diff --git a/doc/catalog.json b/doc/catalog.json
index b3af4a0cd42325e6ec77de90c4b521338f18d5cf..0a78c0e35d2379d76885eeeac4a064f0f393a8dc 100644
--- a/doc/catalog.json
+++ b/doc/catalog.json
@@ -1,8 +1,8 @@
{
"clapp": {
"versions": {
- "stable": "https://www.idiap.ch/software/biosignal/docs/software/clapp/stable/sphinx/",
- "latest": "https://www.idiap.ch/software/biosignal/docs/software/clapp/main/sphinx/"
+ "stable": "https://clapp.readthedocs.io/en/stable/",
+ "latest": "https://clapp.readthedocs.io/en/latest/"
},
"sources": {}
}
diff --git a/src/ptbench/data/hivtb/__init__.py b/src/ptbench/data/hivtb/__init__.py
index d743968d38fc60ee1ee3d6f9f69edc58ac9e4081..dd87f9a4555590851011d7786224a32ceb1295c7 100644
--- a/src/ptbench/data/hivtb/__init__.py
+++ b/src/ptbench/data/hivtb/__init__.py
@@ -34,12 +34,12 @@ _protocols = [
importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
]
-_root_path = load_rc().get("datadir.hivtb", os.path.realpath(os.curdir))
+_datadir = load_rc().get("datadir.hivtb", os.path.realpath(os.curdir))
def _raw_data_loader(sample):
return dict(
- data=load_pil_baw(os.path.join(_root_path, sample["data"])),
+ data=load_pil_baw(os.path.join(_datadir, sample["data"])),
label=sample["label"],
)
diff --git a/src/ptbench/data/indian/__init__.py b/src/ptbench/data/indian/__init__.py
index 80e50dbc8c66fe30e24d682019d1b5ab11251be7..dc1b9d99450f630c6a529ee4949374e3d8a50a1d 100644
--- a/src/ptbench/data/indian/__init__.py
+++ b/src/ptbench/data/indian/__init__.py
@@ -34,12 +34,12 @@ _protocols = [
importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
]
-_root_path = load_rc().get("datadir.indian", os.path.realpath(os.curdir))
+_datadir = load_rc().get("datadir.indian", os.path.realpath(os.curdir))
def _raw_data_loader(sample):
return dict(
- data=load_pil_baw(os.path.join(_root_path, sample["data"])),
+ data=load_pil_baw(os.path.join(_datadir, sample["data"])),
label=sample["label"],
)
diff --git a/src/ptbench/data/montgomery/__init__.py b/src/ptbench/data/montgomery/__init__.py
index fd65f24dbde588d9958b90a488ea56cc4111496e..719941f9206ee53236d1159ab3fabc864cd150ed 100644
--- a/src/ptbench/data/montgomery/__init__.py
+++ b/src/ptbench/data/montgomery/__init__.py
@@ -40,25 +40,19 @@ _protocols = [
importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
]
-_root_path = None
+_datadir = load_rc().get("datadir.montgomery", os.path.realpath(os.curdir))
def _raw_data_loader(sample):
- # hack to allow tests to change "datadir.montgomery"
- global _root_path
- _root_path = _root_path or load_rc().get(
- "datadir.montgomery", os.path.realpath(os.curdir)
- )
-
return dict(
- data=load_pil_baw(os.path.join(_root_path, sample["data"])), # type: ignore
+ data=load_pil_baw(os.path.join(_datadir, sample["data"])), # type: ignore
label=sample["label"],
)
def _loader(context, sample):
# "context" is ignored in this case - database is homogeneous
- # we returned delayed samples to avoid loading all images at once
+ # we return delayed samples to avoid loading all images at once
return make_delayed(sample, _raw_data_loader)
diff --git a/src/ptbench/data/nih_cxr14_re/__init__.py b/src/ptbench/data/nih_cxr14_re/__init__.py
index 5cefea42af0e86de42991e90d90908f8756437ea..8dc3f2232bbe38f9f9219045a10534124830471a 100644
--- a/src/ptbench/data/nih_cxr14_re/__init__.py
+++ b/src/ptbench/data/nih_cxr14_re/__init__.py
@@ -38,7 +38,7 @@ _protocols = [
importlib.resources.files(__name__).joinpath("cardiomegaly.json.bz2"),
]
-_root_path = load_rc().get("datadir.nih_cxr14_re", os.path.realpath(os.curdir))
+_datadir = load_rc().get("datadir.nih_cxr14_re", os.path.realpath(os.curdir))
_idiap_folders = load_rc().get("nih_cxr14_re.idiap_folder_structure", False)
@@ -51,7 +51,7 @@ def _raw_data_loader(sample):
return dict(
data=load_pil_rgb(
os.path.join(
- _root_path,
+ _datadir,
os.path.dirname(sample["data"]),
basename[:5],
basename,
@@ -61,7 +61,7 @@ def _raw_data_loader(sample):
)
else:
return dict(
- data=load_pil_rgb(os.path.join(_root_path, sample["data"])),
+ data=load_pil_rgb(os.path.join(_datadir, sample["data"])),
label=sample["label"],
)
diff --git a/src/ptbench/data/padchest/__init__.py b/src/ptbench/data/padchest/__init__.py
