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()
print("----------------------------------")
start_time = time.time()
UBornCplxR, UBornCplxG, UBornCplxB = rp.RheinbergIllumination(
Refraction + 1j * Absorption, [30, 120], 60, [70, 250])
IntensiteRhein = np.zeros((DIMTOMO, DIMTOMO, DIMTOMO, 3))
IntensiteRhein[:, :, :, 0] = np.abs(UBornCplxR)**2
IntensiteRhein[:, :, :, 1] = np.abs(UBornCplxG)**2
IntensiteRhein[:, :, :, 2] = np.abs(UBornCplxB)**2
print(
f"Rheinberg Contrast processing time: {np.round(time.time() - start_time,decimals=2)} seconds"
)
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"
)
)
print("")
RefractionB = f_reconB.real
AbsorptionB = f_reconB.imag
OTFB = np.zeros_like(mask_sum)
OTFB[mask_sum != 0] = 1
IntensiteB = np.abs(RefractionB + 1j * AbsorptionB)**2
IntensiteRhein[:, :, :, 2] = IntensiteB
OTFRhein[:, :, :, 2] = OTFB
del RefractionB, AbsorptionB, OTFB, IntensiteB
# Writting results
start_time = time.time()
ft.SAVtiffRGBCube(
f"{PROCESSINGFOLDER}/Rheinberg_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
IntensiteRhein, 2 * PIXTHEO * 1e6)
ft.SAVtiffRGBCube(
f"{PROCESSINGFOLDER}/OTFRheinberg_{DIMTOMO}x{DIMTOMO}x{DIMTOMO}.tiff",
OTFRhein, 1. / (OTFRhein.shape[0] * 2 * PIXTHEO * 1e6))
print(f"Data saving: {np.round(time.time() - start_time,decimals=2)} seconds")
viewer = napari.view_image(IntensiteRhein[:, :, :, 2].transpose(-1, 1, 0),
name='Bleu',
colormap='blue')
viewer.add_image(IntensiteRhein[:, :, :, 1].transpose(-1, 1, 0),
name='Rouge',
colormap='red')
viewer.add_image(IntensiteRhein[:, :, :, 0].transpose(-1, 1, 0),
name='Vert',
colormap='green')