sigima 0.0.1.dev0__py3-none-any.whl → 1.0.0__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- sigima/__init__.py +142 -2
- sigima/client/__init__.py +105 -0
- sigima/client/base.py +780 -0
- sigima/client/remote.py +469 -0
- sigima/client/stub.py +814 -0
- sigima/client/utils.py +90 -0
- sigima/config.py +444 -0
- sigima/data/logo/Sigima.svg +135 -0
- sigima/data/tests/annotations.json +798 -0
- sigima/data/tests/curve_fitting/exponential_fit.txt +511 -0
- sigima/data/tests/curve_fitting/gaussian_fit.txt +100 -0
- sigima/data/tests/curve_fitting/piecewiseexponential_fit.txt +1022 -0
- sigima/data/tests/curve_fitting/polynomial_fit.txt +100 -0
- sigima/data/tests/curve_fitting/twohalfgaussian_fit.txt +1000 -0
- sigima/data/tests/curve_formats/bandwidth.txt +201 -0
- sigima/data/tests/curve_formats/boxcar.npy +0 -0
- sigima/data/tests/curve_formats/datetime.txt +1001 -0
- sigima/data/tests/curve_formats/dynamic_parameters.txt +4000 -0
- sigima/data/tests/curve_formats/fw1e2.txt +301 -0
- sigima/data/tests/curve_formats/fwhm.txt +319 -0
- sigima/data/tests/curve_formats/multiple_curves.csv +29 -0
- sigima/data/tests/curve_formats/noised_saw.mat +0 -0
- sigima/data/tests/curve_formats/oscilloscope.csv +111 -0
- sigima/data/tests/curve_formats/other/other2/recursive2.txt +5 -0
- sigima/data/tests/curve_formats/other/recursive1.txt +5 -0
- sigima/data/tests/curve_formats/paracetamol.npy +0 -0
- sigima/data/tests/curve_formats/paracetamol.txt +1010 -0
- sigima/data/tests/curve_formats/paracetamol_dx_dy.csv +1000 -0
- sigima/data/tests/curve_formats/paracetamol_dy.csv +1001 -0
- sigima/data/tests/curve_formats/pulse1.npy +0 -0
- sigima/data/tests/curve_formats/pulse2.npy +0 -0
- sigima/data/tests/curve_formats/simple.txt +5 -0
- sigima/data/tests/curve_formats/spectrum.mca +2139 -0
- sigima/data/tests/curve_formats/square2.npy +0 -0
- sigima/data/tests/curve_formats/step.npy +0 -0
- sigima/data/tests/fabry-perot1.jpg +0 -0
- sigima/data/tests/fabry-perot2.jpg +0 -0
- sigima/data/tests/flower.npy +0 -0
- sigima/data/tests/image_formats/NF 180338201.scor-data +11003 -0
- sigima/data/tests/image_formats/binary_image.npy +0 -0
- sigima/data/tests/image_formats/binary_image.png +0 -0
- sigima/data/tests/image_formats/centroid_test.npy +0 -0
- sigima/data/tests/image_formats/coordinated_text/complex_image.txt +10011 -0
- sigima/data/tests/image_formats/coordinated_text/complex_ref_image.txt +10010 -0
- sigima/data/tests/image_formats/coordinated_text/image.txt +15 -0
- sigima/data/tests/image_formats/coordinated_text/image2.txt +14 -0
- sigima/data/tests/image_formats/coordinated_text/image_no_unit_no_label.txt +14 -0
- sigima/data/tests/image_formats/coordinated_text/image_with_nan.txt +15 -0
- sigima/data/tests/image_formats/coordinated_text/image_with_unit.txt +14 -0
- sigima/data/tests/image_formats/fiber.csv +480 -0
- sigima/data/tests/image_formats/fiber.jpg +0 -0
- sigima/data/tests/image_formats/fiber.png +0 -0
- sigima/data/tests/image_formats/fiber.txt +480 -0
- sigima/data/tests/image_formats/gaussian_spot_with_noise.npy +0 -0
- sigima/data/tests/image_formats/mr-brain.dcm +0 -0
- sigima/data/tests/image_formats/noised_gaussian.mat +0 -0
- sigima/data/tests/image_formats/sif_reader/nd_lum_image_no_glue.sif +0 -0
- sigima/data/tests/image_formats/sif_reader/raman1.sif +0 -0
- sigima/data/tests/image_formats/tiling.txt +10 -0
- sigima/data/tests/image_formats/uint16.tiff +0 -0
- sigima/data/tests/image_formats/uint8.tiff +0 -0
- sigima/data/tests/laser_beam/TEM00_z_13.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_18.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_23.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_30.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_35.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_40.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_45.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_50.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_55.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_60.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_65.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_70.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_75.jpg +0 -0
- sigima/data/tests/laser_beam/TEM00_z_80.jpg +0 -0
- sigima/enums.py +195 -0
- sigima/io/__init__.py +123 -0
- sigima/io/base.py +311 -0
- sigima/io/common/__init__.py +5 -0
- sigima/io/common/basename.py +164 -0
- sigima/io/common/converters.py +189 -0
- sigima/io/common/objmeta.py +181 -0
- sigima/io/common/textreader.py +58 -0
- sigima/io/convenience.py +157 -0
- sigima/io/enums.py +17 -0
- sigima/io/ftlab.py +395 -0
- sigima/io/image/__init__.py +9 -0
- sigima/io/image/base.py +177 -0
- sigima/io/image/formats.py +1016 -0
- sigima/io/image/funcs.py +414 -0
- sigima/io/signal/__init__.py +9 -0
- sigima/io/signal/base.py +129 -0
- sigima/io/signal/formats.py +290 -0
- sigima/io/signal/funcs.py +723 -0
- sigima/objects/__init__.py +260 -0
- sigima/objects/base.py +937 -0
- sigima/objects/image/__init__.py +88 -0
- sigima/objects/image/creation.py +556 -0
- sigima/objects/image/object.py +524 -0
- sigima/objects/image/roi.py +904 -0
- sigima/objects/scalar/__init__.py +57 -0
- sigima/objects/scalar/common.py +215 -0
- sigima/objects/scalar/geometry.py +502 -0
- sigima/objects/scalar/table.py +784 -0
- sigima/objects/shape.py +290 -0
- sigima/objects/signal/__init__.py +133 -0
- sigima/objects/signal/constants.py +27 -0
- sigima/objects/signal/creation.py +1428 -0
- sigima/objects/signal/object.py +444 -0
- sigima/objects/signal/roi.py +274 -0
- sigima/params.py +405 -0
- sigima/proc/__init__.py +96 -0
- sigima/proc/base.py +381 -0
- sigima/proc/decorator.py +330 -0
- sigima/proc/image/__init__.py +513 -0
- sigima/proc/image/arithmetic.py +335 -0
- sigima/proc/image/base.py +260 -0
- sigima/proc/image/detection.py +519 -0
- sigima/proc/image/edges.py +329 -0
- sigima/proc/image/exposure.py +406 -0
- sigima/proc/image/extraction.py +458 -0
- sigima/proc/image/filtering.py +219 -0
- sigima/proc/image/fourier.py +147 -0
- sigima/proc/image/geometry.py +661 -0
- sigima/proc/image/mathops.py +340 -0
- sigima/proc/image/measurement.py +195 -0
- sigima/proc/image/morphology.py +155 -0
- sigima/proc/image/noise.py +107 -0
- sigima/proc/image/preprocessing.py +182 -0
- sigima/proc/image/restoration.py +235 -0
- sigima/proc/image/threshold.py +217 -0
- sigima/proc/image/transformations.py +393 -0
- sigima/proc/signal/__init__.py +376 -0