index eb4ccfe48030beb26aaf77d0a22c7bb5e2b3c428..e52b6dd6f44ea7077faf8214bb3319a2917f5b4e 100644
--- a/src/ptbench/data/padchest/__init__.py
+++ b/src/ptbench/data/padchest/__init__.py
@@ -236,12 +236,12 @@ _protocols = [
importlib.resources.files(__name__).joinpath("cardiomegaly_idiap.json.bz2"),
]
-_root_path = load_rc().get("datadir.padchest", os.path.realpath(os.curdir))
+_datadir = load_rc().get("datadir.padchest", os.path.realpath(os.curdir))
def _raw_data_loader(sample):
return dict(
- data=load_pil(os.path.join(_root_path, sample["data"])),
+ data=load_pil(os.path.join(_datadir, sample["data"])),
label=sample["label"],
)
diff --git a/src/ptbench/data/shenzhen/__init__.py b/src/ptbench/data/shenzhen/__init__.py
index a8bcaa3ac474f300f64a4779c92c6bb45a484cc7..c1488160f553aed8e3e0fab4c882d46d8cffc799 100644
--- a/src/ptbench/data/shenzhen/__init__.py
+++ b/src/ptbench/data/shenzhen/__init__.py
@@ -41,12 +41,12 @@ _protocols = [
importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
]
-_root_path = load_rc().get("datadir.shenzhen", os.path.realpath(os.curdir))
+_datadir = load_rc().get("datadir.shenzhen", os.path.realpath(os.curdir))
def _raw_data_loader(sample):
return dict(
- data=load_pil_baw(os.path.join(_root_path, sample["data"])),
+ data=load_pil_baw(os.path.join(_datadir, sample["data"])),
label=sample["label"],
)
diff --git a/src/ptbench/data/tbpoc/__init__.py b/src/ptbench/data/tbpoc/__init__.py
index 7ee817cfece1337913dcae2422b77113c35751c9..0eba11a3a70388210f8af110dc4f631335dc3e88 100644
--- a/src/ptbench/data/tbpoc/__init__.py
+++ b/src/ptbench/data/tbpoc/__init__.py
@@ -34,12 +34,12 @@ _protocols = [
importlib.resources.files(__name__).joinpath("fold_9.json.bz2"),
]
-_root_path = load_rc().get("datadir.tbpoc", os.path.realpath(os.curdir))
+_datadir = load_rc().get("datadir.tbpoc", os.path.realpath(os.curdir))
def _raw_data_loader(sample):
return dict(
- data=load_pil_baw(os.path.join(_root_path, sample["data"])),
+ data=load_pil_baw(os.path.join(_datadir, sample["data"])),
label=sample["label"],
)
diff --git a/tests/conftest.py b/tests/conftest.py
index f1aa8c926811e1d627dbc052b6f48f76721cfb76..86a852b5064c6491daf116467cb5aea99aa60256 100644
--- a/tests/conftest.py
+++ b/tests/conftest.py
@@ -2,9 +2,12 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
+import os
import pathlib
+import typing
import pytest
+import tomli_w
@pytest.fixture
@@ -67,30 +70,56 @@ def temporary_basedir(tmp_path_factory):
return tmp_path_factory.mktemp("test-cli")
-@pytest.fixture(scope="session")
-def montgomery_datadir(tmp_path_factory) -> pathlib.Path:
- from ptbench.utils.rc import load_rc
-
- database_dir = load_rc().get("datadir.montgomery")
- if database_dir is not None:
- return pathlib.Path(database_dir)
-
- # else, we must extract the LFS component
- archive = (
- pathlib.Path(__file__).parents[0] / "data" / "lfs" / "test-database.zip"
- )
- assert archive.exists(), (
- f"Neither datadir.montgomery is set on the global configuration, "
- f"(typically ~/.config/ptbench.toml), or it is possible to detect "
- f"the presence of {archive}' (did you git submodule init --update "
- f"this submodule?)"
- )
-
- database_dir = tmp_path_factory.mktemp("montgomery_datadir")
+@pytest.fixture(scope="session", autouse=True)
+def ensure_montgomery(
+ tmp_path_factory,
+) -> typing.Generator[None, None, None]:
+ """A pytest fixture that ensures that datadir.montgomery is always
+ available."""
+ import tempfile
import zipfile
- with zipfile.ZipFile(archive) as zf:
- zf.extractall(database_dir)
+ from ptbench.utils.rc import load_rc
+
+ rc = load_rc()
- return database_dir
+ database_dir = rc.get("datadir.montgomery")
+ if database_dir is not None:
+ # if the user downloaded it, use that copy
+ yield
+
+ else:
+ # else, we must extract the LFS component (we are likely on the CI)
+ archive = (
+ pathlib.Path(__file__).parents[0]
+ / "data"
+ / "lfs"
+ / "test-database.zip"
+ )
+ assert archive.exists(), (
+ f"Neither datadir.montgomery is set on the global configuration, "
+ f"(typically ~/.config/ptbench.toml), or it is possible to detect "
+ f"the presence of {archive}' (did you git submodule init --update "
+ f"this submodule?)"
