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# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
"""Image ROI advanced unit tests"""
from __future__ import annotations
import numpy as np
import pytest
from skimage import draw
import sigima.objects
import sigima.params
import sigima.proc.image
from sigima.tests import guiutils
from sigima.tests.data import create_multigaussian_image
from sigima.tests.helpers import print_obj_data_dimensions
def test_image_roi_param() -> None:
"""Test image ROI parameter conversion"""
# Create an image object
obj = create_multigaussian_image()
# Create an image ROI
coords = [100, 150, 200, 250]
roi = sigima.objects.create_image_roi("rectangle", coords, inverse=False)
# Convert to parameters
roiparam = roi.to_params(obj)[0]
assert isinstance(roiparam, sigima.objects.ROI2DParam), (
"Parameter should be ROI2DParam"
)
# Check that converting back to single ROI gives the same coordinates
single_roi = roiparam.to_single_roi(obj)
single_roi_coords = single_roi.get_physical_coords(obj)
assert np.all(single_roi_coords == np.array(coords)), (
"Single ROI coordinates mismatch"
)
def test_image_roi_merge() -> None:
"""Test image ROI merge"""
# Create an image object with a single ROI, and another one with another ROI.
# Compute the average of the two objects, and check if the resulting object
# has the expected ROI (i.e. the union of the original object's ROI).
obj1 = create_multigaussian_image()
obj2 = create_multigaussian_image()
obj2.roi = sigima.objects.create_image_roi(
"rectangle", [600, 800, 1000, 1200], inverse=False
)
obj1.roi = sigima.objects.create_image_roi(
"rectangle", [500, 750, 1000, 1250], inverse=False
)
# Compute the average of the two objects
obj3 = sigima.proc.image.average([obj1, obj2])
assert obj3.roi is not None, "Merged object should have a ROI"
assert len(obj3.roi) == 2, "Merged object should have two single ROIs"
for single_roi in obj3.roi:
assert single_roi.get_indices_coords(obj3) in (
[500, 750, 1000, 1250],
[600, 800, 1000, 1200],
), "Merged object should have the union of the original object's ROIs"
def test_image_roi_combine() -> None:
"""Test `ImageROI.combine_with` method"""
coords1, coords2 = [600, 800, 1000, 1200], [500, 750, 1000, 1250]
roi1 = sigima.objects.create_image_roi(
"rectangle", coords1, indices=True, inverse=False
)
roi2 = sigima.objects.create_image_roi(
"rectangle", coords2, indices=True, inverse=False
)
exp_combined = sigima.objects.create_image_roi(
"rectangle",
[coords1, coords2],
indices=True,
inverse=False,
)
# Check that combining two ROIs results in a new ROI with both coordinates:
roi3 = roi1.combine_with(roi2)
assert roi3 == exp_combined, "Combined ROI should match expected"
# Check that combining again with the same ROI does not change it:
roi3 = roi1.combine_with(roi2)
assert roi3 == exp_combined, "Combining with the same ROI should not change it"
# Check that combining with a signal ROI raises an error:
with pytest.raises(
TypeError, match=r"Cannot combine([\S ]*)ImageROI([\S ]*)SignalROI"
):
roi1.combine_with(sigima.objects.create_signal_roi([50, 100], indices=True))
SIZE = 200
# Image ROIs:
IROI1 = [100, 100, 75, 100] # Rectangle
IROI2 = [66, 100, 50] # Circle
# Polygon (triangle, that is intentionally inside the rectangle, so that this ROI
# has no impact on the mask calculations in the tests)
IROI3 = [100, 100, 100, 150, 150, 133]
def __roi_str(obj: sigima.objects.ImageObj) -> str:
"""Return a string representation of a ImageROI object for context."""
