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Merge pull request #999 from AFM-SPM/tcatley/dna-width
Added average grain width measurement to disordered tracing
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8 changes: 4 additions & 4 deletions
8
tests/_regtest_outputs/test_processing.test_process_scan_above.out
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| image_size_x_m image_size_y_m image_area_m2 image_size_x_px image_size_y_px image_area_px2 grains_number_above grains_per_m2_above grains_number_below grains_per_m2_below rms_roughness | ||
| image | ||
| minicircle_small 1.2646e-07 1.2646e-07 1.5993e-14 64 64 4096 3 1.8758e+14 0 0.0000e+00 6.8208e-10 | ||
| centre_x centre_y grain_number radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret image grain_endpoints grain_junctions total_branch_lengths num_crossings avg_crossing_confidence min_crossing_confidence num_mols writhe_string total_contour_length average_end_to_end_distance | ||
| 0 7.5100e-08 4.7559e-08 0 3.9431e-09 2.5631e-08 1.6016e-08 1.6680e-08 9.1991e-10 2.6422e-09 1.5338e-09 1.5341e-09 1.0543e-24 6.8721e-16 1.3198e-15 2.0539e-08 5.0379e-08 1.0347e-15 4.0769e-01 above 5.0379e-08 2.0539e-08 minicircle_small 1 1 8.4571e-08 1 NaN NaN 2 6.5881e-08 8.8370e-09 | ||
| 1 8.0241e-08 7.8677e-08 1 6.8951e-09 2.7188e-08 1.6272e-08 1.6263e-08 9.0630e-10 2.4586e-09 1.6144e-09 1.6264e-09 1.0352e-24 6.3645e-16 1.5931e-15 2.0174e-08 5.1212e-08 1.0332e-15 3.9394e-01 above 5.1262e-08 2.0174e-08 minicircle_small 0 0 7.3054e-08 0 NaN NaN 1 NaN 5.8272e-08 0.0000e+00 | ||
| 2 4.0012e-08 7.5644e-08 2 9.9461e-09 2.3654e-08 1.7561e-08 1.8364e-08 9.0641e-10 2.1066e-09 1.5939e-09 1.5493e-09 1.1192e-24 7.2236e-16 1.5462e-15 3.3592e-08 4.1496e-08 1.3940e-15 8.0952e-01 above 4.4405e-08 3.2528e-08 minicircle_small 0 0 1.0447e-07 0 NaN NaN 1 NaN 8.7183e-08 0.0000e+00 | ||
| centre_x centre_y grain_number radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret image grain_endpoints grain_junctions total_branch_lengths grain_width_mean num_crossings avg_crossing_confidence min_crossing_confidence num_mols writhe_string total_contour_length average_end_to_end_distance | ||
| 0 7.5100e-08 4.7559e-08 0 3.9431e-09 2.5631e-08 1.6016e-08 1.6680e-08 9.1991e-10 2.6422e-09 1.5338e-09 1.5341e-09 1.0543e-24 6.8721e-16 1.3198e-15 2.0539e-08 5.0379e-08 1.0347e-15 4.0769e-01 above 5.0379e-08 2.0539e-08 minicircle_small 1 1 8.4571e-08 8.2685e-09 1 NaN NaN 2 6.5881e-08 8.8370e-09 | ||
| 1 8.0241e-08 7.8677e-08 1 6.8951e-09 2.7188e-08 1.6272e-08 1.6263e-08 9.0630e-10 2.4586e-09 1.6144e-09 1.6264e-09 1.0352e-24 6.3645e-16 1.5931e-15 2.0174e-08 5.1212e-08 1.0332e-15 3.9394e-01 above 5.1262e-08 2.0174e-08 minicircle_small 0 0 7.3054e-08 7.6154e-09 0 NaN NaN 1 NaN 5.8272e-08 0.0000e+00 | ||
| 2 4.0012e-08 7.5644e-08 2 9.9461e-09 2.3654e-08 1.7561e-08 1.8364e-08 9.0641e-10 2.1066e-09 1.5939e-09 1.5493e-09 1.1192e-24 7.2236e-16 1.5462e-15 3.3592e-08 4.1496e-08 1.3940e-15 8.0952e-01 above 4.4405e-08 3.2528e-08 minicircle_small 0 0 1.0447e-07 7.8033e-09 0 NaN NaN 1 NaN 8.7183e-08 0.0000e+00 |
8 changes: 4 additions & 4 deletions
8
tests/_regtest_outputs/test_processing.test_process_scan_both.out