+ )
+
+ database_dir = tmp_path_factory.mktemp("montgomery_datadir")
+ rc.setdefault("datadir.montgomery", str(database_dir))
+
+ with zipfile.ZipFile(archive) as zf:
+ zf.extractall(database_dir)
+
+ with tempfile.TemporaryDirectory() as tmpdir:
+ config_filename = "ptbench.toml"
+ with open(os.path.join(tmpdir, config_filename), "wb") as f:
+ tomli_w.dump(rc.data, f)
+ f.flush()
+
+ old_config_home = os.environ.get("XDG_CONFIG_HOME")
+ os.environ["XDG_CONFIG_HOME"] = tmpdir
+ yield
+ if old_config_home is None:
+ del os.environ["XDG_CONFIG_HOME"]
+ else:
+ os.environ["XDG_CONFIG_HOME"] = old_config_home
diff --git a/tests/test_cli.py b/tests/test_cli.py
index 6507e3d09e2959bbf952a01a44a9a65b4147b413..3ed16d0843697ebf88a160b1be7622c8da7ce504 100644
--- a/tests/test_cli.py
+++ b/tests/test_cli.py
@@ -7,29 +7,10 @@
import contextlib
import os
import re
-import tempfile
-
-import tomli_w
from click.testing import CliRunner
-@contextlib.contextmanager
-def rc_context(**new_config):
- with tempfile.TemporaryDirectory() as tmpdir:
- config_filename = "ptbench.toml"
- with open(os.path.join(tmpdir, config_filename), "wb") as f:
- tomli_w.dump(new_config, f)
- f.flush()
- old_config_home = os.environ.get("XDG_CONFIG_HOME")
- os.environ["XDG_CONFIG_HOME"] = tmpdir
- yield
- if old_config_home is None:
- del os.environ["XDG_CONFIG_HOME"]
- else:
- os.environ["XDG_CONFIG_HOME"] = old_config_home
-
-
@contextlib.contextmanager
def stdout_logging():
# copy logging messages to std out
@@ -187,261 +168,236 @@ def test_compare_help():
_check_help(compare)
-def test_train_pasa_montgomery(temporary_basedir, montgomery_datadir):
- # Temporarily modifies Montgomery datadir if need be
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.scripts.train import train
-
- runner = CliRunner()
-
- with stdout_logging() as buf:
- output_folder = str(temporary_basedir / "results")
- result = runner.invoke(
- train,
- [
- "pasa",
- "montgomery",
- "-vv",
- "--epochs=1",
- "--batch-size=1",
- "--normalization=current",
- f"--output-folder={output_folder}",
- ],
- )
- _assert_exit_0(result)
+def test_train_pasa_montgomery(temporary_basedir):
+ from ptbench.scripts.train import train
- assert os.path.exists(
- os.path.join(output_folder, "model_final_epoch.pth")
- )
- assert os.path.exists(
- os.path.join(output_folder, "model_lowest_valid_loss.pth")
- )
- assert os.path.exists(
- os.path.join(output_folder, "last_checkpoint")
- )
- assert os.path.exists(os.path.join(output_folder, "constants.csv"))
- assert os.path.exists(os.path.join(output_folder, "trainlog.csv"))
- assert os.path.exists(
- os.path.join(output_folder, "model_summary.txt")
- )
+ runner = CliRunner()
- keywords = {
- r"^Found \(dedicated\) '__train__' set for training$": 1,
- r"^Found \(dedicated\) '__valid__' set for validation$": 1,
- r"^Continuing from epoch 0$": 1,
- r"^Saving model summary at.*$": 1,
- r"^Model has.*$": 1,
- r"^Saving checkpoint": 2,
- r"^Total training time:": 1,
- r"^Z-normalization with mean": 1,
- }
- buf.seek(0)
- logging_output = buf.read()
-
- for k, v in keywords.items():
- assert _str_counter(k, logging_output) == v, (
- f"Count for string '{k}' appeared "
- f"({_str_counter(k, logging_output)}) "
- f"instead of the expected {v}:\nOutput:\n{logging_output}"
- )
-
-
-def test_predict_pasa_montgomery(
- temporary_basedir, montgomery_datadir, datadir
-):
- # Temporarily modifies Montgomery datadir if need be
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.scripts.predict import predict
-
- runner = CliRunner()
-
- with stdout_logging() as buf:
- output_folder = str(temporary_basedir / "predictions")
- result = runner.invoke(
- predict,
- [
- "pasa",
- "montgomery",
- "-vv",
- "--batch-size=1",
- "--relevance-analysis",
- f"--weight={str(datadir / 'lfs' / 'models' / 'pasa.pth')}",
- f"--output-folder={output_folder}",
- ],
- )
- _assert_exit_0(result)
+ with stdout_logging() as buf:
+ output_folder = str(temporary_basedir / "results")
+ result = runner.invoke(
+ train,
+ [
+ "pasa",
+ "montgomery",
+ "-vv",
+ "--epochs=1",
+ "--batch-size=1",
+ "--normalization=current",
+ f"--output-folder={output_folder}",
+ ],
+ )
+ _assert_exit_0(result)
- # check predictions are there
- predictions_file1 = os.path.join(
- output_folder, "train/predictions.csv"
- )
- predictions_file2 = os.path.join(
- output_folder, "validation/predictions.csv"
- )
- predictions_file3 = os.path.join(
- output_folder, "test/predictions.csv"
