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Copy pathLFRayTraceVoxGenerate.py
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LFRayTraceVoxGenerate.py
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import copy
import math
import struct
import matplotlib.pyplot as plt
import numpy as np
import LFRayTraceVoxParams
from LFRayTraceVoxSpace import getVoxelDims, getWorkingDims
# TODO
#from camRayEntrance import camRayEntrance
from utils import timer, sizeOf
# ==================================================================================
# Generate LightFieldVoxelRay Space
# using parameters from LFRayTraceVoxParams
# ==================================================================================
def genMidPtsLengthswithSiddon(entrance_, exit_, voxBox_, voxPitch_):
# Generate mid-points and lengths using Siddon algorithm
import siddon2
midpointsList = []
lengthsList = []
longestMidPts = 0
num_midpts = 0
# for each of 164 rays...
for i in range(len(entrance_)):
x1, y1, z1 = entrance_[i][0], entrance_[i][1], entrance_[i][2]
x2, y2, z2 = exit_[i][0], exit_[i][1], exit_[i][2]
dx, dy, dz = voxPitch_, voxPitch_, voxPitch_
# print("Siddon Input ", x1, y1, z1, x2, y2, z2, dx, dy, dz, voxBox_)
args1 = (x1, y1, z1, x2, y2, z2, dx, dy, dz,
voxBox_[0][0], voxBox_[0][1], voxBox_[1][0], voxBox_[1][1], voxBox_[2][0], voxBox_[2][1])
args = (x1, y1, z1, x2, y2, z2)
# call rayTrace only once, then pass to midPoints and lengths
alist = siddon2.raytrace(*args1)
midpoints = siddon2.midpoints(*args, alist)
lengths = siddon2.intersect_length(*args, alist)
num_midpts = num_midpts + len(midpoints)
if len(midpoints) > longestMidPts:
longestMidPts = len(midpoints)
midpointsList.append(midpoints) # physical coordinates
lengthsList.append(lengths)
print(" longestMidPts: ", longestMidPts)
print(" num_midpts : ", num_midpts)
# 164 camPixX, camPixY,
# return np.array(midpointsList), np.array(lengthsList)
return midpointsList, lengthsList
def showMidPointsAndLengths(camPix, midpointsList, lengthsList):
""" Diagnostic... Display # of midpoints and sum of lengths for cam array 16x16 """
image = np.zeros((16, 16))
for i in range(len(camPix)): # 164 rays
# print("midPtsListLen", i, len(midpointsList[i]))
image[int(camPix[i][0]-1), int(camPix[i][1])-1] = len(midpointsList[i])
plt.figure("Number of MidPoints")
# plt.interactive(False)
plt.show(block=False)
plt.imshow(image, cmap=plt.cm.hot)
plt.show()
image = np.zeros((16, 16))
for i in range(len(camPix)): # 164 rays
image[int(camPix[i][0] - 1), int(camPix[i][1]) - 1] = len(lengthsList[i])
plt.figure("Number of Lengths")
plt.show(block=False)
plt.imshow(image, cmap=plt.cm.hot)
plt.show()
image = np.zeros((16, 16))
for i in range(len(camPix)): # 164 rays
lengthsSum = 0
for j in range(len(lengthsList[i])):
lengthsSum = lengthsSum + lengthsList[i][j]
image[int(camPix[i][0]-1), int(camPix[i][1])-1] = lengthsSum
plt.figure("Lengths Sum")
plt.show(block=False)
plt.imshow(image, cmap=plt.cm.hot)
plt.show()
def generateYZOffsets(midpointsList_, ulenses_, uLensPitch_, voxPitch_):
