refactor: remove pint from models

pyproject.toml

@@ -143,6 +143,7 @@ filterwarnings = [
     "error",
     "ignore:unclosed transport:ResourceWarning",             # only on py3.10... not sure why
     "ignore:Clipping negative intensity values:UserWarning", # when importing FPbase spectra
+    "ignore:__array__ implementation doesn't accept a copy keyword"
 ]
 
 # https://coverage.readthedocs.io/en/6.4/config.html

src/microsim/_field_types.py

@@ -4,7 +4,6 @@
 from typing import TYPE_CHECKING, Annotated, Any, Literal, Protocol
 
 import numpy as np
-from pint.facets.plain import PlainQuantity
 from pydantic import GetCoreSchemaHandler, GetJsonSchemaHandler, functional_validators
 from pydantic_core import core_schema
 
@@ -147,12 +146,12 @@ def __get_pydantic_json_schema__(
 
 # these are all ultimately also numeric and/or array[numeric] types too
 
-Meters = Annotated[PlainQuantity, BeforeValidator(_validators.validate_meters)]
-Microns = Annotated[PlainQuantity, BeforeValidator(_validators.validate_microns)]
-Nanometers = Annotated[PlainQuantity, BeforeValidator(_validators.validate_nm)]
-ExtCoeff = Annotated[PlainQuantity, BeforeValidator(_validators.validate_ext_coeff)]
-Nanoseconds = Annotated[PlainQuantity, BeforeValidator(_validators.validate_ns)]
-Seconds = Annotated[PlainQuantity, BeforeValidator(_validators.validate_seconds)]
+# Meters = Annotated[PlainQuantity, BeforeValidator(_validators.validate_meters)]
+# Microns = Annotated[PlainQuantity, BeforeValidator(_validators.validate_microns)]
+# Nanometers = Annotated[PlainQuantity, BeforeValidator(_validators.validate_nm)]
+# ExtCoeff = Annotated[PlainQuantity, BeforeValidator(_validators.validate_ext_coeff)]
+# Nanoseconds = Annotated[PlainQuantity, BeforeValidator(_validators.validate_ns)]
+# Seconds = Annotated[PlainQuantity, BeforeValidator(_validators.validate_seconds)]
 
-Watts = Annotated[PlainQuantity, BeforeValidator(_validators.validate_watts)]
-Watts_cm2 = Annotated[PlainQuantity, BeforeValidator(_validators.validate_irradiance)]
+# Watts = Annotated[PlainQuantity, BeforeValidator(_validators.validate_watts)]
+# Watts_cm2 = Annotated[PlainQuantity, BeforeValidator(_validators.validate_irradiance)]

src/microsim/fpbase.py

@@ -6,8 +6,6 @@
 
 from pydantic import BaseModel, Field, field_validator, model_validator
 
-from microsim._field_types import ExtCoeff, Nanometers, Nanoseconds
-
 __all__ = ["get_fluorophore", "get_microscope", "FPbaseFluorophore", "FPbaseMicroscope"]
 
 
@@ -42,12 +40,12 @@ class SpectrumOwner(BaseModel):
 
 class State(BaseModel):
     id: int
-    exMax: Nanometers
-    emMax: Nanometers
-    extCoeff: ExtCoeff | None = None
+    exMax: float  # nanometers
+    emMax: float  # nanometers
+    extCoeff: float | None = None  # M^-1 cm^-1
     qy: float | None = None
     spectra: list[Spectrum]
-    lifetime: Nanoseconds | None = None
+    lifetime: float | None = None  # ns
 
     @property
     def excitation_spectrum(self) -> Spectrum | None:

src/microsim/interval_creation.py

@@ -118,11 +118,8 @@ def bin_spectrum(
 
     Returns the binned spectrum as a `DataArray`.
     """
-    wavelengths = spectrum.wavelength.magnitude
-    if isinstance(spectrum.intensity, np.ndarray):
-        intensities = spectrum.intensity
-    else:
-        intensities = spectrum.intensity.magnitude
+    wavelengths = spectrum.wavelength
+    intensities = spectrum.intensity
     if bins is None:
         bins = generate_bins(
             x=wavelengths, y=intensities, num_bins=num_bins, strategy=binning_strategy