if obj.roi is None:
return "None"
if obj.roi.is_empty():
return "Empty"
return ", ".join(
f"{single_roi.__class__.__name__}({single_roi.get_indices_coords(obj)})"
for single_roi in obj.roi.single_rois
)
def __create_test_roi() -> sigima.objects.ImageROI:
"""Create test ROI"""
roi = sigima.objects.create_image_roi("rectangle", IROI1, inverse=False)
roi.add_roi(sigima.objects.create_image_roi("circle", IROI2, inverse=False))
roi.add_roi(sigima.objects.create_image_roi("polygon", IROI3, inverse=False))
return roi
def __create_test_image() -> sigima.objects.ImageObj:
"""Create test image"""
param = sigima.objects.NewImageParam.create(height=SIZE, width=SIZE)
ima = create_multigaussian_image(param)
ima.data += 1 # Ensure that the image has non-zero values (for ROI check tests)
return ima
def __test_processing_in_roi(src: sigima.objects.ImageObj) -> None:
"""Run image processing in ROI
Args:
src: Source image object (with or without ROI)
"""
print_obj_data_dimensions(src)
value = 1
p = sigima.params.ConstantParam.create(value=value)
dst = sigima.proc.image.addition_constant(src, p)
orig = src.data
new = dst.data
context = f" [ROI: {__roi_str(src)}]"
if src.roi is not None and not src.roi.is_empty():
# A ROI has been set in the source image.
assert np.all(
new[IROI1[1] : IROI1[3] + IROI1[1], IROI1[0] : IROI1[2] + IROI1[0]]
== orig[IROI1[1] : IROI1[3] + IROI1[1], IROI1[0] : IROI1[2] + IROI1[0]]
+ value
), f"Image ROI 1 data mismatch{context}"
assert np.all(
new[IROI2[1] : IROI1[1] + 1, IROI2[0] : IROI2[0] + 2 * IROI2[2]]
== orig[IROI2[1] : IROI1[1] + 1, IROI2[0] : IROI2[0] + 2 * IROI2[2]] + value
), f"Image ROI 2 data mismatch{context}"
first_col = min(IROI1[0], IROI2[0] - IROI2[2])
first_row = min(IROI1[1], IROI2[1] - IROI2[2])
last_col = max(IROI1[0] + IROI1[2], IROI2[0] + 2 * IROI2[2])
last_row = max(IROI1[1] + IROI1[3], IROI2[1] + 2 * IROI2[2])
assert np.all(
new[:first_row, :first_col] == np.array(orig[:first_row, :first_col], float)
), f"Image before ROIs data mismatch{context}"
assert np.all(new[:first_row, last_col:] == orig[:first_row, last_col:]), (
f"Image after ROIs data mismatch{context}"
)
assert np.all(new[last_row:, :first_col] == orig[last_row:, :first_col]), (
f"Image before ROIs data mismatch{context}"
)
assert np.all(new[last_row:, last_col:] == orig[last_row:, last_col:]), (
f"Image after ROIs data mismatch{context}"
)
else:
# No ROI has been set in the source image.
assert np.all(new == orig + value), f"Image data mismatch{context}"
def test_image_roi_processing() -> None:
"""Test image ROI processing"""
src = __create_test_image()
base_roi = __create_test_roi()
empty_roi = sigima.objects.ImageROI()
for roi in (empty_roi, base_roi):
src.roi = roi
__test_processing_in_roi(src)
def test_empty_image_roi() -> None:
"""Test empty image ROI"""
src = __create_test_image()
empty_roi = sigima.objects.ImageROI()
for roi in (None, empty_roi):
src.roi = roi
context = f" [ROI: {__roi_str(src)}]"
assert src.roi is None or src.roi.is_empty(), (
f"Source object ROI should be empty or None{context}"
)
if src.roi is not None:
# No ROI has been set in the source image
im1 = sigima.proc.image.extract_roi(src, src.roi.to_params(src))
assert im1.data.shape == (0, 0), f"Extracted image should be empty{context}"
@pytest.mark.validation
def test_image_extract_rois() -> None:
"""Validation test for image ROI extraction into a single object"""
src = __create_test_image()
src.roi = __create_test_roi()
context = f" [ROI: {__roi_str(src)}]"
nzroi = f"Non-zero values expected in ROI{context}"
zroi = f"Zero values expected outside ROI{context}"
