added a jupyter notebook to show psf & otf profiles

Meizhu-Liang · Mar 24, 2023 · 86a22f6 · 86a22f6
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commit 86a22f6
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Showing 4 changed files with 33 additions and 35 deletions.
diff --git a/Jupyter_SIMulator.ipynb b/Jupyter_SIMulator.ipynb
diff --git a/README.md b/README.md
@@ -17,7 +17,7 @@ The calculation can be GPU-accelerated if the CUPY (tested with cupy 8.3.0) is i
 Currently applies to:
 - conventional 2-beam SIM data with 3 angles and 3 phases
 - 3-beam hexagonal SIM data with 7 phases, as described in the paper
-- 3-beam hexagonal SIM data with 7 phases at right-angles
+- 3-beam hexagonal SIM data with 5 phases at right-angles
 
 ----------------------------------
 
@@ -46,6 +46,7 @@ To install latest development version :
 ## Usage
 
 1) Open napari and create the viewer.
+2) ![raw](https://github.com/Meizhu-Liang/napari-generic-SIMulator/raw/main/images/hex.avi)
 
 
 2) Launch the widget in ***Plugin***

diff --git a/src/napari_generic_simulator/Illumination.py b/src/napari_generic_simulator/Illumination.py
@@ -60,7 +60,7 @@ def jones_vectors(self, astep):
 
     def _ill_obj(self, x, y, pstep, astep):
         """Illumination intensity applied on the object"""
-        ill = self.xp.sum(self._ill_test_vec(x, y, pstep, astep), axis=1)  # take real part and round to 15 decimals
+        ill = self.xp.sum(self._ill_obj_vec(x, y, pstep, astep), axis=1)  # take real part and round to 15 decimals
         return ill
 
     def _ill_obj_vec(self, x, y, pstep, astep):

diff --git a/src/napari_generic_simulator/baseSIMulator.py b/src/napari_generic_simulator/baseSIMulator.py
@@ -344,12 +344,13 @@ def raw_image_stack_brownian(self):
             otf_x = self.xp.fft.fftn(self.xp.fft.fftshift(psf_x, axes=0))  # need to set plane zero as in-focus here
             otf_y = self.xp.fft.fftn(self.xp.fft.fftshift(psf_y, axes=0))  # need to set plane zero as in-focus here
             otf_z = self.xp.fft.fftn(self.xp.fft.fftshift(psf_z, axes=0))  # need to set plane zero as in-focus here
-        aotf = abs(self.xp.fft.fftshift(otf))  # absolute otf
+        aotf = abs(self.xp.fft.fftshift(otf))  # absolute otf, also modulus of otf (MTF)
+        self.aotffile = np.sum(aotf, axis=(1, 2))
         if self.acc == 3:
             aotf = cp.asnumpy(aotf)
         m = max(aotf.flatten())
 
-        self.aotf = np.log(aotf + aotf.max() / 1000)  # 3d aotx with log
+        self.aotf = np.log(aotf + aotf.max() / 1000)  # 3d aotf with log
         if self.acc == 3:
             self.aotf = cp.asnumpy(self.aotf)