src/microsim/psf.py

@@ -3,12 +3,11 @@
 import logging
 import os
 from functools import cache
-from typing import TYPE_CHECKING, cast
+from typing import TYPE_CHECKING
 
 import numpy as np
 import numpy.typing as npt
 import tqdm
-from pint import Quantity
 
 from microsim.schema.backend import NumpyAPI
 from microsim.schema.lens import ObjectiveKwargs, ObjectiveLens
@@ -351,7 +350,7 @@
     space: SpaceProtocol,
     channel: OpticalConfig,
     objective: ObjectiveLens,
-    em_wvl: Quantity | None = None,
+    em_wvl_nm: float | None = None,
     pinhole_au: float | None = None,
     max_au_relative: float | None = None,
     xp: NumpyAPI | None = None,
@@ -370,16 +369,16 @@
     if em is None:
         em = ex
 
-    if em_wvl is None:
-        em_wvl = cast(Quantity, em.center_wave())
+    if em_wvl_nm is None:
+        em_wvl_nm = em.center_wave()
 
     return cached_psf(
         nz=nz,
         nx=nx,
         dx=dx,
         dz=dz,
-        ex_wvl_um=ex.center_wave().to("um").magnitude,
-        em_wvl_um=em_wvl.to("um").magnitude,
+        ex_wvl_um=ex.center_wave() * 1e-3,  # nm to um
+        em_wvl_um=em_wvl_nm * 1e-3,  # nm to um
         objective=_cast_objective(objective),
         pinhole_au=pinhole_au,
         max_au_relative=max_au_relative,

src/microsim/schema/_emission.py

@@ -59,14 +59,15 @@
     if not (fluor_ex_spectrum := fluor.excitation_spectrum):
         raise NotImplementedError("Fluorophore has no excitation spectrum.")
 
-    if (ext_coeff := fluor.extinction_coefficient) is None:
-        ext_coeff = _ensure_quantity(55000, "cm^-1/M")
+    if (ec := fluor.extinction_coefficient) is None:
+        ec = 55000
         warnings.warn(
             "No extinction coefficient provided for fluorophore, "
             "using 55,000 M^-1 * cm^-1.",
             stacklevel=2,
         )
 
+    ext_coeff = _ensure_quantity(ec, "cm^-1/M")
     # TODO: derive light power from model
     irradiance = ex_filter_spectrum * _ensure_quantity(light_power, "W/cm^2")
     cross_section = fluor_ex_spectrum * ec_to_cross_section(ext_coeff)

src/microsim/schema/lens.py

@@ -3,8 +3,6 @@
 import numpy as np
 from pydantic import Field, model_validator
 
-from microsim._field_types import Microns
-
 from ._base_model import SimBaseModel
 
 
@@ -28,12 +26,9 @@ class ObjectiveLens(SimBaseModel):
     immersion_medium_ri: float = 1.515  # immersion medium RI experimental value (ni)
     immersion_medium_ri_spec: float = 1.515  # immersion medium RI design value (ni0)
     specimen_ri: float = 1.47  # specimen refractive index (ns)
-    # um, working distance, design value (ti0)
-    working_distance: Microns = 150.0  # type: ignore
-    # um, coverslip thickness (tg)
-    coverslip_thickness: Microns = 170.0  # type: ignore
-    # um, coverslip thickness design (tg0)
-    coverslip_thickness_spec: Microns = 170.0  # type: ignore
+    working_distance_um: float = 150.0  # um, working distance, design value (ti0)
+    coverslip_thickness_um: float = 170.0  # um, coverslip thickness (tg)
+    coverslip_thickness_spec_um: float = 170.0  # um, coverslip thickness design (tg0)
 
     magnification: float = Field(1, description="magnification of objective lens.")
 
