Modeling of the thickness of the sensor
In this notebook we will re-use the experiment done at ID28 and previously calibrated and model in 3D the detector.
This detector is a Pilatus 1M with a 450µm thick silicon sensor. Let’s first have a look at the absorption coefficients of this sensor material: https://physics.nist.gov/PhysRefData/XrayMassCoef/ElemTab/z14.html
First we retieve the results of the previous step, then calculate the absorption efficiency:
[1]:
%matplotlib inline
# use `widget` instead of `inline` for better user-exeperience. `inline` allows to store plots into notebooks.
[2]:
import time
start_time = time.perf_counter()
from matplotlib.pyplot import subplots
import numpy
import fabio, pyFAI, pyFAI.units, pyFAI.detectors, pyFAI.azimuthalIntegrator
import json
with open("id28.json") as f:
calib = json.load(f)
thickness = 450e-6
wavelength = calib["wavelength"]
dist = calib["param"][calib['param_names'].index("dist")]
poni1 = calib["param"][calib['param_names'].index("poni1")]
poni2 = calib["param"][calib['param_names'].index("poni2")]
energy = pyFAI.units.hc/(wavelength*1e10)
print("wavelength: %.3em,\t dist: %.3em,\t poni1: %.3em,\t poni2: %.3em,\t energy: %.3fkeV" %
(wavelength, dist, poni1, poni2, energy))
wavelength: 6.968e-11m, dist: 2.845e-01m, poni1: 8.865e-02m, poni2: 8.931e-02m, energy: 17.793keV
Absorption coeficient at 17.8 keV
[3]:
# density from https://en.wikipedia.org/wiki/Silicon
rho = 2.3290 # g/cm^3
#Absorption from https://physics.nist.gov/PhysRefData/XrayMassCoef/ElemTab/z14.html
# Nota: enegies are in MeV !
Si_abs = """
2.00000E-03 2.777E+03 2.669E+03
3.00000E-03 9.784E+02 9.516E+02
4.00000E-03 4.529E+02 4.427E+02
5.00000E-03 2.450E+02 2.400E+02
6.00000E-03 1.470E+02 1.439E+02
8.00000E-03 6.468E+01 6.313E+01
1.00000E-02 3.389E+01 3.289E+01
1.50000E-02 1.034E+01 9.794E+00
2.00000E-02 4.464E+00 4.076E+00
3.00000E-02 1.436E+00 1.164E+00
4.00000E-02 7.012E-01 4.782E-01
5.00000E-02 4.385E-01 2.430E-01
6.00000E-02 3.207E-01 1.434E-01
8.00000E-02 2.228E-01 6.896E-02
1.00000E-01 1.835E-01 4.513E-02
1.50000E-01 1.448E-01 3.086E-02
2.00000E-01 1.275E-01 2.905E-02
3.00000E-01 1.082E-01 2.932E-02
4.00000E-01 9.614E-02 2.968E-02
5.00000E-01 8.748E-02 2.971E-02
6.00000E-01 8.077E-02 2.951E-02
8.00000E-01 7.082E-02 2.875E-02
1.00000E+00 6.361E-02 2.778E-02
1.25000E+00 5.688E-02 2.652E-02
1.50000E+00 5.183E-02 2.535E-02
2.00000E+00 4.480E-02 2.345E-02
3.00000E+00 3.678E-02 2.101E-02
4.00000E+00 3.240E-02 1.963E-02
5.00000E+00 2.967E-02 1.878E-02
6.00000E+00 2.788E-02 1.827E-02
8.00000E+00 2.574E-02 1.773E-02
1.00000E+01 2.462E-02 1.753E-02
1.50000E+01 2.352E-02 1.746E-02
2.00000E+01 2.338E-02 1.757E-02 """
data = numpy.array([[float(i) for i in line.split()] for line in Si_abs.split("\n") if line])
energy_tab, mu_over_rho, mu_en_over_rho = data.T
abs_18 = numpy.interp(energy, energy_tab*1e3, mu_en_over_rho)
mu = abs_18*rho*1e+2
eff = 1.0-numpy.exp(-mu*thickness)
print("µ = %f m^-1 hence absorption efficiency for 450µm: %.1f %%"%(mu, eff*100))
µ = 1537.024174 m^-1 hence absorption efficiency for 450µm: 49.9 %
[4]:
depth = numpy.linspace(0, 1000, 100)
res = numpy.exp(-mu*depth*1e-6)
fig, ax = subplots()
ax.plot(depth, res, "-")
ax.set_xlabel("Depth (µm)")
ax.set_ylabel("Residual signal")
ax.set_title("Silicon @ 17.8 keV")
pass
This is consistent with: http://henke.lbl.gov/optical_constants/filter2.html
Now we can model the detector
Modeling of the detector:
The detector is seen as a 2D array of voxel. Let vox, voy and voz be the dimention of the detector in the three dimentions.
