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Merged
giovannivolpe merged 1 commit into from
Sep 8, 2025
+33 −15
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mg/update optics test #427

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48 changes: 33 additions & 15 deletions deeptrack/tests/test_optics.py
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Original file line number Diff line number Diff line change
@@ -1,29 +1,42 @@
import sys

# Use this only when running the test locally.
# import sys
# sys.path.append(".") # Adds the module to path

import unittest

from deeptrack import features
from deeptrack import units_registry as u
from deeptrack import optics
import numpy as np

from deeptrack import optics
from deeptrack.scatterers import PointParticle, Sphere
from deeptrack.image import Image
from deeptrack import units_registry as u

from deeptrack.backend import TORCH_AVAILABLE, xp
from deeptrack.tests import BackendTestBase

import numpy as np
if TORCH_AVAILABLE:
import torch


class TestOptics_NumPy(BackendTestBase):
BACKEND = "numpy"

@property
def array_type(self):
if self.BACKEND == "numpy":
return np.ndarray
elif self.BACKEND == "torch":
return torch.Tensor
else:
raise ValueError(f"Unsupported backend: {self.BACKEND}")

class TestOptics(unittest.TestCase):
def test_Microscope(self):
microscope_type = optics.Fluorescence()
scatterer = PointParticle()
microscope = optics.Microscope(
sample=scatterer, objective=microscope_type,
)
output_image = microscope.get(None)
self.assertIsInstance(output_image, np.ndarray)
self.assertIsInstance(output_image, self.array_type)
self.assertEqual(output_image.shape, (128, 128, 1))

def test_Optics(self):
Expand Down Expand Up @@ -51,7 +64,7 @@ def test_Fluorescence(self):
)
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, np.ndarray)
self.assertIsInstance(output_image, self.array_type)
self.assertEqual(microscope.NA(), 0.7)
self.assertEqual(output_image.shape, (64, 64, 1))

Expand All @@ -74,7 +87,7 @@ def test_Brightfield(self):
)
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, np.ndarray)
self.assertIsInstance(output_image, self.array_type)
self.assertEqual(output_image.shape, (64, 64, 1))

def test_Holography(self):
Expand All @@ -96,7 +109,7 @@ def test_Holography(self):
)
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, np.ndarray)
self.assertIsInstance(output_image, self.array_type)
self.assertEqual(output_image.shape, (64, 64, 1))

def test_ISCAT(self):
Expand All @@ -119,7 +132,7 @@ def test_ISCAT(self):
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertEqual(microscope.illumination_angle(), 3.141592653589793)
self.assertIsInstance(output_image, np.ndarray)
self.assertIsInstance(output_image, self.array_type)
self.assertEqual(output_image.shape, (64, 64, 1))

def test_Darkfield(self):
Expand All @@ -142,7 +155,7 @@ def test_Darkfield(self):
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertEqual(microscope.illumination_angle(), 1.5707963267948966)
self.assertIsInstance(output_image, np.ndarray)
self.assertIsInstance(output_image, self.array_type)
self.assertEqual(output_image.shape, (64, 64, 1))

def test_IlluminationGradient(self):
Expand All @@ -166,7 +179,7 @@ def test_IlluminationGradient(self):
)
imaged_scatterer = microscope(scatterer)
output_image = imaged_scatterer.resolve()
self.assertIsInstance(output_image, np.ndarray)
self.assertIsInstance(output_image, self.array_type)
self.assertEqual(output_image.shape, (64, 64, 1))

def test_upscale_fluorescence(self):
Expand Down Expand Up @@ -237,6 +250,11 @@ def test_upscale_brightfield(self):
).mean() # Mean absolute error
self.assertLess(error, 0.01)

# TODO: Extending the test and setting the backend to torch
# @unittest.skipUnless(TORCH_AVAILABLE, "PyTorch is not installed.")
# class TestOptics_PyTorch(TestOptics_NumPy):
# BACKEND = "torch"
# pass

if __name__ == "__main__":
unittest.main()
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