AMS-BP 0.0.2__py3-none-any.whl

AMS_BP/utils/errors.py

@@ -0,0 +1,37 @@
+# error base classes for SMS_BP
+
+
+class HurstValueError(Exception):
+    """Raised when the Hurst value is not within the range (0, 1)"""
+
+    pass
+
+
+class SpaceLimitError(Exception):
+    """Raised when the space limit is not within the range (-inf, inf)"""
+
+    pass
+
+
+class DiffusionHighError(Exception):
+    """Raised when the diffusion value is too high for the space limit"""
+
+    pass
+
+
+class HurstHighError(Exception):
+    """Raised when the Hurst value is too high for the space limit"""
+
+    pass
+
+
+class ConfigValidationError(Exception):
+    """Exception raised for errors in the configuration validation."""
+
+    pass
+
+
+class ConfigConversionError(Exception):
+    """Exception raised for errors in the configuration conversion process."""
+
+    pass

AMS_BP/utils/maskMaker.py

@@ -0,0 +1,12 @@
+import numpy as np
+
+
+def mask_maker(
+    total_img_dims: np.ndarray, submask_coordinates: np.ndarray, mask_val: int
+) -> np.ndarray:
+    img = np.zeros(total_img_dims)
+    img[
+        submask_coordinates[1][0] : submask_coordinates[1][1],
+        submask_coordinates[0][0] : submask_coordinates[0][1],
+    ] = mask_val
+    return img

