AMS-BP 0.0.25__py3-none-any.whl → 0.0.31__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.25"
+__version__ = "0.0.31"

AMS_BP/motion/movement/fbm_BP.py

@@ -1,6 +1,7 @@
 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,
@@ -161,10 +162,8 @@ 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(self.dt * 2 * self._diff_a_n)
-            * (self.dt ** (2 * self._hurst_n))
+        gn = np.random.normal(0, 1, self.n) * np.sqrt(
+            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=1,
+            dt=self.oversample_motion_time / 1000.0,
             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=1,
+            dt=self.oversample_motion_time / 1000.0,
             hurst_parameters=hurst_parameters,
             diffusion_parameters=diffusion_parameters,
             diffusion_parameter_transition_matrix=diffusion_transition_matrix,

AMS_BP/optics/lasers/laser_profiles.py

@@ -371,15 +371,16 @@ 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 / 2) / self.dof
-
-        # Use sigmoid function for smooth transition
-        return 1 / (1 + np.exp(normalized_z))
+        # # 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
 
     def calculate_intensity(
         self,
@@ -416,7 +417,7 @@ 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 * 0.01  # 10% of max radius
+        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)
@@ -425,32 +426,6 @@ class WidefieldBeam(LaserProfile):
         return base_intensity * radial_profile * axial_profile
 
 
-# Example usage
-if __name__ == "__main__":
-    # Create parameters for a typical microscope objective
-    params = LaserParameters(
-        wavelength=488,  # 488 nm
-        power=0.001,  # 1 mW
-        beam_width=0.25,  # 250 nm
-        numerical_aperture=1.4,
-        refractive_index=1.518,  # Oil immersion
-    )
-
-    # Create beam object
-    beam = GaussianBeam(params)
-
-    # Get intensity map
-    result = beam.get_intensity_map(
-        volume_size=(5, 5, 10),  # 5x5x10 microns
-        voxel_size=0.1,  # 100 nm voxels
-        t=0,  # t=0 seconds
-    )
-
-    # print(f"Beam waist: {params.beam_width:.3f} µm")
-    # print(f"Rayleigh range: {params.rayleigh_range:.3f} µm")
-    # print(f"Diffraction limit: {params.diffraction_limited_width:.3f} µm")
-
-
 class HiLoBeam(LaserProfile):
     """
     Highly Inclined Laminated Optical (HiLo) illumination profile.
@@ -552,143 +527,3 @@ class HiLoBeam(LaserProfile):
         lamination_factor = np.exp(-np.abs(z_shifted) / (2 * self.axial_resolution))
 