- sigima/proc/signal/analysis.py +206 -0
- sigima/proc/signal/arithmetic.py +551 -0
- sigima/proc/signal/base.py +262 -0
- sigima/proc/signal/extraction.py +60 -0
- sigima/proc/signal/features.py +310 -0
- sigima/proc/signal/filtering.py +484 -0
- sigima/proc/signal/fitting.py +276 -0
- sigima/proc/signal/fourier.py +259 -0
- sigima/proc/signal/mathops.py +420 -0
- sigima/proc/signal/processing.py +580 -0
- sigima/proc/signal/stability.py +175 -0
- sigima/proc/title_formatting.py +227 -0
- sigima/proc/validation.py +272 -0
- sigima/tests/__init__.py +7 -0
- sigima/tests/common/__init__.py +0 -0
- sigima/tests/common/arithmeticparam_unit_test.py +26 -0
- sigima/tests/common/basename_unit_test.py +126 -0
- sigima/tests/common/client_unit_test.py +412 -0
- sigima/tests/common/converters_unit_test.py +77 -0
- sigima/tests/common/decorator_unit_test.py +176 -0
- sigima/tests/common/examples_unit_test.py +104 -0
- sigima/tests/common/kernel_normalization_unit_test.py +242 -0
- sigima/tests/common/roi_basic_unit_test.py +73 -0
- sigima/tests/common/roi_geometry_unit_test.py +171 -0
- sigima/tests/common/scalar_builder_unit_test.py +142 -0
- sigima/tests/common/scalar_unit_test.py +991 -0
- sigima/tests/common/shape_unit_test.py +183 -0
- sigima/tests/common/stat_unit_test.py +138 -0
- sigima/tests/common/title_formatting_unit_test.py +338 -0
- sigima/tests/common/tools_coordinates_unit_test.py +60 -0
- sigima/tests/common/transformations_unit_test.py +178 -0
- sigima/tests/common/validation_unit_test.py +205 -0
- sigima/tests/conftest.py +129 -0
- sigima/tests/data.py +998 -0
- sigima/tests/env.py +280 -0
- sigima/tests/guiutils.py +163 -0
- sigima/tests/helpers.py +532 -0
- sigima/tests/image/__init__.py +28 -0
- sigima/tests/image/binning_unit_test.py +128 -0
- sigima/tests/image/blob_detection_unit_test.py +312 -0
- sigima/tests/image/centroid_unit_test.py +170 -0
- sigima/tests/image/check_2d_array_unit_test.py +63 -0
- sigima/tests/image/contour_unit_test.py +172 -0
- sigima/tests/image/convolution_unit_test.py +178 -0
- sigima/tests/image/datatype_unit_test.py +67 -0
- sigima/tests/image/edges_unit_test.py +155 -0
- sigima/tests/image/enclosingcircle_unit_test.py +88 -0
- sigima/tests/image/exposure_unit_test.py +223 -0
- sigima/tests/image/fft2d_unit_test.py +189 -0
- sigima/tests/image/filtering_unit_test.py +166 -0
- sigima/tests/image/geometry_unit_test.py +654 -0
- sigima/tests/image/hough_circle_unit_test.py +147 -0
- sigima/tests/image/imageobj_unit_test.py +737 -0
- sigima/tests/image/morphology_unit_test.py +71 -0
- sigima/tests/image/noise_unit_test.py +57 -0
- sigima/tests/image/offset_correction_unit_test.py +72 -0
- sigima/tests/image/operation_unit_test.py +518 -0
- sigima/tests/image/peak2d_limits_unit_test.py +41 -0
- sigima/tests/image/peak2d_unit_test.py +133 -0
- sigima/tests/image/profile_unit_test.py +159 -0
- sigima/tests/image/projections_unit_test.py +121 -0
- sigima/tests/image/restoration_unit_test.py +141 -0
- sigima/tests/image/roi2dparam_unit_test.py +53 -0
- sigima/tests/image/roi_advanced_unit_test.py +588 -0
- sigima/tests/image/roi_grid_unit_test.py +279 -0
- sigima/tests/image/spectrum2d_unit_test.py +40 -0
- sigima/tests/image/threshold_unit_test.py +91 -0
- sigima/tests/io/__init__.py +0 -0
- sigima/tests/io/addnewformat_unit_test.py +125 -0
- sigima/tests/io/convenience_funcs_unit_test.py +470 -0
- sigima/tests/io/coordinated_text_format_unit_test.py +495 -0
- sigima/tests/io/datetime_csv_unit_test.py +198 -0
- sigima/tests/io/imageio_formats_test.py +41 -0
- sigima/tests/io/ioregistry_unit_test.py +69 -0
- sigima/tests/io/objmeta_unit_test.py +87 -0
- sigima/tests/io/readobj_unit_test.py +130 -0
- sigima/tests/io/readwriteobj_unit_test.py +67 -0
- sigima/tests/signal/__init__.py +0 -0
- sigima/tests/signal/analysis_unit_test.py +135 -0
- sigima/tests/signal/check_1d_arrays_unit_test.py +169 -0
- sigima/tests/signal/convolution_unit_test.py +404 -0
- sigima/tests/signal/datetime_unit_test.py +176 -0
- sigima/tests/signal/fft1d_unit_test.py +303 -0
- sigima/tests/signal/filters_unit_test.py +403 -0
- sigima/tests/signal/fitting_unit_test.py +929 -0
- sigima/tests/signal/fwhm_unit_test.py +111 -0
- sigima/tests/signal/noise_unit_test.py +128 -0
- sigima/tests/signal/offset_correction_unit_test.py +34 -0
- sigima/tests/signal/operation_unit_test.py +489 -0
- sigima/tests/signal/peakdetection_unit_test.py +145 -0
- sigima/tests/signal/processing_unit_test.py +657 -0
- sigima/tests/signal/pulse/__init__.py +112 -0
- sigima/tests/signal/pulse/crossing_times_unit_test.py +123 -0
- sigima/tests/signal/pulse/plateau_detection_unit_test.py +102 -0
- sigima/tests/signal/pulse/pulse_unit_test.py +1824 -0
- sigima/tests/signal/roi_advanced_unit_test.py +392 -0
- sigima/tests/signal/signalobj_unit_test.py +603 -0
- sigima/tests/signal/stability_unit_test.py +431 -0
- sigima/tests/signal/uncertainty_unit_test.py +611 -0
- sigima/tests/vistools.py +1030 -0
- sigima/tools/__init__.py +59 -0
- sigima/tools/checks.py +290 -0
- sigima/tools/coordinates.py +308 -0
- sigima/tools/datatypes.py +26 -0
- sigima/tools/image/__init__.py +97 -0
- sigima/tools/image/detection.py +451 -0
- sigima/tools/image/exposure.py +77 -0
- sigima/tools/image/extraction.py +48 -0
- sigima/tools/image/fourier.py +260 -0
- sigima/tools/image/geometry.py +190 -0
- sigima/tools/image/preprocessing.py +165 -0
- sigima/tools/signal/__init__.py +86 -0
- sigima/tools/signal/dynamic.py +254 -0
- sigima/tools/signal/features.py +135 -0
- sigima/tools/signal/filtering.py +171 -0
- sigima/tools/signal/fitting.py +1171 -0
- sigima/tools/signal/fourier.py +466 -0
- sigima/tools/signal/interpolation.py +70 -0
- sigima/tools/signal/peakdetection.py +126 -0
- sigima/tools/signal/pulse.py +1626 -0
- sigima/tools/signal/scaling.py +50 -0
- sigima/tools/signal/stability.py +258 -0
- sigima/tools/signal/windowing.py +90 -0
- sigima/worker.py +79 -0
- sigima-1.0.0.dist-info/METADATA +233 -0
- sigima-1.0.0.dist-info/RECORD +262 -0
- {sigima-0.0.1.dev0.dist-info → sigima-1.0.0.dist-info}/licenses/LICENSE +29 -29
- sigima-0.0.1.dev0.dist-info/METADATA +0 -60
- sigima-0.0.1.dev0.dist-info/RECORD +0 -6
- {sigima-0.0.1.dev0.dist-info → sigima-1.0.0.dist-info}/WHEEL +0 -0
- {sigima-0.0.1.dev0.dist-info → sigima-1.0.0.dist-info}/top_level.txt +0 -0
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# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
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"""Unit tests for image operations."""
