From 451950dd5063e5bb7afd9c767ca7dfbc02df413e Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Mon, 24 Jun 2024 10:50:02 +0200
Subject: [PATCH] Revamp tests; Delete outdated; Make common conftest.py;
Improve segmentation tests; Allow segmentation tests to run on CI
---
.gitmodules | 0
pyproject.toml | 2 +-
tests/classification/data/lfs/.gitattributes | 6 -
tests/classification/data/lfs/.gitignore | 1 -
tests/classification/data/lfs/README.md | 14 -
.../data/lfs/models/logreg.ckpt | Bin 3211 -> 0 bytes
.../data/lfs/models/signstotb.ckpt | Bin 6363 -> 0 bytes
...test_cli_classification.py => test_cli.py} | 0
tests/classification/test_hivtb.py | 1 +
tests/classification/test_indian.py | 1 +
tests/classification/test_montgomery.py | 1 +
tests/classification/test_nih_cxr14.py | 1 +
tests/classification/test_padchest.py | 1 +
tests/classification/test_shenzhen.py | 1 +
tests/classification/test_tbpoc.py | 1 +
tests/common/__init__.py | 0
tests/common/conftest.py | 26 --
tests/common/data/iris-test.csv | 75 ------
tests/common/data/iris-train.csv | 75 ------
tests/{classification => }/conftest.py | 39 ++-
tests/{common => }/data/16bits.png | Bin
tests/{common => }/data/iris.json | 0
tests/{classification => }/data/mednet.toml | 14 +-
.../data/raw_with_black_border.png | Bin
.../data/raw_with_elastic_deformation.png | Bin
.../data/raw_without_black_border.png | Bin
.../data/raw_without_elastic_deformation.png | Bin
tests/segmentation/conftest.py | 253 ------------------
tests/segmentation/test_chasedb1.py | 7 +-
.../{test_cli_segmentation.py => test_cli.py} | 0
tests/segmentation/test_cxr8.py | 5 +-
tests/segmentation/test_drhagis.py | 7 +-
tests/segmentation/test_drionsdb.py | 7 +-
tests/segmentation/test_drishtigs1.py | 13 +-
tests/segmentation/test_drive.py | 7 +-
tests/segmentation/test_hrf.py | 7 +-
tests/segmentation/test_iostar.py | 7 +-
tests/segmentation/test_jsrt.py | 7 +-
tests/segmentation/test_montgomery.py | 6 +-
tests/segmentation/test_refuge.py | 7 +-
tests/segmentation/test_rimoner3.py | 10 +-
tests/segmentation/test_shenzhen.py | 7 +-
tests/segmentation/test_stare.py | 7 +-
tests/{common => }/test_database_split.py | 0
tests/{common => }/test_image_utils.py | 0
tests/{common => }/test_resource_monitor.py | 0
tests/{common => }/test_transforms.py | 0
47 files changed, 135 insertions(+), 481 deletions(-)
delete mode 100644 .gitmodules
delete mode 100644 tests/classification/data/lfs/.gitattributes
delete mode 100644 tests/classification/data/lfs/.gitignore
delete mode 100644 tests/classification/data/lfs/README.md
delete mode 100644 tests/classification/data/lfs/models/logreg.ckpt
delete mode 100644 tests/classification/data/lfs/models/signstotb.ckpt
rename tests/classification/{test_cli_classification.py => test_cli.py} (100%)
delete mode 100644 tests/common/__init__.py
delete mode 100644 tests/common/conftest.py
delete mode 100644 tests/common/data/iris-test.csv
delete mode 100644 tests/common/data/iris-train.csv
rename tests/{classification => }/conftest.py (86%)
rename tests/{common => }/data/16bits.png (100%)
rename tests/{common => }/data/iris.json (100%)
rename tests/{classification => }/data/mednet.toml (50%)
rename tests/{common => }/data/raw_with_black_border.png (100%)
rename tests/{common => }/data/raw_with_elastic_deformation.png (100%)
rename tests/{common => }/data/raw_without_black_border.png (100%)
rename tests/{common => }/data/raw_without_elastic_deformation.png (100%)
delete mode 100644 tests/segmentation/conftest.py
rename tests/segmentation/{test_cli_segmentation.py => test_cli.py} (100%)
rename tests/{common => }/test_database_split.py (100%)
rename tests/{common => }/test_image_utils.py (100%)
rename tests/{common => }/test_resource_monitor.py (100%)
rename tests/{common => }/test_transforms.py (100%)
diff --git a/.gitmodules b/.gitmodules
deleted file mode 100644
index e69de29b..00000000
diff --git a/pyproject.toml b/pyproject.toml
index 95f54b8d..34b75b6a 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -151,7 +151,7 @@ test = "pytest -sv tests/"
test-slow = { cmd = "pytest -sv tests/", env = { PYTEST_ADDOPTS = "-m slow" } }
test-fast = { cmd = "pytest -sv tests/", env = { PYTEST_ADDOPTS = "-m '(not slow)'" } }
test-cov = "pytest -sv --cov-report 'html:html/coverage' tests/"
-test-ci = "cp tests/classification/data/mednet.toml $XDG_CONFIG_HOME && pytest -sv --cov-report 'html:html/coverage' --cov-report 'xml:coverage.xml' --junitxml 'junit-coverage.xml' --ignore '.profile' tests/"
+test-ci = "cp tests/data/mednet.toml $XDG_CONFIG_HOME && pytest -sv --cov-report 'html:html/coverage' --cov-report 'xml:coverage.xml' --junitxml 'junit-coverage.xml' --ignore '.profile' tests/"
[tool.pixi.feature.build.dependencies]
hatch = "*"
diff --git a/tests/classification/data/lfs/.gitattributes b/tests/classification/data/lfs/.gitattributes
deleted file mode 100644
index ebbbf5f9..00000000
--- a/tests/classification/data/lfs/.gitattributes
+++ /dev/null
@@ -1,6 +0,0 @@
-_test_densenetrs_checkpoint.pth filter=lfs diff=lfs merge=lfs -text