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,7 +1,7 @@ | ||
| image_size_x_m image_size_y_m image_area_m2 image_size_x_px image_size_y_px image_area_px2 grains_number_above grains_per_m2_above grains_number_below grains_per_m2_below rms_roughness | ||
| image | ||
| minicircle_small 1.2646e-07 1.2646e-07 1.5993e-14 64 64 4096 3 1.8758e+14 0 0.0000e+00 6.8208e-10 | ||
| centre_x centre_y grain_number radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret image grain_endpoints grain_junctions total_branch_lengths total_contour_length average_end_to_end_distance | ||
| 0 7.5100e-08 4.7559e-08 0 3.9431e-09 2.5631e-08 1.6016e-08 1.6680e-08 9.1991e-10 2.6422e-09 1.5338e-09 1.5341e-09 1.0543e-24 6.8721e-16 1.3198e-15 2.0539e-08 5.0379e-08 1.0347e-15 4.0769e-01 above 5.0379e-08 2.0539e-08 minicircle_small 1.0000e+00 1.0000e+00 8.4571e-08 6.5881e-08 8.8370e-09 | ||
| 1 8.0241e-08 7.8677e-08 1 6.8951e-09 2.7188e-08 1.6272e-08 1.6263e-08 9.0630e-10 2.4586e-09 1.6144e-09 1.6264e-09 1.0352e-24 6.3645e-16 1.5931e-15 2.0174e-08 5.1212e-08 1.0332e-15 3.9394e-01 above 5.1262e-08 2.0174e-08 minicircle_small 0.0000e+00 0.0000e+00 7.3054e-08 5.8272e-08 0.0000e+00 | ||
| 2 4.0012e-08 7.5644e-08 2 9.9461e-09 2.3654e-08 1.7561e-08 1.8364e-08 9.0641e-10 2.1066e-09 1.5939e-09 1.5493e-09 1.1192e-24 7.2236e-16 1.5462e-15 3.3592e-08 4.1496e-08 1.3940e-15 8.0952e-01 above 4.4405e-08 3.2528e-08 minicircle_small 0.0000e+00 0.0000e+00 1.0447e-07 8.7183e-08 0.0000e+00 | ||
| centre_x centre_y grain_number radius_min radius_max radius_mean radius_median height_min height_max height_median height_mean volume area area_cartesian_bbox smallest_bounding_width smallest_bounding_length smallest_bounding_area aspect_ratio threshold max_feret min_feret image grain_endpoints grain_junctions total_branch_lengths grain_width_mean total_contour_length average_end_to_end_distance | ||
| 0 7.5100e-08 4.7559e-08 0 3.9431e-09 2.5631e-08 1.6016e-08 1.6680e-08 9.1991e-10 2.6422e-09 1.5338e-09 1.5341e-09 1.0543e-24 6.8721e-16 1.3198e-15 2.0539e-08 5.0379e-08 1.0347e-15 4.0769e-01 above 5.0379e-08 2.0539e-08 minicircle_small 1.0000e+00 1.0000e+00 8.4571e-08 8.2685e-09 6.5881e-08 8.8370e-09 | ||
| 1 8.0241e-08 7.8677e-08 1 6.8951e-09 2.7188e-08 1.6272e-08 1.6263e-08 9.0630e-10 2.4586e-09 1.6144e-09 1.6264e-09 1.0352e-24 6.3645e-16 1.5931e-15 2.0174e-08 5.1212e-08 1.0332e-15 3.9394e-01 above 5.1262e-08 2.0174e-08 minicircle_small 0.0000e+00 0.0000e+00 7.3054e-08 7.6154e-09 5.8272e-08 0.0000e+00 | ||
| 2 4.0012e-08 7.5644e-08 2 9.9461e-09 2.3654e-08 1.7561e-08 1.8364e-08 9.0641e-10 2.1066e-09 1.5939e-09 1.5493e-09 1.1192e-24 7.2236e-16 1.5462e-15 3.3592e-08 4.1496e-08 1.3940e-15 8.0952e-01 above 4.4405e-08 3.2528e-08 minicircle_small 0.0000e+00 0.0000e+00 1.0447e-07 7.8033e-09 8.7183e-08 0.0000e+00 |
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tests/resources/tracing/disordered_tracing/catenanes_disordered_tracing_grainstats.csv
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tests/resources/tracing/disordered_tracing/catenanes_disordered_tracing_stats.csv
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tests/resources/tracing/disordered_tracing/rep_int_disordered_tracing_grainstats.csv
