AMS-BP 0.2.0__py3-none-any.whl → 0.3.1__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.2.0"
+__version__ = "0.3.1"

AMS_BP/cells/budding_yeast_cell.py

@@ -37,7 +37,7 @@ class BuddingCell(BaseCell):
     bud_distance: float
     neck_radius: float
 
-    def is_point_inside(
+    def contains_point_fallback(
         self, x: float, y: float, z: float, tolerance: float = 1e-3
     ) -> bool:
         """

AMS_BP/cells/cell_factory.py

@@ -40,7 +40,7 @@ _CELL_CREATION_MAP: Dict[CellType, Tuple[Callable, List[str]]] = {
     CellType.RECTANGULAR: (make_RectangularCell, ["bounds"]),
     CellType.OVOID: (
         make_OvoidCell,
-        ["center", "direction", "xradius", "yradius", "zradius"],
+        ["center", "xradius", "yradius", "zradius"],
     ),
     CellType.BUDDINGYEAST: (
         make_BuddingCell,

AMS_BP/configio/configmodels.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, List, Literal, Union
+from typing import Any, Dict, List, Literal, Optional, Union
 
 import numpy as np
 from pydantic import BaseModel, Field, field_validator
@@ -85,8 +85,8 @@ class OutputParameters(BaseModel):
 
 
 class ConfigList(BaseModel):
-    CellParameters: CellParameters
-    MoleculeParameters: MoleculeParameters
-    GlobalParameters: GlobalParameters
-    CondensateParameters: CondensateParameters
-    OutputParameters: OutputParameters
+    CellParameter: Optional[CellParameters] = None
+    MoleculeParameter: Optional[MoleculeParameters] = None
+    GlobalParameter: GlobalParameters
+    CondensateParameter: Optional[CondensateParameters] = None
+    OutputParameter: Optional[OutputParameters] = None

AMS_BP/configio/convertconfig.py

@@ -647,11 +647,11 @@ class ConfigLoader:
         # base config
         self.populate_dataclass_schema()
         base_config = ConfigList(
-            CellParameters=self.cell_params,
-            MoleculeParameters=self.molecule_params,
-            GlobalParameters=self.global_params,
-            CondensateParameters=self.condensate_params,
-            OutputParameters=self.output_params,
+            CellParameter=self.cell_params,
+            MoleculeParameter=self.molecule_params,
+            GlobalParameter=self.global_params,
+            CondensateParameter=self.condensate_params,
+            OutputParameter=self.output_params,
         )
 
         # fluorophore config
@@ -666,41 +666,41 @@ class ConfigLoader:
         detector, qe = self.create_detector_from_config(self.config)
 
         # make cell
-        cell = make_cell(cell_params=base_config.CellParameters)
+        cell = make_cell(cell_params=base_config.CellParameter)
 
         # make initial sample plane
         sample_plane = make_sample(
-            global_params=base_config.GlobalParameters,
+            global_params=base_config.GlobalParameter,
             cell=cell,
         )
 
         # make condensates_dict
         condensates_dict = make_condensatedict(
-            condensate_params=base_config.CondensateParameters, cell=cell
+            condensate_params=base_config.CondensateParameter, cell=cell
         )
 
         # make sampling function
         sampling_functions = make_samplingfunction(
-            condensate_params=base_config.CondensateParameters, cell=cell
+            condensate_params=base_config.CondensateParameter, cell=cell
         )
 
         # create initial positions
         initial_molecule_positions = gen_initial_positions(
-            molecule_params=base_config.MoleculeParameters,
+            molecule_params=base_config.MoleculeParameter,
             cell=cell,
-            condensate_params=base_config.CondensateParameters,
+            condensate_params=base_config.CondensateParameter,
             sampling_functions=sampling_functions,
         )
 
         # create the track generator
         track_generators = create_track_generator(
-            global_params=base_config.GlobalParameters, cell=cell
+            global_params=base_config.GlobalParameter, cell=cell
         )
 