- )
- assert os.path.exists(predictions_file1)
- assert os.path.exists(predictions_file2)
- assert os.path.exists(predictions_file3)
-
- keywords = {
- r"^Loading checkpoint from.*$": 1,
- r"^Total time:.*$": 3,
- r"^Relevance analysis.*$": 3,
- }
- buf.seek(0)
- logging_output = buf.read()
-
- for k, v in keywords.items():
- assert _str_counter(k, logging_output) == v, (
- f"Count for string '{k}' appeared "
- f"({_str_counter(k, logging_output)}) "
- f"instead of the expected {v}:\nOutput:\n{logging_output}"
- )
-
-
-def test_predtojson(datadir, temporary_basedir, montgomery_datadir):
- # Temporarily modify Montgomery datadir if need be
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.scripts.predtojson import predtojson
-
- runner = CliRunner()
-
- with stdout_logging() as buf:
- predictions = str(datadir / "test_predictions.csv")
- output_folder = str(temporary_basedir / "pred_to_json")
- result = runner.invoke(
- predtojson,
- [
- "-vv",
- "train",
- f"{predictions}",
- "test",
- f"{predictions}",
- f"--output-folder={output_folder}",
- ],
- )
- _assert_exit_0(result)
-
- # check json file is there
- assert os.path.exists(os.path.join(output_folder, "dataset.json"))
-
- keywords = {
- f"Output folder: {output_folder}": 1,
- r"Saving JSON file...": 1,
- r"^Loading predictions from.*$": 2,
- }
- buf.seek(0)
- logging_output = buf.read()
-
- for k, v in keywords.items():
- assert _str_counter(k, logging_output) == v, (
- f"Count for string '{k}' appeared "
- f"({_str_counter(k, logging_output)}) "
- f"instead of the expected {v}:\nOutput:\n{logging_output}"
- )
-
-
-def test_evaluate_pasa_montgomery(temporary_basedir, montgomery_datadir):
- # Temporarily modify Montgomery datadir if need be
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.scripts.evaluate import evaluate
-
- runner = CliRunner()
-
- with stdout_logging() as buf:
- prediction_folder = str(temporary_basedir / "predictions")
- output_folder = str(temporary_basedir / "evaluations")
- result = runner.invoke(
- evaluate,
- [
- "-vv",
- "montgomery",
- f"--predictions-folder={prediction_folder}",
- f"--output-folder={output_folder}",
- "--threshold=train",
- "--steps=2000",
- ],
+ assert os.path.exists(
+ os.path.join(output_folder, "model_final_epoch.pth")
+ )
+ assert os.path.exists(
+ os.path.join(output_folder, "model_lowest_valid_loss.pth")
+ )
+ assert os.path.exists(os.path.join(output_folder, "last_checkpoint"))
+ assert os.path.exists(os.path.join(output_folder, "constants.csv"))
+ assert os.path.exists(os.path.join(output_folder, "trainlog.csv"))
+ assert os.path.exists(os.path.join(output_folder, "model_summary.txt"))
+
+ keywords = {
+ r"^Found \(dedicated\) '__train__' set for training$": 1,
+ r"^Found \(dedicated\) '__valid__' set for validation$": 1,
+ r"^Continuing from epoch 0$": 1,
+ r"^Saving model summary at.*$": 1,
+ r"^Model has.*$": 1,
+ r"^Saving checkpoint": 2,
+ r"^Total training time:": 1,
+ r"^Z-normalization with mean": 1,
+ }
+ buf.seek(0)
+ logging_output = buf.read()
+
+ for k, v in keywords.items():
+ assert _str_counter(k, logging_output) == v, (
+ f"Count for string '{k}' appeared "
+ f"({_str_counter(k, logging_output)}) "
+ f"instead of the expected {v}:\nOutput:\n{logging_output}"
)
- _assert_exit_0(result)
- # check evaluations are there
- assert os.path.exists(os.path.join(output_folder, "test.csv"))
- assert os.path.exists(os.path.join(output_folder, "train.csv"))
- assert os.path.exists(
- os.path.join(output_folder, "test_score_table.pdf")
+
+def test_predict_pasa_montgomery(temporary_basedir, datadir):
+ from ptbench.scripts.predict import predict
+
+ runner = CliRunner()
+
+ with stdout_logging() as buf:
+ output_folder = str(temporary_basedir / "predictions")
+ result = runner.invoke(
+ predict,
+ [
+ "pasa",
+ "montgomery",
+ "-vv",
+ "--batch-size=1",
+ "--relevance-analysis",
+ f"--weight={str(datadir / 'lfs' / 'models' / 'pasa.pth')}",
+ f"--output-folder={output_folder}",
+ ],
+ )
+ _assert_exit_0(result)
+
+ # check predictions are there
+ predictions_file1 = os.path.join(output_folder, "train/predictions.csv")
+ predictions_file2 = os.path.join(
+ output_folder, "validation/predictions.csv"
+ )
+ predictions_file3 = os.path.join(output_folder, "test/predictions.csv")
+ assert os.path.exists(predictions_file1)
+ assert os.path.exists(predictions_file2)
+ assert os.path.exists(predictions_file3)
+
+ keywords = {
