AMS-BP 0.0.2__py3-none-any.whl → 0.0.11__py3-none-any.whl

AMS_BP/__init__.py

@@ -10,4 +10,4 @@ Last updated: 2024-12-16
 
 """
 
-__version__ = "0.0.2"
+__version__ = "0.0.11"

AMS_BP/configio/configmodels.py

@@ -60,22 +60,19 @@ class GlobalParameters(BaseModel):
 
 
 class CondensateParameters(BaseModel):
-    initial_centers: List[List[List[float]]] = Field(
-        description="Initial centers in um"
-    )
-    initial_scale: List[List[float]] = Field(description="Initial scale in um")
-    diffusion_coefficient: List[List[float]] = Field(
+    initial_centers: List[List[float]] = Field(description="Initial centers in um")
+    initial_scale: List[float] = Field(description="Initial scale in um")
+    diffusion_coefficient: List[float] = Field(
         description="Diffusion coefficients in um^2/s"
     )
-    hurst_exponent: List[List[float]]
-    density_dif: List[int]
-
-    # @field_validator(
-    #     "initial_centers", "initial_scale", "diffusion_coefficient", "hurst_exponent"
-    # )
-    # def convert_to_array(cls, v):
-    #     return np.array(v)
-    #
+    hurst_exponent: List[float]
+    density_dif: int
+
+    @field_validator(
+        "initial_centers", "initial_scale", "diffusion_coefficient", "hurst_exponent"
+    )
+    def convert_to_array(cls, v):
+        return np.array(v)
 
 
 class OutputParameters(BaseModel):

AMS_BP/configio/convertconfig.py

@@ -680,7 +680,7 @@ class ConfigLoader:
         )
 
         # make sampling function
-        sampling_functions = make_samplingfunction(
+        sampling_function = make_samplingfunction(
             condensate_params=base_config.CondensateParameters, cell=cell
         )
 
@@ -689,7 +689,7 @@ class ConfigLoader:
             molecule_params=base_config.MoleculeParameters,
             cell=cell,
             condensate_params=base_config.CondensateParameters,
-            sampling_functions=sampling_functions,
+            sampling_function=sampling_function,
         )
 
         # create the track generator
@@ -776,42 +776,34 @@ def make_sample(global_params, cell_params) -> SamplePlane:
     return sample_plane
 
 
-def make_condensatedict(condensate_params, cell) -> List[dict]:
-    condensates_dict = []
-    for i in range(len(condensate_params.initial_centers)):
-        condensates_dict.append(
-            create_condensate_dict(
-                initial_centers=condensate_params.initial_centers[i],
-                initial_scale=condensate_params.initial_scale[i],
-                diffusion_coefficient=condensate_params.diffusion_coefficient[i],
-                hurst_exponent=condensate_params.hurst_exponent[i],
-                cell=cell,
-            )
-        )
+def make_condensatedict(condensate_params, cell) -> dict:
+    condensates_dict = create_condensate_dict(
+        initial_centers=condensate_params.initial_centers,
+        initial_scale=condensate_params.initial_scale,
+        diffusion_coefficient=condensate_params.diffusion_coefficient,
+        hurst_exponent=condensate_params.hurst_exponent,
+        cell=cell,
+    )
     return condensates_dict
 
 
-def make_samplingfunction(condensate_params, cell) -> List[Callable]:
-    sampling_functions = []
-    for i in range(len(condensate_params.initial_centers)):
-        sampling_functions.append(
-            tp(
-                num_subspace=len(condensate_params.initial_centers[i]),
-                subspace_centers=condensate_params.initial_centers[i],
-                subspace_radius=condensate_params.initial_scale[i],
-                density_dif=condensate_params.density_dif[i],
-                cell=cell,
-            )
-        )
-    return sampling_functions
+def make_samplingfunction(condensate_params, cell) -> Callable:
+    sampling_function = tp(
+        num_subspace=len(condensate_params.initial_centers),
+        subspace_centers=condensate_params.initial_centers,
+        subspace_radius=condensate_params.initial_scale,
+        density_dif=condensate_params.density_dif,
+        cell=cell,
+    )
+    return sampling_function
 