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# pylint: disable=invalid-name # Allows short reference names like x, y, ...
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from __future__ import annotations
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import warnings
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from typing import Generator
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import numpy as np
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import pytest
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import sigima.objects
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import sigima.params
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import sigima.proc.image
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from sigima.enums import AngleUnit, MathOperator
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from sigima.objects.image import ImageObj
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from sigima.proc.base import AngleUnitParam
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from sigima.proc.image import complex_from_magnitude_phase, complex_from_real_imag
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from sigima.tests import guiutils
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from sigima.tests.data import (
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create_noisy_gaussian_image,
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iterate_noisy_image_couples,
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iterate_noisy_images,
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)
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from sigima.tests.env import execenv
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from sigima.tests.helpers import check_array_result
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from sigima.tools.coordinates import polar_to_complex
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def __create_n_images(n: int = 100) -> list[sigima.objects.ImageObj]:
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"""Create a list of N different images for testing."""
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images = []
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for i in range(n):
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param = sigima.objects.NewImageParam.create(
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dtype=sigima.objects.ImageDatatypes.FLOAT32,
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height=128,
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width=128,
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)
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img = create_noisy_gaussian_image(param, level=(i + 1) * 0.1)
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images.append(img)
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return images
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@pytest.mark.validation
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def test_image_addition() -> None:
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"""Image addition test."""
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execenv.print("*** Testing image addition:")
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for ima1, ima2 in iterate_noisy_image_couples(size=128):
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dtype1, dtype2 = ima1.data.dtype, ima2.data.dtype
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execenv.print(f" {dtype1} += {dtype2}: ", end="")
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exp = ima1.data.astype(float) + ima2.data.astype(float)
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ima3 = sigima.proc.image.addition([ima1, ima2])
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check_array_result("Image addition", ima3.data, exp)
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imalist = __create_n_images()
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n = len(imalist)
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ima3 = sigima.proc.image.addition(imalist)
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res = ima3.data
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exp = np.zeros_like(ima3.data)
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for ima in imalist:
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exp += ima.data
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check_array_result(f" Addition of {n} images", res, exp)
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@pytest.mark.validation
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def test_image_average() -> None:
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"""Image average test."""
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execenv.print("*** Testing image average:")
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for ima1, ima2 in iterate_noisy_image_couples(size=128):
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dtype1, dtype2 = ima1.data.dtype, ima2.data.dtype
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execenv.print(f" µ({dtype1},{dtype2}): ", end="")
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exp = (ima1.data.astype(float) + ima2.data.astype(float)) / 2.0
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ima3 = sigima.proc.image.average([ima1, ima2])
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check_array_result("Image average", ima3.data, exp)
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imalist = __create_n_images()
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n = len(imalist)
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ima3 = sigima.proc.image.average(imalist)
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res = ima3.data
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exp = np.zeros_like(ima3.data)
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for ima in imalist:
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exp += ima.data
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exp /= n
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check_array_result(f" Average of {n} images", res, exp)
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@pytest.mark.validation
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def test_image_standard_deviation() -> None:
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"""Image standard deviation test."""
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n = len(imalist)
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s1 = sigima.proc.image.standard_deviation(imalist)
|
|
94
|
+
assert s1.data is not None
|
|
95
|
+
exp = np.zeros_like(s1.data)
|
|
96
|
+
average = np.mean([ima.data for ima in imalist if ima.data is not None], axis=0)
|
|
97
|
+
for ima in imalist:
|
|
98
|
+
exp += (ima.data - average) ** 2
|
|
99
|
+
exp = np.sqrt(exp / n)
|
|
100
|
+
check_array_result(f"Standard Deviation of {n} images", s1.data, exp)
|
|
101
|
+
|
|
102
|
+
|
|
103
|
+
@pytest.mark.validation
|
|
104
|
+
def test_image_difference() -> None:
|
|
105
|
+
"""Image difference test."""
|
|
106
|
+
execenv.print("*** Testing image difference:")
|
|
107
|
+
for ima1, ima2 in iterate_noisy_image_couples(size=128):
|
|
108
|
+
dtype1, dtype2 = ima1.data.dtype, ima2.data.dtype
|
|
109
|
+
execenv.print(f" {dtype1} -= {dtype2}: ", end="")
|
|
110
|
+
exp = ima1.data.astype(float) - ima2.data.astype(float)
|
|
111
|
+
ima3 = sigima.proc.image.difference(ima1, ima2)
|
|
112
|
+
check_array_result("Image difference", ima3.data, exp)
|
|
113
|
+
|
|
114
|
+
|
|
115
|
+
@pytest.mark.validation
|
|
116
|
+
def test_image_quadratic_difference() -> None:
|
|
117
|
+
"""Quadratic difference test."""
|
|
118
|
+
execenv.print("*** Testing quadratic difference:")
|
|
119
|
+
for ima1, ima2 in iterate_noisy_image_couples(size=128):
|
|
120
|
+
dtype1, dtype2 = ima1.data.dtype, ima2.data.dtype
|
|
121
|
+
execenv.print(f" ({dtype1} - {dtype2})/√2: ", end="")
|
|
122
|
+
exp = (ima1.data.astype(float) - ima2.data.astype(float)) / np.sqrt(2)
|
|
123
|
+
ima3 = sigima.proc.image.quadratic_difference(ima1, ima2)
|
|
124
|
+
check_array_result("Image quadratic difference", ima3.data, exp)
|
|
125
|
+
|
|
126
|
+
|
|
127
|
+
@pytest.mark.validation
|
|
128
|
+
def test_image_product() -> None:
|
|
129
|
+
"""Image multiplication test."""