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tests/resources/tracing/disordered_tracing/rep_int_disordered_tracing_stats.csv
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...test_outputs/test_disordered_tracing.test_trace_image_disordered_dataframes[catenane].out
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,28 @@ | ||
| image grain_number grain_endpoints grain_junctions total_branch_lengths grain_width_mean | ||
| 0 test_image 0 0 14 5.7552e-07 4.3883e-09 | ||
| 1 test_image 1 0 12 5.7479e-07 4.4161e-09 | ||
| image grain_number branch_distance branch_type connected_segments mean_pixel_value stdev_pixel_value min_value median_value middle_value | ||
| 0 test_image 0 2.9858e+01 2 [1, 2, 6] 2.6683e+00 3.5767e-01 1.9935e+00 2.6465e+00 2.6744e+00 | ||
| 1 test_image 0 2.8645e+01 2 [0, 2, 6] 2.7290e+00 2.1545e-01 2.5507e+00 2.6838e+00 2.6580e+00 | ||
| 2 test_image 0 1.8683e+00 2 [0, 1, 3, 4] 4.0675e+00 1.6906e-01 3.7890e+00 4.1385e+00 4.1396e+00 | ||
| 3 test_image 0 1.4661e+02 2 [2, 4, 9] 2.6694e+00 2.9476e-01 1.2200e+00 2.7080e+00 2.9116e+00 | ||
| 4 test_image 0 2.6170e+01 2 [2, 3, 9] 2.8350e+00 3.4364e-01 2.5354e+00 2.7608e+00 2.7651e+00 | ||
| 5 test_image 0 2.2459e+02 2 [6, 7, 10, 11] 2.7010e+00 2.6534e-01 1.7874e+00 2.7330e+00 2.2574e+00 | ||
| 6 test_image 0 6.9504e+00 2 [0, 1, 5, 7] 3.6264e+00 6.4067e-01 2.5888e+00 3.8420e+00 3.8420e+00 | ||
| 7 test_image 0 3.1203e+01 2 [5, 6, 8, 11] 2.8436e+00 5.5729e-01 2.1307e+00 2.7052e+00 2.7530e+00 | ||
| 8 test_image 0 3.1287e+01 2 [7, 9, 10, 11] 2.7443e+00 3.8223e-01 2.4149e+00 2.6535e+00 2.4707e+00 | ||
| 9 test_image 0 5.5701e+00 2 [3, 4, 8, 10] 2.7309e+00 4.9010e-02 2.6526e+00 2.7379e+00 2.7495e+00 | ||
| 10 test_image 0 3.8188e+01 2 [5, 8, 9, 11] 2.7864e+00 1.5142e-01 2.4451e+00 2.7710e+00 2.6967e+00 | ||
| 11 test_image 0 4.5941e+00 2 [5, 7, 8, 10] 4.1266e+00 3.7134e-01 3.3511e+00 4.2387e+00 4.2387e+00 | ||
| 0 test_image 1 3.7700e+01 2 [1, 2, 3, 6] 2.7733e+00 1.3491e-01 2.4451e+00 2.7690e+00 2.7142e+00 | ||
| 1 test_image 1 2.2389e+02 2 [0, 2, 4, 9] 2.6966e+00 2.6111e-01 1.8203e+00 2.7314e+00 2.2744e+00 | ||
| 2 test_image 1 5.0821e+00 2 [0, 1, 3, 4] 4.0290e+00 4.6381e-01 3.0770e+00 4.1850e+00 4.1850e+00 | ||
| 3 test_image 1 3.1001e+01 2 [0, 2, 4, 6] 2.7462e+00 4.0205e-01 2.4439e+00 2.6516e+00 2.4439e+00 | ||
| 4 test_image 1 3.1405e+01 2 [1, 2, 3, 9] 2.8423e+00 5.6226e-01 2.1307e+00 2.6942e+00 2.7530e+00 | ||
| 5 test_image 1 1.4750e+02 2 [6, 7, 11] 2.6728e+00 2.9408e-01 1.2200e+00 2.7122e+00 2.9467e+00 | ||
| 6 test_image 1 5.7723e+00 2 [0, 3, 5, 7] 2.7226e+00 5.1362e-02 2.6526e+00 2.7128e+00 2.7181e+00 | ||
| 7 test_image 1 2.5682e+01 2 [5, 6, 11] 2.8513e+00 3.6310e-01 2.5354e+00 2.7618e+00 2.7705e+00 | ||
| 8 test_image 1 2.7871e+01 2 [9, 10, 11] 2.7169e+00 1.7984e-01 2.5507e+00 2.6864e+00 2.6580e+00 | ||
| 9 test_image 1 6.9504e+00 2 [1, 4, 8, 10] 3.6794e+00 5.9509e-01 2.6486e+00 3.8420e+00 3.8420e+00 | ||
| 10 test_image 1 2.9370e+01 2 [8, 9, 11] 2.6403e+00 3.1060e-01 1.9935e+00 2.6483e+00 2.6828e+00 | ||
| 11 test_image 1 2.5584e+00 2 [5, 7, 8, 10] 3.9748e+00 2.3924e-01 3.6041e+00 4.0751e+00 4.0751e+00 |
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