# pre-calculates y and z components of the shifted midpoints so as to accelerate
# the calculation in genLightFieldVoxels...
# Generate offsets in voxels
voxPitchOver1 = 1.0 / voxPitch_
Xmin = 10000
Xmax = 0
Ymin = 10000
Ymax = 0
Zmin = 10000
Zmax = 0
# Z =======================
# extract the Z components
midsZ= []
for n in range(len(midpointsList_)):
midsZ.append([])
for m in range(len(midpointsList_[n])):
midsZ[n].append(midpointsList_[n][m][2])
# Generate Offset Z List =================
midsOffZ = [[] for i in range(ulenses_)]
# TODO added 0.5 ???
for l in range(ulenses_):
offsetZ = (l + 0.5 - ulenses_ / 2) * uLensPitch_
midsOffZ[l] = copy.deepcopy(midsZ)
# print("l, offsetZ", l, offsetZ)
for n in range(len(midsOffZ[l])):
for m in range(len(midsOffZ[l][n])):
z = midsOffZ[l][n][m]
zOff = math.ceil((z + offsetZ) * voxPitchOver1)
midsOffZ[l][n][m] = zOff
if midsOffZ[l][n][m] > Zmax: Zmax = midsOffZ[l][n][m]
if midsOffZ[l][n][m] < Zmin: Zmin = midsOffZ[l][n][m]
# Y ========================
# extract the Y components
midsY= []
for n in range(len(midpointsList_)):
midsY.append([])
for m in range(len(midpointsList_[n])):
midsY[n].append(midpointsList_[n][m][1])
# Generate Offset Y List =================
midsOffY = [[] for i in range(ulenses_)]
for l in range(ulenses_):
offsetY = (l + 0.5 - ulenses_ / 2) * uLensPitch_
midsOffY[l] = copy.deepcopy(midsY)
for n in range(len(midsOffY[l])):
for m in range(len(midsOffY[l][n])):
midsOffY[l][n][m] = math.ceil((midsOffY[l][n][m] + offsetY) * voxPitchOver1)
if midsOffY[l][n][m] > Ymax: Ymax = midsOffZ[l][n][m]
if midsOffY[l][n][m] < Ymin: Ymin = midsOffZ[l][n][m]
# X =============================
# Generate (not Offset) X List
midsX= []
for n in range(len(midpointsList_)):
midsX.append([])
for m in range(len(midpointsList_[n])):
x = math.ceil(midpointsList_[n][m][0] * voxPitchOver1)
midsX[n].append(x)
#midsX[n].append(math.ceil(midpointsList_[n][m][0] * voxPitchOver1))
if x > Xmax: Xmax = x
if x < Xmin: Xmin = x
print("Xmin,Xmax,Ymin,Ymax,Zmin,Zmax:", Xmin, Xmax, Ymin, Ymax, Zmin, Zmax)
return midsX, midsOffY, midsOffZ
def genLightFieldVoxels(workingBox, ulenses, camPix, midsX, midsOffY, midsOffZ, lengthsList, anglesList):
# [ulenses,ulenses,len(camPix)] each containing [length, alt, azim]
# Array of empty lists -> voxel = [[[[] for iZ in xrange(nZ)] for iY in xrange(nY)] for iX in xrange(nX)]
wbx = workingBox[0][1] - workingBox[0][0]
wbyz = workingBox[1][1] - workingBox[1][0]
voxel = np.empty([wbx, wbyz, wbyz], dtype='object')
# voxel[ [x,y,z], has list of rays passing through it: [ray(nRay, nZ, nY, len)] ]
# ??? class Ray(Structure):_fields_ = [('nRay', c_ubyte), ('nZ', c_ubyte), ('nY', c_ubyte), ('len', c_ubyte)]
# TODO parallelization... uLenses / numProcs
def process_for_k(chunk_):
# sub-process for each k
for k in chunk_:
for j in range(ulenses):
nZ = k
nY = j
for nRay in range(len(camPix)): # iterate over the 164 rays
# print("nRay, # of Mids", nRay, len(midsX[nRay]))
for midpt in range(len(midsX[nRay])): # number of midpoints on this ray