|
|
130
|
+
execenv.print("*** Testing image multiplication:")
|
|
131
|
+
for ima1, ima2 in iterate_noisy_image_couples(size=128):
|
|
132
|
+
dtype1, dtype2 = ima1.data.dtype, ima2.data.dtype
|
|
133
|
+
execenv.print(f" {dtype1} *= {dtype2}: ", end="")
|
|
134
|
+
exp = ima1.data.astype(float) * ima2.data.astype(float)
|
|
135
|
+
ima3 = sigima.proc.image.product([ima1, ima2])
|
|
136
|
+
check_array_result("Image multiplication", ima3.data, exp)
|
|
137
|
+
imalist = __create_n_images()
|
|
138
|
+
n = len(imalist)
|
|
139
|
+
ima3 = sigima.proc.image.product(imalist)
|
|
140
|
+
res = ima3.data
|
|
141
|
+
exp = np.ones_like(ima3.data)
|
|
142
|
+
for ima in imalist:
|
|
143
|
+
exp *= ima.data
|
|
144
|
+
check_array_result(f" Multiplication of {n} images", res, exp)
|
|
145
|
+
|
|
146
|
+
|
|
147
|
+
@pytest.mark.validation
|
|
148
|
+
def test_image_division() -> None:
|
|
149
|
+
"""Image division test."""
|
|
150
|
+
execenv.print("*** Testing image division:")
|
|
151
|
+
for ima1, ima2 in iterate_noisy_image_couples(size=128):
|
|
152
|
+
ima2.data = np.ones_like(ima2.data)
|
|
153
|
+
dtype1, dtype2 = ima1.data.dtype, ima2.data.dtype
|
|
154
|
+
execenv.print(f" {dtype1} /= {dtype2}: ", end="")
|
|
155
|
+
exp = ima1.data.astype(float) / ima2.data.astype(float)
|
|
156
|
+
ima3 = sigima.proc.image.division(ima1, ima2)
|
|
157
|
+
if not np.allclose(ima3.data, exp):
|
|
158
|
+
guiutils.view_images_side_by_side_if_gui(
|
|
159
|
+
[ima1.data, ima2.data, ima3.data], ["ima1", "ima2", "ima3"]
|
|
160
|
+
)
|
|
161
|
+
check_array_result("Image division", ima3.data, exp)
|
|
162
|
+
|
|
163
|
+
|
|
164
|
+
def __constparam(value: float) -> sigima.params.ConstantParam:
|
|
165
|
+
"""Create a constant parameter."""
|
|
166
|
+
return sigima.params.ConstantParam.create(value=value)
|
|
167
|
+
|
|
168
|
+
|
|
169
|
+
def __iterate_image_with_constant() -> Generator[
|
|
170
|
+
tuple[sigima.objects.ImageObj, sigima.params.ConstantParam], None, None
|
|
171
|
+
]:
|
|
172
|
+
"""Iterate over all possible image and constant couples for testing."""
|
|
173
|
+
size = 128
|
|
174
|
+
for dtype in sigima.objects.ImageDatatypes:
|
|
175
|
+
param = sigima.objects.NewImageParam.create(
|
|
176
|
+
dtype=dtype, height=size, width=size
|
|
177
|
+
)
|
|
178
|
+
ima = create_noisy_gaussian_image(param, level=0.0)
|
|
179
|
+
for value in (-1.0, 3.14, 5.0):
|
|
180
|
+
p = __constparam(value)
|
|
181
|
+
yield ima, p
|
|
182
|
+
|
|
183
|
+
|
|
184
|
+
@pytest.mark.validation
|
|
185
|
+
def test_image_addition_constant() -> None:
|
|
186
|
+
"""Image addition with constant test."""
|
|
187
|
+
execenv.print("*** Testing image addition with constant:")
|
|
188
|
+
for ima1, p in __iterate_image_with_constant():
|
|
189
|
+
dtype1 = ima1.data.dtype
|
|
190
|
+
execenv.print(f" {dtype1} += constant ({p.value}): ", end="")
|
|
191
|
+
expvalue = np.array(p.value).astype(dtype=dtype1)
|
|
192
|
+
exp = ima1.data.astype(float) + expvalue
|
|
193
|
+
ima2 = sigima.proc.image.addition_constant(ima1, p)
|
|
194
|
+
check_array_result(f"Image + constant ({p.value})", ima2.data, exp)
|
|
195
|
+
|
|
196
|
+
|
|
197
|
+
@pytest.mark.validation
|
|
198
|
+
def test_image_difference_constant() -> None:
|
|
199
|
+
"""Image difference with constant test."""
|
|
200
|
+
execenv.print("*** Testing image difference with constant:")
|
|
201
|
+
for ima1, p in __iterate_image_with_constant():
|
|
202
|
+
dtype1 = ima1.data.dtype
|
|
203
|
+
execenv.print(f" {dtype1} -= constant ({p.value}): ", end="")
|
|
204
|
+
expvalue = np.array(p.value).astype(dtype=dtype1)
|
|
205
|
+
exp = ima1.data.astype(float) - expvalue
|
|
206
|
+
ima2 = sigima.proc.image.difference_constant(ima1, p)
|
|
207
|
+
check_array_result(f"Image - constant ({p.value})", ima2.data, exp)
|
|
208
|
+
|
|
209
|
+
|
|
210
|
+
@pytest.mark.validation
|
|
211
|
+
def test_image_product_constant() -> None:
|
|
212
|
+
"""Image multiplication by constant test."""
|
|
213
|
+
execenv.print("*** Testing image multiplication by constant:")
|
|
214
|
+
for ima1, p in __iterate_image_with_constant():
|
|
215
|
+
dtype1 = ima1.data.dtype
|
|
216
|
+
execenv.print(f" {dtype1} *= constant ({p.value}): ", end="")
|
|
217
|
+
exp = ima1.data.astype(float) * p.value
|
|
218
|
+
ima2 = sigima.proc.image.product_constant(ima1, p)
|
|
219
|
+
check_array_result(f"Image x constant ({p.value})", ima2.data, exp)
|
|
220
|
+
|
|
221
|
+
|
|
222
|
+
@pytest.mark.validation
|
|
223
|
+
def test_image_division_constant() -> None:
|
|
224
|
+
"""Image division by constant test."""
|
|
225
|
+
execenv.print("*** Testing image division by constant:")
|
|
226
|
+
for ima1, p in __iterate_image_with_constant():
|
|
227
|
+
dtype1 = ima1.data.dtype
|
|
228
|
+
execenv.print(f" {dtype1} /= constant ({p.value}): ", end="")
|
|
229
|
+
exp = ima1.data.astype(float) / p.value
|
|
230
|
+
ima2 = sigima.proc.image.division_constant(ima1, p)
|
|
231
|
+
check_array_result(f"Image / constant ({p.value})", ima2.data, exp)
|
|
232
|
+
|
|
233
|
+
|
|
234
|
+
@pytest.mark.validation
|
|
235
|
+
def test_image_arithmetic() -> None:
|
|
236
|
+
"""Image arithmetic test."""