-_test_fpasa_checkpoint.pth filter=lfs diff=lfs merge=lfs -text
-_test_logreg_checkpoint.pth filter=lfs diff=lfs merge=lfs -text
-_test_signstotb_checkpoint.pth filter=lfs diff=lfs merge=lfs -text
-_testdb.zip filter=lfs diff=lfs merge=lfs -text
-pasa.pth filter=lfs diff=lfs merge=lfs -text
diff --git a/tests/classification/data/lfs/.gitignore b/tests/classification/data/lfs/.gitignore
deleted file mode 100644
index b25c15b8..00000000
--- a/tests/classification/data/lfs/.gitignore
+++ /dev/null
@@ -1 +0,0 @@
-*~
diff --git a/tests/classification/data/lfs/README.md b/tests/classification/data/lfs/README.md
deleted file mode 100644
index bc66bf5e..00000000
--- a/tests/classification/data/lfs/README.md
+++ /dev/null
@@ -1,14 +0,0 @@
-# Assets for Testing biosignal/software/mednet>
-
-This package contains test unit assets used by the test suit of
-biosignal/software/mednet>.
-
-
-## Updating
-
-To update the contents of this package, use [git-lfs](https://git-lfs.com),
-following the workflow described at the [GitLab support
-page](https://docs.gitlab.com/ee/topics/git/lfs/).
-
-Cloning and updating the repository, in particular, works the same as before
-and should not impose any workflow changes.
diff --git a/tests/classification/data/lfs/models/logreg.ckpt b/tests/classification/data/lfs/models/logreg.ckpt
deleted file mode 100644
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diff --git a/tests/classification/test_cli_classification.py b/tests/classification/test_cli.py
similarity index 100%
rename from tests/classification/test_cli_classification.py
rename to tests/classification/test_cli.py
diff --git a/tests/classification/test_hivtb.py b/tests/classification/test_hivtb.py
index 91258839..547346fd 100644
--- a/tests/classification/test_hivtb.py
+++ b/tests/classification/test_hivtb.py
@@ -103,6 +103,7 @@ def test_loading(database_checkers, name: str, dataset: str):
prefixes=("HIV-TB_Algorithm_study_X-rays",),
possible_labels=(0, 1),
expected_num_labels=1,
+ expected_meta_size=2,
)
limit -= 1
diff --git a/tests/classification/test_indian.py b/tests/classification/test_indian.py
index 952bc9b7..dcd4236f 100644
--- a/tests/classification/test_indian.py
+++ b/tests/classification/test_indian.py
@@ -108,6 +108,7 @@ def test_loading(database_checkers, name: str, dataset: str):
prefixes=("DatasetA/Training", "DatasetA/Testing"),
possible_labels=(0, 1),
expected_num_labels=1,
+ expected_meta_size=2,
)
limit -= 1
diff --git a/tests/classification/test_montgomery.py b/tests/classification/test_montgomery.py
index ef8715ea..494528dc 100644
--- a/tests/classification/test_montgomery.py
+++ b/tests/classification/test_montgomery.py
@@ -108,6 +108,7 @@ def test_loading(database_checkers, name: str, dataset: str):
prefixes=("CXR_png/MCUCXR_0",),
possible_labels=(0, 1),
expected_num_labels=1,
+ expected_meta_size=2,
)
limit -= 1
diff --git a/tests/classification/test_nih_cxr14.py b/tests/classification/test_nih_cxr14.py
index da5504ba..1d2c2222 100644
--- a/tests/classification/test_nih_cxr14.py
+++ b/tests/classification/test_nih_cxr14.py
@@ -83,6 +83,7 @@ def test_loading(database_checkers, name: str, dataset: str, num_labels: int):
possible_labels=(0, 1),
expected_num_labels=num_labels,
expected_image_shape=(1, 1024, 1024),
+ expected_meta_size=2,
)
limit -= 1
diff --git a/tests/classification/test_padchest.py b/tests/classification/test_padchest.py
index af6007df..78ce812a 100644
--- a/tests/classification/test_padchest.py
+++ b/tests/classification/test_padchest.py
@@ -88,6 +88,7 @@ def test_loading(database_checkers, name: str, dataset: str, num_labels: int):
prefixes=("",),
possible_labels=(0, 1),
expected_num_labels=num_labels,
+ expected_meta_size=2,
)
limit -= 1
diff --git a/tests/classification/test_shenzhen.py b/tests/classification/test_shenzhen.py
index afc55032..2c31ac26 100644
--- a/tests/classification/test_shenzhen.py
+++ b/tests/classification/test_shenzhen.py
@@ -105,6 +105,7 @@ def test_loading(database_checkers, name: str, dataset: str):
prefixes=("CXR_png/CHNCXR_0",),
possible_labels=(0, 1),
expected_num_labels=1,
+ expected_meta_size=2,
)
limit -= 1
diff --git a/tests/classification/test_tbpoc.py b/tests/classification/test_tbpoc.py
index 81288179..66dcd46a 100644
--- a/tests/classification/test_tbpoc.py
+++ b/tests/classification/test_tbpoc.py
@@ -109,6 +109,7 @@ def test_loading(database_checkers, name: str, dataset: str):
),
possible_labels=(0, 1),
expected_num_labels=1,
+ expected_meta_size=2,
)
limit -= 1
diff --git a/tests/common/__init__.py b/tests/common/__init__.py
deleted file mode 100644
index e69de29b..00000000
diff --git a/tests/common/conftest.py b/tests/common/conftest.py
deleted file mode 100644
index e9c23ab2..00000000
--- a/tests/common/conftest.py
+++ /dev/null
@@ -1,26 +0,0 @@
-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-import pathlib
-
-import pytest
-
-
-@pytest.fixture
-def datadir(request) -> pathlib.Path:
- """Return the directory in which the test is sitting. Check the pytest
- documentation for more information.