         # get all the tracks
         tracks, points_per_time = get_tracks(
-            molecule_params=base_config.MoleculeParameters,
-            global_params=base_config.GlobalParameters,
+            molecule_params=base_config.MoleculeParameter,
+            global_params=base_config.GlobalParameter,
             initial_positions=initial_molecule_positions,
             track_generator=track_generators,
         )

AMS_BP/run_cell_simulation.py

@@ -196,7 +196,7 @@ def run_cell_simulation(
 
         # save
         save_config_frames(
-            metadata, frames, setup_config["base_config"].OutputParameters
+            metadata, frames, setup_config["base_config"].OutputParameter
         )
 
         progress.update(task_2, completed=None)

AMS_BP/sim_microscopy.py

@@ -132,8 +132,8 @@ class VirtualMicroscope:
             self._set_laser_positions(laser_positions=laser_position)
 
         duration_total, exposure_time, interval_time = timeValidator(
-            self.config.GlobalParameters.exposure_time,
-            self.config.GlobalParameters.interval_time,
+            self.config.GlobalParameter.exposure_time,
+            self.config.GlobalParameter.interval_time,
             self.sample_plane.dt,
             self.sample_plane.t_end,
             self._time,

{ams_bp-0.2.0.dist-info → ams_bp-0.3.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.2.0
+Version: 0.3.1
 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
@@ -9,7 +9,7 @@ Maintainer-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
 License-File: LICENSE
 Keywords: SMS
 Requires-Python: >=3.12
-Requires-Dist: boundedfbm>=0.2.0
+Requires-Dist: boundedfbm>=0.4.0
 Requires-Dist: jsonschema>=4.23.0
 Requires-Dist: numpy>=1.21.2
 Requires-Dist: pydantic>=2.9.2
@@ -29,8 +29,24 @@ Description-Content-Type: text/markdown
 
 AMS-BP is a powerful simulation tool for advanced fluorescence microscopy experiments. This guide covers both command-line usage and library integration.
 
-> **_NOTE:_** Please note that this application DOES NOT currently model the process of stimulated emission, and as such is not suitable for simulating stimulated emission microscopy ([STED](https://en.wikipedia.org/wiki/STED_microscopy))-type experiments. Work in this area is ongoing.
+## Overview of Simulation Workflow
+<img align = "left" src="./docs/assets/figures/Fig1_Schema.svg" width="500"/>
+
+*A ground truth is created, **a**, with $`f_{n}`$ fluorophore types of $`N_{f_{n}}`$ molecules each. If applicable, the motion of these molecules is modelled using a 3D bounded FBM with fluctuating generalized diffusion coefficients and Hurst parameters. Variations are modelled as a Markov Chain and require rate constants as parameters. Different fluorophores can have different motion models. The resolution of the motion models is $`\Delta t`$ and cannot be smaller than 1 ms (for computational efficiency). Given the microscope parameters specific to the experimental procedure to simulate, at every time $`t_{j}`$, the excitation intensity for each channel (**b**) is calculated at each fluorophore's location, **c**. For $`t_{j} \rightarrow t_{j+\Delta t}`$, the photophysical state trajectory of the fluorophore is simulated using the light intensity at the molecule's location as input for any light-dependent transition rates, **d**. For the duration that the shutter is open and light is emitted from the sample, emission filters for each channel are applied before the convolution with PSF models, **e**. The incident photons on the detector are then converted to photoelectrons and finally to digital units using the detector models provided, **f**.*
+
+## API Reference and Docs
+Find detailed API references for the library at: [joemans3/github.io/AMS_BP](https://joemans3.github.io/AMS_BP/)
+> 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/FRAP_methods.ipynb) which is possible by the use of compositions of modules in this simulation library.
 