+ r"^Loading checkpoint from.*$": 1,
+ r"^Total time:.*$": 3,
+ r"^Relevance analysis.*$": 3,
+ }
+ buf.seek(0)
+ logging_output = buf.read()
+
+ for k, v in keywords.items():
+ assert _str_counter(k, logging_output) == v, (
+ f"Count for string '{k}' appeared "
+ f"({_str_counter(k, logging_output)}) "
+ f"instead of the expected {v}:\nOutput:\n{logging_output}"
)
- assert os.path.exists(
- os.path.join(output_folder, "train_score_table.pdf")
+
+
+def test_predtojson(datadir, temporary_basedir):
+ from ptbench.scripts.predtojson import predtojson
+
+ runner = CliRunner()
+
+ with stdout_logging() as buf:
+ predictions = str(datadir / "test_predictions.csv")
+ output_folder = str(temporary_basedir / "pred_to_json")
+ result = runner.invoke(
+ predtojson,
+ [
+ "-vv",
+ "train",
+ f"{predictions}",
+ "test",
+ f"{predictions}",
+ f"--output-folder={output_folder}",
+ ],
+ )
+ _assert_exit_0(result)
+
+ # check json file is there
+ assert os.path.exists(os.path.join(output_folder, "dataset.json"))
+
+ keywords = {
+ f"Output folder: {output_folder}": 1,
+ r"Saving JSON file...": 1,
+ r"^Loading predictions from.*$": 2,
+ }
+ buf.seek(0)
+ logging_output = buf.read()
+
+ for k, v in keywords.items():
+ assert _str_counter(k, logging_output) == v, (
+ f"Count for string '{k}' appeared "
+ f"({_str_counter(k, logging_output)}) "
+ f"instead of the expected {v}:\nOutput:\n{logging_output}"
)
- keywords = {
- r"^Skipping dataset '__train__'": 1,
- r"^Evaluating threshold on.*$": 1,
- r"^Maximum F1-score of.*$": 4,
- r"^Set --f1_threshold=.*$": 1,
- r"^Set --eer_threshold=.*$": 1,
- }
- buf.seek(0)
- logging_output = buf.read()
-
- for k, v in keywords.items():
- assert _str_counter(k, logging_output) == v, (
- f"Count for string '{k}' appeared "
- f"({_str_counter(k, logging_output)}) "
- f"instead of the expected {v}:\nOutput:\n{logging_output}"
- )
-
-
-def test_compare_pasa_montgomery(temporary_basedir, montgomery_datadir):
- # Temporarily modify Montgomery datadir if need be
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.scripts.compare import compare
-
- runner = CliRunner()
-
- with stdout_logging() as buf:
- predictions_folder = str(temporary_basedir / "predictions")
- output_folder = str(temporary_basedir / "comparisons")
- result = runner.invoke(
- compare,
- [
- "-vv",
- "train",
- f"{predictions_folder}/train/predictions.csv",
- "test",
- f"{predictions_folder}/test/predictions.csv",
- f"--output-figure={output_folder}/compare.pdf",
- f"--output-table={output_folder}/table.txt",
- "--threshold=0.5",
- ],
+
+def test_evaluate_pasa_montgomery(temporary_basedir):
+ from ptbench.scripts.evaluate import evaluate
+
+ runner = CliRunner()
+
+ with stdout_logging() as buf:
+ prediction_folder = str(temporary_basedir / "predictions")
+ output_folder = str(temporary_basedir / "evaluations")
+ result = runner.invoke(
+ evaluate,
+ [
+ "-vv",
+ "montgomery",
+ f"--predictions-folder={prediction_folder}",
+ f"--output-folder={output_folder}",
+ "--threshold=train",
+ "--steps=2000",
+ ],
+ )
+ _assert_exit_0(result)
+
+ # check evaluations are there
+ assert os.path.exists(os.path.join(output_folder, "test.csv"))
+ assert os.path.exists(os.path.join(output_folder, "train.csv"))
+ assert os.path.exists(
+ os.path.join(output_folder, "test_score_table.pdf")
+ )
+ assert os.path.exists(
+ os.path.join(output_folder, "train_score_table.pdf")
+ )
+
+ keywords = {
+ r"^Skipping dataset '__train__'": 1,
+ r"^Evaluating threshold on.*$": 1,
+ r"^Maximum F1-score of.*$": 4,
+ r"^Set --f1_threshold=.*$": 1,
+ r"^Set --eer_threshold=.*$": 1,
+ }
+ buf.seek(0)
+ logging_output = buf.read()
+
+ for k, v in keywords.items():
+ assert _str_counter(k, logging_output) == v, (
+ f"Count for string '{k}' appeared "
+ f"({_str_counter(k, logging_output)}) "
+ f"instead of the expected {v}:\nOutput:\n{logging_output}"
)
- _assert_exit_0(result)
- # check comparisons are there
- assert os.path.exists(os.path.join(output_folder, "compare.pdf"))
- assert os.path.exists(os.path.join(output_folder, "table.txt"))
- keywords = {
- r"^Dataset '\*': threshold =.*$": 1,
- r"^Loading predictions from.*$": 2,
- r"^Tabulating performance summary...": 1,
- }
- buf.seek(0)
- logging_output = buf.read()
+def test_compare_pasa_montgomery(temporary_basedir):
+ from ptbench.scripts.compare import compare
+
+ runner = CliRunner()
+
+ with stdout_logging() as buf:
+ predictions_folder = str(temporary_basedir / "predictions")