-
- Parameters
- ----------
- request
- Information of the requesting test function.
-
- Returns
- -------
- pathlib.Path
- The directory in which the test is sitting.
- """
-
- return pathlib.Path(request.module.__file__).parents[0] / "data"
diff --git a/tests/common/data/iris-test.csv b/tests/common/data/iris-test.csv
deleted file mode 100644
index 27d1b05a..00000000
--- a/tests/common/data/iris-test.csv
+++ /dev/null
@@ -1,75 +0,0 @@
-5,3,1.6,0.2,Iris-setosa
-5,3.4,1.6,0.4,Iris-setosa
-5.2,3.5,1.5,0.2,Iris-setosa
-5.2,3.4,1.4,0.2,Iris-setosa
-4.7,3.2,1.6,0.2,Iris-setosa
-4.8,3.1,1.6,0.2,Iris-setosa
-5.4,3.4,1.5,0.4,Iris-setosa
-5.2,4.1,1.5,0.1,Iris-setosa
-5.5,4.2,1.4,0.2,Iris-setosa
-4.9,3.1,1.5,0.1,Iris-setosa
-5,3.2,1.2,0.2,Iris-setosa
-5.5,3.5,1.3,0.2,Iris-setosa
-4.9,3.1,1.5,0.1,Iris-setosa
-4.4,3,1.3,0.2,Iris-setosa
-5.1,3.4,1.5,0.2,Iris-setosa
-5,3.5,1.3,0.3,Iris-setosa
-4.5,2.3,1.3,0.3,Iris-setosa
-4.4,3.2,1.3,0.2,Iris-setosa
-5,3.5,1.6,0.6,Iris-setosa
-5.1,3.8,1.9,0.4,Iris-setosa
-4.8,3,1.4,0.3,Iris-setosa
-5.1,3.8,1.6,0.2,Iris-setosa
-4.6,3.2,1.4,0.2,Iris-setosa
-5.3,3.7,1.5,0.2,Iris-setosa
-5,3.3,1.4,0.2,Iris-setosa
-6.6,3,4.4,1.4,Iris-versicolor
-6.8,2.8,4.8,1.4,Iris-versicolor
-6.7,3,5,1.7,Iris-versicolor
-6,2.9,4.5,1.5,Iris-versicolor
-5.7,2.6,3.5,1,Iris-versicolor
-5.5,2.4,3.8,1.1,Iris-versicolor
-5.5,2.4,3.7,1,Iris-versicolor
-5.8,2.7,3.9,1.2,Iris-versicolor
-6,2.7,5.1,1.6,Iris-versicolor
-5.4,3,4.5,1.5,Iris-versicolor
-6,3.4,4.5,1.6,Iris-versicolor
-6.7,3.1,4.7,1.5,Iris-versicolor
-6.3,2.3,4.4,1.3,Iris-versicolor
-5.6,3,4.1,1.3,Iris-versicolor
-5.5,2.5,4,1.3,Iris-versicolor
-5.5,2.6,4.4,1.2,Iris-versicolor
-6.1,3,4.6,1.4,Iris-versicolor
-5.8,2.6,4,1.2,Iris-versicolor
-5,2.3,3.3,1,Iris-versicolor
-5.6,2.7,4.2,1.3,Iris-versicolor
-5.7,3,4.2,1.2,Iris-versicolor
-5.7,2.9,4.2,1.3,Iris-versicolor
-6.2,2.9,4.3,1.3,Iris-versicolor
-5.1,2.5,3,1.1,Iris-versicolor
-5.7,2.8,4.1,1.3,Iris-versicolor
-7.2,3.2,6,1.8,Iris-virginica
-6.2,2.8,4.8,1.8,Iris-virginica
-6.1,3,4.9,1.8,Iris-virginica
-6.4,2.8,5.6,2.1,Iris-virginica
-7.2,3,5.8,1.6,Iris-virginica
-7.4,2.8,6.1,1.9,Iris-virginica
-7.9,3.8,6.4,2,Iris-virginica
-6.4,2.8,5.6,2.2,Iris-virginica
-6.3,2.8,5.1,1.5,Iris-virginica
-6.1,2.6,5.6,1.4,Iris-virginica
-7.7,3,6.1,2.3,Iris-virginica
-6.3,3.4,5.6,2.4,Iris-virginica
-6.4,3.1,5.5,1.8,Iris-virginica
-6,3,4.8,1.8,Iris-virginica
-6.9,3.1,5.4,2.1,Iris-virginica
-6.7,3.1,5.6,2.4,Iris-virginica
-6.9,3.1,5.1,2.3,Iris-virginica
-5.8,2.7,5.1,1.9,Iris-virginica
-6.8,3.2,5.9,2.3,Iris-virginica
-6.7,3.3,5.7,2.5,Iris-virginica
-6.7,3,5.2,2.3,Iris-virginica
-6.3,2.5,5,1.9,Iris-virginica
-6.5,3,5.2,2,Iris-virginica
-6.2,3.4,5.4,2.3,Iris-virginica
-5.9,3,5.1,1.8,Iris-virginica
diff --git a/tests/common/data/iris-train.csv b/tests/common/data/iris-train.csv
deleted file mode 100644
index 82d5b134..00000000
--- a/tests/common/data/iris-train.csv
+++ /dev/null
@@ -1,75 +0,0 @@
-5.1,3.5,1.4,0.2,Iris-setosa
-4.9,3,1.4,0.2,Iris-setosa
-4.7,3.2,1.3,0.2,Iris-setosa
-4.6,3.1,1.5,0.2,Iris-setosa
-5,3.6,1.4,0.2,Iris-setosa
-5.4,3.9,1.7,0.4,Iris-setosa
-4.6,3.4,1.4,0.3,Iris-setosa
-5,3.4,1.5,0.2,Iris-setosa
-4.4,2.9,1.4,0.2,Iris-setosa
-4.9,3.1,1.5,0.1,Iris-setosa
-5.4,3.7,1.5,0.2,Iris-setosa
-4.8,3.4,1.6,0.2,Iris-setosa
-4.8,3,1.4,0.1,Iris-setosa
-4.3,3,1.1,0.1,Iris-setosa
-5.8,4,1.2,0.2,Iris-setosa
-5.7,4.4,1.5,0.4,Iris-setosa
-5.4,3.9,1.3,0.4,Iris-setosa
-5.1,3.5,1.4,0.3,Iris-setosa
-5.7,3.8,1.7,0.3,Iris-setosa
-5.1,3.8,1.5,0.3,Iris-setosa
-5.4,3.4,1.7,0.2,Iris-setosa
-5.1,3.7,1.5,0.4,Iris-setosa
-4.6,3.6,1,0.2,Iris-setosa
-5.1,3.3,1.7,0.5,Iris-setosa
-4.8,3.4,1.9,0.2,Iris-setosa
-7,3.2,4.7,1.4,Iris-versicolor