[5]:
detector= pyFAI.detector_factory(calib["detector"])
print(detector)
vox = detector.pixel2 # this is not a typo
voy = detector.pixel1 # x <--> axis 2
voz = thickness
print(vox, voy, voz)
Detector Pilatus 1M PixelSize= 172µm, 172µm BottomRight (3)
0.000172 0.000172 0.00045
The intensity grabbed in this voxel is the triple integral of the absorbed signal coming from this pixel or from the neighboring ones.
There are 3 ways to perform this intergral: * Volumetric analytic integral. Looks feasible with a change of variable in the depth * Slice per slice, the remaining intensity depand on the incidence angle + pixel splitting between neighbooring pixels * raytracing: the decay can be solved analytically for each ray, one has to throw many ray to average out the signal.
For sake of simplicity, this integral will be calculated numerically using this raytracing algorithm. http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.42.3443&rep=rep1&type=pdf
Knowing the input position for a X-ray on the detector and its propagation vector, this algorithm allows us to calculate the length of the path in all voxel it crosses in a fairly efficient way.
To speed up the calculation, we will use a few tricks: * One ray never crosses more than 16 pixels, which is reasonable considering the incidance angle * we use numba to speed-up the calculation of loops in python * We will allocate the needed memory by chuncks of 1 million elements
[6]:
! pip install numba
Requirement already satisfied: numba in /home/edgar1993a/miniforge3/envs/edgar/lib/python3.11/site-packages (0.60.0)
Requirement already satisfied: llvmlite<0.44,>=0.43.0dev0 in /home/edgar1993a/miniforge3/envs/edgar/lib/python3.11/site-packages (from numba) (0.43.0)
Requirement already satisfied: numpy<2.1,>=1.22 in /home/edgar1993a/miniforge3/envs/edgar/lib/python3.11/site-packages (from numba) (1.26.4)
[7]:
from numba import jit
BLOCK_SIZE = 1<<20 # 1 million
BUFFER_SIZE = 16
BIG = numpy.finfo(numpy.float32).max
mask = numpy.load("mask.npy").astype(numpy.int8)
from scipy.sparse import csr_matrix, csc_matrix, linalg
[8]:
@jit(nopython=True)
def calc_one_ray(entx, enty,
kx, ky, kz,
vox, voy, voz):
"""For a ray, entering at position (entx, enty), with a propagation vector (kx, ky,kz),
calculate the length spent in every voxel where energy is deposited from a bunch of photons comming in the detector
at a given position and and how much energy they deposit in each voxel.
