AMS-BP 0.0.31__py3-none-any.whl → 0.0.251__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.31"
+__version__ = "0.0.251"

AMS_BP/motion/movement/fbm_BP.py

@@ -1,7 +1,6 @@
 import numpy as np
-
+from .boundary_conditions import _refecting_boundary, _absorbing_boundary
 from ...probabilityfuncs.markov_chain import MCMC_state_selection
-from .boundary_conditions import _absorbing_boundary, _refecting_boundary
 
 BOUNDARY_CONDITIONS = {
     "reflecting": _refecting_boundary,
@@ -162,8 +161,10 @@ class FBM_BP:
         phi = np.zeros(self.n)
         psi = np.zeros(self.n)
         # construct a gaussian noise vector
-        gn = np.random.normal(0, 1, self.n) * np.sqrt(
-            2 * self._diff_a_n * (self.dt ** (2 * self._hurst_n))
+        gn = (
+            np.random.normal(0, 1, self.n)
+            * np.sqrt(self.dt * 2 * self._diff_a_n)
+            * (self.dt ** (2 * self._hurst_n))
         )
         # catch is all hurst are 0.5 then use the gaussian noise vector corresponding to the scale defined by the diffusion parameter
         if np.all(self._hurst_n == 0.5):

AMS_BP/motion/track_gen.py

@@ -124,12 +124,12 @@ class Track_generator:
             rel_space_lim[i] = self.space_lim[i] - initials[i]
 
         # convert the diffusion_coefficients
-        # diffusion_coefficient = self._convert_diffcoef_um2s_um2xms(
-        #     diffusion_coefficient
-        # )
+        diffusion_coefficient = self._convert_diffcoef_um2s_um2xms(
+            diffusion_coefficient
+        )
         fbm = FBM_BP(
             n=track_length,
-            dt=self.oversample_motion_time / 1000.0,
+            dt=1,
             hurst_parameters=[hurst_exponent],
             diffusion_parameters=[diffusion_coefficient],
             diffusion_parameter_transition_matrix=[1],
@@ -216,11 +216,11 @@ class Track_generator:
         for i in range(3):
             rel_space_lim[i] = self.space_lim[i] - initials[i]
         # convert the diffusion_coefficients
-        # diffusion_parameters = self._convert_diffcoef_um2s_um2xms(diffusion_parameters)
+        diffusion_parameters = self._convert_diffcoef_um2s_um2xms(diffusion_parameters)
         # initialize the fbm class
         fbm = FBM_BP(
             n=track_length,
-            dt=self.oversample_motion_time / 1000.0,
+            dt=1,
             hurst_parameters=hurst_parameters,
             diffusion_parameters=diffusion_parameters,
             diffusion_parameter_transition_matrix=diffusion_transition_matrix,

AMS_BP/optics/lasers/laser_profiles.py

@@ -371,16 +371,15 @@ class WidefieldBeam(LaserProfile):
         Returns:
             Intensity scaling factor between 0 and 1
         """
-        # # Use error function for smooth transition at DoF boundaries
-        # # Scale factor determines how sharp the transition is
-        # scale_factor = 2.0  # Adjust this to change transition sharpness
-        #
-        # # Normalize z by DoF and create smooth falloff
-        # normalized_z = scale_factor * (np.abs(z)) / self.dof
-        #
-        # # Use sigmoid function for smooth transition
-        # return 1 / (1 + np.exp(normalized_z))
-        return 1.0
+        # Use error function for smooth transition at DoF boundaries
+        # Scale factor determines how sharp the transition is
+        scale_factor = 2.0  # Adjust this to change transition sharpness
+
+        # Normalize z by DoF and create smooth falloff
+        normalized_z = scale_factor * (np.abs(z) - self.dof / 2) / self.dof
+
+        # Use sigmoid function for smooth transition
+        return 1 / (1 + np.exp(normalized_z))
 
     def calculate_intensity(
         self,
@@ -417,7 +416,7 @@ class WidefieldBeam(LaserProfile):
         base_intensity = power / (np.pi * self.max_radius**2)
 
         # Apply radial intensity profile with smooth falloff at edges
-        edge_width = self.max_radius * 0.00001
+        edge_width = self.max_radius * 0.00001 
         radial_profile = 0.5 * (1 - np.tanh((r - self.max_radius) / edge_width))
         # Apply DoF-based axial intensity profile
         axial_profile = self._calculate_dof_profile(z_shifted)

AMS_BP/optics/psf/psf_engine.py

@@ -85,19 +85,15 @@ class PSFEngine:
         self._grid_xy = _generate_grid(self._psf_size, self.params.pixel_size)
 