-6.4,3.2,4.5,1.5,Iris-versicolor
-6.9,3.1,4.9,1.5,Iris-versicolor
-5.5,2.3,4,1.3,Iris-versicolor
-6.5,2.8,4.6,1.5,Iris-versicolor
-5.7,2.8,4.5,1.3,Iris-versicolor
-6.3,3.3,4.7,1.6,Iris-versicolor
-4.9,2.4,3.3,1,Iris-versicolor
-6.6,2.9,4.6,1.3,Iris-versicolor
-5.2,2.7,3.9,1.4,Iris-versicolor
-5,2,3.5,1,Iris-versicolor
-5.9,3,4.2,1.5,Iris-versicolor
-6,2.2,4,1,Iris-versicolor
-6.1,2.9,4.7,1.4,Iris-versicolor
-5.6,2.9,3.6,1.3,Iris-versicolor
-6.7,3.1,4.4,1.4,Iris-versicolor
-5.6,3,4.5,1.5,Iris-versicolor
-5.8,2.7,4.1,1,Iris-versicolor
-6.2,2.2,4.5,1.5,Iris-versicolor
-5.6,2.5,3.9,1.1,Iris-versicolor
-5.9,3.2,4.8,1.8,Iris-versicolor
-6.1,2.8,4,1.3,Iris-versicolor
-6.3,2.5,4.9,1.5,Iris-versicolor
-6.1,2.8,4.7,1.2,Iris-versicolor
-6.4,2.9,4.3,1.3,Iris-versicolor
-6.3,3.3,6,2.5,Iris-virginica
-5.8,2.7,5.1,1.9,Iris-virginica
-7.1,3,5.9,2.1,Iris-virginica
-6.3,2.9,5.6,1.8,Iris-virginica
-6.5,3,5.8,2.2,Iris-virginica
-7.6,3,6.6,2.1,Iris-virginica
-4.9,2.5,4.5,1.7,Iris-virginica
-7.3,2.9,6.3,1.8,Iris-virginica
-6.7,2.5,5.8,1.8,Iris-virginica
-7.2,3.6,6.1,2.5,Iris-virginica
-6.5,3.2,5.1,2,Iris-virginica
-6.4,2.7,5.3,1.9,Iris-virginica
-6.8,3,5.5,2.1,Iris-virginica
-5.7,2.5,5,2,Iris-virginica
-5.8,2.8,5.1,2.4,Iris-virginica
-6.4,3.2,5.3,2.3,Iris-virginica
-6.5,3,5.5,1.8,Iris-virginica
-7.7,3.8,6.7,2.2,Iris-virginica
-7.7,2.6,6.9,2.3,Iris-virginica
-6,2.2,5,1.5,Iris-virginica
-6.9,3.2,5.7,2.3,Iris-virginica
-5.6,2.8,4.9,2,Iris-virginica
-7.7,2.8,6.7,2,Iris-virginica
-6.3,2.7,4.9,1.8,Iris-virginica
-6.7,3.3,5.7,2.1,Iris-virginica
diff --git a/tests/classification/conftest.py b/tests/conftest.py
similarity index 86%
rename from tests/classification/conftest.py
rename to tests/conftest.py
index 97d42378..36e5fa5b 100644
--- a/tests/classification/conftest.py
+++ b/tests/conftest.py
@@ -44,7 +44,7 @@ def pytest_configure(config):
config.addinivalue_line(
"markers",
"skip_if_rc_var_not_set(name): this mark skips the test if a certain "
- "~/.config/mednet.libs.classification.toml variable is not set",
+ "~/.config/mednet.toml variable is not set",
)
config.addinivalue_line("markers", "slow: this mark indicates slow tests")
@@ -134,14 +134,19 @@ class DatabaseCheckers:
assert len(split[k]) == lengths[k]
for s in split[k]:
- assert any([s[0].startswith(k) for k in prefixes]), (
- f"Sample with name {s[0]} does not start with any of the "
- f"prefixes in {prefixes}"
- )
- if isinstance(s[1], list):
- assert all([k in possible_labels for k in s[1]])
- else:
- assert s[1] in possible_labels
+ # check filename prefixes match, if prefixes were passed
+ if prefixes:
+ assert any([s[0].startswith(k) for k in prefixes]), (
+ f"Sample with name {s[0]} does not start with any of the "
+ f"prefixes in {prefixes}"
+ )
+
+ # check if labels match, if labels were passed
+ if possible_labels:
+ if isinstance(s[1], list):
+ assert all([k in possible_labels for k in s[1]])
+ else:
+ assert s[1] in possible_labels
@staticmethod
def check_loaded_batch(
@@ -151,6 +156,7 @@ class DatabaseCheckers:
prefixes: typing.Sequence[str],
possible_labels: typing.Sequence[int],
expected_num_labels: int,
+ expected_meta_size: int,
expected_image_shape: tuple[int, ...] | None = None,
):
"""Check the consistency of an individual (loaded) batch.
@@ -170,6 +176,9 @@ class DatabaseCheckers:
These are the list of possible labels contained in any split.
expected_num_labels
The expected number of labels each sample should have.
+ expected_meta_size
+ The expected number of elements on the meta-information dictionary
+ on every sample.
expected_image_shape
The expected shape of the image (num_channels, width, height).
"""