+ output_folder = str(temporary_basedir / "comparisons")
+ result = runner.invoke(
+ compare,
+ [
+ "-vv",
+ "train",
+ f"{predictions_folder}/train/predictions.csv",
+ "test",
+ f"{predictions_folder}/test/predictions.csv",
+ f"--output-figure={output_folder}/compare.pdf",
+ f"--output-table={output_folder}/table.txt",
+ "--threshold=0.5",
+ ],
+ )
+ _assert_exit_0(result)
+
+ # check comparisons are there
+ assert os.path.exists(os.path.join(output_folder, "compare.pdf"))
+ assert os.path.exists(os.path.join(output_folder, "table.txt"))
+
+ keywords = {
+ r"^Dataset '\*': threshold =.*$": 1,
+ r"^Loading predictions from.*$": 2,
+ r"^Tabulating performance summary...": 1,
+ }
+ buf.seek(0)
+ logging_output = buf.read()
- for k, v in keywords.items():
- assert _str_counter(k, logging_output) == v, (
- f"Count for string '{k}' appeared "
- f"({_str_counter(k, logging_output)}) "
- f"instead of the expected {v}:\nOutput:\n{logging_output}"
- )
+ for k, v in keywords.items():
+ assert _str_counter(k, logging_output) == v, (
+ f"Count for string '{k}' appeared "
+ f"({_str_counter(k, logging_output)}) "
+ f"instead of the expected {v}:\nOutput:\n{logging_output}"
+ )
def test_train_signstotb_montgomery_rs(temporary_basedir, datadir):
@@ -638,115 +594,108 @@ def test_predict_logreg_montgomery_rs(temporary_basedir, datadir):
)
-def test_aggregpred(temporary_basedir, montgomery_datadir):
- # Temporarily modify Montgomery datadir if need be
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.scripts.aggregpred import aggregpred
+def test_aggregpred(temporary_basedir):
+ from ptbench.scripts.aggregpred import aggregpred
- runner = CliRunner()
+ runner = CliRunner()
- with stdout_logging() as buf:
- predictions = str(
- temporary_basedir / "predictions" / "train" / "predictions.csv"
- )
- output_folder = str(temporary_basedir / "aggregpred")
- result = runner.invoke(
- aggregpred,
- [
- "-vv",
- f"{predictions}",
- f"{predictions}",
- f"--output-folder={output_folder}",
- ],
- )
- _assert_exit_0(result)
+ with stdout_logging() as buf:
+ predictions = str(
+ temporary_basedir / "predictions" / "train" / "predictions.csv"
+ )
+ output_folder = str(temporary_basedir / "aggregpred")
+ result = runner.invoke(
+ aggregpred,
+ [
+ "-vv",
+ f"{predictions}",
+ f"{predictions}",
+ f"--output-folder={output_folder}",
+ ],
+ )
+ _assert_exit_0(result)
- # check csv file is there
- assert os.path.exists(os.path.join(output_folder, "aggregpred.csv"))
+ # check csv file is there
+ assert os.path.exists(os.path.join(output_folder, "aggregpred.csv"))
- keywords = {
- f"Output folder: {output_folder}": 1,
- r"Saving aggregated CSV file...": 1,
- r"^Loading predictions from.*$": 2,
- }
- buf.seek(0)
- logging_output = buf.read()
+ keywords = {
+ f"Output folder: {output_folder}": 1,
+ r"Saving aggregated CSV file...": 1,
+ r"^Loading predictions from.*$": 2,
+ }
+ buf.seek(0)
+ logging_output = buf.read()
- for k, v in keywords.items():
- assert _str_counter(k, logging_output) == v, (
- f"Count for string '{k}' appeared "
- f"({_str_counter(k, logging_output)}) "
- f"instead of the expected {v}:\nOutput:\n{logging_output}"
- )
+ for k, v in keywords.items():
+ assert _str_counter(k, logging_output) == v, (
+ f"Count for string '{k}' appeared "
+ f"({_str_counter(k, logging_output)}) "
+ f"instead of the expected {v}:\nOutput:\n{logging_output}"
+ )
# Not enough RAM available to do this test
-# def test_predict_densenetrs_montgomery(temporary_basedir, montgomery_datadir, datadir):
-
-# # Temporarily modify Montgomery datadir if need be
-# new_value = {"datadir.montgomery": str(montgomery_datadir)}
-# with rc_context(**new_value):
-
-# from ptbench.scripts.predict import predict
-
-# runner = CliRunner()
-
-# with stdout_logging() as buf:
-
-# output_folder = str(temporary_basedir / "predictions")
-# result = runner.invoke(
-# predict,
-# [
-# "densenet_rs",
-# "montgomery_f0_rgb",
-# "-vv",
-# "--batch-size=1",
-# f"--weight={str(datadir / 'lfs' / 'models' / 'densenetrs.pth')}",
-# f"--output-folder={output_folder}",
-# "--grad-cams"
-# ],
-# )
-# _assert_exit_0(result)
-
-# # check predictions are there
-# predictions_file1 = os.path.join(output_folder, "train/predictions.csv")
-# predictions_file2 = os.path.join(output_folder, "validation/predictions.csv")
-# predictions_file3 = os.path.join(output_folder, "test/predictions.csv")
-# assert os.path.exists(predictions_file1)