AMS_BP/utils/util_functions.py

@@ -0,0 +1,319 @@
+import json
+import os
+import pickle
+
+import numpy as np
+import skimage as skimage
+from PIL import Image
+
+from ..utils.decorators import cache
+
+
+def convert_arrays_to_lists(obj: np.ndarray | dict) -> list | dict:
+    """
+    Recursively convert NumPy arrays to lists.
+
+    Parameters:
+    -----------
+    obj : np.ndarray | dict
+        Object to be converted.
+
+    Returns:
+    --------
+    list | dict
+        Converted object with NumPy arrays replaced by lists.
+    """
+    if isinstance(obj, np.ndarray):
+        return obj.tolist()
+    elif isinstance(obj, dict):
+        return {k: convert_arrays_to_lists(v) for k, v in obj.items()}
+    else:
+        return obj
+
+
+# Function to recursively convert lists to NumPy arrays
+def convert_lists_to_arrays(obj: list | dict) -> np.ndarray | dict:
+    """
+    Recursively convert lists to NumPy arrays.
+
+    Parameters:
+    -----------
+    obj : list | dict
+        Object to be converted.
+
+    Returns:
+    --------
+    np.ndarray | dict
+        Converted object with lists replaced by NumPy arrays.
+    """
+    if isinstance(obj, list):
+        return np.array(obj)
+    elif isinstance(obj, dict):
+        return {k: convert_lists_to_arrays(v) for k, v in obj.items()}
+    else:
+        return obj
+
+
+def save_tiff(
+    image: np.ndarray, path: str, img_name: str | None = None, tifffile_args: dict = {}
+) -> None:
+    """
+    Save the image as a TIFF file.
+
+    Parameters:
+    -----------
+    image : np.ndarray
+        Image to be saved.
+    path : str
+        Path where the image will be saved.
+    img_name : str, optional
+        Name of the image file (without extension), by default None.
+    tifffile_args: dict(str, val)
+        named arguments passed to the tifffile plugin as a dict.
+
+    Returns:
+    --------
+    None
+    """
+    if img_name is None:
+        skimage.io.imsave(path, image)
+    else:
+        skimage.io.imsave(
+            os.path.join(path, img_name + ".tiff"),
+            image,
+            plugin="tifffile",
+            plugin_args=tifffile_args,
+        )
+    return
+
+
+def binning_array(
+    array_to_bin: np.ndarray, binning_size: int, mode: str = "sum"
+) -> np.ndarray:
+    """
+    Bin an N-dimensional array by summing values in each bin.
+
+    Parameters:
+    -----------
+    array_to_bin: numpy.ndarray
+        Input N-dimensional array to be binned
+    binning_size : int
+        Size of the binning window (e.g., 2 for 2x2 binning)
+    mode : str, optional
+        Method for binning. Currently only supports 'sum'
+
+    Returns:
+    --------
+    numpy.ndarray
+        Binned array with reduced dimensions
+    """
+    if binning_size == 1:
+        return array_to_bin
+    if mode != "sum":
+        raise ValueError("Only 'sum' mode is currently supported")
+
+    # Get the shape of the input array
+    original_shape = np.array(array_to_bin.shape)
+
+    # Calculate the shape of the output array
+    # We need to handle both cases where the dimension is divisible by binning_size
+    # and where it's not
+    output_shape = np.ceil(original_shape / binning_size).astype(int)
+
+    # Calculate the effective shape that we can fully bin
+    # This handles cases where the array dimensions aren't perfectly divisible
+    effective_shape = (output_shape * binning_size) - original_shape
+
+    # Pad the array if necessary to make it divisible by binning_size
+    if np.any(effective_shape > 0):
+        pad_width = np.array([(0, int(s)) for s in effective_shape])
+        array_to_bin = np.pad(array_to_bin, pad_width, mode="constant")
+
+    # Generate slicing for the reshape operation
+    new_shape = []
+    for dim in array_to_bin.shape:
+        new_shape.extend([dim // binning_size, binning_size])
+
+    # Reshape and sum along the appropriate axes
+    reshaped = array_to_bin.reshape(new_shape)
+
+    # Calculate the axes to sum over
+    # For N dimensions, we want to sum over axes 1, 3, 5, etc.
+    sum_axes = tuple(range(1, len(new_shape), 2))
+
+    # Perform the binning by summing
+    binned = reshaped.sum(axis=sum_axes)
+
+    return binned
+
+
+# function to perform the subsegmentation
+def sub_segment(
+    img: np.ndarray,
+    subsegment_num: int,
+    img_name: str | None = None,
+    subsegment_type: str = "mean",
+) -> list[np.ndarray]:
+    """
+    Perform subsegmentation on the image.
+
+    Parameters:
+    -----------
+    img : np.ndarray
+        Image to be subsegmented.
+    subsegment_num : int
+        Number of subsegments to be created.
+    img_name : str, optional
+        Name of the image, by default None.
+    subsegment_type : str, optional
+        Type of subsegmentation to be performed. Options are "mean", "max", "std". Default is "mean".
+
+    Returns:
+    --------
+    list[np.ndarray]
