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Gv/final/optics+scatteres+image #423

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6d7c00b
Update optics.py
giovannivolpe Sep 6, 2025
d9b6f9c
Update optics.py
giovannivolpe Sep 6, 2025
9afc670
Update test_scatterers.py
giovannivolpe Sep 6, 2025
0827274
Update optics.py
giovannivolpe Sep 8, 2025
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153 changes: 98 additions & 55 deletions deeptrack/optics.py
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Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -137,10 +137,11 @@ def _pad_volume(
from __future__ import annotations

from pint import Quantity
from typing import Any
from typing import Any, TYPE_CHECKING
import warnings

import numpy as np
from numpy.typing import NDArray
from scipy.ndimage import convolve

from deeptrack.backend.units import (
Expand All @@ -158,6 +159,9 @@ def _pad_volume(
from deeptrack import image
from deeptrack import units_registry as u

if TYPE_CHECKING:
import torch


#TODO ***??*** revise Microscope - torch, typing, docstring, unit test
class Microscope(StructuralFeature):
Expand Down Expand Up @@ -207,59 +211,60 @@ class Microscope(StructuralFeature):

__distributed__ = False

_sample: Feature
_objective: Feature

def __init__(
self: Microscope,
sample: Feature,
objective: Feature,
**kwargs: Any,
):
"""Initialize the `Microscope` instance.
"""Initialize a microscope feature combining sample and optics.

This constructor attaches a sample feature (typically a combination of
scatterers) and an objective feature (optical system) to the
microscope.

Parameters
----------
sample: Feature
A feature-set resolving a list of images describing the sample to be
imaged.
Feature that resolves one or more scatterer volumes or fields
representing the sample to be imaged.
objective: Feature
A feature-set defining the optical device that images the sample.
Feature describing the optical system used to image the sample
(e.g., brightfield, fluorescence).
**kwargs: Any
Additional parameters passed to the base `StructuralFeature` class.

Attributes
----------
_sample: Feature
The feature-set defining the sample to be imaged.
_objective: Feature
The feature-set defining the optical system imaging the sample.
Additional keyword arguments passed to the base `StructuralFeature`
class.

"""

super().__init__(**kwargs)

self._sample = self.add_feature(sample)
self._objective = self.add_feature(objective)

#TODO: erase following line when rid of Image
self._sample.store_properties()

def get(
self: Microscope,
image: Image | None,
input: Any = None, # Ignored, kept for API compatibility
**kwargs: Any,
) -> Image:
) -> NDArray[Any] | torch.Tensor:
"""Generate an image of the sample using the defined optical system.

This method processes the sample through the optical system to
produce a simulated image.

Parameters
----------
image: Image | None
The input image to be processed. If None, a new image is created.
image: Any, optional
Ignored. Kept for API compatibility. Defaults to None.
**kwargs: Any
Additional parameters for the imaging process.

Returns
-------
Image: Image
array or tensor
The processed image after applying the optical system.

Examples
Expand All @@ -277,94 +282,131 @@ def get(

"""

# Grab properties from the objective to pass to the sample
additional_sample_kwargs = self._objective.properties()
# Grab objective properties to pass to sample
objective_properties = self._objective.properties()

# Calculate required output image for the given upscale
# This way of providing the upscale will be deprecated in the future
# in favor of dt.Upscale().
_upscale_given_by_optics = additional_sample_kwargs["upscale"]
#TODO: TBE
"""
# Calculate required output image for the given upscale.
# This upscale way will be deprecated in favor of dt.Upscale().
_upscale_given_by_optics = objective_properties["upscale"]
if np.array(_upscale_given_by_optics).size == 1:
_upscale_given_by_optics = (_upscale_given_by_optics,) * 3

with u.context(
create_context(
*additional_sample_kwargs["voxel_size"], *_upscale_given_by_optics
*objective_properties["voxel_size"], *_upscale_given_by_optics
)
):
"""

upscale = np.round(get_active_scale())

output_region = additional_sample_kwargs.pop("output_region")
additional_sample_kwargs["output_region"] = [
int(o * upsc)
for o, upsc in zip(
output_region, (upscale[0], upscale[1], upscale[0], upscale[1])
)
]
with u.context(create_context(*objective_properties["voxel_size"])):

padding = additional_sample_kwargs.pop("padding")
additional_sample_kwargs["padding"] = [
int(p * upsc)
for p, upsc in zip(
padding, (upscale[0], upscale[1], upscale[0], upscale[1])
)
]
upscale = np.round(get_active_scale())

def _scale_region_2d(
region: list[int],
upscale: tuple[float, float, float],
) -> list[int]:
"""Scale a 4-tuple region (x_min, y_min, x_max, y_max) or
padding using the lateral upscale factors (ux, uy)."""
ux, uy, _ = upscale
return [int(v * f) for v, f in zip(region, (ux, uy, ux, uy))]

# Scale output region from optics into sample voxel units.
output_region = objective_properties.pop("output_region")
objective_properties["output_region"] = _scale_region_2d(
output_region,
upscale,
)
self._objective.output_region.set_value(
additional_sample_kwargs["output_region"]
objective_properties["output_region"]
)
self._objective.padding.set_value(additional_sample_kwargs["padding"])

# Scale padding region in the same way (left, top, right, bottom).
padding = objective_properties.pop("padding")
objective_properties["padding"] = _scale_region_2d(
padding,
upscale,
)
self._objective.padding.set_value(objective_properties["padding"])