# x, y, z = int(midsX[nRay][midpt]), \
# int(midsOffY[nY][nRay][midpt]), \
# int(midsOffZ[nZ][nRay][midpt])
#print("type(midsOffY[nZ][nRay][midpt])", type(midsOffY[nZ][nRay][midpt]))
#print("type(workingBox[0][0])", type(workingBox[0][0]))
# print(" MidPt: ", midpt, ":",
# midsX[nRay][midpt],
# midsOffY[nY][nRay][midpt],
# midsOffZ[nZ][nRay][midpt],
# " ",
# workingBox[0][0],
# workingBox[1][0],
# workingBox[2][0]
# )
# add this ray in EX space to list of rays for the corresponding voxel coord in working space
# x, y, z = int(midsX[nRay][midpt] - workingBox[0][0]), \
# int(midsOffY[nY][nRay][midpt] - workingBox[1][0]), \
# int(midsOffZ[nZ][nRay][midpt] - workingBox[2][0])
x, y, z = int(midsX[nRay][midpt] - workingBox[0][0]-1), \
int(midsOffY[nY][nRay][midpt] - workingBox[1][0]-1), \
int(midsOffZ[nZ][nRay][midpt] - workingBox[2][0]-1)
if 0 <= x < wbx and 0 <= y < wbyz and 0 <= z < wbyz:
#print(" nZ, nY, nRay, x, y, z: ", nZ, nY, nRay, " ", x, y, z)
packedRay = struct.pack('BBBH', nRay, nZ, nY,
int(lengthsList[nRay][midpt] * LFRayTraceVoxParams.length_div))
if voxel[x][y][z] is None:
voxel[x][y][z] = [packedRay]
else:
voxel[x][y][z].append(packedRay)
#else:
# print(" * nZ, nY, nRay, x, y, z: ", nZ, nY, nRay, " ", x, y, z)
# def chunks(l, n):
#number_of_rays = 0
numProc = LFRayTraceVoxParams.getNumProcs()
l = list(range(ulenses))
chunks_of_k = [l[x: x + numProc] for x in range(0, len(l), numProc)]
for chunk in chunks_of_k:
process_for_k(chunk)
#print("number_of_rays:", number_of_rays)
return voxel
# def generateLightFieldVoxelRaySpace(ulenses_, uLensPitch_, voxPitch_, entrance_, exits_, workingBox_):
# timer.startTime()
# # Rays - Generate midpoints and lengths for the 164 rays... These are in micron, physical dimensions
# midpointsList, lengthsList = genMidPtsLengthswithSiddon(entrance_, exits_, workingBox_, voxPitch_)
# print("workingBox_:", workingBox_)
# print(" len(midpointsList) :",len(midpointsList))
# print(" max(lengthsList) :", max(lengthsList))
# print(" max(max(lengthsList)):", max(max(lengthsList)))
# anglesList = LFRayTraceVoxParams.genRayAngles(entrance_, exits_)
# timer.endTime(" Siddon")
# # diagnostic...
# showMidPointsAndLengths(camPix, midpointsList, lengthsList)
# # given uLenses, gen offsets
# timer.startTime()
# midsX, midsOffY, midsOffZ = generateYZOffsets(midpointsList, ulenses_, uLensPitch_, voxPitch_)
# timer.endTime(" generateOffsets")
# print(" midsX :", len(midsX))
# print(" midsOffY:", len(midsOffY))
# print(" midsOffZ:", len(midsOffZ))
# # print("lengthsList,angleList: ", len(lengthsList), len(anglesList))
#
# timer.startTime()
# voxel = genLightFieldVoxels(workingBox_, ulenses_, camPix, midsX, midsOffY, midsOffZ, lengthsList, anglesList)
# timer.endTime(" genLightFieldVoxels")
#sizeOfLFVox(voxel)
#print("voxel size: ", sizeOf.getsize(voxel))
# return voxel
# ======================================================
# Saving/Loading LFRTVs
# TODO We may also need to specify: voxPitch, ulenses, entranceExitX, entranceExitYZ, objectSpaceX, objectSpaceYZ
def saveLightFieldVoxelRaySpace(filename, voxel):