         # Pre-calculate normalized sigma values
-        self._norm_sigma_xy = self._sigma_xy / 2.0
-        self._norm_sigma_z = self._sigma_z / 2.0
+        self._norm_sigma_xy = self._sigma_xy / 2.355
+        self._norm_sigma_z = self._sigma_z / 2.355
 
         # Generate pinhole mask if specified
         if self.params.pinhole_radius is not None:
             if self.params.pinhole_radius < AIRYFACTOR * self._sigma_xy:
-                RuntimeWarning(
+                raise ValueError(
                     f"Pinhole size ({self.params.pinhole_radius} um) is smaller than {AIRYFACTOR} times the Airy lobe. This will diffract the emission light in the pinhole; an ideal pinhole size for this setup is {self._sigma_xy} um."
                 )
-                #
-                # raise ValueError(
-                #     f"Pinhole size ({self.params.pinhole_radius} um) is smaller than {AIRYFACTOR} times the Airy lobe. This will diffract the emission light in the pinhole; an ideal pinhole size for this setup is {self._sigma_xy} um."
-                # )
             self._pinhole_mask = self._generate_pinhole_mask()
         else:
             self._pinhole_mask = None
@@ -120,9 +116,7 @@ class PSFEngine:
         return (r <= self.params.pinhole_radius).astype(np.float64)
 
     @lru_cache(maxsize=128)
-    def psf_z(
-        self, x_val: float, y_val: float, z_val: float, norm_scale: bool = True
-    ) -> NDArray[np.float64]:
+    def psf_z(self, z_val: float) -> NDArray[np.float64]:
         """Calculate the PSF at the detector for a point source at z_val.
 
         This represents how light from a point source at position z_val
@@ -130,28 +124,17 @@ class PSFEngine:
         detector. If a pinhole is present, it spatially filters this pattern.
 
         Args:
-            x_val: x-position of the point source in micrometers
-            y_val: y-position of the point source in micrometers
             z_val: Z-position of the point source in micrometers
 
         Returns:
             2D array containing the light intensity pattern at the detector
         """
         x, y = self._grid_xy
-        sigma_xy_z_squared = (self._norm_sigma_xy**2) * (
-            1 + (z_val / self._norm_sigma_z) ** 2
-        )
 
         # Calculate how light from the point source diffracts through collection optics
-        r_squared = (x - x_val % self.params.pixel_size) ** 2 + (
-            y - y_val % self.params.pixel_size
-        ) ** 2
-        psf_at_detector = np.exp(-0.5 * (r_squared / sigma_xy_z_squared))
-
-        if norm_scale:
-            psf_at_detector = self.normalize_psf(
-                psf_at_detector, mode="sum"
-            ) * self.psf_z_xy0(z_val)
+        r_squared = (x / self._norm_sigma_xy) ** 2 + (y / self._norm_sigma_xy) ** 2
+        z_term = (z_val / self._norm_sigma_z) ** 2
+        psf_at_detector = np.exp(-0.5 * (r_squared + z_term))
 
         if self._pinhole_mask is not None:
             # Apply pinhole's spatial filtering
@@ -269,7 +252,7 @@ def calculate_psf_size(
         Tuple of dimensions (z,y,x) or (y,x) for the PSF calculation
     """
     # Calculate radius to capture important features (2x Airy radius)
-    r_psf = 3 * sigma_xy
+    r_psf = 2 * sigma_xy
 
     # Convert to pixels and ensure odd number
     pixels_xy = int(np.ceil(r_psf / pixel_size))

AMS_BP/photophysics/photon_physics.py

@@ -168,11 +168,11 @@ class incident_photons:
                 photons_n = self.transmission_photon_rate.values[i] * dt
                 photons += photons_n
                 psf_gen = (
-                    self.generator[i].psf_z(
-                        x_val=self.position[0],
-                        y_val=self.position[1],
-                        z_val=self.position[2],
+                    self.generator[i].normalize_psf(
+                        self.generator[i].psf_z(z_val=self.position[2]),
+                        mode="sum",
                     )
+                    * self.generator[i].psf_z_xy0(z_val=self.position[2])
                     * photons_n
                 )
 

{ams_bp-0.0.31.dist-info → ams_bp-0.0.251.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.31
+Version: 0.0.251
 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-0.0.31.dist-info → ams_bp-0.0.251.dist-info}/RECORD

