AMS-BP 0.0.26__py3-none-any.whl → 0.0.231__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.26"
+__version__ = "0.0.231"

AMS_BP/optics/lasers/laser_profiles.py

@@ -96,10 +96,7 @@ class LaserParameters:
             Power in watts
         """
         if callable(self.power):
-            power = self.power(t)
-            if power < 0:
-                raise ValueError("Laser Power Cannot be Negative")
-            return power
+            return self.power(t)
         return self.power
 
     def get_position(self, t: float) -> Tuple[float, float, float]:
@@ -371,16 +368,15 @@ 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 +413,7 @@ 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 * 0.1  # 10% of max radius
         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)
@@ -426,6 +422,32 @@ 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.
@@ -527,3 +549,143 @@ 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

@@ -116,7 +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) -> 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
@@ -124,8 +124,6 @@ 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:
@@ -134,9 +132,7 @@ class PSFEngine:
         x, y = self._grid_xy
 
         # Calculate how light from the point source diffracts through collection optics
-        r_squared = (
-            (x - x_val % self.params.pixel_size) / self._norm_sigma_xy
-        ) ** 2 + ((y - y_val % self.params.pixel_size) / self._norm_sigma_xy) ** 2
+        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))
 
@@ -256,7 +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/photophysics/state_kinetics.py

@@ -27,7 +27,6 @@ class StateTransitionCalculator:
         self.current_global_time = current_global_time  # ms (oversample motion time)
         self.laser_intensity_generator = laser_intensity_generator
         self.fluorescent_state_history = {}  # {fluorescent.state.name : [delta time (seconds), laser_intensites], ...}
-        self.current_global_time_s = self.current_global_time * 1e-3
 
     def __call__(
         self,
@@ -49,9 +48,7 @@ class StateTransitionCalculator:
         time = 0
         transitions = self.flurophoreobj.state_history[self.current_global_time][2]
         final_state_name = transitions[0].from_state
-        laser_intensities = self._initialize_state_hist(
-            self.current_global_time, time + self.current_global_time_s
-        )
+        laser_intensities = self._initialize_state_hist(self.current_global_time, time)
 
         while time < self.time_duration:
             stateTransitionMatrixR = [

AMS_BP/sim_microscopy.py

@@ -73,9 +73,7 @@ class VirtualMicroscope:
     def _set_laser_powers(self, laser_power: Dict[str, float]) -> None:
         if laser_power is not None:
             for laser in laser_power.keys():
-                if isinstance(self.lasers[laser].params.power, float) and isinstance(
-                    laser_power[laser], float
-                ):
+                if isinstance(self.lasers[laser].params.power, float):
                     if laser_power[laser] > self.lasers[laser].params.max_power:
                         raise ValueError(
                             "Provided laser power for laser: {} nm, is larger than the maximum power: {}".format(

{ams_bp-0.0.26.dist-info → ams_bp-0.0.231.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.26
+Version: 0.0.231
 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
@@ -171,5 +171,3 @@ frames, metadata = function_exp(microscope=microscope, config=config_exp)
 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). 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-0.0.26.dist-info → ams_bp-0.0.231.dist-info}/RECORD

@@ -1,7 +1,7 @@
-AMS_BP/__init__.py,sha256=PRd0eVcZs7H8ezQRMXS-q-AES78dJ-DWPSQZT3j5QP0,327
+AMS_BP/__init__.py,sha256=rqdkAwhLvzoA4UNC7EgJOgze5vTlp72Cm62WfiIINCc,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
+AMS_BP/sim_microscopy.py,sha256=0UZfyT44nrB4JdfnFnRPTVBm3tPbCyOnPXiBBZs8xIc,18617
 AMS_BP/cells/__init__.py,sha256=yWFScBC1uOGDkeC8i1m1ZBtIREcyt4JHxYa72LxbBZU,177
 AMS_BP/cells/base_cell.py,sha256=FIPB9J8F40tb53vv7C6qG-SaAFLOI8-MGIk1mmZ-gnI,1503
 AMS_BP/cells/rectangular_cell.py,sha256=5yGxvTXYvgldLXyWXpE_SD9Zx2NLerC-I2j02reHsJ0,2515
@@ -29,12 +29,12 @@ 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=J9czY646XcW8GzXx9Eb16mG7tQdWw4oVYveOrihZCeY,22745
 AMS_BP/optics/psf/__init__.py,sha256=ezrKPgpTeR4gTHOvF0mhF6u2zMMTd8Bgp8PGeOf11fA,121
-AMS_BP/optics/psf/psf_engine.py,sha256=CDtnZpUvYexIih6ssBZsd5s1RUSa5fjUxgzEVELo6CE,9684
+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/state_kinetics.py,sha256=IdZtlHCLs--iSjLwDu2IQA617qXC4la8VpqosrM-vgQ,5401
+AMS_BP/photophysics/photon_physics.py,sha256=QRG_QIZ4csJ3g5qGP9Wtk7kzqm8_MUbVHfFef6cMtHQ,6671
+AMS_BP/photophysics/state_kinetics.py,sha256=0cc7Vc4LtAbEdGDeg22IJmRGLsONOty4c32hXHO-TSU,5281
 AMS_BP/probabilityfuncs/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
 AMS_BP/probabilityfuncs/markov_chain.py,sha256=LV6KGr8Lv4NIvBPJqsR0CEynssa_mPH30qLaK85GObA,4339
 AMS_BP/probabilityfuncs/probability_functions.py,sha256=j_rIxrupGBf_FKkQBh1TvEa34A44jAasaZQRg2u3FuY,11793
@@ -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-0.0.26.dist-info/METADATA,sha256=aaB17p23_wqvfOqQQfb90g7zFD1MrgpdXwoCsbYx37s,5869
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-ams_bp-0.0.26.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
-ams_bp-0.0.26.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.0.26.dist-info/RECORD,,
+ams_bp-0.0.231.dist-info/METADATA,sha256=Rs9gQc6T1-ZcguRTLWfsl42ZsTmJCtVgXRn-pcL7noY,5284
+ams_bp-0.0.231.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.0.231.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
+ams_bp-0.0.231.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.0.231.dist-info/RECORD,,