AMS-BP 0.0.22__py3-none-any.whl → 0.0.24__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.22"
+__version__ = "0.0.24"

AMS_BP/configio/configmodels.py

@@ -21,9 +21,7 @@ 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]]]
@@ -33,9 +31,7 @@ class MoleculeParameters(BaseModel):
 
     @field_validator(
         "diffusion_coefficient",
-        "diffusion_track_amount",
         "hurst_exponent",
-        "hurst_track_amount",
         "state_probability_diffusion",
         "state_probability_hurst",
     )

AMS_BP/motion/condensate_movement.py

@@ -20,7 +20,6 @@ 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
@@ -310,47 +309,3 @@ 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/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 != input_shape:
+        if array.shape != tuple(input_shape):
             raise ValueError(
                 f"Input array shape {array.shape} does not match expected shape {input_shape}"
             )

AMS_BP/optics/lasers/laser_profiles.py

@@ -96,7 +96,10 @@ class LaserParameters:
             Power in watts
         """
         if callable(self.power):
-            return self.power(t)
+            power = self.power(t)
+            if power < 0:
+                raise ValueError("Laser Power Cannot be Negative")
+            return power
         return self.power
 
     def get_position(self, t: float) -> Tuple[float, float, float]:

AMS_BP/optics/psf/psf_engine.py

@@ -100,12 +100,19 @@ class PSFEngine:
 
     def _generate_pinhole_mask(self) -> NDArray[np.float64]:
         """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.
+        The pinhole is centered on the grid, blocking emission light based on position
+        in the image plane, affecting what portion of the diffracted light reaches
+        the detector.
         """
         x, y = self._grid_xy
-        r = np.sqrt(x**2 + y**2)
+
+        # Calculate the grid center
+        x_center = (x.max() + x.min()) / 2
+        y_center = (y.max() + y.min()) / 2
+
+        # Calculate radial distance from grid center
+        r = np.sqrt((x - x_center) ** 2 + (y - y_center) ** 2)
+
         return (r <= self.params.pinhole_radius).astype(np.float64)
 
     @lru_cache(maxsize=128)

AMS_BP/photophysics/state_kinetics.py

@@ -27,6 +27,7 @@ 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,
@@ -48,7 +49,9 @@ 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)
+        laser_intensities = self._initialize_state_hist(
+            self.current_global_time, time + self.current_global_time_s
+        )
 
         while time < self.time_duration:
             stateTransitionMatrixR = [

AMS_BP/sim_config.toml

@@ -23,18 +23,8 @@ diffusion_coefficient = [
         0.0,
     ],
 ] # um^2/s, size of each index (eg. len(...[0]) is the # of diffusion coefficients the system can explore.
-diffusion_track_amount = [
-    [
-        0.5,
-        0.5,
-    ],
-    [
-        0.5,
-        0.5,
-    ],
-] # only usefull for initial distribution of diffusion coefficients to trajectories.
+
 hurst_exponent = [[0.5], [0.5]]
-hurst_track_amount = [[1.0], [1.0]]
 allow_transition_probability = [true, true] # bool
 transition_matrix_time_step = [
     20,
@@ -193,12 +183,6 @@ to_state = "triplet"
 photon_dependent = false
 base_rate = 1            # 1/s
 
-[fluorophores.PAmCherry.transitions.triplet_to_bleached]
-from_state = "triplet"
-to_state = "bleached"
-photon_dependent = false
-base_rate = 1            # 1/s
-
 [fluorophores.PAmCherry.transitions.triplet_to_dark]
 from_state = "triplet"
 to_state = "dark"

{ams_bp-0.0.22.dist-info → ams_bp-0.0.24.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.22
+Version: 0.0.24
 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
@@ -10,7 +10,6 @@ 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
@@ -172,3 +171,5 @@ 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)