         return intensity * lamination_factor
-
-
-class ConfocalBeam(LaserProfile):
-    """
-    Confocal microscopy beam profile with point scanning and pinhole characteristics.
-
-    Implements key optical principles of confocal microscopy:
-    - Point scanning illumination
-    - Pinhole-based rejection of out-of-focus light
-    - Depth-resolved imaging capabilities
-    """
-
-    def __init__(
-        self,
-        params: LaserParameters,
-        pinhole_diameter: float,  # Pinhole diameter in microns
-        scanning_mode: str = "point",  # 'point' or 'line'
-        line_orientation: str = "horizontal",  # 'horizontal' or 'vertical'
-    ):
-        """
-        Initialize Confocal beam profile.
-
-        Args:
-            params: LaserParameters for the beam
-            pinhole_diameter: Diameter of the detection pinhole in microns
-            scanning_mode: Scanning method ('point' or 'line')
-            line_orientation: Orientation for line scanning
-        """
-        super().__init__(params)
-
-        # Validate numerical aperture
-        if params.numerical_aperture is None:
-            raise ValueError(
-                "Numerical aperture must be specified for confocal microscopy"
-            )
-
-        # Pinhole and optical characteristics
-        self.pinhole_diameter = pinhole_diameter
-        self.scanning_mode = scanning_mode
-        self.line_orientation = line_orientation
-
-        # Calculate optical parameters
-        wavelength_microns = params.wavelength / 1000.0
-        na = params.numerical_aperture
-
-        # Theoretical resolution calculations
-        self.lateral_resolution = 0.61 * wavelength_microns / na
-        self.axial_resolution = 0.5 * wavelength_microns / (na**2)
-
-        # Pinhole transmission calculation
-        # Airy disk radius calculation
-        self.airy_radius = 1.22 * wavelength_microns / (2 * na)
-
-        # Transmission through pinhole
-        def pinhole_transmission(z):
-            """
-            Calculate pinhole transmission as a function of z-position.
-            Uses an error function to model smooth transition.
-            """
-            # Normalized z-position relative to focal plane
-            z_norm = z / self.axial_resolution
-
-            # Smooth transition function
-            return 0.5 * (1 + np.tanh(-z_norm))
-
-        self.pinhole_transmission = pinhole_transmission
-
-        # print("Confocal Microscopy Configuration:")
-        # print(f"  Scanning Mode: {scanning_mode}")
-        # print(f"  Pinhole Diameter: {pinhole_diameter:.2f} µm")
-        # print(f"  Lateral Resolution: {self.lateral_resolution:.3f} µm")
-        # print(f"  Axial Resolution: {self.axial_resolution:.3f} µm")
-        # print(f"  Airy Disk Radius: {self.airy_radius:.3f} µm")
-
-    def calculate_intensity(
-        self,
-        x: np.ndarray | float,
-        y: np.ndarray | float,
-        z: np.ndarray | float,
-        t: float,
-    ) -> np.ndarray:
-        """
-        Calculate the confocal illumination intensity distribution.
-
-        Args:
-            x: X coordinates in microns (3D array)
-            y: Y coordinates in microns (3D array)
-            z: Z coordinates in microns (3D array)
-            t: Time in seconds
-
-        Returns:
-            3D array of intensities in W/µm²
-        """
-        # Get time-dependent parameters
-        power = self.params.get_power(t)
-        pos = self.params.get_position(t)
-
-        # Shift coordinates based on current beam position
-        x_shifted = x - pos[0]
-        y_shifted = y - pos[1]
-        z_shifted = z - pos[2]
-
-        # Base beam parameters
-        w0 = self.params.beam_width  # Beam waist
-        zR = self.params.rayleigh_range  # Rayleigh range
-
-        # Calculate beam width at z
-        w_z = w0 * np.sqrt(1 + (z_shifted / zR) ** 2)
-
-        # Peak intensity calculation
-        I0 = 2 * power / (np.pi * w0**2)
-
-        # Scanning mode intensity modification
-        if self.scanning_mode == "point":
-            # Point scanning: standard Gaussian beam
-            radial_intensity = (
-                I0
-                * (w0 / w_z) ** 2
-                * np.exp(-2 * (x_shifted**2 + y_shifted**2) / w_z**2)
-            )
-        elif self.scanning_mode == "line":
-            # Line scanning: different intensity distribution
-            if self.line_orientation == "horizontal":
-                line_intensity = (
-                    I0 * (w0 / w_z) ** 2 * np.exp(-2 * y_shifted**2 / w_z**2)
-                )
-                radial_intensity = line_intensity
-            else:  # vertical line scanning
-                line_intensity = (
-                    I0 * (w0 / w_z) ** 2 * np.exp(-2 * x_shifted**2 / w_z**2)
-                )
-                radial_intensity = line_intensity
-        else:
-            raise ValueError(f"Unknown scanning mode: {self.scanning_mode}")
-
-        # Pinhole transmission effect
-        pinhole_effect = self.pinhole_transmission(z_shifted)
-
-        # Final intensity calculation
-        return radial_intensity * pinhole_effect

AMS_BP/optics/psf/psf_engine.py

@@ -85,15 +85,19 @@ 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 / 2.355
-        self._norm_sigma_z = self._sigma_z / 2.355
+        self._norm_sigma_xy = self._sigma_xy / 2.0
+        self._norm_sigma_z = self._sigma_z / 2.0
 
         # Generate pinhole mask if specified
         if self.params.pinhole_radius is not None:
             if self.params.pinhole_radius < AIRYFACTOR * self._sigma_xy:
-                raise ValueError(
+                RuntimeWarning(
                     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
@@ -116,7 +120,9 @@ class PSFEngine:
         return (r <= self.params.pinhole_radius).astype(np.float64)
 
