del UBornCplxR, UBornCplxG, UBornCplxB
start_time = time.time()
ft.SAVtiffRGBCube(
f"{PROCESSINGFOLDER}/IntensiteRheinSpec_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
IntensiteRhein, 2 * PIXTHEO * 1e6)
print(
f"Data saving: {np.round(time.time() - start_time,decimals=2)} seconds"
)
# Darkfield processing
if "DARKFIELD" == MethodUsed:
DarkF = abs(UBornCplxDark)**2
start_time = time.time()
ft.SAVtiffCube(
f"{PROCESSINGFOLDER}/Darkfield_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
DarkF, 2 * PIXTHEO * 1e6)
print(
f"Data saving: {np.round(time.time() - start_time,decimals=2)} seconds"
)
if "BASE" == MethodUsed:
Base = np.abs(Refraction + 1j * Absorption)**2
start_time = time.time()
ft.SAVtiffCube(
f"{PROCESSINGFOLDER}/Brightfield_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
Base, 2 * PIXTHEO * 1e6)
print(
f"Data saving: {np.round(time.time() - start_time,decimals=2)} seconds"
)
CPT += 1
if "RHEINBERG" == MethodUsed:
StackRGB[:,:,int((Z+1200)/80),0] = SumHoloR
StackRGB[:,:,int((Z+1200)/80),1] = SumHoloG
StackRGB[:,:,int((Z+1200)/80),2] = SumHoloB
else :
Stack[:,:,int((Z+1200)/80)] = SumHolo
CPTSUM += 1
print(f"Slice {CPTSUM} out of {Stack.shape[2]}")
print(f"Pre-Processing time for {CPTSUM} Slices: "
f"{np.round(time.time() - start_time,decimals=2)} seconds")
if "RHEINBERG" == MethodUsed:
ft.SAVtiffRGBCube(f"{PROCESSINGFOLDER}/{MethodUsed}_{2*dimHolo}x{2*dimHolo}x{StackRGB.shape[2]}.tiff",
StackRGB, 2*M.PIX*1e6)
else:
ft.SAVtiffCube(f"{PROCESSINGFOLDER}/{MethodUsed}_{2*dimHolo}x{2*dimHolo}x{Stack.shape[2]}.tiff",
Stack, 2*M.PIX*1e6)
# Center recording and file closing
fidParams.write(f"nb_angle {CPT_EXIST-1}\n")
fidParams.write(f"fmaxHolo {fmaxHolo}\n")
fidParams.write(f"dimHolo {dimHolo}\n")
fidParams.write(f"pixTheo {M.PIX/Gtot}\n")
tf.imwrite(CHEMINSAV_CENTRES, np.float32(np.int32(Centres)))
fidCentrestxt.close()
fidParams.close()
NMAX = 0.05
KAPPAMIN = 0
KAPPAMAX = 0
# Gerchberg reconstruction
del Absorption, Refraction
start_time = time.time()
FilteredObj = rp.Gerchberg(Rec_Object, OTF, NMIN, NMAX, KAPPAMIN, KAPPAMAX,
NBITER)
print("")
print(f"Reconstruction time for {NBITER} iterations: "
f"{np.round(time.time() - start_time,decimals=2)} seconds")
print("")
# plt.imshow(Rec_Object[:, :, DIMHOLO].real, cmap="gray")
# plt.show()
# plt.imshow(Rec_Object[:, :, DIMHOLO].imag, cmap="gray")
# plt.show()
# Data saving
start_time = time.time()
ft.SAVtiffCube(
f"{GERCHBERGFOLDER}/RefractionGerch_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
Rec_Object.real.transpose(1, 0, -1), 2 * PIXTHEO * 1e6)
print(f"Data saving: {np.round(time.time() - start_time,decimals=2)} seconds")
# Visualization
viewer = napari.view_image(Rec_Object.real.transpose(-1, 1, 0),
name='Refraction',
colormap='magma',
axis_labels=["z", "y", "x"])
print(
f"3D-FFT computation time : {np.round(time.time() - start_time, decimals=2)} seconds"
)
fdm, sdzm, dxm, dym = rp.Calc_fd(FMAXHOLO, REWALD)
HOLO = np.zeros((DIMHOLO, DIMHOLO, NB_HOLO), dtype=np.complex128)
start_time = time.time()
for cpt in range(NB_HOLO):
if cpt % 100 == 0:
print(f"Hologram = {cpt} out of {NB_HOLO}")
TF_Holo = np.zeros((DIMHOLO, DIMHOLO), dtype=np.complex128)
k_inc = np.array([fi[0, cpt], fi[1, cpt]])
TF_Holo = st.Calc_TF_Holo(TomoSpectrum, TF_Holo, fdm, sdzm, dxm, dym,
FMAXHOLO, k_inc, REWALD, 632.8e-9, nimm)
decal = np.array([-k_inc[0] + DIMHOLO / 2,
-k_inc[1] + DIMHOLO / 2]).astype(int)
TF_Holo_r = rp.decal_TF_holo(TF_Holo, decal, TF_Holo.shape[0], roll=True)
HOLO[:, :, cpt] = (ifftn(TF_Holo_r)) / (UBornPitch**2 * FMAXHOLO**2)
# plt.imshow(np.abs(HOLO), cmap="gray")
# plt.show()
print(
f"Simulation time for {NB_HOLO} holograms: {np.round(time.time() - start_time, decimals=2)} seconds"
)
print("")
# ft.SAVtiffCube(CHEMIN_RE_UBORN, HOLO, PIXTHEO*1e6)
ft.SAVtiffCube(CHEMIN_RE_UBORN, HOLO.real, PIXTHEO * 1e6)
ft.SAVtiffCube(CHEMIN_IM_UBORN, HOLO.imag, PIXTHEO * 1e6)
print(
f"Execution time: {np.round(time.time() - total_time, decimals=2)} seconds"
)
print("")
Refraction = f_recon.real
Absorption = f_recon.imag
OTF = np.zeros_like(mask_sum)
OTF[mask_sum != 0] = 1
# TFVolfilt = np.zeros_like(OTF)
# TFVolfilt[TFVol != 0] = 1
viewer = napari.Viewer()
viewer.add_image(Absorption.transpose(-1, 1, 0),
name='Absorption',
colormap='magma')
viewer.add_image(Refraction.transpose(-1, 1, 0),
name='Refraction',
colormap='magma')
# Writting results
start_time = time.time()
ft.SAVtiffCube(
f"{PROCESSINGFOLDER}/Refraction_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
Refraction, 2 * PIXTHEO * 1e6)
ft.SAVtiffCube(
f"{PROCESSINGFOLDER}/Absorption_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
Absorption, 2 * PIXTHEO * 1e6)
ft.SAVtiffCube(f"{PROCESSINGFOLDER}/OTF_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
OTF, 1. / (Refraction.shape[0] * 2 * PIXTHEO * 1e6))
# ft.SAVtiffCube(f"{PROCESSINGFOLDER}/Spectrum_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
# fftshift(np.log10(abs(TFVol*1e17+1e-10)**2)), 1./(Refraction.shape[0]*2*PIXTHEO*1e6))
print(f"Data saving: {np.round(time.time() - start_time,decimals=2)} seconds")