Direct implementation of http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.42.3443&rep=rep1&type=pdf
:param entx, enty: coordinate of the entry point in meter (2 components, x,y)
:param kx, ky, kz: vector with the direction of the photon (3 components, x,y,z)
:param vox, voy, voz: size of the voxel in meter (3 components, x,y,z)
:return: coordinates voxels in x, y and length crossed when leaving the associated voxel
"""
array_x = numpy.empty(BUFFER_SIZE, dtype=numpy.int32)
array_x[:] = -1
array_y = numpy.empty(BUFFER_SIZE, dtype=numpy.int32)
array_y[:] = -1
array_len = numpy.empty(BUFFER_SIZE, dtype=numpy.float32)
#normalize the input propagation vector
n = numpy.sqrt(kx*kx + ky*ky + kz*kz)
kx /= n
ky /= n
kz /= n
#assert kz>0
step_X = -1 if kx<0.0 else 1
step_Y = -1 if ky<0.0 else 1
#assert vox>0
#assert voy>0
#assert voz>0
X = int(entx//vox)
Y = int(enty//voy)
if kx>0.0:
t_max_x = ((entx//vox+1)*(vox)-entx)/ kx
elif kx<0.0:
t_max_x = ((entx//vox)*(vox)-entx)/ kx
else:
t_max_x = BIG
if ky>0.0:
t_max_y = ((enty//voy+1)*(voy)-enty)/ ky
elif ky<0.0:
t_max_y = ((enty//voy)*(voy)-enty)/ ky
else:
t_max_y = BIG
#Only one case for z as the ray is travelling in one direction only
t_max_z = voz / kz
t_delta_x = abs(vox/kx) if kx!=0 else BIG
t_delta_y = abs(voy/ky) if ky!=0 else BIG
t_delta_z = voz/kz
finished = False
last_id = 0
array_x[last_id] = X
array_y[last_id] = Y
while not finished:
if t_max_x < t_max_y:
if t_max_x < t_max_z:
array_len[last_id] = t_max_x
last_id+=1
X += step_X
array_x[last_id] = X
array_y[last_id] = Y
t_max_x += t_delta_x
else:
array_len[last_id] = t_max_z
finished = True
else:
if t_max_y < t_max_z:
array_len[last_id] = t_max_y
last_id+=1
Y += step_Y
array_x[last_id] = X
array_y[last_id] = Y
t_max_y += t_delta_y
else:
array_len[last_id] = t_max_z
finished = True
if last_id>=array_len.size-1:
print("resize arrays")
old_size = len(array_len)
new_size = (old_size//BUFFER_SIZE+1)*BUFFER_SIZE
new_array_x = numpy.empty(new_size, dtype=numpy.int32)
new_array_x[:] = -1
new_array_y = numpy.empty(new_size, dtype=numpy.int32)
new_array_y[:] = -1
new_array_len = numpy.empty(new_size, dtype=numpy.float32)
new_array_x[:old_size] = array_x
new_array_y[:old_size] = array_y
new_array_len[:old_size] = array_len
array_x = new_array_x
array_y = new_array_y
array_len = new_array_len
return array_x[:last_id], array_y[:last_id], array_len[:last_id]
print(calc_one_ray(0.0,0.0, 1,1,1, 172e-6, 172e-6, 450e-6))
import random
%timeit calc_one_ray(10+random.random(),11+random.random(),\
random.random()-0.5,random.random()-0.5,0.5+random.random(), \
vox, voy, voz)
%timeit calc_one_ray.py_func(10+random.random(),11+random.random(),\
random.random()-0.5,random.random()-0.5,0.5+random.random(), \
vox, voy, voz)
(array([0, 0, 1, 1], dtype=int32), array([0, 1, 1, 2], dtype=int32), array([0.00029791, 0.00029791, 0.00059583, 0.00059583], dtype=float32))
The slowest run took 8.26 times longer than the fastest. This could mean that an intermediate result is being cached.
7.27 μs ± 7.97 μs per loop (mean ± std. dev. of 7 runs, 1 loop each)
8.15 μs ± 183 ns per loop (mean ± std. dev. of 7 runs, 100,000 loops each)
Now that we are able to perform raytracing for any ray comming in the detector, we can calculate the contribution to the neighboring pixels, using the absorption law (the length travelled is already known). To average-out the signal, we will sample a few dozens of rays per pixel to get an approximatation of the volumic integrale.
Now we need to store the results so that this transformation can be represented as a sparse matrix multiplication:
b = M.a
Where b is the recorded image (blurred) and a is the “perfect” signal. M being the sparse matrix where every pixel of a gives a limited number of contribution to b.