|
|
237
|
+
execenv.print("*** Testing image arithmetic:")
|
|
238
|
+
# pylint: disable=too-many-nested-blocks
|
|
239
|
+
for ima1, ima2 in iterate_noisy_image_couples(size=128):
|
|
240
|
+
dtype1 = ima1.data.dtype
|
|
241
|
+
p = sigima.params.ArithmeticParam.create()
|
|
242
|
+
for o in MathOperator:
|
|
243
|
+
p.operator = o
|
|
244
|
+
for a in (0.0, 1.0, 2.0):
|
|
245
|
+
p.factor = a
|
|
246
|
+
for b in (0.0, 1.0, 2.0):
|
|
247
|
+
p.constant = b
|
|
248
|
+
ima2.data = np.clip(ima2.data, 1, None) # Avoid division by zero
|
|
249
|
+
ima3 = sigima.proc.image.arithmetic(ima1, ima2, p)
|
|
250
|
+
if o in (MathOperator.MULTIPLY, MathOperator.DIVIDE) and a == 0.0:
|
|
251
|
+
exp = np.ones_like(ima1.data) * b
|
|
252
|
+
elif o == MathOperator.ADD:
|
|
253
|
+
exp = np.add(ima1.data, ima2.data, dtype=float) * a + b
|
|
254
|
+
elif o == MathOperator.MULTIPLY:
|
|
255
|
+
exp = np.multiply(ima1.data, ima2.data, dtype=float) * a + b
|
|
256
|
+
elif o == MathOperator.SUBTRACT:
|
|
257
|
+
exp = np.subtract(ima1.data, ima2.data, dtype=float) * a + b
|
|
258
|
+
elif o == MathOperator.DIVIDE:
|
|
259
|
+
exp = np.divide(ima1.data, ima2.data, dtype=float) * a + b
|
|
260
|
+
if p.restore_dtype:
|
|
261
|
+
if np.issubdtype(dtype1, np.integer):
|
|
262
|
+
iinfo1 = np.iinfo(dtype1)
|
|
263
|
+
exp = np.clip(exp, iinfo1.min, iinfo1.max)
|
|
264
|
+
exp = exp.astype(dtype1)
|
|
265
|
+
check_array_result(
|
|
266
|
+
f"Arithmetic [{p.get_operation()}]", ima3.data, exp
|
|
267
|
+
)
|
|
268
|
+
|
|
269
|
+
|
|
270
|
+
@pytest.mark.validation
|
|
271
|
+
def test_image_inverse() -> None:
|
|
272
|
+
"""Image inverse test."""
|
|
273
|
+
execenv.print("*** Testing image inverse:")
|
|
274
|
+
for ima1 in iterate_noisy_images(size=128):
|
|
275
|
+
execenv.print(f" 1/({ima1.data.dtype}): ", end="")
|
|
276
|
+
with warnings.catch_warnings():
|
|
277
|
+
warnings.simplefilter("ignore", category=RuntimeWarning)
|
|
278
|
+
exp = np.reciprocal(ima1.data, dtype=float)
|
|
279
|
+
exp[np.isinf(exp)] = np.nan
|
|
280
|
+
ima2 = sigima.proc.image.inverse(ima1)
|
|
281
|
+
check_array_result("Image inverse", ima2.data, exp)
|
|
282
|
+
|
|
283
|
+
|
|
284
|
+
@pytest.mark.validation
|
|
285
|
+
def test_image_absolute() -> None:
|
|
286
|
+
"""Image absolute value test."""
|
|
287
|
+
execenv.print("*** Testing image absolute value:")
|
|
288
|
+
for ima1 in iterate_noisy_images(size=128):
|
|
289
|
+
execenv.print(f" abs({ima1.data.dtype}): ", end="")
|
|
290
|
+
exp = np.abs(ima1.data)
|
|
291
|
+
ima2 = sigima.proc.image.absolute(ima1)
|
|
292
|
+
check_array_result("Absolute value", ima2.data, exp)
|
|
293
|
+
|
|
294
|
+
|
|
295
|
+
@pytest.mark.validation
|
|
296
|
+
def test_image_real() -> None:
|
|
297
|
+
"""Image real part test."""
|
|
298
|
+
execenv.print("*** Testing image real part:")
|
|
299
|
+
for ima1 in iterate_noisy_images(size=128):
|
|
300
|
+
execenv.print(f" re({ima1.data.dtype}): ", end="")
|
|
301
|
+
exp = np.real(ima1.data)
|
|
302
|
+
ima2 = sigima.proc.image.real(ima1)
|
|
303
|
+
check_array_result("Real part", ima2.data, exp)
|
|
304
|
+
|
|
305
|
+
|
|
306
|
+
@pytest.mark.validation
|
|
307
|
+
def test_image_imag() -> None:
|
|
308
|
+
"""Image imaginary part test."""
|
|
309
|
+
execenv.print("*** Testing image imaginary part:")
|
|
310
|
+
for ima1 in iterate_noisy_images(size=128):
|
|
311
|
+
execenv.print(f" im({ima1.data.dtype}): ", end="")
|
|
312
|
+
exp = np.imag(ima1.data)
|
|
313
|
+
ima2 = sigima.proc.image.imag(ima1)
|
|
314
|
+
check_array_result("Imaginary part", ima2.data, exp)
|
|
315
|
+
|
|
316
|
+
|
|
317
|
+
@pytest.mark.validation
|
|
318
|
+
def test_image_complex_from_real_imag() -> None:
|
|
319
|
+
"""Test :py:func:`sigima.proc.image.complex_from_real_imag`."""
|
|
320
|
+
real = np.ones((4, 4))
|
|
321
|
+
ima = np.arange(16).reshape(4, 4)
|
|
322
|
+
ima_real = ImageObj("real")
|
|
323
|
+
ima_real.data = real
|
|
324
|
+
ima_imag = ImageObj("imag")
|
|
325
|
+
ima_imag.data = ima
|
|
326
|
+
result = complex_from_real_imag(ima_real, ima_imag)
|
|
327
|
+
check_array_result(
|
|
328
|
+
"complex_from_real_imag",
|
|
329
|
+
result.data,
|
|
330
|
+
real + 1j * ima,
|
|
331
|
+
)
|
|
332
|
+
|
|
333
|
+
|
|
334
|
+
@pytest.mark.validation
|
|
335
|
+
def test_image_phase() -> None:
|
|
336
|
+
"""Image phase test."""
|
|
337
|
+
execenv.print("*** Testing image phase:")
|
|
338
|
+
for base_image in iterate_noisy_images():
|
|
339
|
+
# Create a complex image for testing
|
|
340
|
+
assert base_image.data is not None, "Input image data is None."