im1 = sigima.proc.image.extract_rois(src, src.roi.to_params(src))
mask1 = np.zeros(shape=(SIZE, SIZE), dtype=bool)
mask1[IROI1[1] : IROI1[1] + IROI1[3], IROI1[0] : IROI1[0] + IROI1[2]] = 1
xc, yc, r = IROI2
mask2 = np.zeros(shape=(SIZE, SIZE), dtype=bool)
rr, cc = draw.disk((yc, xc), r)
mask2[rr, cc] = 1
mask = mask1 | mask2
row_min = int(min(IROI1[1], IROI2[1] - r))
col_min = int(min(IROI1[0], IROI2[0] - r))
row_max = int(max(IROI1[1] + IROI1[3], IROI2[1] + r))
col_max = int(max(IROI1[0] + IROI1[2], IROI2[0] + r))
mask = mask[row_min:row_max, col_min:col_max]
assert np.all(im1.data[mask] != 0), nzroi
assert np.all(im1.data[~mask] == 0), zroi
# Bug fix verification: extracted image should not have ROI defined
assert im1.roi is None, f"Extracted image should not have ROI defined{context}"
@pytest.mark.validation
def test_image_extract_roi() -> None:
"""Validation test for image ROI extraction into multiple objects"""
src = __create_test_image()
src.roi = __create_test_roi()
context = f" [ROI: {__roi_str(src)}]"
nzroi = f"Non-zero values expected in ROI{context}"
roisham = f"ROI shape mismatch{context}"
images: list[sigima.objects.ImageObj] = []
for index, single_roi in enumerate(src.roi):
roiparam = single_roi.to_param(src, index)
image = sigima.proc.image.extract_roi(src, roiparam)
images.append(image)
assert len(images) == 3, f"Three images expected{context}"
im1, im2 = images[:2] # pylint: disable=unbalanced-tuple-unpacking
assert np.all(im1.data != 0), nzroi
assert im1.data.shape == (IROI1[3], IROI1[2]), roisham
assert np.all(im2.data != 0), nzroi
assert im2.data.shape == (IROI2[2] * 2, IROI2[2] * 2), roisham
mask2 = np.zeros(shape=im2.data.shape, dtype=bool)
xc = yc = r = IROI2[2] # Adjust for ROI origin
rr, cc = draw.disk((yc, xc), r, shape=im2.data.shape)
mask2[rr, cc] = 1
assert np.all(im2.maskdata == ~mask2), f"Mask data mismatch{context}"
# Bug fix verification: extracted images should handle ROI correctly
# - For rectangular ROI: no ROI should be defined
# - For circular/polygonal ROI: a new ROI should be created (not copied from source)
assert images[0].roi is None, f"Rectangular extraction should not have ROI{context}"
# For circular and polygonal, roi should exist but be different from source
for idx in [1, 2]:
if images[idx].roi is not None:
err_msg = f"Extracted image {idx} ROI should not be same as source{context}"
assert images[idx].roi is not src.roi, err_msg
def test_roi_coordinates_validation() -> None:
"""Test ROI coordinates validation"""
# Create a 20x20 Gaussian image
param = sigima.objects.Gauss2DParam.create(a=10.0, height=20, width=20)
src = sigima.objects.create_image_from_param(param)
# Create ROI coordinates
rect_coords = np.array([4.5, 4.5, 10.0, 10.0])
circ_coords = np.array([9.5, 9.5, 5.0])
poly_coords = np.array([5.1, 15.1, 14.7, 12.0, 12.5, 7.0, 5.2, 4.9])
# Create ROIs
rect_roi = sigima.objects.create_image_roi(
"rectangle", rect_coords, title="rectangular"
)
circ_roi = sigima.objects.create_image_roi("circle", circ_coords, title="circular")
poly_roi = sigima.objects.create_image_roi(
"polygon", poly_coords, title="polygonal"
)
# Check that coordinates are correct
assert np.all(rect_roi.get_single_roi(0).get_physical_coords(src) == rect_coords)
assert np.all(circ_roi.get_single_roi(0).get_physical_coords(src) == circ_coords)
assert np.all(poly_roi.get_single_roi(0).get_physical_coords(src) == poly_coords)
# Check that extracted images have correct data
for roi in (rect_roi, circ_roi, poly_roi):
extracted = sigima.proc.image.extract_roi(src, roi.to_params(src)[0])
assert np.all(extracted.data != 0), "Extracted image should have non-zero data"