Each pixel in b is represented by one line in M and we store the indices of a of interest with the coefficients of the matrix. So if a pixel i,j contributes to (i,j), (i+1,j), (i+1,j+1), there are only 3 elements in the line. This is advantagous for storage.
We will use the CSR sparse matrix representation: https://en.wikipedia.org/wiki/Sparse_matrix#Compressed_sparse_row_.28CSR.2C_CRS_or_Yale_format.29 where there are 3 arrays: * data: containing the actual non zero values * indices: for a given line, it contains the column number of the assocated data (at the same indice) * idptr: this array contains the index of the start of every line.
[9]:
from numba.experimental import jitclass
from numba import int8, int32, int64, float32, float64
spec = [("vox",float64),("voy",float64),("voz",float64),("mu",float64),
("dist",float64),("poni1",float64),("poni2",float64),
("width", int64),("height", int64),("mask", int8[:,:]),
("sampled", int64), ("data", float32[:]),("indices", int32[:]),("idptr", int32[:]),
]
@jitclass(spec)
class ThickDetector(object):
"Calculate the point spread function as function of the geometry of the experiment"
def __init__(self, vox, voy, thickness, mask, mu,
dist, poni1, poni2):
"""Constructor of the class:
:param vox, voy: detector pixel size in the plane
:param thickness: thickness of the sensor in meters
:param mask:
:param mu: absorption coefficient of the sensor material
:param dist: sample detector distance as defined in the geometry-file
:param poni1, poni2: coordinates of the PONI as defined in the geometry
"""
self.vox = vox
self.voy = voy
self.voz = thickness
self.mu = mu
self.dist=dist
self.poni1 = poni1
self.poni2 = poni2
self.width = mask.shape[-1]
self.height = mask.shape[0]
self.mask = mask
self.sampled = 0
self.data = numpy.zeros(BLOCK_SIZE, dtype=numpy.float32)
self.indices = numpy.zeros(BLOCK_SIZE,dtype=numpy.int32)
self.idptr = numpy.zeros(self.width*self.height+1, dtype=numpy.int32)
def calc_one_ray(self, entx, enty):
"""For a ray, entering at position (entx, enty), with a propagation vector (kx, ky,kz),
calculate the length spent in every voxel where energy is deposited from a bunch of photons comming in the detector
at a given position and and how much energy they deposit in each voxel.
Direct implementation of http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.42.3443&rep=rep1&type=pdf
:param entx, enty: coordinate of the entry point in meter (2 components, x,y)
:return: coordinates voxels in x, y and length crossed when leaving the associated voxel
"""
array_x = numpy.empty(BUFFER_SIZE, dtype=numpy.int32)
array_x[:] = -1
array_y = numpy.empty(BUFFER_SIZE, dtype=numpy.int32)
array_y[:] = -1
array_len = numpy.empty(BUFFER_SIZE, dtype=numpy.float32)
#normalize the input propagation vector
kx = entx - self.poni2
ky = enty - self.poni1
kz = self.dist
n = numpy.sqrt(kx*kx + ky*ky + kz*kz)
kx /= n
ky /= n
kz /= n
step_X = -1 if kx<0.0 else 1
step_Y = -1 if ky<0.0 else 1
X = int(entx/self.vox)
Y = int(enty/self.voy)
if kx>0.0:
t_max_x = ((entx//self.vox+1)*(self.vox)-entx)/ kx
elif kx<0.0:
t_max_x = ((entx//self.vox)*(self.vox)-entx)/ kx
else:
t_max_x = BIG
if ky>0.0:
t_max_y = ((enty//self.voy+1)*(self.voy)-enty)/ ky
elif ky<0.0:
t_max_y = ((enty//self.voy)*(self.voy)-enty)/ ky