+## Examples (Click on the image buttons to be taken to the Jupyter notebooks):
+
+> !!ATTENTION!! - Please note that you NEED to install the developmental dependencies to run the examples in full. This is mainly for installing the Jupyter notebook extensions, matplotlib and other visualization packages.
+
+[<img src="./docs/assets/buttons/ButtonFigure_FRAP.svg" width="300" height="120"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_fPALM_NPC.svg" width="300"/>](./examples/QuantitativeExperiments/FRAP/FRAP_methods.ipynb)
+
+[<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_widefield.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Widefield/widefield_twocolor.ipynb) [<img src="./docs/assets/buttons/ButtonFigure_zstack_twocolor_confocal.svg" width="300"/>](./examples/QuantitativeExperiments/TwoColor/Confocal/confocal_twocolor.ipynb)
+
+[<img align="middle" src="./docs/assets/buttons/ButtonFigure_sptPALM_mmaple.svg" width="300"/>](./examples/QuantitativeExperiments/PALM/sptPALM/motionmodels_sptmmaple.ipynb)
 ## Table of Contents
 - [Installation](#installation)
 - [Command Line Interface](#command-line-interface)
@@ -81,13 +97,6 @@ run_AMS_BP runsim CONFIG_FILE
 - `-o, --output_path PATH`: Specify the output directory for the configuration file
 - `-r, --recursive_o`: Create output directory if it doesn't exist
 
-## Overview of Simulation Workflow
-![Overview Schematic](./docs/assets/figures/Fig1_Schema.svg)
-*A ground truth is created, **a**, with $`f_{n}`$ fluorophore types of $`N_{f_{n}}`$ molecules each. If applicable, the motion of these molecules is modelled using a 3D bounded FBM with fluctuating generalized diffusion coefficients and Hurst parameters. Variations are modelled as a Markov Chain and require rate constants as parameters. Different fluorophores can have different motion models. The resolution of the motion models is $`\Delta t`$ and cannot be smaller than 1 ms (for computational efficiency). Given the microscope parameters specific to the experimental procedure to simulate, at every time $`t_{j}`$, the excitation intensity for each channel (**b**) is calculated at each fluorophore's location, **c**. For $`t_{j} \rightarrow t_{j+\Delta t}`$, the photophysical state trajectory of the fluorophore is simulated using the light intensity at the molecule's location as input for any light-dependent transition rates, **d**. For the duration that the shutter is open and light is emitted from the sample, emission filters for each channel are applied before the convolution with PSF models, **e**. The incident photons on the detector are then converted to photoelectrons and finally to digital units using the detector models provided, **f**.*
-
-
-
-
 
 ## Configuration File
 
@@ -155,7 +164,17 @@ laser_names_active = ["red", "blue"]
 laser_powers_active = [0.5, 0.05]
 laser_positions_active = [[5, 5, 0], [5, 5, 0]]
 ```
-
+To run the default configuration:
+1. Make sure you followed the uv tool installation.
+2. Make a copy of the default configuration file using the command:
+```bash
+run_AMS_BP config
+```
+3. Run the sim:
+```bash
+run_AMS_BP runsim sim_config.toml
+```
+4. View the results in the newly created folder, whose name is defined in the config file.
 ## Advanced Usage
 
 ### Using AMS-BP as a Library
@@ -181,13 +200,10 @@ 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)
 ```
-
-## API Reference and Docs
-Find detailed API references for the library at: [joemans3/github.io/AMS_BP](https://joemans3.github.io/AMS_BP/)
-> 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.
+> **_NOTE:_** Please note that this application DOES NOT currently model the process of stimulated emission, and as such is not suitable for simulating stimulated emission microscopy ([STED](https://en.wikipedia.org/wiki/STED_microscopy))-type experiments. Work in this area is ongoing.
 