     @lru_cache(maxsize=128)
-    def psf_z(self, z_val: float) -> NDArray[np.float64]:
+    def psf_z(
+        self, x_val: float, y_val: float, z_val: float, norm_scale: bool = True
+    ) -> 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
@@ -124,17 +130,28 @@ 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 / 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))
+        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)
 
         if self._pinhole_mask is not None:
             # Apply pinhole's spatial filtering
@@ -252,7 +269,7 @@ 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 = 2 * sigma_xy
+    r_psf = 3 * 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].normalize_psf(
-                        self.generator[i].psf_z(z_val=self.position[2]),
-                        mode="sum",
+                    self.generator[i].psf_z(
+                        x_val=self.position[0],
+                        y_val=self.position[1],
+                        z_val=self.position[2],
                     )
-                    * self.generator[i].psf_z_xy0(z_val=self.position[2])
                     * photons_n
                 )
 

{ams_bp-0.0.25.dist-info → ams_bp-0.0.31.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.25
+Version: 0.0.31
 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
@@ -172,4 +172,4 @@ from AMS_BP.configio.saving import save_config_frames
 save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
 ```
 
-> A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb)
+> A more detailed example is provided in the jupyter notebook in the examples. For starters refer to the [VisualizingIndividualModules](examples/VisualizingIndividualModules/modules_explained.ipynb). Then head over to the [laser modulation module](examples/VisualizingIndividualModules/laser_modulation.ipynb) which will show how to change the laser power over time in the simulations. Then view an example of a complex experiment setup for [FRAP](examples/QuantitativeExperiments/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.

{ams_bp-0.0.25.dist-info → ams_bp-0.0.31.dist-info}/RECORD

@@ -1,4 +1,4 @@
-AMS_BP/__init__.py,sha256=yp6QnMO5sZo0vrYRjuOtHAlUVullfFuge7Vs5jrt0zI,327
+AMS_BP/__init__.py,sha256=iU9u6S7CcnHsXcUjS8BDRGWvPnqK-wceLqo-pkKOSrk,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=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=Z3QJLVMP1gX4SlgOXFxBg8sJhBG0Xq25ixnBoEHEAZI,19462
+AMS_BP/motion/track_gen.py,sha256=2ssg8BXxZUEufycqgziL2BOeKOInTmmjzsthfS80gfI,19540
 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=dH-JZiAInnIaZXH1wAAo8dOIX9zafclqnZ4dOhKtnO0,9327
+AMS_BP/motion/movement/fbm_BP.py,sha256=47d2ph4r8Izso_mBxxgQYH9xjEqj_zXUzIGpEXPEhFM,9292
 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=lJG4LPCYFmGYVKPTfCiyCctppHUAlrSlNCvPLSYBZZk,22865
+AMS_BP/optics/lasers/laser_profiles.py,sha256=7mqf5VMpb0VN_veqYEdeiakr0kaOilfGzNq5mzFQuRw,17136
 AMS_BP/optics/psf/__init__.py,sha256=ezrKPgpTeR4gTHOvF0mhF6u2zMMTd8Bgp8PGeOf11fA,121
-AMS_BP/optics/psf/psf_engine.py,sha256=Do54D1jMbSrj5uljdTrrEttCvxq3qbVT74acRuOk15c,9434
+AMS_BP/optics/psf/psf_engine.py,sha256=FbR4VHQ-VgCWrrDj8AHPPnVgwVUGs-OP19w_TjcbMcU,10215
 AMS_BP/photophysics/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/photophysics/photon_physics.py,sha256=QRG_QIZ4csJ3g5qGP9Wtk7kzqm8_MUbVHfFef6cMtHQ,6671
+AMS_BP/photophysics/photon_physics.py,sha256=9FWBXaxuSRaSxW8bY0x1d5R5buooibZbRdYTuQcMXhQ,6624
 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-0.0.25.dist-info/METADATA,sha256=DV7dXicn4eT0pVFdX-Mvj66iF1nJ5-iIjq_DOucP5Ig,5483
-ams_bp-0.0.25.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ams_bp-0.0.25.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
-ams_bp-0.0.25.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.0.25.dist-info/RECORD,,
+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,,