 
-def gen_initial_positions(molecule_params, cell, condensate_params, sampling_functions):
+def gen_initial_positions(molecule_params, cell, condensate_params, sampling_function):
     initials = []
     for i in range(len(molecule_params.num_molecules)):
         num_molecules = molecule_params.num_molecules[i]
         initial_positions = gen_points(
-            pdf=sampling_functions[i],
+            pdf=sampling_function,
             total_points=num_molecules,
             min_x=cell.origin[0],
             max_x=cell.origin[0] + cell.dimensions[0],
@@ -819,7 +811,7 @@ def gen_initial_positions(molecule_params, cell, condensate_params, sampling_fun
             max_y=cell.origin[1] + cell.dimensions[1],
             min_z=-cell.dimensions[2] / 2,
             max_z=cell.dimensions[2] / 2,
-            density_dif=condensate_params.density_dif[i],
+            density_dif=condensate_params.density_dif,
         )
         initials.append(initial_positions)
     return initials

AMS_BP/sim_config.toml

@@ -77,49 +77,20 @@ oversample_motion_time = 20 # ms
 [Condensate_Parameters]
 initial_centers = [
     [
-        [
-            5.5,
-            5,
-            0.05,
-        ],
-        [
-            5,
-            5,
-            -0.15,
-        ],
-        [
-            5,
-            6,
-            -0.15,
-        ],
-        [
-            5,
-            5.5,
-            -0.15,
-        ],
-        [
-            6,
-            5.5,
-            -0.15,
-        ],
+        5.5,
+        5,
+        0.05,
     ],
     [
-        [
-            5.5,
-            5,
-            0.05,
-        ],
-        [
-            5,
-            7,
-            -0.15,
-        ],
+        5,
+        7,
+        -0.15,
     ],
-] # um. First dimension is the types of molecules as in Molecule Parameters.num_molecules. second dimension is the # of condentates. center = [x,y,z]
-initial_scale = [[0.26, 0.26, 0.13, 0.13, 0.26], [0.26, 0.26]] # um
-diffusion_coefficient = [[0, 0, 0, 0, 0], [0, 0]] # um^2/s
-hurst_exponent = [[0.2, 0.2, 0.2, 0.2, 0.2], [0.2, 0.2]]
-density_dif = [10, 10] # density of the condensate vs the background.
+] # um, first dimension is the # of condentates. center = [x,y,z]
+initial_scale = [0.26, 0.26] # um
+diffusion_coefficient = [0, 0] # um^2/s
+hurst_exponent = [0.2, 0.2]
+density_dif = 10 # density of the condensate vs the background.
 
 [Output_Parameters]
 output_path = "<YOUR-PATH-HERE-CAN-BE-ABSOLUTE-OR-RELATIVE>"

{ams_bp-0.0.2.dist-info → ams_bp-0.0.11.dist-info}/METADATA

@@ -1,7 +1,7 @@
 Metadata-Version: 2.4
 Name: AMS_BP
-Version: 0.0.2
-Summary: Advanced Microscopy Simulations developed for the Weber Lab by Baljyot Singh Parmar
+Version: 0.0.11
+Summary: Advanced Molecule Simulations and 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
 Author-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
@@ -19,16 +19,11 @@ Requires-Dist: tomli>=2.0.2
 Requires-Dist: typer>=0.12.5
 Description-Content-Type: text/markdown
 
-# AMS-BP
-<p>
-<img src="./docs/assets/icons/drawing.svg" alt="AMS-BP Logo" width="500" height="200">
-</p>
-## Advanced Fluorescence Microscopy Simulation Tool
+# AMS-BP User Guide
+## Advanced Molecule Simulation Tool
 
 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.
-
 ## Table of Contents
 - [Installation](#installation)
 - [Command Line Interface](#command-line-interface)
@@ -54,14 +49,6 @@ uv tool install AMS_BP
     - `run_AMS_BP config` : This is a helper tool to generate a template config file for the simulation. (see `run_AMS_BP config --help` for more details)
     - Note: using `run_AMS_BP --help` will show you all the available commands.
 4. You can now use these tools (they are isolated in their own env created by uv, which is cool).
-
-### ***PyPi***
-
-1. Run:
-```bash
-pip install AMS_BP
-```
-
 ## Command Line Interface
 
 AMS-BP provides a command-line interface with two main commands:
@@ -83,7 +70,7 @@ run_AMS_BP runsim CONFIG_FILE
 
 The configuration file (sim_config.toml) is divided into several key sections:
 
