From e79d73697efcf4bb02b924254eefd79572069fe9 Mon Sep 17 00:00:00 2001
From: Talley Lambert <talley.lambert@gmail.com>
Date: Thu, 31 Oct 2024 12:34:39 +0100
Subject: [PATCH] refactor: update settings

---
 src/microsim/schema/modality/__init__.py      |  2 +-
 .../modality/{_simple.py => _simple_psf.py}   |  0
 src/microsim/schema/settings.py               | 40 ++-----------------
 3 files changed, 4 insertions(+), 38 deletions(-)
 rename src/microsim/schema/modality/{_simple.py => _simple_psf.py} (100%)

diff --git a/src/microsim/schema/modality/__init__.py b/src/microsim/schema/modality/__init__.py
index 43679bf..2215099 100644
--- a/src/microsim/schema/modality/__init__.py
+++ b/src/microsim/schema/modality/__init__.py
@@ -1,4 +1,4 @@
-from ._simple import Confocal, Identity, Widefield
+from ._simple_psf import Confocal, Identity, Widefield
 
 Modality = Confocal | Widefield | Identity
 
diff --git a/src/microsim/schema/modality/_simple.py b/src/microsim/schema/modality/_simple_psf.py
similarity index 100%
rename from src/microsim/schema/modality/_simple.py
rename to src/microsim/schema/modality/_simple_psf.py
diff --git a/src/microsim/schema/settings.py b/src/microsim/schema/settings.py
index 80fd38f..ec46654 100644
--- a/src/microsim/schema/settings.py
+++ b/src/microsim/schema/settings.py
@@ -1,5 +1,5 @@
 import random
-from typing import Any, ClassVar, Literal
+from typing import Any, ClassVar
 
 from pydantic import Field, model_validator
 from pydantic_settings import BaseSettings, SettingsConfigDict
@@ -35,7 +35,7 @@ class Settings(SimBaseModel, BaseSettings):
         default_factory=lambda: random.randint(0, 2**32 - 1)
     )
     max_psf_radius_aus: float | None = Field(
-        8,
+        6,
         description=(
             "When simulating, restrict generated lateral PSF size to no more than this "
             "many Airy units. Decreasing this can *dramatically* speed up simulations, "
@@ -44,18 +44,8 @@ class Settings(SimBaseModel, BaseSettings):
         ),
     )
     cache: CacheSettings = Field(default_factory=CacheSettings)
-    binning_strategy: Literal["equal_area", "equal_space"] = Field(
-        "equal_space",
-        description=(
-            "The strategy to use for binning data. `'equal_area'` will divide the "
-            "spectrum into intervals with intensity integral, while `'equal_space'` "
-            "will divide the range of values into equally spaced bins. Note that "
-            "`'equal_area'` is more accurate, but is not supported in the case of "
-            "multiple fluorophores."
-        ),
-    )
     spectral_bins_per_emission_channel: int = Field(
-        4,
+        1,
         description="Number of wavelengths to use (per channel) when simulating the "
         "optical image. By default, a single centroid wavelength is used to approximate"
         "the emission wavelength.  Increasing this will make the simulation more "
@@ -71,30 +61,6 @@ class Settings(SimBaseModel, BaseSettings):
         "intensity above this threshold). Then, the spectrum is discretized into "
         "spectral_bins_per_emission_channel bins.",
     )
-    num_wavelength_bins: int = Field(
-        32,
-        description=(
-            "Number of bins to use when discretizing the wavelength spectrum."
-            "It regards the wavelength range for illumination and excitation spectra."
-            "Increasing this will increase accuracy but also increase memory usage."
-        ),
-    )
-    min_wavelength: int = Field(
-        300,
-        description=(
-            "Minimum wavelength to consider in the simulation."
-            "It is used to define the range of the wavelength spectrum when "
-            "fluorophores are not defined."
-        ),
-    )
-    max_wavelength: int = Field(
-        800,
-        description=(
-            "Maximum wavelength to consider in the simulation."
-            "It is used to define the range of the wavelength spectrum when "
-            "fluorophores are not defined."
-        ),
-    )
 
     model_config: ClassVar[SettingsConfigDict] = SettingsConfigDict(
         validate_assignment=True,