Skip to content

Commit

Permalink
tests(tracing): Split and update tests of disordered traces
Browse files Browse the repository at this point in the history 
Splits `test_trace_image_disordered` into two tests, the original compares dictionaries, the newer (suffixed with
`_dataframes`) compares the dataframes/csv files that are produced, of which there are two and one needed updating to
include the `grain_width_mean` column that #999 introduces.
  • Loading branch information
@ns-rse
ns-rse committed Nov 18, 2024
1 parent 09e10d1 commit 20cf3c0
Show file tree
Hide file tree
Showing 7 changed files with 152 additions and 75 deletions.
3 changes: 0 additions & 3 deletions tests/resources/tracing/disordered_tracing/catenanes_disordered_tracing_grainstats.csv
View file

This file was deleted.

25 changes: 0 additions & 25 deletions tests/resources/tracing/disordered_tracing/catenanes_disordered_tracing_stats.csv
View file

This file was deleted.

2 changes: 0 additions & 2 deletions tests/resources/tracing/disordered_tracing/rep_int_disordered_tracing_grainstats.csv
View file

This file was deleted.

13 changes: 0 additions & 13 deletions tests/resources/tracing/disordered_tracing/rep_int_disordered_tracing_stats.csv
View file

This file was deleted.

28 changes: 28 additions & 0 deletions ...test_outputs/test_disordered_tracing.test_trace_image_disordered_dataframes[catenane].out
View file
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
15 changes: 15 additions & 0 deletions ...t_disordered_tracing.test_trace_image_disordered_dataframes[replication_intermediate].out
View file
Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
image grain_number grain_endpoints grain_junctions total_branch_lengths grain_width_mean
0 test_image 0 0 13 9.6852e-07 3.0318e-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 1.7269e+02 2 [1, 2, 3, 8] 2.1474e+00 1.8580e-01 1.4118e+00 2.1479e+00 2.1939e+00
1 test_image 0 3.3804e+02 2 [0, 2, 7, 11] 2.1262e+00 1.8417e-01 1.1279e+00 2.1329e+00 2.2363e+00
2 test_image 0 6.9014e-01 2 [0, 1, 3, 4] 3.5129e+00 2.4417e-01 3.2687e+00 3.5129e+00 3.5129e+00
3 test_image 0 7.5415e+01 2 [0, 2, 4, 8] 2.1781e+00 2.2953e-01 1.4118e+00 2.1784e+00 2.2734e+00
4 test_image 0 3.1893e+01 2 [2, 3, 5, 6] 2.1379e+00 3.3898e-01 1.7556e+00 2.0944e+00 2.2880e+00
5 test_image 0 5.1517e+01 2 [4, 6, 7] 2.2339e+00 2.3611e-01 1.7265e+00 2.2070e+00 2.0221e+00
6 test_image 0 1.1781e+00 2 [4, 5, 7] 3.4336e+00 2.9158e-01 3.0268e+00 3.5782e+00 3.6957e+00
7 test_image 0 1.5383e+02 2 [1, 5, 6, 11] 2.1708e+00 2.3399e-01 1.3202e+00 2.1774e+00 2.1908e+00
8 test_image 0 5.8754e+01 2 [0, 3, 10, 11] 2.0020e+00 3.3701e-01 8.8592e-01 2.0826e+00 2.2475e+00
9 test_image 0 3.8962e+01 3 [10] 2.2736e+00 1.7805e-01 2.0016e+00 2.2595e+00 2.2033e+00
10 test_image 0 4.8800e-01 2 [8, 9, 11] 2.8751e+00 9.8813e-03 2.8652e+00 2.8751e+00 2.8751e+00
11 test_image 0 4.5069e+01 2 [1, 7, 8, 10] 2.1855e+00 2.2638e-01 1.2893e+00 2.2271e+00 2.2271e+00
141 changes: 109 additions & 32 deletions tests/tracing/test_disordered_tracing.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -7,7 +7,6 @@

import numpy as np
import numpy.typing as npt
import pandas as pd
import pytest

from topostats.io import dict_almost_equal # pylint: disable=no-name-in-module import-error
Expand All @@ -16,6 +15,7 @@
# pylint: disable=too-many-arguments
# pylint: disable=too-many-locals
# pylint: disable=too-many-lines
# pylint: disable=too-many-positional-arguments
# pylint: disable=unspecified-encoding

BASE_DIR = Path.cwd()
Expand Down Expand Up @@ -1294,9 +1294,7 @@ def test_disordered_trace_grain(
"skeletonisation_params",
"pruning_params",
"expected_disordered_crop_data_filename",
"expected_disordered_tracing_grainstats_filename",
"expected_all_images_filename",
"expected_disordered_tracing_stats_filename",
),
[
pytest.param(
Expand Down Expand Up @@ -1326,9 +1324,7 @@ def test_disordered_trace_grain(
"method_outlier": "mean_abs",
},
"catenanes_disordered_tracing_crop_data.pkl",
"catenanes_disordered_tracing_grainstats.csv",
"catenanes_disordered_tracing_all_images.pkl",
"catenanes_disordered_tracing_stats.csv",
id="catenane",
),
pytest.param(
Expand Down Expand Up @@ -1358,9 +1354,7 @@ def test_disordered_trace_grain(
"method_outlier": "mean_abs",
},
"rep_int_disordered_tracing_crop_data.pkl",
"rep_int_disordered_tracing_grainstats.csv",
"rep_int_disordered_tracing_all_images.pkl",
"rep_int_disordered_tracing_stats.csv",
id="replication intermediate",
),
],
Expand All @@ -1374,9 +1368,7 @@ def test_trace_image_disordered(
skeletonisation_params: dict,
pruning_params: dict,
expected_disordered_crop_data_filename: str,
expected_disordered_tracing_grainstats_filename: str,
expected_all_images_filename: str,
expected_disordered_tracing_stats_filename: str,
) -> None:
"""Test the trace image disordered method."""
# Load the image
Expand All @@ -1385,9 +1377,9 @@ def test_trace_image_disordered(

