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| import pytest | |
| from path_analysis.analyse import * | |
| from path_analysis.data_preprocess import RemovedPeakData | |
| import numpy as np | |
| from math import pi | |
| import xml.etree.ElementTree as ET | |
| from PIL import ImageChops | |
| from pathlib import Path | |
| import matplotlib | |
| matplotlib.use('Agg') | |
| def script_loc(request): | |
| '''Return the directory of the currently running test script''' | |
| return Path(request.fspath).parent | |
| def test_image_1(script_loc): | |
| config = { 'sphere_radius': 0.1984125, | |
| 'peak_threshold': 0.4, | |
| 'xy_res': 0.0396825, | |
| 'z_res': 0.0909184, | |
| 'threshold_type': 'per-cell', | |
| 'use_corrected_positions': True, | |
| 'screening_distance': 10, | |
| } | |
| data_loc = script_loc.parent.parent / 'test_data' / 'hei10 ++ 15.11.19 p22s2 image 9' | |
| image_input = data_loc / 'HEI10.tif' | |
| path_input = data_loc / 'SNT_Data.traces' | |
| paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config) | |
| assert np.allclose(extracted_peaks['SNT_trace_length(um)'], [61.47, 70.40, 51.93, 43.94, 62.24], atol=1e-2 ) | |
| assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 ) | |
| assert list(extracted_peaks['Trace_foci_number']) == [2,3,2,2,3] | |
| def test_image_2(script_loc): | |
| config = { 'sphere_radius': 0.1984125, | |
| 'peak_threshold': 0.4, | |
| 'xy_res': 0.0396825, | |
| 'z_res': 0.0909184, | |
| 'threshold_type': 'per-cell', | |
| 'use_corrected_positions': True, | |
| 'screening_distance': 10, | |
| } | |
| data_loc = script_loc.parent.parent / 'test_data' / 'z-optimised' | |
| image_input = data_loc / 'HEI10.tif' | |
| path_input = data_loc / 'ZYP1.traces' | |
| paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config) | |
| assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 ) | |
| assert list(extracted_peaks['Trace_foci_number']) == [2,2,1,2,1] | |
| def test_image_3(script_loc): | |
| config = { 'sphere_radius': 0.1984125, | |
| 'peak_threshold': 0.4, | |
| 'xy_res': 0.0396825, | |
| 'z_res': 0.1095510, | |
| 'threshold_type': 'per-trace', | |
| 'use_corrected_positions': True, | |
| 'screening_distance': 10, | |
| } | |
| data_loc = script_loc.parent.parent / 'test_data' / 'arenosa SN A1243 image 18-20230726T142725Z-001' / 'arenosa SN A1243 image 18' | |
| image_input = data_loc / 'HEI10.tif' | |
| path_input = data_loc / 'SNT_Data.traces' | |
| paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config) | |
| assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 ) | |
| assert list(extracted_peaks['Trace_foci_number']) == [2,1,1,1,2,1,1,1] | |
| def test_image_4(script_loc): | |
| config = { 'sphere_radius': 10., | |
| 'peak_threshold': 0.4, | |
| 'xy_res': 1, | |
| 'z_res': 1, | |
| 'threshold_type': 'per-trace', | |
| 'use_corrected_positions': True, | |
| 'screening_distance': 10, | |
| } | |
| data_loc = script_loc.parent.parent / 'test_data' / 'mammalian 2D-20230821T180708Z-001' / 'mammalian 2D' / '1' | |
| image_input = data_loc / 'C2-Pachytene SIM-1.tif' | |
| path_input = data_loc / 'SNT_Data.traces' | |
| paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config) | |
| assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 ) | |
| valid_results = [{1}, {1}, {2, 3}, {1, 2}, {1, 2}, {1}, {1}, {2}, {1}, {1}, {1, 2}, {1}, {1, 2}, {1, 2}, {1}, {1}, {1}, {1}, {1}] | |
| measured = extracted_peaks['Trace_foci_number'] | |
| print(measured) | |
| assert len(measured) == len(valid_results) | |
| assert(all(m in v for m,v in zip(measured, valid_results))) | |
| def test_image_5(script_loc): | |
| config = { 'sphere_radius': 0.3, | |
| 'peak_threshold': 0.4, | |
| 'xy_res': 0.1023810, | |
| 'z_res': 1, | |
| 'threshold_type': 'per-trace', | |
| 'use_corrected_positions': True, | |
| 'screening_distance': 10, | |
| } | |
| data_loc = script_loc.parent.parent / 'test_data' / 'mammalian 2D-20230821T180708Z-001' / 'mammalian 2D' / '2' | |
| image_input = data_loc / 'C1-CNTD1FHFH CSHA 1in5000 22612 Slide 6-102-1.tif' | |
| path_input = data_loc / 'SNT_Data.traces' | |
| paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config) | |
| assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 ) | |
| valid_results = [1, 1, 1, 1, 1, 1, 2, 1, 1, 2, 1, 1, 2, 1, 2, 1, 2, 1, 1] | |
| measured = extracted_peaks['Trace_foci_number'] | |
| assert list(measured) == valid_results | |