@@ -186,18 +195,20 @@ class DatabaseCheckers:
)
assert isinstance(batch[1], dict) # metadata
- assert len(batch[1]) == 2 # label and name
+ assert len(batch[1]) == expected_meta_size
assert "target" in batch[1]
- assert all([k in possible_labels for k in batch[1]["target"]])
+ if possible_labels:
+ assert all([k in possible_labels for k in batch[1]["target"]])
if expected_num_labels:
assert len(batch[1]["target"]) == expected_num_labels
assert "name" in batch[1]
- assert all(
- [any([k.startswith(j) for j in prefixes]) for k in batch[1]["name"]],
- )
+ if prefixes:
+ assert all(
+ [any([k.startswith(j) for j in prefixes]) for k in batch[1]["name"]],
+ )
# use the code below to view generated images
# from torchvision.transforms.functional import to_pil_image
diff --git a/tests/common/data/16bits.png b/tests/data/16bits.png
similarity index 100%
rename from tests/common/data/16bits.png
rename to tests/data/16bits.png
diff --git a/tests/common/data/iris.json b/tests/data/iris.json
similarity index 100%
rename from tests/common/data/iris.json
rename to tests/data/iris.json
diff --git a/tests/classification/data/mednet.toml b/tests/data/mednet.toml
similarity index 50%
rename from tests/classification/data/mednet.toml
rename to tests/data/mednet.toml
index 283c0998..6096cb4b 100644
--- a/tests/classification/data/mednet.toml
+++ b/tests/data/mednet.toml
@@ -1,6 +1,16 @@
[datadir]
+# classification
+indian = "/idiap/resource/database/TBXpredict"
+tbx11k = "/idiap/resource/database/tbx11k"
+
+# segmentation
+chasedb1 = "/idiap/resource/database/CHASE-DB1"
+drive = "/idiap/resource/database/DRIVE"
+hrf = "/idiap/resource/database/HRF"
+jsrt = "/idiap/resource/database/JSRT"
+stare = "/idiap/resource/database/STARE"
+
+# classification and segmentation
#montgomery = "/idiap/resource/database/MontgomeryXraySet"
montgomery = "/idiap/resource/database/montgomery-preprocessed"
shenzhen = "/idiap/resource/database/ShenzhenXraySet"
-indian = "/idiap/resource/database/TBXpredict"
-tbx11k = "/idiap/resource/database/tbx11k"
diff --git a/tests/common/data/raw_with_black_border.png b/tests/data/raw_with_black_border.png
similarity index 100%
rename from tests/common/data/raw_with_black_border.png
rename to tests/data/raw_with_black_border.png
diff --git a/tests/common/data/raw_with_elastic_deformation.png b/tests/data/raw_with_elastic_deformation.png
similarity index 100%
rename from tests/common/data/raw_with_elastic_deformation.png
rename to tests/data/raw_with_elastic_deformation.png
diff --git a/tests/common/data/raw_without_black_border.png b/tests/data/raw_without_black_border.png
similarity index 100%
rename from tests/common/data/raw_without_black_border.png
rename to tests/data/raw_without_black_border.png
diff --git a/tests/common/data/raw_without_elastic_deformation.png b/tests/data/raw_without_elastic_deformation.png
similarity index 100%
rename from tests/common/data/raw_without_elastic_deformation.png
rename to tests/data/raw_without_elastic_deformation.png
diff --git a/tests/segmentation/conftest.py b/tests/segmentation/conftest.py
deleted file mode 100644
index ce7e932f..00000000
--- a/tests/segmentation/conftest.py
+++ /dev/null
@@ -1,253 +0,0 @@
-# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
-#
-# SPDX-License-Identifier: GPL-3.0-or-later
-
-import pathlib
-import typing
-
-import numpy
-import pytest
-import torch
-from mednet.libs.common.data.split import JSONDatabaseSplit
-from mednet.libs.common.data.typing import DatabaseSplit
-
-
-@pytest.fixture
-def datadir(request) -> pathlib.Path:
- """Return the directory in which the test is sitting. Check the pytest
- documentation for more information.