assert extracted.data.shape == (10, 10), "Extracted image shape mismatch"
# Display the original image and the ROIs
if guiutils.is_gui_enabled():
images = [src]
titles = ["Original Image"]
for inverse in (False, True):
for roi in (rect_roi, circ_roi, poly_roi):
src2 = src.copy()
roi.get_single_roi(0).inverse = inverse
src2.roi = roi
images.append(src2)
roi_title = roi.get_single_roi(0).title
mask_str = "mask inside" if inverse else "mask outside"
titles.append(f"Image with {roi_title} ROI ({mask_str})")
guiutils.view_images_side_by_side_if_gui(
images, titles, rows=2, title="Image ROIs"
)
def test_create_image_roi_inverse_parameter() -> None:
"""Test create_image_roi function with inverse parameter functionality"""
# Test 1: Single ROI with inverse=True (mask inside)
roi1 = sigima.objects.create_image_roi("rectangle", [10, 20, 30, 40], inverse=True)
assert len(roi1) == 1, "Should create one ROI"
assert roi1.single_rois[0].inverse is True, "ROI should have inverse=True"
# Test 2: Single ROI with inverse=False (default)
roi2 = sigima.objects.create_image_roi("rectangle", [10, 20, 30, 40])
assert roi2.single_rois[0].inverse is False, "Default should be False"
# Test 3: Multiple ROIs with global inverse parameter
coords = [[10, 20, 30, 40], [50, 60, 70, 80]]
roi3 = sigima.objects.create_image_roi("rectangle", coords, inverse=True)
assert len(roi3) == 2, "Should create two ROIs"
assert all(single_roi.inverse is True for single_roi in roi3.single_rois), (
"All ROIs should have inverse=True (internal representation)"
)
# Test 4: Multiple ROIs with individual inverse parameters
inverse_values = [True, False] # mask inside, then mask outside
roi4 = sigima.objects.create_image_roi("rectangle", coords, inverse=inverse_values)
assert len(roi4) == 2, "Should create two ROIs"
assert roi4.single_rois[0].inverse is True, "First ROI should be True"
assert roi4.single_rois[1].inverse is False, "Second ROI should be False"
# Test 5: Circle ROIs with mixed inverse parameters
circle_coords = [[50, 50, 25], [150, 150, 30]]
roi5 = sigima.objects.create_image_roi(
"circle",
circle_coords,
inverse=[False, True], # mask outside, then mask inside
)
assert len(roi5) == 2, "Should create two circle ROIs"
assert roi5.single_rois[0].inverse is False, "First circle should be False"
assert roi5.single_rois[1].inverse is True, "Second circle should be True"
# Test 6: Polygon ROIs with varying vertex counts and mixed inverse parameters
polygon_coords = [
[0, 0, 10, 0, 5, 8], # Triangle (3 vertices)
[20, 20, 30, 20, 30, 30, 20, 30], # Rectangle (4 vertices)
]
roi6 = sigima.objects.create_image_roi(
"polygon",
polygon_coords,
inverse=[True, False], # mask inside, then mask outside
)
assert len(roi6) == 2, "Should create two polygon ROIs"
assert roi6.single_rois[0].inverse is True, "Triangle should be True"
assert roi6.single_rois[1].inverse is False, "Rectangle should be False"
def test_create_image_roi_inverse_parameter_errors() -> None:
"""Test error handling for inverse parameter in create_image_roi"""
# Test error when inverse parameter count doesn't match ROI count
coords = [[10, 20, 30, 40], [50, 60, 70, 80], [90, 100, 110, 120]]
# Only 2 values for 3 ROIs
inverse_params = [
True, # mask inside
False, # mask outside
]
with pytest.raises(
ValueError,
match=r"Number of inverse values \(2\) must match number of ROIs \(3\)",
):
sigima.objects.create_image_roi("rectangle", coords, inverse=inverse_params)
# Test with too many inverse values
# 4 values for 3 ROIs
inverse_params_too_many = [
True, # mask inside
False, # mask outside
True, # mask inside
False, # mask outside
