AMS-BP 0.0.3__tar.gz → 0.0.21__tar.gz

{ams_bp-0.0.3 → ams_bp-0.0.21}/.github/workflows/lint.yml

@@ -21,5 +21,6 @@ jobs:
       # Update output format to enable automatic inline annotations.
       - name: Run Ruff
         run: |
+          ruff check --fix
           ruff format
           ruff format --check --diff

{ams_bp-0.0.3 → ams_bp-0.0.21}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.3
+Version: 0.0.21
 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
@@ -10,6 +10,7 @@ License-File: LICENSE
 Keywords: SMS
 Requires-Python: >=3.10
 Requires-Dist: jsonschema>=4.23.0
+Requires-Dist: matplotlib>=3.6.0
 Requires-Dist: numpy>=1.21.2
 Requires-Dist: pydantic>=2.9.2
 Requires-Dist: scikit-image>=0.18.3
@@ -171,5 +172,3 @@ 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-0.0.3 → ams_bp-0.0.21}/README.md

@@ -151,5 +151,3 @@ 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-0.0.3 → ams_bp-0.0.21}/docs/API_Documentation/configio/configmodels.md

@@ -41,10 +41,18 @@ class MoleculeParameters(BaseModel)
   - Description: Diffusion coefficients in μm²/s
   - 2D array automatically converted to numpy array
 
+- `diffusion_track_amount: List[List[float]]`
+  - Description: Amount of diffusive tracking for each state
+  - 2D array automatically converted to numpy array
+
 - `hurst_exponent: List[List[float]]`
   - Description: Hurst exponents for fractional Brownian motion
   - 2D array automatically converted to numpy array
 
+- `hurst_track_amount: List[List[float]]`
+  - Description: Amount of Hurst tracking for each state
+  - 2D array automatically converted to numpy array
+
 - `allow_transition_probability: List[bool]`
   - Description: Whether to allow state transitions
 

{ams_bp-0.0.3 → ams_bp-0.0.21}/docs/API_Documentation/optics/psf/psf_engine.md

@@ -12,35 +12,14 @@ This module provides functionality for generating Point Spread Functions (PSFs)
   - [_calculate_sigma_z](#_calculate_sigma_z)
   - [_generate_grid](#_generate_grid)
   - [calculate_psf_size](#calculate_psf_size)
-  - [_generate_pinhole_mask](#_generate_pinhole_mask)
 
 ---
 
 ## Classes
 
 ### `PSFParameters`
-#### Description
-This is a frozen dataclass (enum-ish?) with the following parameters / cached properties
-```python
-emission_wavelength: float
-numerical_aperture: float
-pixel_size: float
-z_step: float
-refractive_index: float = 1.0
-pinhole_diameter: Optional[float] = None  # um
-
-@cached_property
-def wavelength_um(self) -> float:
-    """Emission wavelength in micrometers."""
-    return self.emission_wavelength / 1000.0
-@cached_property
-def pinhole_radius(self) -> Optional[float]:
-  """Pinhole radius in micrometers."""
-  return (
-    self.pinhole_diameter / 2.0 if self.pinhole_diameter is not None else None
-  )
-```
-### `PSFEngine`
+
+
 #### Methods
 
 - **`__init__`**: Initializes the PSF engine with the given parameters.
@@ -50,7 +29,6 @@ def pinhole_radius(self) -> Optional[float]:
 - **`_3d_normalization_A`**: Computes the normalization factor for a 3D Gaussian PSF.
 - **`_2d_normalization_A`**: Computes the normalization factor for a 2D Gaussian PSF.
 - **`normalize_psf`**: Normalizes the PSF using different schemes.
-- **`_generate_pinhole_mask`**: Generate a binary mask representing the pinhole's spatial filtering.
 
 ---
 
@@ -127,21 +105,4 @@ Calculates the appropriate PSF size based on physical parameters.
 
 #### Returns
 
-- **`Tuple[int, ...]`**: Tuple of dimensions (z, y, x) or (y, x) for the PSF calculation.
-
----
-
-### `_generate_pinhole_mask`
-
-
-#### Description
-
-Generate a binary mask representing the pinhole's spatial filtering.
-
-The pinhole blocks emission light based on position in the image plane,
-affecting what portion of the diffracted light reaches the detector.
-
-#### Parameters
-#### Returns
-
-- **`NDArray[np.float64]`**: Same dimensions as the psf generated but with binary values (0,1) indicating the transmittance of the psf due to the pinhole. Note, if the pinhole size is smaller than 1*airy disk diameter, then diffraction due to the pinhole is NOT non negligiable and diffraction effects will be introduced. A ValueError is thrown if this is the case.   
+- **`Tuple[int, ...]`**: Tuple of dimensions (z, y, x) or (y, x) for the PSF calculation.

{ams_bp-0.0.3 → ams_bp-0.0.21}/docs/API_Documentation/sim_config.md

@@ -224,7 +224,6 @@ Each fluorophore has transitions defined with the following parameters:
 - **Properties**:
   - **`numerical_aperture`**: The numerical aperture (typical range: 0.1 - 1.5).
   - **`refractive_index`**: The refractive index (default is air: 1.0).
-  - **`pinhole_diameter`**: None or float. In units of um. None = no pinhole before the detector.
 