-
- Parameters
- ----------
- request
- Information of the requesting test function.
-
- Returns
- -------
- pathlib.Path
- The directory in which the test is sitting.
- """
-
- return pathlib.Path(request.module.__file__).parents[0] / "data"
-
-
-def pytest_configure(config):
- """This function is run once for pytest setup.
-
- Parameters
- ----------
- config
- Configuration values. Check the pytest documentation for more
- information.
- """
-
- config.addinivalue_line(
- "markers",
- "skip_if_rc_var_not_set(name): this mark skips the test if a certain "
- "~/.config/mednet.libs.segmentation.toml variable is not set",
- )
-
- config.addinivalue_line("markers", "slow: this mark indicates slow tests")
-
-
-def pytest_runtest_setup(item):
- """This function is run for every test candidate in this directory.
-
- The test is run if this function returns ``None``. To skip a test,
- call ``pytest.skip()``, specifying a reason.
-
- Parameters
- ----------
- item
- A test invocation item. Check the pytest documentation for more
- information.
- """
-
- from mednet.libs.common.utils.rc import load_rc
-
- rc = load_rc()
-
- # iterates over all markers for the item being examined, get the first
- # argument and accumulate these names
- rc_names = [
- mark.args[0] for mark in item.iter_markers(name="skip_if_rc_var_not_set")
- ]
-
- # checks all names mentioned are set in ~/.config/mednet.libs.segmentation.toml, otherwise,
- # skip the test
- if rc_names:
- missing = [k for k in rc_names if rc.get(k) is None]
- if any(missing):
- pytest.skip(
- f"Test skipped because {', '.join(missing)} is **not** "
- f"set in ~/.config/mednet.libs.segmentation.toml",
- )
-
-
-def rc_variable_set(name):
- from mednet.libs.common.utils.rc import load_rc
-
- rc = load_rc()
- pytest.mark.skipif(
- name not in rc,
- reason=f"RC variable '{name}' is not set",
- )
-
-
-@pytest.fixture(scope="session")
-def temporary_basedir(tmp_path_factory):
- return tmp_path_factory.mktemp("test-cli")
-
-
-class DatabaseCheckers:
- """Helpers for database tests."""
-
- @staticmethod
- def check_split(
- split: DatabaseSplit,
- lengths: dict[str, int],
- prefixes: typing.Sequence[str] = None,
- ):
- """Run a simple consistency check on the data split.
-
- Parameters
- ----------
- split
- An instance of DatabaseSplit.
- lengths
- A dictionary that contains keys matching those of the split (this
- will be checked). The values of the dictionary should correspond
- to the sizes of each of the datasets in the split.
- prefixes
- Each file named in a split should start with at least one of these
- prefixes.
- """
-
- assert len(split) == len(lengths)
-
- for k in lengths.keys():
- # dataset must have been declared
- assert k in split
-
- assert len(split[k]) == lengths[k]
- for s in split[k]:
- if prefixes is not None:
- assert any([s[0].startswith(k) for k in prefixes]), (
- f"Sample with name {s[0]} does not start with any of the "
- f"prefixes in {prefixes}"
- )
-
- @staticmethod
- def check_loaded_batch(
- batch,
- batch_size: int,
- color_planes: int,
- expected_num_targets: int,
- prefixes: typing.Sequence[str] = None,
- expected_image_shape: tuple[int, ...] | None = None,
- ):
- """Check the consistency of an individual (loaded) batch.
-
- Parameters
- ----------
- batch
- The loaded batch to be checked.
- batch_size
- The mini-batch size.
- color_planes
- The number of color planes in the images.
- expected_num_targets
- The expected number of labels each sample should have.
- prefixes
- Each file named in a split should start with at least one of these
- prefixes.
- expected_image_shape
- The expected shape of the image (num_channels, width, height).