]
with pytest.raises(
ValueError,
match=r"Number of inverse values \(4\) must match number of ROIs \(3\)",
):
sigima.objects.create_image_roi(
"rectangle", coords, inverse=inverse_params_too_many
)
def test_roi_inverse_affects_mask_generation() -> None:
"""Test that inverse parameter affects mask generation correctly"""
# Create a test image
img = __create_test_image()
# Test rectangle ROI with inverse=True vs inverse=False
rect_coords = [75, 75, 50, 50] # Rectangle that should be inside image bounds
# ROI with inverse=True (mask is True inside the rectangle)
roi_inside = sigima.objects.create_image_roi("rectangle", rect_coords, inverse=True)
mask_inside = roi_inside.to_mask(img)
# ROI with inverse=False (mask is True outside the rectangle)
roi_outside = sigima.objects.create_image_roi(
"rectangle", rect_coords, inverse=False
)
mask_outside = roi_outside.to_mask(img)
# The two masks should be inverse of each other
assert np.array_equal(mask_inside, ~mask_outside), (
"Inside and outside masks should be inverse of each other"
)
# Check that inside mask has True values inside the rectangle region
# For a rectangle [x0, y0, dx, dy], the region is [x0:x0+dx, y0:y0+dy]
x0, y0, dx, dy = rect_coords
expected_inside_region = np.zeros_like(img.data, dtype=bool)
expected_inside_region[y0 : y0 + dy, x0 : x0 + dx] = True
assert np.array_equal(mask_inside, expected_inside_region), (
"Inside mask should match expected rectangular region"
)
def test_roi_inverse_serialization() -> None:
"""Test that inverse parameter is preserved during
serialization/deserialization"""
# Create ROIs with mixed inverse parameters
coords = [[10, 20, 30, 40], [50, 60, 70, 80]]
inverse_params = [
True, # mask inside
False, # mask outside
]
original_roi = sigima.objects.create_image_roi(
"rectangle", coords, inverse=inverse_params
)
# Serialize to dictionary
roi_dict = original_roi.to_dict()
# Deserialize from dictionary
restored_roi = sigima.objects.ImageROI.from_dict(roi_dict)
# Check that inverse parameters are preserved
assert len(restored_roi) == len(original_roi), "ROI count should be preserved"
for i in range(len(original_roi)):
original_inverse = original_roi.single_rois[i].inverse
restored_inverse = restored_roi.single_rois[i].inverse
assert original_inverse == restored_inverse, (
f"inverse parameter for ROI {i} should be preserved "
f"(expected {original_inverse}, got {restored_inverse})"
)
def test_roi_inverse_parameter_conversion() -> None:
"""Test that inverse parameter works correctly with parameter conversion"""
img = __create_test_image()
# Create ROI with inverse=True (mask inside)
roi = sigima.objects.create_image_roi("rectangle", [50, 50, 40, 40], inverse=True)
# Convert to parameters
params = roi.to_params(img)
assert len(params) == 1, "Should create one parameter"
# Check that inverse parameter is preserved in the parameter
param = params[0]
assert hasattr(param, "inverse"), "Parameter should have inverse attribute"
assert param.inverse is True, "Parameter should preserve inverse=True"
# Create ROI from parameter and check inverse is preserved
new_roi = sigima.objects.ImageROI.from_params(img, params)
assert len(new_roi) == 1, "Should recreate one ROI"
assert new_roi.single_rois[0].inverse is True, (
"Recreated ROI should have inverse=True (internal representation)"
)
def test_multiple_rois_inverse_true() -> None:
"""Test multiple ROIs with inverse=True on distinct areas
This test checks that when multiple ROIs are defined with inverse=True
on distinct areas of an image, the resulting mask should have True values
in BOTH ROI areas, not just their intersection.