-#### For a detailed description of the configuration file, refer to the [Configuration File Reference](https://joemans3.github.io/AMS_BP/API_Documentation/sim_config/).
+#### For a detailed description of the configuration file, refer to the [Configuration File Reference](./API_Documentation/sim_config.md).
 ### Basic Units
 ```toml
 version = "0.1"
@@ -171,3 +158,40 @@ 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)
 ```
+
+### Key Components When Using as Library
+
+1. **ConfigLoader**: Handles configuration file parsing and validation
+2. **Microscope**: Represents the virtual microscope setup
+3. **Experiment Functions**: Control experiment execution
+4. **Save Functions**: Handle data output
+
+### Custom Experiment Types
+
+When using AMS-BP as a library, you can create custom experiment types by:
+
+1. Extending the base experiment class
+2. Implementing custom scanning patterns
+3. Defining new molecule behaviors
+4. Creating specialized analysis routines
+
+## Tips and Best Practices
+
+1. **Configuration Management**
+   - Keep separate config files for different experiment types
+   - Version control your configurations
+   - Document any custom modifications
+
+2. **Resource Usage**
+   - Monitor memory usage for large simulations
+   - Use appropriate sampling rates
+
+3. **Data Output**
+   - Set appropriate output paths
+   - Use meaningful naming conventions
+   - Consider data format requirements for analysis
+
+## Troubleshooting
+
+Common issues and their solutions:
+TODO

{ams_bp-0.0.2.dist-info → ams_bp-0.0.11.dist-info}/RECORD

@@ -1,6 +1,6 @@
-AMS_BP/__init__.py,sha256=Uf1hFjP3Vh5NQoJm1cL3TnbYf94ZH26bCPr6jYrrSrc,326
+AMS_BP/__init__.py,sha256=RIbrP3fesid1_nRkAUmjla1c4p2K5T-2exkbTTssitg,327
 AMS_BP/run_cell_simulation.py,sha256=fPU1Tuu7hBupGtMk07j2t8QYo_TjFLMJRU9fwmAgU9c,7502
-AMS_BP/sim_config.toml,sha256=FD-OcSDAgRuNIalFe0pC8sbsaSwM-9DV2DNswds2q54,11976
+AMS_BP/sim_config.toml,sha256=raxr-VSoVdTbaQX09rkLEiMWY2UfPShpv9v5MSVB4_g,11383
 AMS_BP/sim_microscopy.py,sha256=7JQ6NQlgNZCvFE-FC1f9Ehh6DoJgn7bLzeqS_Mamq9Y,18619
 AMS_BP/cells/__init__.py,sha256=yWFScBC1uOGDkeC8i1m1ZBtIREcyt4JHxYa72LxbBZU,177
 AMS_BP/cells/base_cell.py,sha256=FIPB9J8F40tb53vv7C6qG-SaAFLOI8-MGIk1mmZ-gnI,1503
@@ -8,8 +8,8 @@ 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/convertconfig.py,sha256=lS7FTDheESdbpaZ0K1LcE8rkdJOKLjzIvcmWpjeebSs,34654
+AMS_BP/configio/configmodels.py,sha256=KK5A9aFzRuXBWlwEGr84_x3LY60p7cddRgBsSkx5iS8,2986
+AMS_BP/configio/convertconfig.py,sha256=OHm9GnKXXObGWIEpeFfHOYJTHNWhjZKhoopLG85zWgY,34271
 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
@@ -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-0.0.2.dist-info/METADATA,sha256=3W89MwItnt2sZhSvLQpGF0u2Cr1aX_DzcM80V1RlNWM,5314
-ams_bp-0.0.2.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
-ams_bp-0.0.2.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
-ams_bp-0.0.2.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
-ams_bp-0.0.2.dist-info/RECORD,,
+ams_bp-0.0.11.dist-info/METADATA,sha256=unqrYIrskb0xGCrHhqiJtQ8VNxvSRvAzjizx4WUSWxg,5918
+ams_bp-0.0.11.dist-info/WHEEL,sha256=qtCwoSJWgHk21S1Kb4ihdzI2rlJ1ZKaIurTj_ngOhyQ,87
+ams_bp-0.0.11.dist-info/entry_points.txt,sha256=MFUK9bZWW61djfsavqopMqiVPVn4lJtt6v8qzyEFyNM,76
+ams_bp-0.0.11.dist-info/licenses/LICENSE,sha256=k_-JV1DQKvO0FR8WjvOisqdTl0kp6VJ7RFM3YZhao0c,1071
+ams_bp-0.0.11.dist-info/RECORD,,