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Added average grain width measurement to disordered tracing #999

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merged 28 commits into from
Dec 4, 2024
Merged

Added average grain width measurement to disordered tracing #999

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992ebf4
initial testing
tcatley Nov 8, 2024
c0b7b60
further testing
tcatley Nov 11, 2024
4e74d58
testing
tcatley Nov 12, 2024
47f09c0
package: Unpin topoly version
ns-rse Nov 11, 2024
e115d0d
tests: Peg pytest-regtest to 2.3.1 as failing on OSX
ns-rse Nov 11, 2024
f84f198
added dna width measurement in disordered tracing
tcatley Nov 14, 2024
8ce3932
[pre-commit.ci] Fixing issues with pre-commit
pre-commit-ci[bot] Nov 14, 2024
c8b8294
Merge branch 'main' into ns-rse/994-unpin-topoly
ns-rse Nov 15, 2024
39305c5
tests(processing): Update regression test targets to include dna width
tcatley Nov 15, 2024
3ed5d53
tests(processing): Update regression test targets to include dna widt…
tcatley Nov 15, 2024
b0e72da
ci: Adds a Pull Request template
ns-rse Nov 15, 2024
1706c7c
ci: Clarify docs to be updated in PR template
ns-rse Nov 15, 2024
ec786ef
initial testing
tcatley Nov 8, 2024
0b76fa7
further testing
tcatley Nov 11, 2024
ec27115
testing
tcatley Nov 12, 2024
d81f92c
added dna width measurement in disordered tracing
tcatley Nov 14, 2024
8ffed0d
[pre-commit.ci] Fixing issues with pre-commit
pre-commit-ci[bot] Nov 14, 2024
0fb3067
tests(processing): Update regression test targets to include dna width
tcatley Nov 15, 2024
9e2d0f5
tests(processing): Update regression test targets to include dna widt…
tcatley Nov 15, 2024
b90f2af
tests(tracing): Split and update tests of disordered traces
ns-rse Nov 18, 2024
a99c9f0
tests(processing): Update tests to account for grain_width_mean
ns-rse Nov 18, 2024
c97bee4
Merge branch 'main' into tcatley/dna-width
ns-rse Nov 18, 2024
6226b27
Merge branch 'tcatley/dna-width' into ns-rse/999-split-and-update-tests
ns-rse Nov 18, 2024
c813dda
Merge pull request #1002 from AFM-SPM/ns-rse/999-split-and-update-tests
ns-rse Nov 18, 2024
7acb413
added basic square tests for calculate_dna_width()
MaxGamill-Sheffield Nov 19, 2024
3eab5ca
chg result to expected
MaxGamill-Sheffield Nov 19, 2024
52b5101
style: Tidying calculate_dna_width()
ns-rse Dec 4, 2024
8d38ae8
Merge pull request #1035 from AFM-SPM/ns-rse/dna-width-tidy
ns-rse Dec 4, 2024
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2 changes: 1 addition & 1 deletion pyproject.toml
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Original file line number Diff line number Diff line change
Expand Up @@ -55,7 +55,7 @@ dependencies = [
"snoop",
"tensorflow",
"tifffile",
"topoly==1.0.2",
"topoly",
"tqdm",
]

Expand Down
8 changes: 4 additions & 4 deletions 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 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
3 changes: 0 additions & 3 deletions tests/resources/tracing/disordered_tracing/catenanes_disordered_tracing_grainstats.csv
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25 changes: 0 additions & 25 deletions tests/resources/tracing/disordered_tracing/catenanes_disordered_tracing_stats.csv
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2 changes: 0 additions & 2 deletions tests/resources/tracing/disordered_tracing/rep_int_disordered_tracing_grainstats.csv
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13 changes: 0 additions & 13 deletions tests/resources/tracing/disordered_tracing/rep_int_disordered_tracing_stats.csv
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Binary file modified tests/resources/tracing/ordered_tracing/catenanes_ordered_tracing_data.pkl
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8 changes: 4 additions & 4 deletions tests/resources/tracing/ordered_tracing/catenanes_ordered_tracing_molstats.csv
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@@ -1,5 +1,5 @@
,image,grain_number,molecule_number,circular,topology,topology_flip,processing
0,catenane,0,0,True,4^2_1,2^2_1,nodestats
1,catenane,0,1,True,4^2_1,2^2_1,nodestats
2,catenane,1,0,True,2^2_1,0_1U0_1,nodestats
3,catenane,1,1,True,2^2_1,0_1U0_1,nodestats
0,catenane,0,0,True,L4a1,L2a1,nodestats
1,catenane,0,1,True,L4a1,L2a1,nodestats
2,catenane,1,0,True,L2a1,0_1U0_1,nodestats
3,catenane,1,1,True,L2a1,0_1U0_1,nodestats
28 changes: 28 additions & 0 deletions ...test_outputs/test_disordered_tracing.test_trace_image_disordered_dataframes[catenane].out
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@@ -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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