else:
t_max_y = BIG
#Only one case for z as the ray is travelling in one direction only
t_max_z = self.voz / kz
t_delta_x = abs(self.vox/kx) if kx!=0 else BIG
t_delta_y = abs(self.voy/ky) if ky!=0 else BIG
t_delta_z = self.voz/kz
finished = False
last_id = 0
array_x[last_id] = X
array_y[last_id] = Y
while not finished:
if t_max_x < t_max_y:
if t_max_x < t_max_z:
array_len[last_id] = t_max_x
last_id+=1
X += step_X
array_x[last_id] = X
array_y[last_id] = Y
t_max_x += t_delta_x
else:
array_len[last_id] = t_max_z
last_id+=1
finished = True
else:
if t_max_y < t_max_z:
array_len[last_id] = t_max_y
last_id+=1
Y += step_Y
array_x[last_id] = X
array_y[last_id] = Y
t_max_y += t_delta_y
else:
array_len[last_id] = t_max_z
last_id+=1
finished = True
if last_id>=array_len.size-1:
print("resize arrays")
old_size = len(array_len)
new_size = (old_size//BUFFER_SIZE+1)*BUFFER_SIZE
new_array_x = numpy.empty(new_size, dtype=numpy.int32)
new_array_x[:] = -1
new_array_y = numpy.empty(new_size, dtype=numpy.int32)
new_array_y[:] = -1
new_array_len = numpy.empty(new_size, dtype=numpy.float32)
new_array_x[:old_size] = array_x
new_array_y[:old_size] = array_y
new_array_len[:old_size] = array_len
array_x = new_array_x
array_y = new_array_y
array_len = new_array_len
return array_x[:last_id], array_y[:last_id], array_len[:last_id]
def one_pixel(self, row, col, sample):
"""calculate the contribution of one pixel to the sparse matrix and populate it.
:param row: row index of the pixel of interest
:param col: column index of the pixel of interest
:param sample: Oversampling rate, 10 will thow 10x10 ray per pixel
:return: the extra number of pixel allocated
"""
if self.mask[row, col]:
return (numpy.empty(0, dtype=numpy.int32),
numpy.empty(0, dtype=numpy.float32))
counter = 0
tmp_size = 0
last_buffer_size = BUFFER_SIZE
tmp_idx = numpy.empty(last_buffer_size, dtype=numpy.int32)
tmp_idx[:] = -1
tmp_coef = numpy.zeros(last_buffer_size, dtype=numpy.float32)
pos = row * self.width + col
start = self.idptr[pos]
for i in range(sample):
posx = (col+1.0*i/sample)*vox
for j in range(sample):
posy = (row+1.0*j/sample)*voy
array_x, array_y, array_len = self.calc_one_ray(posx, posy)
rem = 1.0
for i in range(array_x.size):
x = array_x[i]
y = array_y[i]
l = array_len[i]
if (x<0) or (y<0) or (y>=self.height) or (x>=self.width):
break
elif (self.mask[y, x]):
continue
idx = x + y*self.width
dos = numpy.exp(-self.mu*l)
value = rem - dos
rem = dos
for j in range(last_buffer_size):
if tmp_size >= last_buffer_size:
#Increase buffer size
new_buffer_size = last_buffer_size + BUFFER_SIZE
new_idx = numpy.empty(new_buffer_size, dtype=numpy.int32)
new_coef = numpy.zeros(new_buffer_size, dtype=numpy.float32)
new_idx[:last_buffer_size] = tmp_idx
new_idx[last_buffer_size:] = -1
new_coef[:last_buffer_size] = tmp_coef
last_buffer_size = new_buffer_size
tmp_idx = new_idx
tmp_coef = new_coef
if tmp_idx[j] == idx:
tmp_coef[j] += value
break
elif tmp_idx[j] < 0:
tmp_idx[j] = idx
tmp_coef[j] = value
tmp_size +=1
break
return tmp_idx[:tmp_size], tmp_coef[:tmp_size]
def calc_csr(self, sample):
"""Calculate the CSR matrix for the whole image
:param sample: Oversampling factor
:return: CSR matrix
"""
size = self.width * self.height
allocated_size = BLOCK_SIZE
