Merge branch 'full_vectorial'

# Conflicts:
#	src/napari_generic_simulator/_widget.py

README.md

@@ -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***

src/napari_generic_simulator/Illumination.py

@@ -58,20 +58,26 @@ def jones_vectors(self, astep):
             f_p = self.xp.array(self.polarised_field(phi_S))
             self.S[:, i, :] = self.xp.transpose(self.rotation(phi_S, self.theta) @ f_p)
 
-    def _ill_test(self, x, y, pstep, astep):
+    def _ill_obj(self, x, y, pstep, astep):
+        """Illumination intensity applied on the object"""
+        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):
+        """Vectorised illumination intensity applied on the object"""
         p = [0, pstep * 2 * np.pi / self._phaseStep, pstep * (-4) * np.pi / self._phaseStep]
-        E = self.xp.zeros((self.npoints, self._n_beams, 3), dtype=self.xp.complex64)
+        E = self.xp.zeros((self.npoints, self._n_beams, 3), dtype=self.xp.complex64)  # exponential terms of field
         for i in range(self._n_beams):
             phi_E = i * self._beam_a + astep * 2 * np.pi / self._angleStep + self.angle_error[i, astep]
             xyz = self.xp.transpose(self.xp.stack([x, y, self.xp.zeros(self.npoints)]))
             e = self.xp.exp(-1j * (xyz @ self.rotation(phi_E, self.theta) @ self.xp.array([0, 0, self.k0]) + p[i] +
                                    self.phase_error[i, astep, pstep]))
             E[:, i, :] = self.xp.transpose(self.xp.array([e, ] * 3))
-        F = self.xp.sum(self.S * E, axis=1, dtype=self.xp.complex64)
-        ill = self.xp.sum(F * self.xp.conjugate(F), axis=1).real  # the dot multiplication
+        F = self.xp.sum(self.S * E, axis=1, dtype=self.xp.complex64)  # field of illumination
+        # to calculate intensity: ill = F @ F_conjugate
+        ill = (F * self.xp.conjugate(F)).real.round(15)  # take real part and round to 15 decimals
         return ill
 
-
 class ConIll(Illumination):
     def __init__(self):
         self._phaseStep = 3

src/napari_generic_simulator/_widget.py

@@ -186,7 +186,8 @@ class Pol(Enum):
 
 class Psf_calc(Enum):
     SCALAR = 0
-    VECTOR_in_development = 1
+    VEC_FLEXI = 1
+    VEC_RIGID = 2
 
 
 class Accel(Enum):
@@ -250,6 +251,7 @@ def parameters(self):
         self.fwhmz = FloatSpinBox(value=3.0, name='spin', label='fwhmz(μm)', min=0.0, max=10.0)
         self.random_seed = SpinBox(value=123, name='spin', label='random seed')
         self.drift = FloatSpinBox(value=0.0, name='spin', label='drift(nm)', min=0.0, max=1000.0, step=5)
+        self.defocus = FloatSpinBox(value=0.0, name='spin', label='de-focus(μm)', min=-10.0, max=10, step=5)
         self.sph_abb = FloatSpinBox(value=0.0, name='spin', label='spherical(rad)', min=-10.0, max=10, step=0.5)
         self.lable = Label(value='aberration')
 
@@ -259,7 +261,7 @@ def par_list(self):
                 self.Psf.value, self.N.value, self.pixel_size.value, self.magnification.value, self.ill_NA.value,
                 self.det_NA.value, self.n.value, self.ill_wavelength.value, self.det_wavelength.value,
                 self.zrange.value, self.tpoints.value, self.xdrift.value, self.zdrift.value,
-                self.fwhmz.value, self.random_seed.value, self.drift.value, self.sph_abb.value]
+                self.fwhmz.value, self.random_seed.value, self.drift.value, self.defocus.value, self.sph_abb.value]
 
     def set_att(self):
         """Sets attributes in the simulation class. Executed frequently to update the parameters"""
@@ -299,8 +301,10 @@ def set_att(self):
             if self.Acceleration.value == Accel.CUPY:
                 self.sim.acc = 3
 
