From 513bed9df5b13eed930d3d49592a26d0cdb54084 Mon Sep 17 00:00:00 2001
From: Andre Anjos <andre.dos.anjos@gmail.com>
Date: Wed, 2 Aug 2023 21:02:33 +0200
Subject: [PATCH] [tests.test_nih_cxr14] Adapt to new datamodule syntax
---
tests/test_nih_cxr14.py | 135 +++++++++++++------------
tests/{test_pc.py => test_padchest.py} | 0
2 files changed, 70 insertions(+), 65 deletions(-)
rename tests/{test_pc.py => test_padchest.py} (100%)
diff --git a/tests/test_nih_cxr14.py b/tests/test_nih_cxr14.py
index d7cc149a..242ac7e9 100644
--- a/tests/test_nih_cxr14.py
+++ b/tests/test_nih_cxr14.py
@@ -1,72 +1,77 @@
# SPDX-FileCopyrightText: Copyright © 2023 Idiap Research Institute <contact@idiap.ch>
#
# SPDX-License-Identifier: GPL-3.0-or-later
-"""Tests for NIH CXR14 dataset."""
+"""Tests for NIH CXR-14 dataset."""
-import pytest
-
-
-@pytest.mark.skip(reason="Test need to be updated")
-def test_protocol_consistency():
- from ptbench.data.nih_cxr14_re import dataset
-
- # Default protocol
- subset = dataset.subsets("default")
- assert len(subset) == 3
-
- assert "train" in subset
- assert len(subset["train"]) == 98637
- for s in subset["train"]:
- assert s.key.startswith("images/000")
-
- assert "validation" in subset
- assert len(subset["validation"]) == 6350
- for s in subset["validation"]:
- assert s.key.startswith("images/000")
-
- assert "test" in subset
- assert len(subset["test"]) == 4054
- for s in subset["test"]:
- assert s.key.startswith("images/000")
-
- # Check labels
- for s in subset["train"]:
- for element in list(set(s.label)):
- assert element in [0.0, 1.0]
+import importlib
- for s in subset["validation"]:
- for element in list(set(s.label)):
- assert element in [0.0, 1.0]
-
- for s in subset["test"]:
- for element in list(set(s.label)):
- assert element in [0.0, 1.0]
-
-
-@pytest.mark.skip(reason="Test need to be updated")
-@pytest.mark.skip_if_rc_var_not_set("datadir.nih_cxr14_re")
-def test_loading():
- from ptbench.data.nih_cxr14_re import dataset
-
- def _check_size(size):
- if size == (1024, 1024):
- return True
- return False
-
- def _check_sample(s):
- data = s.data
- assert isinstance(data, dict)
- assert len(data) == 2
-
- assert "data" in data
- assert _check_size(data["data"].size) # Check size
- assert data["data"].mode == "RGB" # Check colors
-
- assert "label" in data
- assert len(data["label"]) == 14 # Check labels
+import pytest
- limit = 30 # use this to limit testing to first images only, else None
- subset = dataset.subsets("default")
- for s in subset["train"][:limit]:
- _check_sample(s)
+def id_function(val):
+ if isinstance(val, dict):
+ return str(val)
+ return repr(val)
+
+
+@pytest.mark.parametrize(
+ "split,lenghts",
+ [
+ ("default", dict(train=98637, validation=6350, test=4054)),
+ ],
+ ids=id_function, # just changes how pytest prints it
+)
+def test_protocol_consistency(
+ database_checkers, split: str, lenghts: dict[str, int]
+):
+ from ptbench.data.nih_cxr14.datamodule import make_split
+
+ database_checkers.check_split(
+ make_split(f"{split}.json.bz2"),
+ lengths=lenghts,
+ prefixes=("images/000",),
+ possible_labels=(0, 1),
+ )
+
+
+@pytest.mark.skip_if_rc_var_not_set("datadir.nih_cxr14")
+@pytest.mark.parametrize(
+ "dataset",
+ [
+ "train",
+ "validation",
+ "test",
+ ],
+)
+@pytest.mark.parametrize(
+ "name",
+ [
+ "default",
+ ],
+)
+def test_loading(database_checkers, name: str, dataset: str):
+ datamodule = importlib.import_module(
+ f".{name}", "ptbench.data.nih_cxr14"
+ ).datamodule
+
+ datamodule.model_transforms = [] # should be done before setup()
+ datamodule.setup("predict") # sets up all datasets
+
+ loader = datamodule.predict_dataloader()[dataset]
+
+ limit = 3 # limit load checking
+ for batch in loader:
+ if limit == 0:
+ break
+ database_checkers.check_loaded_batch(
+ batch,
+ batch_size=1,
+ color_planes=1,
+ prefixes=("images/000",),
+ possible_labels=(0, 1),
+ )
+ limit -= 1
+
+
+# TODO: check size 1024x1024
+# TODO: check there are 14 binary labels (0, 1)
diff --git a/tests/test_pc.py b/tests/test_padchest.py
similarity index 100%
rename from tests/test_pc.py
rename to tests/test_padchest.py
--
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