# Propagate all relevant properties from the objective to the
# sample graph. This ensures scatterers are evaluated in the
# same voxel size, output region, and padding as the optics.
# The extra flag `return_fft=True` is forced here because most
# objectives (e.g., Brightfield, Holography) operate in Fourier
# space, and they require scatterers to provide Fourier-domain
# data in addition to real-space volumes.
propagate_data_to_dependencies(
self._sample, **{"return_fft": True, **additional_sample_kwargs}
self._sample,
**{"return_fft": True, **objective_properties},
)

# Evaluate the sample feature to obtain scatterers.
# The result may be a single scatterer or a list of them.
list_of_scatterers = self._sample()

if not isinstance(list_of_scatterers, list):
list_of_scatterers = [list_of_scatterers]

# All scatterers that are defined as volumes.
volume_samples = [
# Volume scatterers occupy voxels in 3D (e.g. PointParticle).
volume_scatterers = [
scatterer
for scatterer in list_of_scatterers
if not scatterer.get_property("is_field", default=False)
]

# All scatterers that are defined as fields.
field_samples = [
# Field scatterers provide a complex field directly,
# bypassing volume merge.
field_scatterers = [
scatterer
for scatterer in list_of_scatterers
if scatterer.get_property("is_field", default=False)
]








# Merge all volumes into a single volume.
sample_volume, limits = _create_volume(
volume_samples,
**additional_sample_kwargs,
volume_scatterers,
**objective_properties,
)
sample_volume = Image(sample_volume)

# Merge all properties into the volume.
for scatterer in volume_samples + field_samples:
for scatterer in volume_scatterers + field_scatterers:
sample_volume.merge_properties_from(scatterer)

# Let the objective know about the limits of the volume and all the fields.
propagate_data_to_dependencies(
self._objective,
limits=limits,
fields=field_samples,
fields=field_scatterers,
)

imaged_sample = self._objective.resolve(sample_volume)

# Upscale given by the optics needs to be handled separately.
#TODO: TBE
"""
# Handling separately upscale given by optics.
# This upscale way will be deprecated in favor of dt.Upscale().
if _upscale_given_by_optics != (1, 1, 1):
imaged_sample = AveragePooling((*_upscale_given_by_optics[:2], 1))(
imaged_sample
)
"""

return imaged_sample

"""
#TODO: erase rest of the method
# Merge with input
if not image:
if not self._wrap_array_with_image and isinstance(imaged_sample, Image):
Expand All @@ -377,6 +419,7 @@ def get(
for i in range(len(image)):
image[i].merge_properties_from(imaged_sample)
return image
"""

# def _no_wrap_format_input(self, *args, **kwargs) -> list:
# return self._image_wrapped_format_input(*args, **kwargs)
Expand Down
16 changes: 15 additions & 1 deletion deeptrack/tests/test_scatterers.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -68,6 +68,8 @@ def test_Ellipse(self):
self.assertEqual(output_image.shape, (64, 64, 1))

def test_EllipseUpscale(self):
pass #TODO: adapt test with dt.Upscale()
"""
optics = Fluorescence(
NA=0.7,
wavelength=680e-9,
Expand Down Expand Up @@ -105,8 +107,11 @@ def test_EllipseUpscale(self):
imaged_scatterer.resolve()
scatterer_volume = scatterer()
self.assertEqual(scatterer_volume.shape, (39, 79, 1))
"""

def test_EllipseUpscaleAsymmetric(self):
pass #TODO: adapt test with dt.Upscale()
"""
optics = Fluorescence(
NA=0.7,
wavelength=680e-9,
Expand Down Expand Up @@ -144,6 +149,7 @@ def test_EllipseUpscaleAsymmetric(self):
imaged_scatterer.resolve()
scatterer_volume = scatterer()
self.assertEqual(scatterer_volume.shape, (19, 39, 1))
"""

def test_Sphere(self):
optics = Fluorescence(
Expand All @@ -166,7 +172,8 @@ def test_Sphere(self):
self.assertEqual(output_image.shape, (64, 64, 1))

def test_SphereUpscale(self):

pass #TODO: adapt test with dt.Upscale()
"""
optics = Fluorescence(
NA=0.7,
wavelength=680e-9,
Expand All @@ -185,6 +192,7 @@ def test_SphereUpscale(self):
imaged_scatterer.resolve()
scatterer_volume = scatterer()
self.assertEqual(scatterer_volume.shape, (40, 40, 40))
"""

def test_Ellipsoid(self):
optics = Fluorescence(
Expand All @@ -208,6 +216,8 @@ def test_Ellipsoid(self):
self.assertEqual(output_image.shape, (64, 64, 1))

def test_EllipsoidUpscale(self):
pass #TODO: adapt test with dt.Upscale()
"""
optics = Fluorescence(
NA=0.7,
wavelength=680e-9,
Expand All @@ -227,8 +237,11 @@ def test_EllipsoidUpscale(self):
imaged_scatterer.resolve()
scatterer_volume = scatterer()
self.assertEqual(scatterer_volume.shape, (19, 39, 9))
"""

def test_EllipsoidUpscaleAsymmetric(self):
pass #TODO: adapt test with dt.Upscale()
"""
optics = Fluorescence(
NA=0.7,
wavelength=680e-9,
Expand Down Expand Up @@ -288,6 +301,7 @@ def test_EllipsoidUpscaleAsymmetric(self):
imaged_scatterer.resolve()
scatterer_volume = scatterer()
self.assertEqual(scatterer_volume.shape, (19, 39, 19))
"""

def test_MieSphere(self):
optics_1 = Brightfield(
Expand Down
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