|
|
341
|
+
complex_data = base_image.data.astype(np.complex128)
|
|
342
|
+
complex_data += 1j * (0.5 * base_image.data + 1.0)
|
|
343
|
+
complex_image = base_image.copy()
|
|
344
|
+
complex_image.data = complex_data
|
|
345
|
+
|
|
346
|
+
# Test phase extraction in radians without unwrapping
|
|
347
|
+
param_rad = sigima.params.PhaseParam.create(unit=AngleUnit.RADIAN, unwrap=False)
|
|
348
|
+
result_rad = sigima.proc.image.phase(complex_image, param_rad)
|
|
349
|
+
assert result_rad.data is not None, "Phase in radians data is None."
|
|
350
|
+
expected_rad = np.angle(complex_image.data, deg=False)
|
|
351
|
+
check_array_result("Phase in radians", result_rad.data, expected_rad)
|
|
352
|
+
|
|
353
|
+
# Test phase extraction in degrees without unwrapping
|
|
354
|
+
param_deg = sigima.params.PhaseParam.create(unit=AngleUnit.DEGREE, unwrap=False)
|
|
355
|
+
result_deg = sigima.proc.image.phase(complex_image, param_deg)
|
|
356
|
+
assert result_deg.data is not None, "Phase in degrees data is None."
|
|
357
|
+
expected_deg = np.angle(complex_image.data, deg=True)
|
|
358
|
+
check_array_result("Phase in degrees", result_deg.data, expected_deg)
|
|
359
|
+
|
|
360
|
+
# Test phase extraction in radians with unwrapping
|
|
361
|
+
param_rad_unwrap = sigima.params.PhaseParam.create(
|
|
362
|
+
unit=AngleUnit.RADIAN, unwrap=True
|
|
363
|
+
)
|
|
364
|
+
result_rad_unwrap = sigima.proc.image.phase(complex_image, param_rad_unwrap)
|
|
365
|
+
expected_rad_unwrap = np.unwrap(np.angle(complex_image.data, deg=False))
|
|
366
|
+
assert result_rad_unwrap.data is not None, (
|
|
367
|
+
"Phase in radians with unwrapping data is None."
|
|
368
|
+
)
|
|
369
|
+
check_array_result(
|
|
370
|
+
"Phase in radians with unwrapping",
|
|
371
|
+
result_rad_unwrap.data,
|
|
372
|
+
expected_rad_unwrap,
|
|
373
|
+
)
|
|
374
|
+
|
|
375
|
+
# Test phase extraction in degrees with unwrapping
|
|
376
|
+
param_deg_unwrap = sigima.params.PhaseParam.create(
|
|
377
|
+
unit=AngleUnit.DEGREE, unwrap=True
|
|
378
|
+
)
|
|
379
|
+
result_deg_unwrap = sigima.proc.image.phase(complex_image, param_deg_unwrap)
|
|
380
|
+
expected_deg_unwrap = np.unwrap(
|
|
381
|
+
np.angle(complex_image.data, deg=True), period=360.0
|
|
382
|
+
)
|
|
383
|
+
assert result_deg_unwrap.data is not None, (
|
|
384
|
+
"Phase in degrees with unwrapping data is None."
|
|
385
|
+
)
|
|
386
|
+
check_array_result(
|
|
387
|
+
"Phase in degrees with unwrapping",
|
|
388
|
+
result_deg_unwrap.data,
|
|
389
|
+
expected_deg_unwrap,
|
|
390
|
+
)
|
|
391
|
+
|
|
392
|
+
|
|
393
|
+
MAGNITUDE_PHASE_TEST_CASES = [
|
|
394
|
+
(np.linspace(0, np.pi, 16).reshape(4, 4), AngleUnit.RADIAN),
|
|
395
|
+
(np.linspace(0, 360, 16).reshape(4, 4), AngleUnit.DEGREE),
|
|
396
|
+
]
|
|
397
|
+
|
|
398
|
+
|
|
399
|
+
@pytest.mark.parametrize("phase, unit", MAGNITUDE_PHASE_TEST_CASES)
|
|
400
|
+
@pytest.mark.validation
|
|
401
|
+
def test_image_complex_from_magnitude_phase(phase: np.ndarray, unit: AngleUnit) -> None:
|
|
402
|
+
"""Test :py:func:`sigima.proc.image.complex_from_magnitude_phase`.
|
|
403
|
+
|
|
404
|
+
Args:
|
|
405
|
+
phase (np.ndarray): Angles in radians or degrees.
|
|
406
|
+
unit (AngleUnit): Unit of the angles, either radian or degree.
|
|
407
|
+
"""
|
|
408
|
+
magnitude = np.full((4, 4), 2.0)
|
|
409
|
+
# Create image instances for magnitude and phase
|
|
410
|
+
ima_mag = ImageObj("magnitude")
|
|
411
|
+
ima_mag.data = magnitude
|
|
412
|
+
ima_phase = ImageObj("phase")
|
|
413
|
+
ima_phase.data = phase
|
|
414
|
+
# Create complex signal from magnitude and phase
|
|
415
|
+
p = AngleUnitParam.create(unit=unit)
|
|
416
|
+
result = complex_from_magnitude_phase(ima_mag, ima_phase, p)
|
|
417
|
+
unit_str = "rad" if p.unit == AngleUnit.RADIAN else "°"
|
|
418
|
+
check_array_result(
|
|
419
|
+
"complex_from_magnitude_phase",
|
|
420
|
+
result.data,
|
|
421
|
+
polar_to_complex(magnitude, phase, unit=unit_str),
|
|
422
|
+
)
|
|
423
|
+
|
|
424
|
+
|
|
425
|
+
def __test_all_complex_from_magnitude_phase() -> None:
|
|
426
|
+
"""Test all combinations of magnitude and phase."""
|
|
427
|
+
for phase, unit in MAGNITUDE_PHASE_TEST_CASES:
|
|
428
|
+
test_image_complex_from_magnitude_phase(phase, unit)
|
|
429
|
+
|
|
430
|
+
|
|
431
|
+
def __get_numpy_info(dtype: np.dtype) -> np.generic:
|
|
432
|
+
"""Get numpy info for a given data type."""
|
|
433
|
+
if np.issubdtype(dtype, np.integer):
|
|
434
|
+
return np.iinfo(dtype)
|
|
435
|
+
return np.finfo(dtype)
|
|
436
|
+
|
|
437
|
+
|
|
438
|
+
@pytest.mark.validation
|
|
439
|
+
def test_image_astype() -> None:
|
|
440
|
+
"""Image type conversion test."""
