Randomisation

examples/article_figures/fig1_hiv_examples.py

@@ -114,6 +114,7 @@
     central_axis=False,
     use_dol=True,
     axis_object = ax,
+    random_seed=seed
     )
 
 filename = my_experiment.date_as_string + 'vlab4mic_hiv_antibody.png'

examples/article_figures/fig3_abc_panels.py

@@ -101,7 +101,7 @@ def create_parameter_grid_as_list(h_positions, v_positions, margin=0.1, min_z =
 ax.set_xticklabels([])
 ax.set_yticklabels([])
 
-filename = myexperiment2.date_as_string + 'vlab4mic_fig3_panelA.png'
+filename = myexperiment2.date_as_string + 'vlab4mic_fig3_panelB.png'
 filename2 = os.path.join(myexperiment2.output_directory, filename)
 fig.savefig(filename2,dpi=300, bbox_inches='tight')
 plt.close()
@@ -153,7 +153,7 @@ def create_parameter_grid_as_list(h_positions, v_positions, margin=0.1, min_z =
 myexperiment2.particle.gen_axis_plot(axis_object=ax4, with_sources=False, source_plotsize=0, source_plotmarker="o", view_init=[90,0,0],
                                      xlim=[0,1000], ylim=[0,1000], zlim=[0,600], emitter_plotsize=1)
 
-filename = myexperiment2.date_as_string + 'vlab4mic_fig3_panelB.png'
+filename = myexperiment2.date_as_string + 'vlab4mic_fig3_panel_AC.png'
 filename2 = os.path.join(myexperiment2.output_directory, filename)
 fig2.savefig(filename2,dpi=300, bbox_inches='tight')
 plt.close()

examples/article_figures/fig3_de_panels.py

@@ -46,6 +46,6 @@
 axs[3].set_title(title)
 
 
-filename = os.path.join(sweep_gen.output_directory, 'vlab4mic_fig3B.png')
+filename = os.path.join(sweep_gen.output_directory, 'vlab4mic_fig3E.png')
 fig.savefig(filename, dpi=300, bbox_inches='tight')
 plt.close()

examples/article_figures/figS_image_for_positioning.py

@@ -45,8 +45,8 @@
 plt.close()
 
 
-
-img_mask = np.random.rand(100,100)
+rng_ = np.random.default_rng(seed=random_seed)
+img_mask = rng_.random([100,100])
 p = 0.99
 img_mask[img_mask >= p] = 1
 img_mask[img_mask < p] = 0

src/vlab4mic/experiments.py

@@ -617,7 +617,7 @@ def _build_coordinate_field(
         if use_self_particle and self.generators_status("particle"):
             print("creating field from existing particle")
             exported_field, fieldobject = field_from_particle(
-                self.particle, **self.virtualsample_params, **kwargs
+                self.particle, **self.virtualsample_params, random_seed=self.random_seed, **kwargs
             )
             self.virtualsample_params["minimal_distance"] = (
                 fieldobject.molecules_params["minimal_distance"]
@@ -631,7 +631,7 @@ def _build_coordinate_field(
         else:
             # create minimal field
             fieldobject = coordinates_field.create_min_field(
-                **self.virtualsample_params, **kwargs
+                **self.virtualsample_params, random_seed=self.random_seed, **kwargs
             )
             exported_field = fieldobject.export_field()
             if keep:

src/vlab4mic/generate/coordinates_field.py

@@ -121,7 +121,7 @@ def init_from_file(self, field_yaml):
         self.set_molecules_params(**molecules)
 
