AMS-BP 0.2.0__py3-none-any.whl → 0.3.0__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.2.0"
+__version__ = "0.3.0"

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-0.2.0.dist-info → ams_bp-0.3.0.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.2.0
+Version: 0.3.0
 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
@@ -155,7 +155,17 @@ 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
@@ -187,7 +197,7 @@ Find detailed API references for the library at: [joemans3/github.io/AMS_BP](htt
 > 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.
 
 ## 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-0.3.0.dist-info}/RECORD

@@ -1,10 +1,10 @@
-AMS_BP/__init__.py,sha256=pj8JaDmWwnqBAxuQAgDPFFVkI2FOkCRpIN4GlyKBTQw,326
+AMS_BP/__init__.py,sha256=qZJ3LMMRzoxLqWhvaesLzGNyIIJtQf64R5bjLywCTqw,326
 AMS_BP/run_cell_simulation.py,sha256=7InopFikjo0HfaLO2siXskBIbyCIte9avG4YXjjaWCI,7420
 AMS_BP/sim_config.toml,sha256=G0wW9qsxciZA1Y0Zm6YgZ00ZDBEBBLw_XXq4gsVRjSY,11778
 AMS_BP/sim_microscopy.py,sha256=Vsga9lTWqP0pjEnfFj0qKaSz7YZ_F4E3TqsaErwhi3E,19991
 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
@@ -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-0.3.0.dist-info/METADATA,sha256=Lqmx2IoHSTQyYMyjOfjJnGS54A9q8l-E06ifUrYFT8Q,8033
+ams_bp-0.3.0.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.3.0.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
+ams_bp-0.3.0.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.3.0.dist-info/RECORD,,