 ---
 

{ams_bp-0.0.3 → ams_bp-0.0.21}/pyproject.toml

@@ -22,6 +22,7 @@ maintainers = [
 
 dependencies = [
   "numpy>=1.21.2",
+  "matplotlib>=3.6.0",
   "scipy>=1.7.1",
   "scikit-image>=0.18.3",
   "typer>=0.12.5",
@@ -40,10 +41,8 @@ venv = ".venv"
 
 [tool.uv]
 dev-dependencies = [
-  "matplotlib>=3.10.0",
   "mkdocs-material==9.5.40",
   "mkdocstrings-python>=1.12.2",
-  "notebook>=7.3.2",
   "pymdown-extensions>=10.11",
   "pyright>=1.1.384",
   "pytest>=8.3.3",

{ams_bp-0.0.3 → ams_bp-0.0.21}/src/AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.3"
+__version__ = "0.0.21"

{ams_bp-0.0.3 → ams_bp-0.0.21}/src/AMS_BP/configio/configmodels.py

@@ -21,7 +21,9 @@ class MoleculeParameters(BaseModel):
     diffusion_coefficient: List[List[float]] = Field(
         description="Diffusion coefficients in um^2/s"
     )
+    diffusion_track_amount: List[List[float]]
     hurst_exponent: List[List[float]]
+    hurst_track_amount: List[List[float]]
     allow_transition_probability: List[bool]
     transition_matrix_time_step: List[int] = Field(description="Time step in ms")
     diffusion_transition_matrix: List[List[List[float]]]
@@ -31,7 +33,9 @@ class MoleculeParameters(BaseModel):
 
     @field_validator(
         "diffusion_coefficient",
+        "diffusion_track_amount",
         "hurst_exponent",
+        "hurst_track_amount",
         "state_probability_diffusion",
         "state_probability_hurst",
     )

{ams_bp-0.0.3 → ams_bp-0.0.21}/src/AMS_BP/configio/convertconfig.py

@@ -324,12 +324,11 @@ class ConfigLoader:
         ):
             # Create PSFParameters instance
             parameters = PSFParameters(
-                emission_wavelength=wavelength,
+                wavelength=wavelength,
                 numerical_aperture=float(params_config["numerical_aperture"]),
                 pixel_size=pixel_size,
                 z_step=float(params_config["z_step"]) if z_step is None else z_step,
                 refractive_index=float(params_config.get("refractive_index", 1.0)),
-                pinhole_diameter=params_config.get("pinhole_diameter", None),
             )
 
             # Create PSF engine

{ams_bp-0.0.3 → ams_bp-0.0.21}/src/AMS_BP/metadata/metadata.py

@@ -1,4 +1,4 @@
-from typing import Dict, Iterator, List, Literal, Union
+from typing import Iterator, List, Literal, Union
 
 from pydantic import BaseModel
 
@@ -77,7 +77,7 @@ class MetaData(BaseModel):
     PhysicalSizeXUnit: Literal["nm", "m"]
     PhysicalSizeY: float
     PhysicalSizeYUnit: Literal["nm", "m"]
-    Channel: Dict[Literal["Name"], List[str]]
+    # Channel: Dict[Literal["Name"], List[str]]
 
     def __post_init__(self):
         if isinstance(self.notes, (list, str)):

{ams_bp-0.0.3 → ams_bp-0.0.21}/src/AMS_BP/motion/condensate_movement.py

@@ -20,6 +20,7 @@ Usage:
         condensate(times, time_unit) -> dict{"Position":np.ndarray, "Scale":float}
 """
 
+import matplotlib.pyplot as plt
 import numpy as np
 
 from ..cells.rectangular_cell import RectangularCell
@@ -309,3 +310,47 @@ class Condensate:
         # make array of length time with the last scale
         scale = np.full(time.shape, last_scale)
         return scale
+
+    def plot_condensate(self, ax, **kwargs):
+        """
+        Plots the condensate
+
+        Parameters:
+        -----------
+        ax: plt.Axes
+            Axes to plot the condensate on.
+        **kwargs:
+            Keyword arguments to pass to the plot function.
+        """
+        # check if the _condensate_positions exists
+        if not hasattr(self, "_condensate_positions"):
+            # if it doesn't then we need to generate the condensate positions
+            self.times = np.array([self.initial_time])
+            self.condensate_positions = np.array([self.initial_position])
+            self.scale = np.array([self.initial_scale])
+
+        # plot the condensate positions
+        ax.plot(
+            self.condensate_positions[:, 0], self.condensate_positions[:, 1], **kwargs
+        )
+
+        # plot a circle at all the positions with the scale as the radius
+        for i in range(len(self.condensate_positions)):
+            ax.add_patch(
+                plt.Circle(
+                    self.condensate_positions[i], self.scale[i], color="r", fill=False
+                )
+            )
+
+        # plot the initial position in a different colour
+        ax.scatter(self.initial_position[0], self.initial_position[1], color="g")
+        # plot the final position in a different colour
+        ax.scatter(
+            self.condensate_positions[-1][0],
+            self.condensate_positions[-1][1],
+            color="b",
+        )
+        if "save_path" in kwargs:
+            plt.savefig(kwargs["save_path"])
+        # plt.show()
+        return ax

{ams_bp-0.0.3 → ams_bp-0.0.21}/src/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-0.0.3 → ams_bp-0.0.21}/src/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-0.0.3 → ams_bp-0.0.21}/src/AMS_BP/optics/camera/detectors.py

@@ -305,7 +305,7 @@ def create_binning_function(input_shape, binning_size, mode="sum"):
         numpy.ndarray
             Binned array
         """
-        if array.shape != tuple(input_shape):
+        if array.shape != input_shape:
             raise ValueError(
                 f"Input array shape {array.shape} does not match expected shape {input_shape}"
             )

{ams_bp-0.0.3 → ams_bp-0.0.21}/src/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