     def create_minimal_field(
-        self, nmolecules=1, random_placing=False, random_orientations=False, random_rotations=False, **kwargs
+        self, nmolecules=1, random_placing=False, random_orientations=False, random_rotations=False, random_seed=None, **kwargs
     ):
         """
         Create a minimal field with a specified number of molecules and placement options.
@@ -163,7 +163,7 @@ def create_minimal_field(
             # if no list was passed, then we will use the default nmolecules parameter
             # having more than one particle necesarily use random placing
             self.random_placing = True
-            self.generate_random_positions()
+            self.generate_random_positions(random_seed=random_seed)
             self._gen_abs_from_rel_positions()
             self.fluorophre_emitters = {
                 fluo_name: self.get_molecule_param("absolute_positions")
@@ -174,7 +174,7 @@ def create_minimal_field(
             self.set_molecule_param("nMolecules", 1)
             if random_placing:
                 self.random_placing = True
-                self.generate_random_positions()
+                self.generate_random_positions(random_seed=random_seed)
             self._gen_abs_from_rel_positions()
             point = self.get_molecule_param("absolute_positions")
             self.fluorophre_emitters = {fluo_name: point.reshape(1, 3)}
@@ -296,6 +296,7 @@ def set_molecules_params(
         random_positions,
         random_orientations,
         random_rotations,
+        random_seed=None,
         **kwargs,
     ):
         """
@@ -317,11 +318,11 @@ def set_molecules_params(
         # self.change_number_of_molecules(nMolecules)
         self.set_molecule_param("nMolecules", nMolecules)
         if random_positions:
-            self.generate_random_positions()
+            self.generate_random_positions(random_seed=random_seed)
         if random_orientations:
-            self.generate_random_orientations()
+            self.generate_random_orientations(random_seed=random_seed)
         if random_rotations:
-            self.initialise_random_rotations()
+            self.initialise_random_rotations(random_seed=random_seed)
         for key, value in kwargs.items():
             self.molecules_params[key] = value
 
@@ -337,7 +338,7 @@ def show_params(self):
             print(key, ": ", val)
 
     # methods to prime molecule positions, orientations...
-    def generate_random_positions(self):
+    def generate_random_positions(self, random_seed=None):
         """
         Generate random positions for molecules within the field, optionally enforcing a minimal distance.
         """
@@ -359,23 +360,23 @@ def generate_random_positions(self):
             self.molecules_params["relative_positions"] = rand
             self._gen_abs_from_rel_positions()
 
-    def randomise_axial_position(self):
-        rng = np.random.default_rng()
+    def randomise_axial_position(self, random_seed=None):
+        rng = np.random.default_rng(seed=random_seed)
         nmolecules = self.get_molecule_param("nMolecules")
         axial_offsets = rng.choice(self.axial_offset, nmolecules, replace=True)
         for i, zpos in enumerate(axial_offsets):
             self.molecules_params["absolute_positions"][i][2] = zpos + self.z_offset
 
 
-    def generate_random_orientations(self):
+    def generate_random_orientations(self, random_seed=None):
         """
         Generate random orientations for all molecules in the field.
         """
         # give new orientation
         norientations = self.get_molecule_param("nMolecules")
         orientations = []
         unconstrained = True
-        rng = np.random.default_rng()
+        rng = np.random.default_rng(seed=random_seed)
         xy_orientation_changes = np.zeros((norientations,))
         if self.xy_orientations is not None:
             xy_orientation_changes =  rng.choice(self.xy_orientations, norientations, replace=True)
@@ -403,12 +404,12 @@ def generate_random_orientations(self):
             self.set_molecule_param("orientations_planewise", orientations_planewise)
             self.set_molecule_param("orientations", None)
 
-    def initialise_random_rotations(self, rotation_angles: list = None):
+    def initialise_random_rotations(self, rotation_angles: list = None, random_seed=None):
         """
         Generate random rotations around central axis for all molecules in the field.
         """
         nrotations = self.get_molecule_param("nMolecules")
-        rng = np.random.default_rng()
+        rng = np.random.default_rng(seed=random_seed)
         if self.rotation_angles is None:
             print("random unconstrained rotations")
             rotations = rng.integers(360, size=nrotations) 
@@ -531,7 +532,7 @@ def get_fluorophore_params(self):
         return self.fluoparams
 
     # working with macromolecules
-    def create_molecules_from_InstanceObject(self, InstancePrototype: LabeledInstance):
+    def create_molecules_from_InstanceObject(self, InstancePrototype: LabeledInstance, random_seed=None):
         """
         Create molecules in the field from a prototype instance.
 