@@ -54,9 +49,9 @@ def __hash__(self) -> int:
                 self.immersion_medium_ri,
                 self.immersion_medium_ri_spec,
                 self.specimen_ri,
-                self.working_distance,
-                self.coverslip_thickness,
-                self.coverslip_thickness_spec,
+                self.working_distance_um,
+                self.coverslip_thickness_um,
+                self.coverslip_thickness_spec_um,
                 self.magnification,
             )
         )
@@ -91,15 +86,15 @@ def ng(self) -> float:
 
     @property
     def tg(self) -> float:
-        return float(self.coverslip_thickness.to("meters").magnitude)
+        return self.coverslip_thickness_um * 1e-6  # convert to meters
 
     @property
     def tg0(self) -> float:
-        return float(self.coverslip_thickness_spec.to("meters").magnitude)
+        return self.coverslip_thickness_spec_um * 1e-6  # convert to meters
 
     @property
     def ti0(self) -> float:
-        return float(self.working_distance.to("meters").magnitude)
+        return self.working_distance_um * 1e-6  # convert to meters
 
     @property
     def ng0(self) -> float:

src/microsim/schema/modality/_simple.py

@@ -1,8 +1,6 @@
 from typing import Annotated, Any, Literal
 
-import pint
 from annotated_types import Ge
-from pint import Quantity
 
 from microsim._data_array import ArrayProtocol, DataArray, xrDataArray
 from microsim.psf import make_psf
@@ -23,7 +21,7 @@ def psf(
         objective_lens: ObjectiveLens,
         settings: Settings,
         xp: NumpyAPI,
-        em_wvl: Quantity | None = None,
+        em_wvl_nm: float | None = None,
     ) -> ArrayProtocol:
         # default implementation is a widefield PSF
         return make_psf(
@@ -32,7 +30,7 @@ def psf(
             objective=objective_lens,
             max_au_relative=settings.max_psf_radius_aus,
             xp=xp,
-            em_wvl=em_wvl,
+            em_wvl_nm=em_wvl_nm,
         )
 
     def render(
@@ -44,7 +42,6 @@ def render(
         xp: NumpyAPI,
     ) -> xrDataArray:
         convolved: Any = 0
-        ureg = pint.application_registry.get()  # type: ignore
         for fluor_idx in range(truth.sizes[Axis.F]):
             convolved_fluor: Any = 0
             for bin_idx in range(truth.sizes[Axis.W]):
@@ -53,14 +50,13 @@ def render(
                     # NOTE: there can be bins for which there is no data in one of the
                     #  fluorophores
                     continue
-                em_wvl = binned_flux[Axis.W].values.item().mid * ureg.nm
                 psf = self.psf(
                     truth.attrs["space"],
                     channel,
                     objective_lens,
                     settings,
                     xp,
-                    em_wvl=em_wvl,
+                    em_wvl_nm=binned_flux[Axis.W].values.item().mid,
                 )
                 convolved_fluor += xp.fftconvolve(
                     binned_flux.isel({Axis.C: 0}), psf, mode="same"
@@ -91,7 +87,7 @@ def psf(
         objective_lens: ObjectiveLens,
         settings: Settings,
         xp: NumpyAPI,
-        em_wvl: Quantity | None = None,
+        em_wvl_nm: float | None = None,
     ) -> ArrayProtocol:
         return make_psf(
             space=space,
@@ -100,7 +96,7 @@ def psf(
             pinhole_au=self.pinhole_au,
             max_au_relative=settings.max_psf_radius_aus,
             xp=xp,
-            em_wvl=em_wvl,
+            em_wvl_nm=em_wvl_nm,
         )
 
 

src/microsim/schema/optical_config/config.py

@@ -4,7 +4,6 @@
 
 from pydantic import Field, model_validator
 
-from microsim._field_types import Watts, Watts_cm2
 from microsim.fpbase import SpectrumOwner
 from microsim.schema._base_model import SimBaseModel
 from microsim.schema.spectrum import Spectrum
@@ -15,7 +14,7 @@
 class LightSource(SimBaseModel):
     name: str = ""
     spectrum: Spectrum
-    power: Watts | Watts_cm2 | None = None
+    power: float | None = None  # W/cm^2
 
     @classmethod
     def from_fpbase(cls, light: SpectrumOwner) -> "LightSource":
@@ -135,7 +134,7 @@ def plot(self, show: bool = True) -> None:
 
         legend = []
         for filt in self.filters:
-            ax.plot(filt.spectrum.wavelength.magnitude, filt.spectrum.intensity)
+            ax.plot(filt.spectrum.wavelength, filt.spectrum.intensity)
             legend.append(filt.name)
         if any(legend):
             ax.legend(legend)