@@ -1,4 +1,4 @@
-AMS_BP/__init__.py,sha256=iU9u6S7CcnHsXcUjS8BDRGWvPnqK-wceLqo-pkKOSrk,327
+AMS_BP/__init__.py,sha256=qv5C9LGYuQzZP9NQ_ST5KH4IuqGwi8PVl44IypUo97w,328
 AMS_BP/run_cell_simulation.py,sha256=7InopFikjo0HfaLO2siXskBIbyCIte9avG4YXjjaWCI,7420
 AMS_BP/sim_config.toml,sha256=3IqOQIJYmP5g4okk15nqQiNZb3ij7Pt63HbpI-5tySw,11672
 AMS_BP/sim_microscopy.py,sha256=u60ApTA6MTUmqSAd7EsAxweKya_Typput8NumDq9fp8,18697
@@ -16,10 +16,10 @@ AMS_BP/metadata/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/metadata/metadata.py,sha256=YDumjc5sI3lY_UZx8f0ZhMqbG2qKQkysXwl7CY4ZtnY,2927
 AMS_BP/motion/__init__.py,sha256=cy3W-wCRjjlN1DrTqYc-JltYwcE8SZCXMVPJ2o6q_BQ,178
 AMS_BP/motion/condensate_movement.py,sha256=eig4WtD7o1cvIafWMjOk6pqxyhe_IIucgLcBEoDvasU,11648
-AMS_BP/motion/track_gen.py,sha256=2ssg8BXxZUEufycqgziL2BOeKOInTmmjzsthfS80gfI,19540
+AMS_BP/motion/track_gen.py,sha256=Z3QJLVMP1gX4SlgOXFxBg8sJhBG0Xq25ixnBoEHEAZI,19462
 AMS_BP/motion/movement/__init__.py,sha256=PqovpG4dAuFFIP9M2_kt-6egQJX3P5ig4MMWVzNaswg,278
 AMS_BP/motion/movement/boundary_conditions.py,sha256=jpfK3AEUY8btrTsu19bpUfx-jri7_HfyxqMFjMoxAVM,2200
-AMS_BP/motion/movement/fbm_BP.py,sha256=47d2ph4r8Izso_mBxxgQYH9xjEqj_zXUzIGpEXPEhFM,9292
+AMS_BP/motion/movement/fbm_BP.py,sha256=dH-JZiAInnIaZXH1wAAo8dOIX9zafclqnZ4dOhKtnO0,9327
 AMS_BP/optics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/optics/camera/__init__.py,sha256=eCoDUFHcoCWgbgYdLn8EH7AULM53A3XWTXNZnV8QxeY,182
 AMS_BP/optics/camera/detectors.py,sha256=_815Ovo7Aj375OZh5Xim8pFuZEEcSVtSdnLRYFqb3_8,10355
@@ -29,11 +29,11 @@ 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=7mqf5VMpb0VN_veqYEdeiakr0kaOilfGzNq5mzFQuRw,17136
+AMS_BP/optics/lasers/laser_profiles.py,sha256=DM3YDh6JccgQk8fjBRh6J3bDpTChm8Im_AE5z9EK3EI,17101
 AMS_BP/optics/psf/__init__.py,sha256=ezrKPgpTeR4gTHOvF0mhF6u2zMMTd8Bgp8PGeOf11fA,121
-AMS_BP/optics/psf/psf_engine.py,sha256=FbR4VHQ-VgCWrrDj8AHPPnVgwVUGs-OP19w_TjcbMcU,10215
+AMS_BP/optics/psf/psf_engine.py,sha256=Do54D1jMbSrj5uljdTrrEttCvxq3qbVT74acRuOk15c,9434
 AMS_BP/photophysics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/photophysics/photon_physics.py,sha256=9FWBXaxuSRaSxW8bY0x1d5R5buooibZbRdYTuQcMXhQ,6624
+AMS_BP/photophysics/photon_physics.py,sha256=QRG_QIZ4csJ3g5qGP9Wtk7kzqm8_MUbVHfFef6cMtHQ,6671
 AMS_BP/photophysics/state_kinetics.py,sha256=IdZtlHCLs--iSjLwDu2IQA617qXC4la8VpqosrM-vgQ,5401
 AMS_BP/probabilityfuncs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/probabilityfuncs/markov_chain.py,sha256=LV6KGr8Lv4NIvBPJqsR0CEynssa_mPH30qLaK85GObA,4339
@@ -48,8 +48,8 @@ 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=jI6WBh09_khdABnEoVK7SK1WRvCLHuw40f5ALyflzlc,9478
-ams_bp-0.0.31.dist-info/METADATA,sha256=_BrdW-rInQ_BfbnMgpegzioE8C7ksXy3Z0guJdZxWxA,5869
-ams_bp-0.0.31.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ams_bp-0.0.31.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
-ams_bp-0.0.31.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.0.31.dist-info/RECORD,,
+ams_bp-0.0.251.dist-info/METADATA,sha256=lSmQVE_Aaw13hf692nC4MuTZplqmg5vBqjap8PTnow0,5870
+ams_bp-0.0.251.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.0.251.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
+ams_bp-0.0.251.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.0.251.dist-info/RECORD,,