|
|
441
|
+
execenv.print("*** Testing image type conversion:")
|
|
442
|
+
for ima1 in iterate_noisy_images(size=128):
|
|
443
|
+
for dtype_str in sigima.objects.ImageObj.get_valid_dtypenames():
|
|
444
|
+
dtype1_str = str(ima1.data.dtype)
|
|
445
|
+
execenv.print(f" {dtype1_str} -> {dtype_str}: ", end="")
|
|
446
|
+
dtype_exp = np.dtype(dtype_str)
|
|
447
|
+
info_exp = __get_numpy_info(dtype_exp)
|
|
448
|
+
info_ima1 = __get_numpy_info(ima1.data.dtype)
|
|
449
|
+
if info_exp.min < info_ima1.min or info_exp.max > info_ima1.max:
|
|
450
|
+
continue
|
|
451
|
+
exp = np.clip(ima1.data, info_exp.min, info_exp.max).astype(dtype_exp)
|
|
452
|
+
p = sigima.params.DataTypeIParam.create(dtype_str=dtype_str)
|
|
453
|
+
ima2 = sigima.proc.image.astype(ima1, p)
|
|
454
|
+
check_array_result(
|
|
455
|
+
f"Image astype({dtype1_str}->{dtype_str})", ima2.data, exp
|
|
456
|
+
)
|
|
457
|
+
|
|
458
|
+
|
|
459
|
+
@pytest.mark.validation
|
|
460
|
+
def test_image_exp() -> None:
|
|
461
|
+
"""Image exponential test."""
|
|
462
|
+
execenv.print("*** Testing image exponential:")
|
|
463
|
+
with np.errstate(over="ignore"):
|
|
464
|
+
for ima1 in iterate_noisy_images(size=128):
|
|
465
|
+
execenv.print(f" exp({ima1.data.dtype}): ", end="")
|
|
466
|
+
exp = np.exp(ima1.data)
|
|
467
|
+
ima2 = sigima.proc.image.exp(ima1)
|
|
468
|
+
check_array_result("Image exp", ima2.data, exp)
|
|
469
|
+
|
|
470
|
+
|
|
471
|
+
@pytest.mark.validation
|
|
472
|
+
def test_image_log10() -> None:
|
|
473
|
+
"""Image base-10 logarithm test."""
|
|
474
|
+
execenv.print("*** Testing image base-10 logarithm:")
|
|
475
|
+
with np.errstate(over="ignore"):
|
|
476
|
+
for ima1 in iterate_noisy_images(size=128):
|
|
477
|
+
execenv.print(f" log10({ima1.data.dtype}): ", end="")
|
|
478
|
+
exp = np.log10(np.exp(ima1.data))
|
|
479
|
+
ima2 = sigima.proc.image.log10(sigima.proc.image.exp(ima1))
|
|
480
|
+
check_array_result("Image log10", ima2.data, exp)
|
|
481
|
+
|
|
482
|
+
|
|
483
|
+
@pytest.mark.validation
|
|
484
|
+
def test_image_log10_z_plus_n() -> None:
|
|
485
|
+
"""Image log(1+n) test."""
|
|
486
|
+
execenv.print("*** Testing image log(1+n):")
|
|
487
|
+
with np.errstate(over="ignore"):
|
|
488
|
+
for ima1 in iterate_noisy_images(size=128):
|
|
489
|
+
execenv.print(f" log1p({ima1.data.dtype}): ", end="")
|
|
490
|
+
p = sigima.params.Log10ZPlusNParam.create(n=2.0)
|
|
491
|
+
exp = np.log10(ima1.data + p.n)
|
|
492
|
+
ima2 = sigima.proc.image.log10_z_plus_n(ima1, p)
|
|
493
|
+
check_array_result("Image log1p", ima2.data, exp)
|
|
494
|
+
|
|
495
|
+
|
|
496
|
+
if __name__ == "__main__":
|
|
497
|
+
guiutils.enable_gui()
|
|
498
|
+
test_image_addition()
|
|
499
|
+
test_image_average()
|
|
500
|
+
test_image_product()
|
|
501
|
+
test_image_division()
|
|
502
|
+
test_image_difference()
|
|
503
|
+
test_image_quadratic_difference()
|
|
504
|
+
test_image_addition_constant()
|
|
505
|
+
test_image_product_constant()
|
|
506
|
+
test_image_difference_constant()
|
|
507
|
+
test_image_division_constant()
|
|
508
|
+
test_image_arithmetic()
|
|
509
|
+
test_image_inverse()
|
|
510
|
+
test_image_absolute()
|
|
511
|
+
test_image_real()
|
|
512
|
+
test_image_imag()
|
|
513
|
+
test_image_phase()
|
|
514
|
+
__test_all_complex_from_magnitude_phase()
|
|
515
|
+
test_image_astype()
|
|
516
|
+
test_image_exp()
|
|
517
|
+
test_image_log10()
|
|
518
|
+
test_image_log10_z_plus_n()
|
|
@@ -0,0 +1,41 @@
|
|
|
1
|
+
# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
|
|
2
|
+
|
|
3
|
+
"""
|
|
4
|
+
Image peak detection test: testing algorithm limits
|
|
5
|
+
"""
|
|
6
|
+
|
|
7
|
+
# pylint: disable=invalid-name # Allows short reference names like x, y, ...
|
|
8
|
+
|
|
9
|
+
import pytest
|
|
10
|
+
|
|
11
|
+
from sigima.tests.data import get_peak2d_data
|
|
12
|
+
from sigima.tests.env import execenv
|
|
13
|
+
from sigima.tests.image.peak2d_unit_test import (
|
|
14
|
+
exec_image_peak_detection_func,
|
|
15
|
+
)
|
|
16
|
+
from sigima.tools.image import get_2d_peaks_coords
|
|
17
|
+
|
|
18
|
+
|
|
19
|
+
@pytest.mark.skip(reason="Limit testing, not required for automated testing")
|
|
20
|
+
def test_peak2d_limit():
|
|
21
|
+
"""2D peak detection test"""
|
|
22
|
+
# pylint: disable=import-outside-toplevel
|
|
23
|
+
from guidata.qthelpers import qt_app_context
|
|
24
|
+
|
|
25
|
+
with qt_app_context():
|
|
26
|
+
execenv.print("Testing peak detection algorithm with random generated data:")
|
|
27
|
+
for idx in range(100):
|
|
28
|
+
execenv.print(f" Iteration #{idx:02d}: ", end="")
|
|
29
|
+
generated_data, _coords = get_peak2d_data(multi=True)
|
|
30
|
+
coords = get_2d_peaks_coords(generated_data)
|
|
31
|
+
if coords.shape[0] != 4:
|
|
32
|
+
execenv.print(f"KO - {coords.shape[0]}/4 peaks were detected")
|
|
33
|
+
exec_image_peak_detection_func(generated_data)
|
|
34
|
+
else:
|
|
35
|
+
execenv.print("OK")
|
|
36
|
+
# Showing results for last generated sample
|
|
37
|
+
exec_image_peak_detection_func(generated_data)
|
|
38
|
+
|
|
39
|
+
|
|
40
|
+
if __name__ == "__main__":
|
|
41
|
+
test_peak2d_limit()
|
|
@@ -0,0 +1,133 @@
|
|
|
1
|
+
# Copyright (c) DataLab Platform Developers, BSD 3-Clause license, see LICENSE file.
|
|
2
|
+
|
|
3
|
+
"""
|
|
4
|
+
Image peak detection test
|
|
5
|
+
"""