+        List of subsegmented images.
+
+    Raises:
+    -------
+    ValueError
+        If the subsegment type is not supported.
+    """
+    supported_subsegment_types = ["mean", "max", "std"]
+    if subsegment_type not in supported_subsegment_types:
+        raise ValueError(
+            f"Subsegment type {subsegment_type} is not supported. Supported types are {supported_subsegment_types}"
+        )
+    # get the dimensions of the image
+    dims = img.shape
+    # get the number of frames
+    num_frames = dims[0]
+    # find the number of frames per subsegment
+    frames_per_subsegment = int(num_frames / subsegment_num)
+    hold_img = []
+    for j in np.arange(subsegment_num):
+        if subsegment_type == "mean":
+            hold_img.append(
+                np.mean(
+                    img[
+                        int(j * frames_per_subsegment) : int(
+                            (j + 1) * frames_per_subsegment
+                        )
+                    ],
+                    axis=0,
+                )
+            )
+        elif subsegment_type == "max":
+            hold_img.append(
+                np.max(
+                    img[
+                        int(j * frames_per_subsegment) : int(
+                            (j + 1) * frames_per_subsegment
+                        )
+                    ],
+                    axis=0,
+                )
+            )
+        elif subsegment_type == "std":
+            hold_img.append(
+                np.std(
+                    img[
+                        int(j * frames_per_subsegment) : int(
+                            (j + 1) * frames_per_subsegment
+                        )
+                    ],
+                    axis=0,
+                )
+            )
+    return hold_img
+
+
+def make_directory_structure(
+    cd: str,
+    img_name: str,
+    img: np.ndarray,
+    subsegment_type: str,
+    subsegment_num: int,
+    **kwargs,
+) -> list[np.ndarray]:
+    """
+    Create the directory structure for the simulation, save the image, and perform subsegmentation.
+
+    Parameters:
+    -----------
+    cd : str
+        Directory where the simulation will be saved.
+    img_name : str
+        Name of the image.
+    img : np.ndarray
+        Image to be subsegmented.
+    subsegment_type : str
+        Type of subsegmentation to be performed.
+    subsegment_num : int
+        Number of subsegments to be created.
+    **kwargs : dict
+        Additional keyword arguments, including:
+        - data : dict (optional)
+            Dictionary of data to be saved, keys are "map", "tracks", "points_per_frame".
+        - parameters : dict (optional)
+            Parameters of the simulation to be saved.
+
+    Returns:
+    --------
+    list[np.ndarray]
+        List of subsegmented images.
+
+    Raises:
+    -------
+    None
+    """
+    # make the directory if it does not exist
+    if not os.path.exists(cd):
+        os.makedirs(cd)
+    # track_pickle
+    track_pickle = os.path.join(cd, "Track_dump.pkl")
+    # params_pickle
+    params_pickle = os.path.join(cd, "params_dump.pkl")
+    # params_json
+    params_json = os.path.join(cd, "params_dump.json")
+
+    # saves the data if it is passed as a keyword argument (map,tracks,points_per_frame)
+    with open(track_pickle, "wb+") as f:
+        pickle.dump(kwargs.get("data", {}), f)
+    # saves the parameters used to generate the simulation
+    with open(params_pickle, "wb+") as f:
+        pickle.dump(kwargs.get("parameters", {}), f)
+
+    # in this directory, dump the parameters into a json file
+    with open(params_json, "w") as f:
+        # dump the parameters into a json file
+        # json.dump(convert_arrays_to_lists(kwargs.get("parameters", {})), f)
+        json.dump({}, f)
+
+    # make a diretory inside cd called Analysis if it does not exist
+    if not os.path.exists(os.path.join(cd, "Analysis")):
+        os.makedirs(os.path.join(cd, "Analysis"))
+    # save the img file with its name in the cd directory
+    save_tiff(img, cd, img_name=img_name)
+    # make a directory inside cd called segmented if it does not exist
+    if not os.path.exists(os.path.join(cd, "segmented")):
+        os.makedirs(os.path.join(cd, "segmented"))
+    # perform subsegmentation on the image
+    hold_img = sub_segment(
+        img, subsegment_num, img_name=img_name, subsegment_type=subsegment_type
+    )
+    # create the names for the subsegmented images
+    hold_name = []
+    for i in np.arange(subsegment_num):
+        hold_name.append(
+            os.path.join(cd, "segmented", str(int(i) + 1) + "_" + img_name + ".tif")
+        )
+    # save the subsegmented images
+    for i in np.arange(subsegment_num):
+        img = Image.fromarray(hold_img[i])
+        img.save(hold_name[i])
+    return hold_img
+
+
+@cache
+def ms_to_seconds(time: int | float) -> float:
+    return time * 1e-3