idptr = numpy.zeros(size+1, dtype=numpy.int32)
indices = numpy.zeros(allocated_size, dtype=numpy.int32)
data = numpy.zeros(allocated_size, dtype=numpy.float32)
self.sampled = sample*sample
pos = 0
start = 0
for row in range(self.height):
for col in range(self.width):
line_idx, line_coef = self.one_pixel(row, col, sample)
line_size = line_idx.size
if line_size == 0:
new_size = 0
pos+=1
idptr[pos] = start
continue
stop = start + line_size
if stop >= allocated_size:
new_buffer_size = allocated_size + BLOCK_SIZE
new_idx = numpy.zeros(new_buffer_size, dtype=numpy.int32)
new_coef = numpy.zeros(new_buffer_size, dtype=numpy.float32)
new_idx[:allocated_size] = indices
new_coef[:allocated_size] = data
allocated_size = new_buffer_size
indices = new_idx
data = new_coef
indices[start:stop] = line_idx
data[start:stop] = line_coef
pos+=1
idptr[pos] = stop
start = stop
last = idptr[-1]
self.data = data
self.indices = indices
self.idptr = idptr
return (self.data[:last]/self.sampled, indices[:last], idptr)
[10]:
thick = ThickDetector(vox,voy, thickness=thickness, mu=mu, dist=dist, poni1=poni1, poni2=poni2, mask=mask)
%time thick.calc_csr(1)
CPU times: user 3.12 s, sys: 79.9 ms, total: 3.2 s
Wall time: 3.2 s
[10]:
(array([0., 0., 0., ..., 0., 0., 0.], dtype=float32),
array([ 2, 2, 4, ..., 1023180, 1023181, 1023182],
dtype=int32),
array([ 0, 0, 0, ..., 1902581, 1902582, 1902583],
dtype=int32))
[11]:
thick = ThickDetector(vox,voy, thickness=thickness, mu=mu, dist=dist, poni1=poni1, poni2=poni2, mask=mask)
%time pre_csr = thick.calc_csr(8)
CPU times: user 30 s, sys: 113 ms, total: 30.1 s
Wall time: 30 s
Validation of the CSR matrix obtained:
For this we will build a simple 2D image with one pixel in a regular grid and calculate the effect of the transformation calculated previously on it.
[12]:
dummy_image = numpy.ones(mask.shape, dtype="float32")
dummy_image[::5,::5] = 10
#dummy_image[mask] = -1
csr = csr_matrix(pre_csr)
dummy_blurred = csr.T.dot(dummy_image.ravel()).reshape(mask.shape)
fix, ax = subplots(2,2, figsize=(8,8))
ax[0,0].imshow(dummy_image)
ax[0,1].imshow(dummy_blurred)
ax[1,1].imshow(csr.dot(dummy_blurred.ravel()).reshape(mask.shape))
pass
[13]:
ax[0,0].set_xlim(964,981)
ax[0,0].set_ylim(0,16)
ax[0,1].set_xlim(964,981)
ax[0,1].set_ylim(0,16)
ax[1,1].set_xlim(964,981)
ax[1,1].set_ylim(0,16)
pass
Least squares refinement of the pseudo-inverse
[14]:
blured = dummy_blurred.ravel()
# Invert this matrix: see https://arxiv.org/abs/1006.0758
%time res = linalg.lsmr(csr.T, blured)
restored = res[0].reshape(mask.shape)
ax[1,0].imshow(restored)
ax[1,0].set_xlim(964,981)
ax[1,0].set_ylim(0,16)
print(res[1:])
CPU times: user 13.4 s, sys: 46.7 ms, total: 13.5 s
Wall time: 1.08 s
(1, 30, 0.0046368041028449205, 0.0005109819474116924, 2.1354864217638663, 4.833787403420624, 2175.569104133437)
Pseudo inverse with positivitiy constrain and poissonian noise (MLEM)
The MLEM algorithm was initially developed within the framework of reconstruction of images in emission tomography [Shepp and Vardi, 1982], [Vardi et al., 1985], [Lange and Carson, 1984]. Nowadays, this algorithm is employed in numerous tomographic reconstruction problems and often associated to regularization techniques. It is based on the iterative maximization of the log-likelihood function.