 ## High Priority Features
-1. Irregular cell shapes with motion models
+~~1. Irregular cell shapes with motion models~~ (supported with release of v0.2.0)
 2. Stimulated Emission models
 3. STORM workflow examples
 4. CTRW motion models

{ams_bp-0.2.0.dist-info → ams_bp-0.3.1.dist-info}/RECORD

@@ -1,13 +1,13 @@
-AMS_BP/__init__.py,sha256=pj8JaDmWwnqBAxuQAgDPFFVkI2FOkCRpIN4GlyKBTQw,326
-AMS_BP/run_cell_simulation.py,sha256=7InopFikjo0HfaLO2siXskBIbyCIte9avG4YXjjaWCI,7420
+AMS_BP/__init__.py,sha256=H6Hnoehl90XIkGR-l7GpvZiYTQ6AEXD3EfzjFTtS2Sc,326
+AMS_BP/run_cell_simulation.py,sha256=P_0fHB7S7SQibqXaaqOxRC1UqSunGZdJXs-4thC6DUI,7419
 AMS_BP/sim_config.toml,sha256=G0wW9qsxciZA1Y0Zm6YgZ00ZDBEBBLw_XXq4gsVRjSY,11778
-AMS_BP/sim_microscopy.py,sha256=Vsga9lTWqP0pjEnfFj0qKaSz7YZ_F4E3TqsaErwhi3E,19991
+AMS_BP/sim_microscopy.py,sha256=3BYrFLzjcAevlyBQXAM0PixHM8GA5BnnAHouGVDNbMw,19989
 AMS_BP/cells/__init__.py,sha256=Rd2gpWWUZJxW2u_piI2ZcIqLtYkzVOr_MjU3upiUv8Q,866
-AMS_BP/cells/budding_yeast_cell.py,sha256=BiZ_rML5xjcS8NMP785VzUPVxo41yhihsbvbwSYLQvM,9440
-AMS_BP/cells/cell_factory.py,sha256=Mhk-0KzLVfaub81Asj5PibOcps0s8I24iC4qZs0VVK4,4435
+AMS_BP/cells/budding_yeast_cell.py,sha256=_n0jhiRvrMcPddfoR8Vi4RdOJQTo_nR4JF7ydsrCF98,9448
+AMS_BP/cells/cell_factory.py,sha256=a-M5xHDkYDHoMv3vbQyn4x0KQ-lshO2CEdfrStLGSOU,4422
 AMS_BP/configio/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
-AMS_BP/configio/configmodels.py,sha256=9rPXIYh228fEEf4tDGcE0kSC_RB97VocBaIobhCeuBQ,2998
-AMS_BP/configio/convertconfig.py,sha256=Np2xKMnAKMkqPip_uqGYOUmp7_5BWn1ZnUBesfkyvis,34588
+AMS_BP/configio/configmodels.py,sha256=pp4haDLjGCMoERKq995v6lBXGhpen0-qE3ZWnd99bjM,3071
+AMS_BP/configio/convertconfig.py,sha256=18Xg3nrE0mI0em610FEJxI1dU_N24EQf06EqDstsAVk,34574
 AMS_BP/configio/experiments.py,sha256=HdfaSi0gPPJ_wLF87XcW5ICja19Uezx7-ygFEwNzi30,3995
 AMS_BP/configio/saving.py,sha256=596QgAadV32rzsN4B2FngGFcBWCzCDnLFN-qtQsv3bM,857
 AMS_BP/groundtruth_generators/__init__.py,sha256=UPVmhiB81OfyqAes5LoN-n6XgQuBCYCqRPAGd2jpMfc,99
@@ -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=9Qlr4kjY04fObktR8TrzB0IgoG1yXtcmxPRX9AN34mM,9671
-ams_bp-0.2.0.dist-info/METADATA,sha256=GJLdow0hQ3y6LLNubb0q0xfzw00oSeftbRgfnr_K4u8,7658
-ams_bp-0.2.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ams_bp-0.2.0.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
-ams_bp-0.2.0.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.2.0.dist-info/RECORD,,
+ams_bp-0.3.1.dist-info/METADATA,sha256=mU78kPY_FuQsUMkTcr-JaNB9k2jnAw8gFZOByanZ-Iw,9153
+ams_bp-0.3.1.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.3.1.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
+ams_bp-0.3.1.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.3.1.dist-info/RECORD,,