ams_bp-0.0.2.dist-info/METADATA

@@ -0,0 +1,173 @@
+Metadata-Version: 2.4
+Name: AMS_BP
+Version: 0.0.2
+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
+Author-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
+Maintainer-email: Baljyot Singh Parmar <baljyotparmar@hotmail.com>
+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
+Requires-Dist: scipy>=1.7.1
+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 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)
+- [Configuration File](#configuration-file)
+- [Running Experiments](#running-experiments)
+- [Advanced Usage](#advanced-usage)
+
+## Installation
+
+
+### ***Installing the CLI tool using UV***
+
+
+
+
+1. [Install UV](https://docs.astral.sh/uv/getting-started/installation/).
+2. Run the command:
+```bash
+uv tool install AMS_BP
+```
+3. You will have access to two CLI commands (using the uv interface):
+    - `run_AMS_BP runsim` : This is the main entry point for the simulation. (see `run_AMS_BP runsim --help` for more details)
+    - `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:
+
+```bash
+# Generate a default configuration file
+run_AMS_BP config [OPTIONS]
+
+# Run a simulation using a configuration file
+run_AMS_BP runsim CONFIG_FILE
+```
+
+### Config Command Options
+
+- `-o, --output_path PATH`: Specify the output directory for the configuration file
+- `-r, --recursive_o`: Create output directory if it doesn't exist
+
+## Configuration 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/).
+### Basic Units
+```toml
+version = "0.1"
+length_unit = "um"        # micrometers
+time_unit = "ms"          # milliseconds
+diffusion_unit = "um^2/s" # diffusion coefficient units
+```
+
+### Key Configuration Sections
+
+1. **Cell Parameters**
+   - Define cell space dimensions
+   - Set cell axial radius
+
+2. **Molecule Parameters**
+   - Number of molecules per type
+   - Tracking types (constant/fbm)
+   - Diffusion coefficients
+   - State transition probabilities
+
+3. **Global Parameters**
+   - Sample plane dimensions
+   - Cycle count -> Exposure time + Interval time
+   - Exposure and interval times
+
+4. **Fluorophore Configuration**
+   - Any number of fluorophores
+   - Any number of States per fluorophore
+   - Fluorophore StateType: (bright, dark, bleached) -> All States must be one of these.
+   - Transition parameters
+   - Spectral properties
+
+5. **Optical Configuration**
+   - PSF parameters
+   - Laser settings
+   - Channel configuration
+   - Camera settings
+
+## Running Experiments
+
+AMS-BP supports two types of experiments:
+
+### 1. Time Series
+```toml
+[experiment]
+experiment_type = "time-series"
+z_position = 0.0
+laser_names_active = ["red", "blue"]
+laser_powers_active = [0.5, 0.05]
+laser_positions_active = [[5, 5, 0], [5, 5, 0]]
+```
+
+### 2. Z-Stack
+```toml
+[experiment]
+experiment_type = "z-stack"
+z_position = [-0.5, -0.4, -0.3, -0.2, -0.1, 0, 0.1, 0.2, 0.3, 0.4, 0.5]
+laser_names_active = ["red", "blue"]
+laser_powers_active = [0.5, 0.05]
+laser_positions_active = [[5, 5, 0], [5, 5, 0]]
+```
+
+## Advanced Usage
+
+### Using AMS-BP as a Library
+
+For programmatic control, you can import and use AMS-BP as a Python library:
+
+```python
+from AMS_BP.configio.convertconfig import ConfigLoader
+
+# Configuration loader intialization
+config_loader = ConfigLoader(config_path="path/to/config.toml")
+
+# Setup microscope
+setup_config = config_loader.setup_microscope()
+microscope = setup_config["microscope"]
+config_exp = setup_config["experiment_config"]
+function_exp = setup_config["experiment_func"]
+
+# Run simulation
+frames, metadata = function_exp(microscope=microscope, config=config_exp)
+
+# Save results
+from AMS_BP.configio.saving import save_config_frames
+save_config_frames(metadata, frames, setup_config["base_config"].OutputParameters)
+```

ams_bp-0.0.2.dist-info/RECORD

@@ -0,0 +1,55 @@
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+AMS_BP/sample/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
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+AMS_BP/sample/flurophores/flurophore_schema.py,sha256=j8jnr4w4ltuhXUkjd74IoyyuotyH52mn8FWkgahX5Vw,10886
+AMS_BP/utils/__init__.py,sha256=47DEQpj8HBSa-_TImW-5JCeuQeRkm5NMpJWZG3hSuFU,0
+AMS_BP/utils/constants.py,sha256=-r3cnEiuxb-XzRgGhpOuJshYYhKnDu_hv0YSffkxAfc,273
+AMS_BP/utils/decorators.py,sha256=4qFdvzPJne0dhkhD1znPxRln1Rfr5NX8rdcCDcbATRU,6224
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+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-0.0.2.dist-info/WHEEL

@@ -0,0 +1,4 @@
+Wheel-Version: 1.0
+Generator: hatchling 1.27.0
+Root-Is-Purelib: true
+Tag: py3-none-any

ams_bp-0.0.2.dist-info/entry_points.txt

@@ -0,0 +1,2 @@
+[console_scripts]
+run_AMS_BP = AMS_BP.run_cell_simulation:typer_app_asms_bp

ams_bp-0.0.2.dist-info/licenses/LICENSE

@@ -0,0 +1,21 @@
+MIT License
+
+Copyright (c) 2024 Baljyot Parmar
+
+Permission is hereby granted, free of charge, to any person obtaining a copy
+of this software and associated documentation files (the "Software"), to deal
+in the Software without restriction, including without limitation the rights
+to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+copies of the Software, and to permit persons to whom the Software is
+furnished to do so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.