[15]:
fix, ax = subplots(2,2, figsize=(8,8))
ax[0,0].imshow(dummy_image)
ax[0,1].imshow(dummy_blurred)
ax[1,1].imshow(csr.dot(dummy_blurred.ravel()).reshape(mask.shape))
ax[0,0].set_xlim(964,981)
ax[0,0].set_ylim(0,16)
ax[0,0].set_title("Dummy image")
ax[0,1].set_xlim(964,981)
ax[0,1].set_ylim(0,16)
ax[0,1].set_title("Convolved image (i.e. blurred)")
ax[1,1].set_xlim(964,981)
ax[1,1].set_ylim(0,16)
ax[1,1].set_title("Retro-projected of the blurred")
ax[1,0].set_title("Corrected image")
pass
[16]:
def iterMLEM_scipy(F, M, R):
"Implement one step of MLEM"
#res = F * (R.T.dot(M))/R.dot(F)# / M.sum(axis=-1)
norm = 1/R.T.dot(numpy.ones_like(F))
cor = R.T.dot(M/R.dot(F))
res = norm * F * cor
res[numpy.isnan(res)] = 1.0
return res
def deconv_MLEM(csr, data, thres=0.2, maxiter=1000):
R = csr.T
msk = data<0
img = data.astype("float32")
img[msk] = 0.0 # set masked values to 0, negative values could induce errors
M = img.ravel()
#F0 = numpy.random.random(data.size)#M#
F0 = R.T.dot(M)
F1 = iterMLEM_scipy(F0, M, R)
delta = abs(F1-F0).max()
for i in range(maxiter):
if delta<thres:
break
F2 = iterMLEM_scipy(F1, M, R)
delta = abs(F1-F2).max()
if i%100==0:
print(i, delta)
F1 = F2
i+=1
print(i, delta)
return F2.reshape(img.shape)
[17]:
%time res = deconv_MLEM(csr, dummy_blurred, 1e-4)
ax[1,0].imshow(res)
ax[1,0].set_xlim(964,981)
ax[1,0].set_ylim(0,16)
/tmp/ipykernel_7354/87626099.py:4: RuntimeWarning: divide by zero encountered in divide
norm = 1/R.T.dot(numpy.ones_like(F))
/tmp/ipykernel_7354/87626099.py:5: RuntimeWarning: invalid value encountered in divide
cor = R.T.dot(M/R.dot(F))
/tmp/ipykernel_7354/87626099.py:6: RuntimeWarning: invalid value encountered in multiply
res = norm * F * cor
0 1.7867398
100 0.0016492605
200 0.00027656555
262 9.918213e-05
CPU times: user 5.33 s, sys: 28 ms, total: 5.36 s
Wall time: 5.37 s
[17]:
(0.0, 16.0)
Conclusion of the raytracing part:
We are able to simulate the path and the absorption of the photon in the thickness of the detector. Numba helped substentially to make the raytracing calculation much faster. The signal of each pixel is indeed spread on the neighboors, depending on the position of the PONI and this effect can be inverted using sparse-matrix pseudo-inversion. The MLEM can garanteee that the total signal is conserved and that no pixel gets negative value.
We will now save this sparse matrix to file in order to be able to re-use it in next notebook. But before saving it, it makes sense to spend some time in generating a high quality sparse matrix in throwing thousand rays per pixel in a grid of 64x64.
[18]:
%time pre_csr = thick.calc_csr(64)
hq_csr = csr_matrix(pre_csr)
from scipy.sparse import save_npz
save_npz("csr.npz",hq_csr)
CPU times: user 31min 15s, sys: 5.65 s, total: 31min 21s
Wall time: 31min 11s
[19]:
print(f"Total execution time: {time.perf_counter()-start_time:.3f} s")
Total execution time: 1925.942 s