-        if self.Psf.value == Psf_calc.VECTOR_in_development:
-            self.sim.psf_calc = 'vector'
+        if self.Psf.value == Psf_calc.VEC_RIGID:
+            self.sim.psf_calc = 'vector_rigid'
+        elif self.Psf.value == Psf_calc.VEC_FLEXI:
+                self.sim.psf_calc = 'vector_flexible'
         elif self.Psf.value == Psf_calc.SCALAR:
             self.sim.psf_calc = 'scalar'
 
@@ -324,14 +328,16 @@ def set_att(self):
         self.sim.fwhmz = self.fwhmz.value
         self.sim.drift = self.drift.value
         self.sim.random_seed = self.random_seed.value
+        self.sim.defocus = self.defocus.value
         self.sim.sph_abb = self.sph_abb.value
         self.used_par_list = [self.SIM_mode.value, self.Polarisation.value, self.Acceleration.value,
                               self.Psf.value,
                               self.N.value, self.pixel_size.value, self.magnification.value, self.ill_NA.value,
                               self.det_NA.value,
                               self.n.value, self.ill_wavelength.value, self.det_wavelength.value,
                               self.zrange.value, self.tpoints.value, self.xdrift.value, self.zdrift.value,
-                              self.fwhmz.value, self.random_seed.value, self.drift.value, self.sph_abb.value]
+                              self.fwhmz.value, self.random_seed.value, self.drift.value, self.defocus.value,
+                              self.sph_abb.value]
 
     def start_simulator(self):
         """Starts the raw images generators and create the frequency space"""
@@ -383,7 +389,8 @@ def show_img(data):
                                                  'tpoints': self.tpoints.value, 'xdrift': self.xdrift.value,
                                                  'zdrift': self.zdrift.value, 'fwhmz': self.fwhmz.value,
                                                  'random seed': self.random_seed.value, 'Brownian': self.drift.value,
-                                                 'sph_abb': self.sph_abb.value})
+                                                 'defocus': self.defocus.value, 'sph_abb': self.sph_abb.value
+                                                 })
                 current_step = list(self._viewer.dims.current_step)
                 for dim_idx in [-3, -2, -1]:
                     current_step[dim_idx] = data.shape[dim_idx] // 2
@@ -414,7 +421,8 @@ def wrap_widgets(self):
                                    self.pixel_size, self.ill_NA, self.det_NA, self.n,
                                    self.ill_wavelength, self.det_wavelength]),
                 Container(widgets=[self.magnification, self.zrange, self.tpoints, self.xdrift,
-                                   self.zdrift, self.fwhmz, self.random_seed, self.drift, self.sph_abb])], layout='horizontal')
+                                   self.zdrift, self.fwhmz, self.random_seed, self.drift, self.defocus,
+                                   self.sph_abb])], layout='horizontal')
         w_cal = magicgui(self.get_results, call_button='Calculate raw image stack', auto_call=False)
 
         # 'save and print' widgets
@@ -514,10 +522,9 @@ def on_show_illumination_click():
                     except Exception as e:
                         print(str(e))
 
-        w_save_and_print = Container(widgets=[Container(widgets=[save_tif_with_tags, print_tif]),
-                                              Container(widgets=[show_psf, show_otf, show_illumination])],
-                                     layout='horizontal', labels=None)
+        w_save_and_print = Container(widgets=[save_tif_with_tags, print_tif], layout='horizontal')
+        w_show = Container(widgets=[show_psf, show_otf, show_illumination], layout='horizontal')
         self.messageBox = LineEdit(value='Messages')
         self.w = Container(widgets=[w_parameters, magicgui(self.select_layer, call_button='Calculate results'),
-                                    w_save_and_print, self.messageBox],
+                                    w_save_and_print, w_show, self.messageBox],
                            labels=None)