- """
-
- assert len(batch) == 2 # sample, metadata
-
- assert isinstance(batch[0], torch.Tensor)
- assert batch[0].shape[0] == batch_size # mini-batch size
- assert batch[0].shape[1] == color_planes
- assert all([isinstance(image, torch.Tensor) for image in batch[0]])
-
- if expected_image_shape:
- assert all(
- [data.shape == expected_image_shape for data in batch[0]],
- )
-
- assert isinstance(batch[1], dict) # metadata
- assert len(batch[1]) in [2, 3] # target, Optional(mask), name
-
- assert "target" in batch[1]
- assert all([isinstance(target, torch.Tensor) for target in batch[1]["target"]])
-
- if expected_num_targets:
- assert len(batch[1]["target"]) == expected_num_targets
-
- if "mask" in batch[1]:
- assert all([isinstance(mask, torch.Tensor) for mask in batch[1]["mask"]])
-
- assert "name" in batch[1]
- if prefixes is not None:
- assert all(
- [any([k.startswith(j) for j in prefixes]) for k in batch[1]["name"]],
- )
-
- @staticmethod
- def check_image_quality(
- datamodule,
- reference_histogram_file,
- compare_type="equal",
- pearson_coeff_threshold=0.005,
- ):
- ref_histogram_splits = JSONDatabaseSplit(reference_histogram_file)
-
- for split_name in ref_histogram_splits:
- raw_samples = datamodule.splits[split_name][0][0]
-
- # It is not possible to get a sample from a Dataset by name/path,
- # only by index. This creates a dict of sample name to dataset
- # index.
- raw_samples_indices = {}
- for idx, rs in enumerate(raw_samples):
- raw_samples_indices[rs[0]] = idx
-
- for ref_hist_path, ref_hist_data in ref_histogram_splits[split_name]:
- # Get index in the dataset that will return the data
- # corresponding to the specified sample name
- dataset_sample_index = raw_samples_indices[ref_hist_path]
-
- image_tensor = datamodule._datasets[split_name][ # noqa: SLF001
- dataset_sample_index
- ][0]
-
- histogram = []
- for color_channel in image_tensor:
- color_channel = numpy.multiply(
- color_channel.numpy(),
- 255,
- ).astype(int)
- histogram.extend(
- numpy.histogram(
- color_channel,
- bins=256,
- range=(0, 256),
- )[0].tolist(),
- )
-
- if compare_type == "statistical":
- # Compute pearson coefficients between histogram and
- # reference and check the similarity within a certain
- # threshold
- pearson_coeffs = numpy.corrcoef(histogram, ref_hist_data)
- assert 1 - pearson_coeff_threshold <= pearson_coeffs[0][1] <= 1
-
- else:
- assert histogram == ref_hist_data
-
-
-@pytest.fixture
-def database_checkers():
- return DatabaseCheckers
diff --git a/tests/segmentation/test_chasedb1.py b/tests/segmentation/test_chasedb1.py
index 77c8f2d6..04983002 100644
--- a/tests/segmentation/test_chasedb1.py
+++ b/tests/segmentation/test_chasedb1.py
@@ -33,6 +33,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.chasedb1", f"{split}.json"),
lengths=lengths,
+ prefixes=["Image_"],
+ possible_labels=[],
)
@@ -81,7 +83,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["Image_"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_cli_segmentation.py b/tests/segmentation/test_cli.py
similarity index 100%
rename from tests/segmentation/test_cli_segmentation.py
rename to tests/segmentation/test_cli.py
diff --git a/tests/segmentation/test_cxr8.py b/tests/segmentation/test_cxr8.py
index 1d18d53c..c097557a 100644
--- a/tests/segmentation/test_cxr8.py
+++ b/tests/segmentation/test_cxr8.py
@@ -32,6 +32,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.cxr8", f"{split}.json"),
lengths=lengths,
+ prefixes=[],
+ possible_labels=[],
)
@@ -79,7 +81,8 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
)
limit -= 1
diff --git a/tests/segmentation/test_drhagis.py b/tests/segmentation/test_drhagis.py
index 48001248..8eaf73e0 100644
--- a/tests/segmentation/test_drhagis.py
+++ b/tests/segmentation/test_drhagis.py
@@ -32,6 +32,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.drhagis", f"{split}.json"),
lengths=lengths,
+ prefixes=["Fundus_Images/"],
+ possible_labels=[],
)
@@ -79,7 +81,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["Fundus_Images/"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_drionsdb.py b/tests/segmentation/test_drionsdb.py
index 7d4e14f8..6c04191a 100644
--- a/tests/segmentation/test_drionsdb.py
+++ b/tests/segmentation/test_drionsdb.py
@@ -33,6 +33,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.drionsdb", f"{split}.json"),
lengths=lengths,
+ prefixes=["images/image_"],
+ possible_labels=[],
)
@@ -81,7 +83,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["images/image_"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_drishtigs1.py b/tests/segmentation/test_drishtigs1.py
index 0c099b55..8f704979 100644
--- a/tests/segmentation/test_drishtigs1.py
+++ b/tests/segmentation/test_drishtigs1.py
@@ -33,6 +33,11 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.drishtigs1", f"{split}.json"),
lengths=lengths,
+ prefixes=[
+ "Drishti-GS1_files/Training/Images/drishtiGS_",
+ "Drishti-GS1_files/Test/Images/drishtiGS_",
+ ],
+ possible_labels=[],
)
@@ -83,7 +88,13 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=[
+ "Drishti-GS1_files/Training/Images/drishtiGS_",
+ "Drishti-GS1_files/Test/Images/drishtiGS_",
+ ],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_drive.py b/tests/segmentation/test_drive.py
index 9d356596..33fdd65a 100644
