get_points(self):
# import pdb; pdb.set_trace()
points = np.asarray(self.thisPlane).T
return points, np.ones_like(points)
def pGrid(self, N = None, iL = 1, N2 = None):
#Return a list of points in the plane in polar Coords
if N is None: self.N = self.default_N
else: self.N = N
if N2 is None: self.N2 = self.N
else: self.N2 = N2
return [self.cart2sph(pos) for pos in self.cGrid(N, iL, N2)]
#Generates default grids
class defGrid:
def __init__(self, params=None):
# print('Generating Default Grids...')
#Above the Pole
iL = 1
normal1 = [0,0,1]
offset1 = [1.5, 0, 0]
self.topPlane = plane(normal1, offset1, iL, rotAxis = [0,1,0])
#Slice of the Pole
self.polePlane = plane()
#Smaller slice of the Pole
self.spolePlane = plane(offset = [0,1,-1], iL = 2)
#Bigger Slice of the Pole
self.bpolePlane = plane(iL = 8)
self.sidePlane = plane([1,0,0], [0,16,0], rotAxis = [0,1,0], iL = 20)
#This line goes over the pole without touching it
position, target = [2, np.pi/4, 0.001], [2, -np.pi/4, -0.001]
self.primeLine = sightline(position, target, coords = 'sphere')
#This line goes over the pole without touching it
position, target = [5, 0.001, 1.5], [-5, 0.001, 1.5]
self.primeLineLong = sightline(position, target, coords = 'cart')
#This line goes over the pole without touching it
z = 1.02
position, target = [10, 0.001, z], [-10, 0.001, z]
self.primeLineVLong = sightline(position, target, coords = 'cart')
#This line starts from north pole and goes out radially
self.poleLine = sightline([1,0,0],[101,0,0], coords = 'Sphere')
b = 1.03
self.impLine = sightline([5,1e-8,b],[-5,1e-8,b])
def impactArray(b0, b1, iPoints, spacing='log'):
# Create the impact array
if b1 is not None:
if spacing.casefold() in 'log'.casefold():
logsteps = np.logspace(np.log10(b0 - 1), np.log10(b1 - 1), iPoints)
return np.round(logsteps + 1, 5)
else:
return np.round(np.linspace(b0, b1, iPoints), 4)
else:
return np.round([b0], 4)
def impactLines(N=5, b0 = 1.05, b1= 1.5, len = 50):
#Generate lines with a fixed angle but varying impact parameter
lines = []
x = len
y = 1e-8
#bax = np.logspace(np.log10(b0),np.log10(b1),N)
bax = np.linspace(b0,b1,N)
for zz in bax:
lines.append(sightline([x,y,zz], [-x,y,zz]))
#List of grids, list of labels
return [lines, bax]
def rotLines(N = 20, b = 1.05, offset = 0, x0 = 5, envInd = 0):
#Generate lines with a fixed impact parameter but varying angle
work = []
y0 = 1e-8
angles = np.float16(np.linspace(0, np.pi*(1 - 1/N), N))
for theta in angles:
theta += offset
x = x0 * np.sin(theta) + y0 * np.cos(theta)
y = x0 * np.cos(theta) - y0 * np.sin(theta)
thisLine = sightline([x,y,b], [-x,-y,b], envInd = envInd)
work.append(thisLine)
return work
def image(N = [20,20], rez=[0.5,0.5], target = [0,1.5], len = 10):
yy = np.linspace(target[0] - rez[0]/2, target[0] + rez[0]/2, N[0])
zz = np.linspace(target[1] - rez[1]/2, target[1] + rez[1]/2, N[1])
lines = []
coords = []
yi = 0
ii = 0
for y in yy:
zi = 0
for z in zz:
line = sightline([len,y,z],[-len,y,z])
line.findT = False
line.index = (yi,zi,ii)
lines.append(line)
coords.append((y,z))
zi += 1
ii += 1
yi += 1
return [[lines, coords]], [yy,zz]
def maximizePlot():
try:
mng = plt.get_current_fig_manager()
backend = plt.get_backend()
if backend == 'TkAgg':
try:
mng.window.state('zoomed')
except:
mng.resize(*mng.window.maxsize())
elif backend == 'wxAgg':
mng.frame.Maximize(True)
elif backend[:2].upper() == 'QT':
mng.window.showMaximized()
else:
return False
return True
except:
return False