-# assert os.path.exists(predictions_file2)
-# assert os.path.exists(predictions_file3)
-# # check some grad cams are there
-# cam1 = os.path.join(output_folder, "train/cams/MCUCXR_0002_0_cam.png")
-# cam2 = os.path.join(output_folder, "train/cams/MCUCXR_0126_1_cam.png")
-# cam3 = os.path.join(output_folder, "train/cams/MCUCXR_0275_1_cam.png")
-# cam4 = os.path.join(output_folder, "validation/cams/MCUCXR_0399_1_cam.png")
-# cam5 = os.path.join(output_folder, "validation/cams/MCUCXR_0113_1_cam.png")
-# cam6 = os.path.join(output_folder, "validation/cams/MCUCXR_0013_0_cam.png")
-# cam7 = os.path.join(output_folder, "test/cams/MCUCXR_0027_0_cam.png")
-# cam8 = os.path.join(output_folder, "test/cams/MCUCXR_0094_0_cam.png")
-# cam9 = os.path.join(output_folder, "test/cams/MCUCXR_0375_1_cam.png")
-# assert os.path.exists(cam1)
-# assert os.path.exists(cam2)
-# assert os.path.exists(cam3)
-# assert os.path.exists(cam4)
-# assert os.path.exists(cam5)
-# assert os.path.exists(cam6)
-# assert os.path.exists(cam7)
-# assert os.path.exists(cam8)
-# assert os.path.exists(cam9)
-
-# keywords = {
-# r"^Loading checkpoint from.*$": 1,
-# r"^Total time:.*$": 3,
-# r"^Grad cams folder:.*$": 3,
-# }
-# buf.seek(0)
-# logging_output = buf.read()
-
-# for k, v in keywords.items():
-# assert _str_counter(k, logging_output) == v, (
-# f"Count for string '{k}' appeared "
-# f"({_str_counter(k, logging_output)}) "
-# f"instead of the expected {v}:\nOutput:\n{logging_output}"
-# )
+# def test_predict_densenetrs_montgomery(temporary_basedir, datadir):
+
+# from ptbench.scripts.predict import predict
+
+# runner = CliRunner()
+
+# with stdout_logging() as buf:
+
+# output_folder = str(temporary_basedir / "predictions")
+# result = runner.invoke(
+# predict,
+# [
+# "densenet_rs",
+# "montgomery_f0_rgb",
+# "-vv",
+# "--batch-size=1",
+# f"--weight={str(datadir / 'lfs' / 'models' / 'densenetrs.pth')}",
+# f"--output-folder={output_folder}",
+# "--grad-cams"
+# ],
+# )
+# _assert_exit_0(result)
+
+# # check predictions are there
+# predictions_file1 = os.path.join(output_folder, "train/predictions.csv")
+# predictions_file2 = os.path.join(output_folder, "validation/predictions.csv")
+# predictions_file3 = os.path.join(output_folder, "test/predictions.csv")
+# assert os.path.exists(predictions_file1)
+# assert os.path.exists(predictions_file2)
+# assert os.path.exists(predictions_file3)
+# # check some grad cams are there
+# cam1 = os.path.join(output_folder, "train/cams/MCUCXR_0002_0_cam.png")
+# cam2 = os.path.join(output_folder, "train/cams/MCUCXR_0126_1_cam.png")
+# cam3 = os.path.join(output_folder, "train/cams/MCUCXR_0275_1_cam.png")
+# cam4 = os.path.join(output_folder, "validation/cams/MCUCXR_0399_1_cam.png")
+# cam5 = os.path.join(output_folder, "validation/cams/MCUCXR_0113_1_cam.png")
+# cam6 = os.path.join(output_folder, "validation/cams/MCUCXR_0013_0_cam.png")
+# cam7 = os.path.join(output_folder, "test/cams/MCUCXR_0027_0_cam.png")
+# cam8 = os.path.join(output_folder, "test/cams/MCUCXR_0094_0_cam.png")
+# cam9 = os.path.join(output_folder, "test/cams/MCUCXR_0375_1_cam.png")
+# assert os.path.exists(cam1)
+# assert os.path.exists(cam2)
+# assert os.path.exists(cam3)
+# assert os.path.exists(cam4)
+# assert os.path.exists(cam5)
+# assert os.path.exists(cam6)
+# assert os.path.exists(cam7)
+# assert os.path.exists(cam8)
+# assert os.path.exists(cam9)
+
+# keywords = {
+# r"^Loading checkpoint from.*$": 1,
+# r"^Total time:.*$": 3,
+# r"^Grad cams folder:.*$": 3,
+# }
+# buf.seek(0)
+# logging_output = buf.read()
+
+# for k, v in keywords.items():
+# assert _str_counter(k, logging_output) == v, (
+# f"Count for string '{k}' appeared "
+# f"({_str_counter(k, logging_output)}) "
+# f"instead of the expected {v}:\nOutput:\n{logging_output}"
+# )
diff --git a/tests/test_config.py b/tests/test_config.py
index 6493892baea443210cc8c24410b07ffdb753d2d1..91f52a5a970675adf80d898f17ca71c25c08fcba 100644
--- a/tests/test_config.py
+++ b/tests/test_config.py
@@ -2,13 +2,8 @@
#
# SPDX-License-Identifier: GPL-3.0-or-later
-import contextlib
-import os
-import tempfile
-
import numpy as np
import pytest
-import tomli_w
import torch
from torch.utils.data import ConcatDataset
@@ -21,23 +16,6 @@ from ptbench.configs.datasets import get_positive_weights, get_samples_weights
N = 10
-@contextlib.contextmanager
-def rc_context(**new_config):
- with tempfile.TemporaryDirectory() as tmpdir:
- config_filename = "ptbench.toml"