# Save to file...
print("Saving voxels to file: " + filename)
np.save(filename, voxel)
# def loadLightFieldVoxelRaySpace(filename):
# voxel = np.load(filename+".npy" , allow_pickle=True)
# return voxel
# DIAGNOSTIC ===============================
def showRaysInVoxels(voxel):
# diagnostic: shows number of rays in each voxel
print("voxel.shape:", voxel.shape)
for x in range(voxel.shape[0]):
for y in range(voxel.shape[1]):
for z in range(voxel.shape[2]):
rays = voxel[x][y][z]
if rays is None:
print( x,y,z, " : -----")
else:
print(x, y, z, " : ", len(rays))
for ray in range(len(rays)):
if rays[ray] is not None:
unpackedRay = struct.unpack('BBBH', rays[ray])
nRay = unpackedRay[0]
nZ = unpackedRay[1]
nY = unpackedRay[2]
length = unpackedRay[3]
# print(x,y,z,nRay, nZ, nY, length)
def generateLFRTvoxels(ulenses, voxPitch):
print("Generating lfvox with ulenses: ", ulenses, " voxPitch: ", voxPitch)
voxCtr, voxNrX, voxNrYZ = getVoxelDims(LFRayTraceVoxParams.entranceExitX,
LFRayTraceVoxParams.entranceExitYZ, voxPitch)
print(" EX space specified: (", LFRayTraceVoxParams.entranceExitX, LFRayTraceVoxParams.entranceExitYZ, "microns )")
print(" EX space, voxCtr:", LFRayTraceVoxParams.formatList(voxCtr),
" size: ", voxNrX, voxNrYZ, voxNrYZ)
# camPix, entrance, exits, angles = camRayCoord(voxCtr) # 188 (x,y), (x, y, z) (x, y, z)
# print("lengths of camPix, entrance, exit: ", len(camPix), len(entrance), len(exits))
# anglesList = LFRayTraceVoxParams.genRayAngles(entrance, exits) # ????
angles = LFRayTraceVoxParams.getAngles()
camPix, rayEntrFace, rayExitFace = LFRayTraceVoxParams.camRayCoord(voxCtr, angles)
workingBox = getWorkingDims(voxCtr, ulenses, voxPitch)
print(" Siddon Calcs...")
# Rays - Generate midpoints and lengths for the 164 rays... These are in micron, physical dimensions
midpointsList, lengthsList = genMidPtsLengthswithSiddon(rayEntrFace, rayExitFace, workingBox, voxPitch)
print(" len(midpointsList) :", len(midpointsList))
# print(" max(lengthsList) :", max(lengthsList))
print(" max(max(lengthsList)), longest length:", max(max(lengthsList)))
# showMidPointsAndLengths(camPix, midpointsList, lengthsList)
# given uLenses, gen offsets
print(" Offsets...")
midsX, midsOffY, midsOffZ = generateYZOffsets(midpointsList, ulenses, LFRayTraceVoxParams.uLensPitch, voxPitch)
print(" midsX :", len(midsX))
print(" midsOffY:", len(midsOffY))
print(" midsOffZ:", len(midsOffZ))
# print("lengthsList,angleList: ", len(lengthsList), len(anglesList))
timer.startTime()
voxel = genLightFieldVoxels(workingBox, ulenses, camPix,
midsX, midsOffY, midsOffZ, lengthsList, angles)
timer.endTime(" genLightFieldVoxels")
# save to disk ============================================
parameters, imagepath, lfvoxpath = LFRayTraceVoxParams.file_strings(ulenses, voxPitch)
saveLightFieldVoxelRaySpace(lfvoxpath + "lfvox_" + parameters, voxel)
# LightFieldVoxelRaySpace voxel files are saved in the directory corresponding to its parameters
print(' Saved LightFieldVoxelRaySpace to: ', parameters)
# showRaysInVoxels(voxel) # diagnostic
del voxel
# ======================================================================================
def main():
pass
# globals
lfrtVoxels = None
# midsX, midsOffY, midsOffZ
if __name__ == "__main__":
# import sys
# sys.stdout = open('outputGen.txt', 'wt')
for ulenses in LFRayTraceVoxParams.ulenseses:
for voxPitch in LFRayTraceVoxParams.voxPitches:
generateLFRTvoxels(ulenses, voxPitch)
print("All done Generating LFRTVoxels.")