--- a/tests/segmentation/test_drive.py
+++ b/tests/segmentation/test_drive.py
@@ -33,6 +33,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.drive", f"{split}.json"),
lengths=lengths,
+ prefixes=["training/", "test/"],
+ possible_labels=[],
)
@@ -80,7 +82,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ possible_labels=[],
+ prefixes=["training/", "test/"],
)
limit -= 1
diff --git a/tests/segmentation/test_hrf.py b/tests/segmentation/test_hrf.py
index 416fe434..5f7a29bd 100644
--- a/tests/segmentation/test_hrf.py
+++ b/tests/segmentation/test_hrf.py
@@ -32,6 +32,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.hrf", f"{split}.json"),
lengths=lengths,
+ prefixes=["images/"],
+ possible_labels=[],
)
@@ -79,7 +81,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["images/"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_iostar.py b/tests/segmentation/test_iostar.py
index e50967e0..082131f2 100644
--- a/tests/segmentation/test_iostar.py
+++ b/tests/segmentation/test_iostar.py
@@ -33,6 +33,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.iostar", f"{split}.json"),
lengths=lengths,
+ prefixes=["image/STAR "],
+ possible_labels=[],
)
@@ -78,7 +80,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["image/STAR "],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_jsrt.py b/tests/segmentation/test_jsrt.py
index c096a130..e40b6d18 100644
--- a/tests/segmentation/test_jsrt.py
+++ b/tests/segmentation/test_jsrt.py
@@ -32,6 +32,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.jsrt", f"{split}.json"),
lengths=lengths,
+ prefixes=["All247images/JPC"],
+ possible_labels=[],
)
@@ -80,7 +82,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["All247images/JPC"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_montgomery.py b/tests/segmentation/test_montgomery.py
index 97d30147..df72590c 100644
--- a/tests/segmentation/test_montgomery.py
+++ b/tests/segmentation/test_montgomery.py
@@ -32,6 +32,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.montgomery", f"{split}.json"),
lengths=lengths,
+ prefixes=["CXR_png"],
+ possible_labels=[],
)
@@ -80,8 +82,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
prefixes=["CXR_png"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_refuge.py b/tests/segmentation/test_refuge.py
index 07dedfc2..df854840 100644
--- a/tests/segmentation/test_refuge.py
+++ b/tests/segmentation/test_refuge.py
@@ -32,6 +32,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.refuge", f"{split}.json"),
lengths=lengths,
+ prefixes=["Training400/", "REFUGE-Validation400/V", "Test400/T0"],
+ possible_labels=[],
)
@@ -81,7 +83,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["Training400/", "REFUGE-Validation400/V", "Test400/T0"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_rimoner3.py b/tests/segmentation/test_rimoner3.py
index 6a2327f3..895dc3c0 100644
--- a/tests/segmentation/test_rimoner3.py
+++ b/tests/segmentation/test_rimoner3.py
@@ -35,6 +35,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.rimoner3", f"{split}.json"),
lengths=lengths,
+ prefixes=["Healthy/Stereo Images/N-", "Glaucoma and suspects/Stereo Images/"],
+ possible_labels=[],
)
@@ -85,7 +87,13 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=[
+ "Healthy/Stereo Images/N-",
+ "Glaucoma and suspects/Stereo Images/",
+ ],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_shenzhen.py b/tests/segmentation/test_shenzhen.py
index 9510d3e4..8de3a36e 100644
--- a/tests/segmentation/test_shenzhen.py
+++ b/tests/segmentation/test_shenzhen.py
@@ -32,6 +32,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.shenzhen", f"{split}.json"),
lengths=lengths,
+ prefixes=["CXR_png/CHNCXR_"],
+ possible_labels=[],
)
@@ -80,7 +82,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["CXR_png/CHNCXR_"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/segmentation/test_stare.py b/tests/segmentation/test_stare.py
index 6268ec9f..08697089 100644
--- a/tests/segmentation/test_stare.py
+++ b/tests/segmentation/test_stare.py
@@ -33,6 +33,8 @@ def test_protocol_consistency(
database_checkers.check_split(
make_split("mednet.libs.segmentation.config.data.stare", f"{split}.json"),
lengths=lengths,
+ prefixes=["stare-images/im0"],
+ possible_labels=[],
)
@@ -81,7 +83,10 @@ def test_loading(database_checkers, name: str, dataset: str):
batch,
batch_size=1,
color_planes=3,
- expected_num_targets=1,
+ expected_num_labels=1,
+ expected_meta_size=3,
+ prefixes=["stare-images/im0"],
+ possible_labels=[],
)
limit -= 1
diff --git a/tests/common/test_database_split.py b/tests/test_database_split.py
similarity index 100%
rename from tests/common/test_database_split.py
rename to tests/test_database_split.py
diff --git a/tests/common/test_image_utils.py b/tests/test_image_utils.py
similarity index 100%
rename from tests/common/test_image_utils.py
rename to tests/test_image_utils.py
diff --git a/tests/common/test_resource_monitor.py b/tests/test_resource_monitor.py
similarity index 100%
rename from tests/common/test_resource_monitor.py
rename to tests/test_resource_monitor.py
diff --git a/tests/common/test_transforms.py b/tests/test_transforms.py
similarity index 100%
rename from tests/common/test_transforms.py
rename to tests/test_transforms.py
--
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