{ams_bp-0.0.22.dist-info → ams_bp-0.0.24.dist-info}/RECORD

@@ -1,6 +1,6 @@
-AMS_BP/__init__.py,sha256=NlkysP1_GeDxvsm-dQaJIW9U1iNFB0jI_34DmCYn-bg,327
+AMS_BP/__init__.py,sha256=_0wRoFCXiDI2esMHAgmC0k46izWDlMXa_aqJ_MoW48g,327
 AMS_BP/run_cell_simulation.py,sha256=7InopFikjo0HfaLO2siXskBIbyCIte9avG4YXjjaWCI,7420
-AMS_BP/sim_config.toml,sha256=LVpxp2zv-y6Ic-ve2AG7Ted1Fr_Tni-8yh8l5gp-7oM,12056
+AMS_BP/sim_config.toml,sha256=3IqOQIJYmP5g4okk15nqQiNZb3ij7Pt63HbpI-5tySw,11672
 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
@@ -8,33 +8,33 @@ AMS_BP/cells/rectangular_cell.py,sha256=5yGxvTXYvgldLXyWXpE_SD9Zx2NLerC-I2j02reH
 AMS_BP/cells/rod_cell.py,sha256=jQ1kLEk74Pv2rcXPRJ6-QJJhux-mYiDSytzqlxCNWfA,3181
 AMS_BP/cells/spherical_cell.py,sha256=n3ou3tW0nCxXIwv6uLkVKHkYCfgoNn8VI6CVTLBIll0,2140
 AMS_BP/configio/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/configio/configmodels.py,sha256=Isc6THk3RAIVdjEUBW4c_OD0I122dYufgEvAcGJQ5uo,3046
+AMS_BP/configio/configmodels.py,sha256=Gd2Qdut0u5zS0IpjPwGIB3ur-b4Dfa9e8SbhotBKymc,2894
 AMS_BP/configio/convertconfig.py,sha256=Fg9pOCZSxmWuHnrg-5xZRvhPEK6Qc1kXqu6LL9e9QYw,34741
 AMS_BP/configio/experiments.py,sha256=HdfaSi0gPPJ_wLF87XcW5ICja19Uezx7-ygFEwNzi30,3995
 AMS_BP/configio/saving.py,sha256=596QgAadV32rzsN4B2FngGFcBWCzCDnLFN-qtQsv3bM,857
 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=cGLHIOL7VUJ7U-JrJXetcnUF2v9SepIBznoqu6AQPxU,13252
+AMS_BP/motion/condensate_movement.py,sha256=eig4WtD7o1cvIafWMjOk6pqxyhe_IIucgLcBEoDvasU,11648
 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=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=UJqi7owESw9nkFiQhoAe7Q1LIi_fYCzuvZLgtM3yAPk,10348
+AMS_BP/optics/camera/detectors.py,sha256=_815Ovo7Aj375OZh5Xim8pFuZEEcSVtSdnLRYFqb3_8,10355
 AMS_BP/optics/camera/quantum_eff.py,sha256=ZCvJ8dJESOUbjwblsJIBcCg_b-_DNdhDlkzd7HeGMDg,2378
 AMS_BP/optics/filters/__init__.py,sha256=oYPk2_wuL4KrwbaZy3gktvO5biQUfdQLUColWhkU1lw,337
 AMS_BP/optics/filters/filters.py,sha256=-iw7eqmDO77SEqlFTv5jJNVwpA8y93TLsjy5hhsAfiI,6406
 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=J9czY646XcW8GzXx9Eb16mG7tQdWw4oVYveOrihZCeY,22745
+AMS_BP/optics/lasers/laser_profiles.py,sha256=dLnobLB-zZIG9EyMkU4E2P9CDl3n3OLzgR8Tx5EAd2c,22864
 AMS_BP/optics/psf/__init__.py,sha256=ezrKPgpTeR4gTHOvF0mhF6u2zMMTd8Bgp8PGeOf11fA,121
-AMS_BP/optics/psf/psf_engine.py,sha256=wabdBszY4CcGUtt7ye8e3tQXQQxDJ8griGD7FMgAdIo,9192
+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=QRG_QIZ4csJ3g5qGP9Wtk7kzqm8_MUbVHfFef6cMtHQ,6671
-AMS_BP/photophysics/state_kinetics.py,sha256=0cc7Vc4LtAbEdGDeg22IJmRGLsONOty4c32hXHO-TSU,5281
+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
 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-0.0.22.dist-info/METADATA,sha256=VQheoFTH5ZdmZTZwrb58UxP9YTowy8U7r6zW5kabIMI,5316
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-ams_bp-0.0.22.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
-ams_bp-0.0.22.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.0.22.dist-info/RECORD,,
+ams_bp-0.0.24.dist-info/METADATA,sha256=s8z9bcI32yK1EZINiomMaexx3UFZ1gGJZLDc7412oqk,5483
+ams_bp-0.0.24.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.0.24.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
+ams_bp-0.0.24.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.0.24.dist-info/RECORD,,