AMS-BP 0.0.32__py3-none-any.whl → 0.0.33__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.32"
+__version__ = "0.0.33"

AMS_BP/optics/lasers/laser_profiles.py

@@ -235,7 +235,7 @@ class LaserProfile(ABC):
 class GaussianBeam(LaserProfile):
     """3D Gaussian laser beam profile with time dependence."""
 
-    def calculate_intensity(
+    def calculate_intensity_(
         self,
         x: np.ndarray | float,
         y: np.ndarray | float,
@@ -274,7 +274,7 @@ class GaussianBeam(LaserProfile):
             # * np.cos(phase_terms)
         )
 
-    def calculate_intensity_(
+    def calculate_intensity(
         self,
         x: np.ndarray | float,
         y: np.ndarray | float,
@@ -312,7 +312,7 @@ class GaussianBeam(LaserProfile):
         w_z = self.get_beam_width(z_shifted)
 
         # Calculate peak intensity (z-dependent)
-        I0 = 2 * power / (np.pi * (self.params.beam_width / 2.0) ** 2)
+        I0 = 2 * power / (np.pi * (self.params.beam_width) ** 2)
         I0_z = I0 * (self.params.beam_width / w_z) ** 2
 
         # Calculate phase terms if needed
@@ -504,7 +504,7 @@ class HiLoBeam(LaserProfile):
         z_shifted = z - pos[2]
 
         # Calculate radial distance from optical axis
-        r = np.sqrt(x_shifted**2 + y_shifted**2)
+        r_squared = x_shifted**2 + y_shifted**2
 
         # Base beam parameters
         w0 = self.params.beam_width  # Beam waist
@@ -524,7 +524,7 @@ class HiLoBeam(LaserProfile):
         intensity = (
             I0
             * (w0 / w_z) ** 2  # Beam width scaling
-            * np.exp(-2 * r**2 / w_z**2)  # Gaussian radial profile
+            * np.exp(-2 * r_squared / w_z**2)  # Gaussian radial profile
         )
 
         # Lamination effect: attenuate out-of-focus regions

AMS_BP/sample/sim_sampleplane.py

@@ -207,23 +207,23 @@ class SamplePlane:
         trajectory: Optional[Dict[int, Tuple[float, float, float]]] = None,
     ) -> bool:
         """Add a fluorescent object to the sample plane"""
-        # Verify position is within sample space
-        if not self._space.contains_position(position):
-            return False
-
-        # Verify initial position is within FOV
-        if not self.is_within_fov(position):
-            return False
-
-        # If trajectory provided, verify all positions
-        if trajectory is not None:
-            if not all(
-                self._space.contains_position(pos) for pos in trajectory.values()
-            ):
-                return False
-            if not all(self.is_within_fov(pos) for pos in trajectory.values()):
-                return False
-
+        # # Verify position is within sample space
+        # if not self._space.contains_position(position):
+        #     return False
+        #
+        # # Verify initial position is within FOV
+        # if not self.is_within_fov(position):
+        #     return False
+
+        # # If trajectory provided, verify all positions
+        # if trajectory is not None:
+        #     if not all(
+        #         self._space.contains_position(pos) for pos in trajectory.values()
+        #     ):
+        #         return False
+        #     if not all(self.is_within_fov(pos) for pos in trajectory.values()):
+        #         return False
+        #
         if object_id in self._objects:
             return False
 
@@ -239,11 +239,11 @@ class SamplePlane:
         obj = FluorescentObject(object_id, position, fluorophore, trajectory)
         self._objects[object_id] = obj
 
-        # Update spatial index for all time points
-        for t in self.time_points:
-            pos = trajectory[t]
-            self._update_spatial_index(object_id, pos, t)
-
+        # # Update spatial index for all time points
+        # for t in self.time_points:
+        #     pos = trajectory[t]
+        #     self._update_spatial_index(object_id, pos, t)
+        #
         return True
 
     def get_all_objects(self) -> List[FluorescentObject]:

{ams_bp-0.0.32.dist-info → ams_bp-0.0.33.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.32
+Version: 0.0.33
 Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
 Project-URL: Documentation, https://joemans3.github.io/AMS_BP/
 Project-URL: Source code, https://github.com/joemans3/AMS_BP