- with open(os.path.join(tmpdir, config_filename), "wb") as f:
- tomli_w.dump(new_config, f)
- f.flush()
- old_config_home = os.environ.get("XDG_CONFIG_HOME")
- os.environ["XDG_CONFIG_HOME"] = tmpdir
- yield
- if old_config_home is None:
- del os.environ["XDG_CONFIG_HOME"]
- else:
- os.environ["XDG_CONFIG_HOME"] = old_config_home
-
-
-@pytest.mark.skip_if_rc_var_not_set("datadir.montgomery")
def test_montgomery():
def _check_subset(samples, size):
assert len(samples) == size
@@ -60,20 +38,15 @@ def test_montgomery():
_check_subset(dataset["test"], 28)
-def test_get_samples_weights(montgomery_datadir):
- # Temporarily modify Montgomery datadir
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.configs.datasets.montgomery.default import dataset
+def test_get_samples_weights():
+ from ptbench.configs.datasets.montgomery.default import dataset
- train_samples_weights = get_samples_weights(
- dataset["__train__"]
- ).numpy()
+ train_samples_weights = get_samples_weights(dataset["__train__"]).numpy()
- unique, counts = np.unique(train_samples_weights, return_counts=True)
+ unique, counts = np.unique(train_samples_weights, return_counts=True)
- np.testing.assert_equal(counts, np.array([51, 37]))
- np.testing.assert_equal(unique, np.array(1 / counts, dtype=np.float32))
+ np.testing.assert_equal(counts, np.array([51, 37]))
+ np.testing.assert_equal(unique, np.array(1 / counts, dtype=np.float32))
@pytest.mark.skip_if_rc_var_not_set("datadir.nih_cxr14_re")
@@ -87,22 +60,17 @@ def test_get_samples_weights_multi():
)
-def test_get_samples_weights_concat(montgomery_datadir):
- # Temporarily modify Montgomery datadir
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.configs.datasets.montgomery.default import dataset
+def test_get_samples_weights_concat():
+ from ptbench.configs.datasets.montgomery.default import dataset
- train_dataset = ConcatDataset(
- (dataset["__train__"], dataset["__train__"])
- )
+ train_dataset = ConcatDataset((dataset["__train__"], dataset["__train__"]))
- train_samples_weights = get_samples_weights(train_dataset).numpy()
+ train_samples_weights = get_samples_weights(train_dataset).numpy()
- unique, counts = np.unique(train_samples_weights, return_counts=True)
+ unique, counts = np.unique(train_samples_weights, return_counts=True)
- np.testing.assert_equal(counts, np.array([102, 74]))
- np.testing.assert_equal(unique, np.array(2 / counts, dtype=np.float32))
+ np.testing.assert_equal(counts, np.array([102, 74]))
+ np.testing.assert_equal(unique, np.array(2 / counts, dtype=np.float32))
@pytest.mark.skip_if_rc_var_not_set("datadir.nih_cxr14_re")
@@ -127,19 +95,14 @@ def test_get_samples_weights_multi_concat():
np.testing.assert_equal(train_samples_weights, ref_samples_weights)
-def test_get_positive_weights(montgomery_datadir):
- # Temporarily modify Montgomery datadir
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.configs.datasets.montgomery.default import dataset
+def test_get_positive_weights():
+ from ptbench.configs.datasets.montgomery.default import dataset
- train_positive_weights = get_positive_weights(
- dataset["__train__"]
- ).numpy()
+ train_positive_weights = get_positive_weights(dataset["__train__"]).numpy()
- np.testing.assert_equal(
- train_positive_weights, np.array([51.0 / 37.0], dtype=np.float32)
- )
+ np.testing.assert_equal(
+ train_positive_weights, np.array([51.0 / 37.0], dtype=np.float32)
+ )
@pytest.mark.skip_if_rc_var_not_set("datadir.nih_cxr14_re")
@@ -204,21 +167,16 @@ def test_get_positive_weights_multi():
)
-def test_get_positive_weights_concat(montgomery_datadir):
- # Temporarily modify Montgomery datadir
- new_value = {"datadir.montgomery": str(montgomery_datadir)}
- with rc_context(**new_value):
- from ptbench.configs.datasets.montgomery.default import dataset
+def test_get_positive_weights_concat():
+ from ptbench.configs.datasets.montgomery.default import dataset
- train_dataset = ConcatDataset(
- (dataset["__train__"], dataset["__train__"])
- )
+ train_dataset = ConcatDataset((dataset["__train__"], dataset["__train__"]))
- train_positive_weights = get_positive_weights(train_dataset).numpy()
+ train_positive_weights = get_positive_weights(train_dataset).numpy()
- np.testing.assert_equal(
- train_positive_weights, np.array([51.0 / 37.0], dtype=np.float32)
- )
+ np.testing.assert_equal(
+ train_positive_weights, np.array([51.0 / 37.0], dtype=np.float32)
+ )
@pytest.mark.skip_if_rc_var_not_set("datadir.nih_cxr14_re")