@@ -550,7 +551,7 @@ def create_molecules_from_InstanceObject(self, InstancePrototype: LabeledInstanc
             self._set_molecule_minimal_distance(dist=particle_copy.radial_hindance)
         #self._set_molecule_minimal_distance(dist=min_distance)
         if self.random_placing:
-            self.generate_random_positions()
+            self.generate_random_positions(random_seed=random_seed)
         self._gen_abs_from_rel_positions()
         # due to constraints, the actual number of particles might not be reps
         nmolecules = len(self.molecules_params["absolute_positions"])
@@ -569,9 +570,9 @@ def create_molecules_from_InstanceObject(self, InstancePrototype: LabeledInstanc
         if self.sample_initial_orientation is not None:
             self.generate_global_orientation(self.sample_initial_orientation)
         if self.random_orientations:
-            self.generate_random_orientations()
+            self.generate_random_orientations(random_seed=random_seed)
         if self.random_rotations:
-            self.initialise_random_rotations()
+            self.initialise_random_rotations(random_seed=random_seed)
             # self.relabel_molecules()
         self.relabel_molecules()
 
@@ -943,6 +944,7 @@ def create_min_field(
     random_orientations=False,
     random_rotations=False,
     prints=False,
+    random_seed=None,
     **kwargs,
 ):
     """
@@ -977,6 +979,7 @@ def create_min_field(
         random_placing=random_placing,
         random_orientations=random_orientations,
         random_rotations=random_rotations,
+        random_seed=random_seed,
         **kwargs,
     )
     return coordinates_field

src/vlab4mic/generate/labelled_instance.py

@@ -1001,6 +1001,7 @@ def show_probe(
         use_dol=False,
         exact_dol= None,
         axis_object=None,
+        random_seed=None, 
         **kwargs,
     ):
         """
@@ -1052,6 +1053,7 @@ def show_probe(
             probe_emitters, center, np.array([0, 0, 0])
         )
         if dol is not None and use_dol:
+            rng_ = np.random.default_rng(seed=random_seed) 
             list_reoriented_points = []
             max_emitters = centered_emitters.shape[0]
             emitter_indices = np.arange(max_emitters)
@@ -1060,13 +1062,13 @@ def show_probe(
                 selected_emitters = [emitter_indices[x] for x in exact_dol]
                 #selected_emitters = emitter_indices[exact_dol]
             else:
-                int_dol = np.random.poisson(lam=dol)
+                int_dol = rng_.poisson(lam=dol)
                 if int_dol != 0:
                     if int_dol > max_emitters:
                         # use max value
                         selected_emitters = emitter_indices
                     else:
-                        selected_emitters = np.random.choice(
+                        selected_emitters = rng_.choice(
                             emitter_indices, size=int_dol, replace=False
                         )
             for se in selected_emitters:

src/vlab4mic/workflows.py

@@ -273,7 +273,7 @@ def particle_from_structure(
 
 
 def field_from_particle(
-    particle: labinstance.LabeledInstance, field_config: str = None, **kwargs
+    particle: labinstance.LabeledInstance, field_config: str = None, random_seed=None, **kwargs
 ):
     """
     Create a particle field from an input particle object.
@@ -305,7 +305,7 @@ def field_from_particle(
         # coordinates_field.init_from_file(field_config)
     else:
         coordinates_field = create_min_field(**kwargs)
-    coordinates_field.create_molecules_from_InstanceObject(particle)
+    coordinates_field.create_molecules_from_InstanceObject(particle, random_seed=random_seed)
     coordinates_field.construct_static_field()
     return coordinates_field.export_field(), coordinates_field