(
result_disordered_crop_data,
result_disordered_tracing_grainstats,
_,
result_all_images,
result_disordered_tracing_stats,
_,
) = disordered_tracing.trace_image_disordered(
image=image,
grains_mask=mask,
Expand All @@ -1407,42 +1399,127 @@ def test_trace_image_disordered(
# variable_pruned_skeleton = result_all_images["pruned_skeleton"]
# variable_branch_types = result_all_images["branch_types"]

# Update expected values - CHECK RESULTS WITH EXPERT BEFORE UPDATING
# Pickle result_disordered_crop_data
# # Update expected values - CHECK RESULTS WITH EXPERT BEFORE UPDATING
# # Pickle result_disordered_crop_data
# with open(DISORDERED_TRACING_RESOURCES / expected_disordered_crop_data_filename, "wb") as f:
# pkl.dump(result_disordered_crop_data, f)

# # Save result_disordered_tracing_grainstats as a csv
# result_disordered_tracing_grainstats.to_csv(
# DISORDERED_TRACING_RESOURCES / expected_disordered_tracing_grainstats_filename
# )

# # Save result_all_images as a pickle
# with open(DISORDERED_TRACING_RESOURCES / expected_all_images_filename, "wb") as f:
# pkl.dump(result_all_images, f)

# # Save result_disordered_tracing_stats dataframe as a csv
# result_disordered_tracing_stats.to_csv(DISORDERED_TRACING_RESOURCES / expected_disordered_tracing_stats_filename)

# Load expected values
with Path.open(DISORDERED_TRACING_RESOURCES / expected_disordered_crop_data_filename, "rb") as f:
expected_disordered_crop_data = pkl.load(f)

expected_disordered_tracing_grainstats = pd.read_csv(
DISORDERED_TRACING_RESOURCES / expected_disordered_tracing_grainstats_filename, index_col=0
)

with Path.open(DISORDERED_TRACING_RESOURCES / expected_all_images_filename, "rb") as f:
expected_all_images = pkl.load(f)

expected_disordered_tracing_stats = pd.read_csv(
DISORDERED_TRACING_RESOURCES / expected_disordered_tracing_stats_filename, index_col=0
)

assert dict_almost_equal(result_disordered_crop_data, expected_disordered_crop_data, abs_tol=1e-11)
pd.testing.assert_frame_equal(result_disordered_tracing_grainstats, expected_disordered_tracing_grainstats)
assert dict_almost_equal(result_all_images, expected_all_images, abs_tol=1e-11)
pd.testing.assert_frame_equal(result_disordered_tracing_stats, expected_disordered_tracing_stats)


@pytest.mark.parametrize(
(
"image_filename",
"mask_filename",
"pixel_to_nm_scaling",
"min_skeleton_size",
"mask_smoothing_params",
"skeletonisation_params",
"pruning_params",
),
[
pytest.param(
"example_catenanes.npy",
"example_catenanes_labelled_grain_mask_thresholded.npy",
# Pixel to nm scaling
0.488,
# Min skeleton size
10,
# Mask smoothing parameters
{
"gaussian_sigma": 2,
"dilation_iterations": 2,
"holearea_min_max": [10, None],
},
# Skeletonisation parameters
{
"method": "topostats",
"height_bias": 0.6,
},
# Pruning parameters
{
"method": "topostats",
"max_length": 7.0,
"height_threshold": None,
"method_values": "mid",
"method_outlier": "mean_abs",
},
id="catenane",
),
pytest.param(
"example_rep_int.npy",
"example_rep_int_labelled_grain_mask_thresholded.npy",
# Pixel to nm scaling
0.488,
# Min skeleton size
10,
# Mask smoothing parameters
{
"gaussian_sigma": 2,
"dilation_iterations": 2,
"holearea_min_max": [10, None],
},
# Skeletonisation parameters
{
"method": "topostats",
"height_bias": 0.6,
},
# Pruning parameters
{
"method": "topostats",
"max_length": 20.0,
"height_threshold": None,
"method_values": "mid",
"method_outlier": "mean_abs",
},
id="replication intermediate",
),
],
)
def test_trace_image_disordered_dataframes(
image_filename: str,
mask_filename: str,
pixel_to_nm_scaling: float,
min_skeleton_size: int,
mask_smoothing_params: dict,
skeletonisation_params: dict,
pruning_params: dict,
regtest: callable,
) -> None:
"""Test the trace image disordered method produces correct dataframes (/csv files)."""
# Load the image
image = np.load(GENERAL_RESOURCES / image_filename)
mask = np.load(GENERAL_RESOURCES / mask_filename)

(
_,
result_disordered_tracing_grainstats,
_,
result_disordered_tracing_stats,
) = disordered_tracing.trace_image_disordered(
image=image,
grains_mask=mask,
filename="test_image",
pixel_to_nm_scaling=pixel_to_nm_scaling,
min_skeleton_size=min_skeleton_size,
mask_smoothing_params=mask_smoothing_params,
skeletonisation_params=skeletonisation_params,
pruning_params=pruning_params,
pad_width=1,
)
print(result_disordered_tracing_grainstats.to_string(float_format="{:.4e}".format), file=regtest)
print(result_disordered_tracing_stats.to_string(float_format="{:.4e}".format), file=regtest)


@pytest.mark.skip(reason="Awaiting test to be written 2024-10-15.")
Expand Down

0 comments on commit 20cf3c0

Please sign in to comment.