JFoz/test_path_analysis

1 2import pytest3from path_analysis.analyse import *4from path_analysis.data_preprocess import RemovedPeakData5import numpy as np6from math import pi7import xml.etree.ElementTree as ET8from PIL import ImageChops9 10from pathlib import Path11 12import matplotlib13matplotlib.use('Agg')14 15@pytest.fixture(scope="module")16def script_loc(request):17    '''Return the directory of the currently running test script'''18 19    return Path(request.fspath).parent 20 21def test_image_1(script_loc):22            23    config = {  'sphere_radius': 0.1984125,24                'peak_threshold': 0.4,25                'xy_res': 0.0396825,26                'z_res': 0.0909184,27                'threshold_type': 'per-cell',28                'use_corrected_positions': True,29                'screening_distance': 10,30            }31 32    data_loc = script_loc.parent.parent / 'test_data' / 'hei10 ++ 15.11.19 p22s2 image 9'33 34 35    image_input = data_loc / 'HEI10.tif'36    path_input = data_loc / 'SNT_Data.traces'37 38    paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config)39 40    assert np.allclose(extracted_peaks['SNT_trace_length(um)'], [61.47, 70.40, 51.93, 43.94, 62.24], atol=1e-2 )41    assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 )42    assert list(extracted_peaks['Trace_foci_number']) == [2,3,2,2,3]43 44def test_image_2(script_loc):45            46    config = {  'sphere_radius': 0.1984125,47                'peak_threshold': 0.4,48                'xy_res': 0.0396825,49                'z_res': 0.0909184,50                'threshold_type': 'per-cell',51                'use_corrected_positions': True,52                'screening_distance': 10,53              }54 55    data_loc = script_loc.parent.parent / 'test_data' / 'z-optimised'56 57 58    image_input = data_loc / 'HEI10.tif'59    path_input = data_loc / 'ZYP1.traces'60 61    paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config)62 63    assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 )64    assert list(extracted_peaks['Trace_foci_number']) == [2,2,1,2,1]65    66def test_image_3(script_loc):67            68    config = {  'sphere_radius': 0.1984125,69                'peak_threshold': 0.4,70                'xy_res': 0.0396825,71                'z_res': 0.1095510,72                'threshold_type': 'per-trace',73                'use_corrected_positions': True,74                'screening_distance': 10,75                76            }77 78    data_loc = script_loc.parent.parent / 'test_data' / 'arenosa SN A1243 image 18-20230726T142725Z-001' / 'arenosa SN A1243 image 18'79 80 81    image_input = data_loc / 'HEI10.tif'82    path_input = data_loc / 'SNT_Data.traces'83 84    paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config)85 86    assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 )87    assert list(extracted_peaks['Trace_foci_number']) == [2,1,1,1,2,1,1,1]88 89def test_image_4(script_loc):90            91    config = {  'sphere_radius': 10.,92                'peak_threshold': 0.4,93                'xy_res': 1,94                'z_res': 1,95                'threshold_type': 'per-trace',96                'use_corrected_positions': True,97                'screening_distance': 10,98 99            }100 101    data_loc = script_loc.parent.parent / 'test_data' / 'mammalian 2D-20230821T180708Z-001' / 'mammalian 2D' / '1' 102 103 104    image_input = data_loc / 'C2-Pachytene SIM-1.tif'105    path_input = data_loc / 'SNT_Data.traces'106 107    paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config)108 109    assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 )110 111    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}]112    measured = extracted_peaks['Trace_foci_number']113 114    print(measured)115    assert len(measured) == len(valid_results)116    assert(all(m in v for m,v in zip(measured, valid_results)))117 118 119 120def test_image_5(script_loc):121            122    config = {  'sphere_radius': 0.3,123                'peak_threshold': 0.4,124                'xy_res': 0.1023810,125                'z_res': 1,126                'threshold_type': 'per-trace',127                'use_corrected_positions': True,128                'screening_distance': 10,129 130            }131 132    data_loc = script_loc.parent.parent / 'test_data' / 'mammalian 2D-20230821T180708Z-001' / 'mammalian 2D' / '2' 133 134 135    image_input = data_loc / 'C1-CNTD1FHFH CSHA 1in5000 22612 Slide 6-102-1.tif'136    path_input = data_loc / 'SNT_Data.traces'137 138    paths, traces, fig, extracted_peaks = analyse_paths('Cell', image_input, path_input, config)139 140    assert np.allclose(extracted_peaks['SNT_trace_length(um)'], extracted_peaks['Measured_trace_length(um)'], atol=1e-8 )141 142    valid_results = [1, 1, 1, 1, 1, 1, 2, 1, 1, 2, 1, 1, 2, 1, 2, 1, 2, 1, 1]143    measured = extracted_peaks['Trace_foci_number']144 145    assert list(measured) == valid_results146 147 148    149 150 151