"""
# Create a test image
img = __create_test_image()
# Define two rectangular ROIs on distinct areas of the image
# ROI 1: top-left area
roi1_coords = [30, 30, 40, 40] # x, y, width, height
# ROI 2: bottom-right area (distinct from ROI 1)
roi2_coords = [130, 130, 40, 40] # x, y, width, height
# Create ROI with inverse=True for both rectangles
roi = sigima.objects.create_image_roi(
"rectangle", [roi1_coords, roi2_coords], inverse=True
)
# Generate the mask
mask = roi.to_mask(img)
# Expected behavior: mask should be True in BOTH rectangular areas
# Create expected mask manually
expected_mask = np.zeros_like(img.data, dtype=bool)
# ROI 1 area
x1, y1, w1, h1 = roi1_coords
expected_mask[y1 : y1 + h1, x1 : x1 + w1] = True
# ROI 2 area
x2, y2, w2, h2 = roi2_coords
expected_mask[y2 : y2 + h2, x2 : x2 + w2] = True
# Check that the mask has True values in both ROI areas
assert np.any(mask[y1 : y1 + h1, x1 : x1 + w1]), (
"Mask should have True values in first ROI area"
)
assert np.any(mask[y2 : y2 + h2, x2 : x2 + w2]), (
"Mask should have True values in second ROI area"
)
# Check that the mask matches our expected mask
assert np.array_equal(mask, expected_mask), (
"Mask should have True values in both ROI areas and False elsewhere"
)
# Verify that the two ROI areas don't overlap (test integrity)
roi1_mask = np.zeros_like(img.data, dtype=bool)
roi1_mask[y1 : y1 + h1, x1 : x1 + w1] = True
roi2_mask = np.zeros_like(img.data, dtype=bool)
roi2_mask[y2 : y2 + h2, x2 : x2 + w2] = True
assert not np.any(roi1_mask & roi2_mask), (
"Test integrity: ROI areas should not overlap"
)
def test_multiple_rois_mixed_inverse() -> None:
"""Test multiple ROIs with mixed inverse values
This test checks that when ROIs have mixed inverse values,
the combination logic works correctly.
"""
# Create a test image
img = __create_test_image()
# Define three rectangular ROIs
# ROI 1: top-left area (inverse=True - include this area)
roi1_coords = [30, 30, 40, 40] # x, y, width, height
# ROI 2: top-right area (inverse=False - exclude this area)
roi2_coords = [130, 30, 40, 40] # x, y, width, height
# ROI 3: bottom-left area (inverse=True - include this area)
roi3_coords = [30, 130, 40, 40] # x, y, width, height
# Create ROI with mixed inverse values
roi = sigima.objects.create_image_roi(
"rectangle",
[roi1_coords, roi2_coords, roi3_coords],
inverse=[True, False, True], # include, exclude, include
)
# Generate the mask
mask = roi.to_mask(img)
# Expected behavior:
# - ROI 1 area should have True values (inverse=True)
# - ROI 2 area should have False values (inverse=False)
# - ROI 3 area should have True values (inverse=True)
# - Areas outside all ROIs should have True values (due to ROI 2 being
# inverse=False)
x1, y1, w1, h1 = roi1_coords
x2, y2, w2, h2 = roi2_coords
x3, y3, w3, h3 = roi3_coords
# Check that ROI 1 and ROI 3 areas have True values (inverse=True)
assert np.all(mask[y1 : y1 + h1, x1 : x1 + w1]), (
"ROI 1 area should have True values (inverse=True)"
)
assert np.all(mask[y3 : y3 + h3, x3 : x3 + w3]), (
"ROI 3 area should have True values (inverse=True)"
)
# Check that ROI 2 area has False values (inverse=False)
assert not np.any(mask[y2 : y2 + h2, x2 : x2 + w2]), (
"ROI 2 area should have False values (inverse=False)"
)
# Check that areas outside all ROIs have True values (due to ROI 2)
# For example, the bottom-right corner should be True
assert np.all(mask[170:190, 170:190]), (
"Areas outside all ROIs should have True values"
)
if __name__ == "__main__":
guiutils.enable_gui()
test_roi_coordinates_validation()
# test_image_roi_merge()
# test_image_roi_combine()
# test_image_roi_processing()
# test_empty_image_roi()
# test_image_extract_rois()
# test_image_extract_roi()
# test_create_image_roi_inside_parameter()
# test_create_image_roi_inside_parameter_errors()
# test_roi_inverse()
# test_roi_inside_serialization()
# test_roi_inside_parameter_conversion()
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