|
|
6
|
+
|
|
7
|
+
# pylint: disable=invalid-name # Allows short reference names like x, y, ...
|
|
8
|
+
# pylint: disable=duplicate-code
|
|
9
|
+
|
|
10
|
+
from __future__ import annotations
|
|
11
|
+
|
|
12
|
+
import time
|
|
13
|
+
|
|
14
|
+
import numpy as np
|
|
15
|
+
import pytest
|
|
16
|
+
|
|
17
|
+
import sigima.objects
|
|
18
|
+
import sigima.params
|
|
19
|
+
import sigima.proc.image
|
|
20
|
+
from sigima.tests import guiutils
|
|
21
|
+
from sigima.tests.data import get_peak2d_data
|
|
22
|
+
from sigima.tests.env import execenv
|
|
23
|
+
from sigima.tests.helpers import check_array_result
|
|
24
|
+
from sigima.tools.image import get_2d_peaks_coords
|
|
25
|
+
|
|
26
|
+
|
|
27
|
+
def exec_image_peak_detection_func(data: np.ndarray) -> np.ndarray:
|
|
28
|
+
"""Execute image peak detection function
|
|
29
|
+
|
|
30
|
+
Args:
|
|
31
|
+
data: 2D image data
|
|
32
|
+
|
|
33
|
+
Returns:
|
|
34
|
+
2D array of peak coordinates
|
|
35
|
+
"""
|
|
36
|
+
t0 = time.time()
|
|
37
|
+
coords = get_2d_peaks_coords(data)
|
|
38
|
+
dt = time.time() - t0
|
|
39
|
+
execenv.print(f"Calculation time: {int(dt * 1e3):d} ms")
|
|
40
|
+
execenv.print(f" => {coords.tolist()}")
|
|
41
|
+
return coords
|
|
42
|
+
|
|
43
|
+
|
|
44
|
+
def view_image_peak_detection(data: np.ndarray, coords: np.ndarray) -> None:
|
|
45
|
+
"""View image peak detection results
|
|
46
|
+
|
|
47
|
+
Args:
|
|
48
|
+
data: 2D image data
|
|
49
|
+
coords: Coordinates of detected peaks (shape: (n, 2))
|
|
50
|
+
"""
|
|
51
|
+
# pylint: disable=import-outside-toplevel
|
|
52
|
+
from plotpy.builder import make
|
|
53
|
+
|
|
54
|
+
from sigima.tests.vistools import view_image_items
|
|
55
|
+
|
|
56
|
+
execenv.print("Peak detection results:")
|
|
57
|
+
items = [make.image(data, interpolation="linear", colormap="hsv")]
|
|
58
|
+
for x, y in coords:
|
|
59
|
+
items.append(make.marker((x, y)))
|
|
60
|
+
view_image_items(
|
|
61
|
+
items, name=view_image_peak_detection.__name__, title="Peak Detection"
|
|
62
|
+
)
|
|
63
|
+
|
|
64
|
+
|
|
65
|
+
def test_peak2d_unit():
|
|
66
|
+
"""2D peak detection unit test"""
|
|
67
|
+
data, coords_expected = get_peak2d_data(seed=1, multi=False)
|
|
68
|
+
coords = exec_image_peak_detection_func(data)
|
|
69
|
+
assert coords.shape == coords_expected.shape, (
|
|
70
|
+
f"Expected {coords_expected.shape[0]} peaks, got {coords.shape[0]}"
|
|
71
|
+
)
|
|
72
|
+
# Absolute tolerance is set to 2 pixels, as coordinates are in pixel units
|
|
73
|
+
# and the algorithm may detect peaks at slightly different pixel locations
|
|
74
|
+
# Convert coordinates to float64 for dtype compatibility with expected results
|
|
75
|
+
coords_float = coords.astype(np.float64)
|
|
76
|
+
check_array_result(
|
|
77
|
+
"Peak coords (sigima.tools.image.)",
|
|
78
|
+
coords_float,
|
|
79
|
+
coords_expected,
|
|
80
|
+
atol=2,
|
|
81
|
+
sort=True,
|
|
82
|
+
)
|
|
83
|
+
|
|
84
|
+
|
|
85
|
+
@pytest.mark.validation
|
|
86
|
+
def test_image_peak_detection():
|
|
87
|
+
"""2D peak detection unit test"""
|
|
88
|
+
data, coords_expected = get_peak2d_data(seed=1, multi=False)
|
|
89
|
+
for create_rois in (True, False):
|
|
90
|
+
obj = sigima.objects.create_image("peak2d_unit_test", data=data)
|
|
91
|
+
param = sigima.params.Peak2DDetectionParam.create(create_rois=create_rois)
|
|
92
|
+
geometry = sigima.proc.image.peak_detection(obj, param)
|
|
93
|
+
coords = geometry.coords
|
|
94
|
+
assert coords.shape == coords_expected.shape, (
|
|
95
|
+
f"Expected {coords_expected.shape[0]} peaks, got {coords.shape[0]}"
|
|
96
|
+
)
|
|
97
|
+
# Absolute tolerance is set to 2 pixels, as coordinates are in pixel units
|
|
98
|
+
# and the algorithm may detect peaks at slightly different pixel locations
|
|
99
|
+
check_array_result(
|
|
100
|
+
"Peak coords (comp.)", coords, coords_expected, atol=2, sort=True
|
|
101
|
+
)
|
|
102
|
+
if create_rois:
|
|
103
|
+
assert obj.roi is not None, "ROI should be created"
|
|
104
|
+
assert len(obj.roi) == coords.shape[0], (
|
|
105
|
+
f"Expected {coords.shape[0]} ROIs, got {len(obj.roi)}"
|
|
106
|
+
)
|
|
107
|
+
for i, roi in enumerate(obj.roi):
|
|
108
|
+
# Check that ROIs are rectangles
|
|
109
|
+
assert isinstance(roi, sigima.objects.RectangularROI), (
|
|
110
|
+
f"Expected RectangularROI, got {type(roi)}"
|
|
111
|
+
)
|
|
112
|
+
# Check that ROIs are correctly positioned
|
|
113
|
+
x0, y0, x1, y1 = roi.get_bounding_box(obj)
|
|
114
|
+
x, y = coords[i]
|
|
115
|
+
assert x0 <= x < x1, f"ROI {i} x0={x0}, x={x}, x1={x1} does not match"
|
|
116
|
+
assert y0 <= y < y1, f"ROI {i} y0={y0}, y={y}, y1={y1} does not match"
|
|
117
|
+
else:
|
|
118
|
+
assert obj.roi is None, "ROI should not be created"
|
|
119
|
+
|
|
120
|
+
|
|
121
|
+
@pytest.mark.gui
|
|
122
|
+
def test_peak2d_interactive():
|
|
123
|
+
"""2D peak detection interactive test"""
|
|
124
|
+
data, _coords = get_peak2d_data(multi=False)
|
|
125
|
+
coords = exec_image_peak_detection_func(data)
|
|
126
|
+
with guiutils.lazy_qt_app_context(force=True):
|
|
127
|
+
view_image_peak_detection(data, coords)
|
|
128
|
+
|
|
129
|
+
|
|
130
|
+
if __name__ == "__main__":
|
|
131
|
+
test_peak2d_unit()
|
|
132
|
+
test_image_peak_detection()
|
|
133
|
+
test_peak2d_interactive()
|