{ams_bp-0.0.32.dist-info → ams_bp-0.0.33.dist-info}/RECORD

@@ -1,4 +1,4 @@
-AMS_BP/__init__.py,sha256=cpKNY-v_X4yiqwdfXMUdEc-j-zmY5npRlWs-Q6Sd4eI,327
+AMS_BP/__init__.py,sha256=ZjfBnA_D79EK47UsS4sJAJupBnTC6IELNNcZzSl9FVg,327
 AMS_BP/run_cell_simulation.py,sha256=7InopFikjo0HfaLO2siXskBIbyCIte9avG4YXjjaWCI,7420
 AMS_BP/sim_config.toml,sha256=3IqOQIJYmP5g4okk15nqQiNZb3ij7Pt63HbpI-5tySw,11672
 AMS_BP/sim_microscopy.py,sha256=Vsga9lTWqP0pjEnfFj0qKaSz7YZ_F4E3TqsaErwhi3E,19991
@@ -31,7 +31,7 @@ AMS_BP/optics/filters/filters.py,sha256=-iw7eqmDO77SEqlFTv5jJNVwpA8y93TLsjy5hhsA
 AMS_BP/optics/filters/channels/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/optics/filters/channels/channelschema.py,sha256=SConyA5yVdfnI_8sgcxVC8SV7S8tGUJYPPC6jn7lglU,906
 AMS_BP/optics/lasers/__init__.py,sha256=T7dHohhyLf_pBw4TidarYHWmiwxVXGE71-Bf1aeBbuc,564
-AMS_BP/optics/lasers/laser_profiles.py,sha256=Naz42SSqG_VS7TtLfM6kz7Gs7opDh6wa2An9CdR6C9M,17286
+AMS_BP/optics/lasers/laser_profiles.py,sha256=_h3g_TjolJI5NTg7T_m_ntyNpSFTJvxW0AeXf0svm-I,17284
 AMS_BP/optics/lasers/scanning_patterns.py,sha256=Xen96e5BlYI892HzZDXdwm80id6TbyNCNj-qvnRnSnI,3393
 AMS_BP/optics/psf/__init__.py,sha256=ezrKPgpTeR4gTHOvF0mhF6u2zMMTd8Bgp8PGeOf11fA,121
 AMS_BP/optics/psf/psf_engine.py,sha256=FbR4VHQ-VgCWrrDj8AHPPnVgwVUGs-OP19w_TjcbMcU,10215
@@ -42,7 +42,7 @@ AMS_BP/probabilityfuncs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG
 AMS_BP/probabilityfuncs/markov_chain.py,sha256=LV6KGr8Lv4NIvBPJqsR0CEynssa_mPH30qLaK85GObA,4339
 AMS_BP/probabilityfuncs/probability_functions.py,sha256=j_rIxrupGBf_FKkQBh1TvEa34A44jAasaZQRg2u3FuY,11793
 AMS_BP/sample/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/sample/sim_sampleplane.py,sha256=-Vb3o3vgUuN1qfoLMR8SanTbI7JtbtBvs78QzRdkps0,12826
+AMS_BP/sample/sim_sampleplane.py,sha256=szr0Y9zFsaJy0aY_Gm5AAVBbY8UsRwehxowUGfaK_2Q,12889
 AMS_BP/sample/flurophores/__init__.py,sha256=arLVUx1-yh5T41fH9Mr6RNY8Ao3ZioFQUtsfEZlzQkU,250
 AMS_BP/sample/flurophores/flurophore_schema.py,sha256=j8jnr4w4ltuhXUkjd74IoyyuotyH52mn8FWkgahX5Vw,10886
 AMS_BP/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
@@ -51,8 +51,8 @@ AMS_BP/utils/decorators.py,sha256=4qFdvzPJne0dhkhD1znPxRln1Rfr5NX8rdcCDcbATRU,62
 AMS_BP/utils/errors.py,sha256=7BOd-L4_YeKmWn3Q4EOdTnNF3Bj_exDa3eg5X0yCZrc,759
 AMS_BP/utils/maskMaker.py,sha256=2ca3n2nc8rFtUh1LurKXOJJsUmhrOpWbRnVX7fjRVvs,335
 AMS_BP/utils/util_functions.py,sha256=9Qlr4kjY04fObktR8TrzB0IgoG1yXtcmxPRX9AN34mM,9671
-ams_bp-0.0.32.dist-info/METADATA,sha256=ga6yZDd1sIWFqn1pdMbgjhvw4iEpyU1B4gJTbi7S21w,5869
-ams_bp-0.0.32.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ams_bp-0.0.32.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
-ams_bp-0.0.32.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.0.32.dist-info/RECORD,,
+ams_bp-0.0.33.dist-info/METADATA,sha256=ibqqOX-JYh5DpbV8f6LJPpDKH4IJyldZYuXBi1F5XBQ,5869
+ams_bp-0.0.33.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.0.33.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
+ams_bp-0.0.33.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.0.33.dist-info/RECORD,,