monai-weekly 1.5.dev2506__py3-none-any.whl → 1.5.dev2507__py3-none-any.whl

tests/bundle/test_bundle_trt_export.py

@@ -0,0 +1,147 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import json
+import os
+import tempfile
+import unittest
+from pathlib import Path
+
+from parameterized import parameterized
+
+from monai.bundle import ConfigParser
+from monai.data import load_net_with_metadata
+from monai.networks import save_state
+from monai.utils import optional_import
+from tests.test_utils import (
+    SkipIfBeforeComputeCapabilityVersion,
+    command_line_tests,
+    skip_if_no_cuda,
+    skip_if_quick,
+    skip_if_windows,
+)
+
+_, has_torchtrt = optional_import(
+    "torch_tensorrt",
+    version="1.4.0",
+    descriptor="Torch-TRT is not installed. Are you sure you have a Torch-TensorRT compilation?",
+)
+_, has_tensorrt = optional_import(
+    "tensorrt", descriptor="TensorRT is not installed. Are you sure you have a TensorRT compilation?"
+)
+
+_, has_onnx = optional_import("onnx", descriptor="Onnx is not installed. Will not test the onnx option.")
+
+TEST_CASE_1 = ["fp32", [], []]
+
+TEST_CASE_2 = ["fp16", [], []]
+
+TEST_CASE_3 = ["fp32", [1, 1, 96, 96, 96], [1, 4, 8]]
+
+TEST_CASE_4 = ["fp16", [1, 1, 96, 96, 96], [1, 4, 8]]
+
+
+@skip_if_windows
+@skip_if_no_cuda
+@skip_if_quick
+@SkipIfBeforeComputeCapabilityVersion((7, 5))
+class TestTRTExport(unittest.TestCase):
+    def setUp(self):
+        self.device = os.environ.get("CUDA_VISIBLE_DEVICES")
+        if not self.device:
+            os.environ["CUDA_VISIBLE_DEVICES"] = "0"  # default
+
+    def tearDown(self):
+        if self.device is not None:
+            os.environ["CUDA_VISIBLE_DEVICES"] = self.device
+        else:
+            del os.environ["CUDA_VISIBLE_DEVICES"]  # previously unset
+
+    @parameterized.expand([TEST_CASE_1, TEST_CASE_2, TEST_CASE_3, TEST_CASE_4])
+    @unittest.skipUnless(has_torchtrt and has_tensorrt, "Torch-TensorRT is required for conversion!")
+    def test_trt_export(self, convert_precision, input_shape, dynamic_batch):
+        tests_dir = Path(__file__).resolve().parent
+        meta_file = os.path.join(tests_dir, "testing_data", "metadata.json")
+        config_file = os.path.join(tests_dir, "testing_data", "inference.json")
+        with tempfile.TemporaryDirectory() as tempdir:
+            def_args = {"meta_file": "will be replaced by `meta_file` arg"}
+            def_args_file = os.path.join(tempdir, "def_args.yaml")
+
+            ckpt_file = os.path.join(tempdir, "model.pt")
+            ts_file = os.path.join(tempdir, f"model_trt_{convert_precision}.ts")
+
+            parser = ConfigParser()
+            parser.export_config_file(config=def_args, filepath=def_args_file)
+            parser.read_config(config_file)
+            net = parser.get_parsed_content("network_def")
+            save_state(src=net, path=ckpt_file)
+
+            cmd = ["python", "-m", "monai.bundle", "trt_export", "network_def", "--filepath", ts_file]
+            cmd += ["--meta_file", meta_file, "--config_file", f"['{config_file}','{def_args_file}']", "--ckpt_file"]
+            cmd += [ckpt_file, "--args_file", def_args_file, "--precision", convert_precision]
+            if input_shape:
+                cmd += ["--input_shape", str(input_shape)]
+            if dynamic_batch:
+                cmd += ["--dynamic_batch", str(dynamic_batch)]
+            command_line_tests(cmd)
+            self.assertTrue(os.path.exists(ts_file))
+
+            _, metadata, extra_files = load_net_with_metadata(
+                ts_file, more_extra_files=["inference.json", "def_args.json"]
+            )
+            self.assertIn("schema", metadata)
+            self.assertIn("meta_file", json.loads(extra_files["def_args.json"]))
+            self.assertIn("network_def", json.loads(extra_files["inference.json"]))
+
+    @parameterized.expand([TEST_CASE_3, TEST_CASE_4])
+    @unittest.skipUnless(
+        has_onnx and has_torchtrt and has_tensorrt, "Onnx and TensorRT are required for onnx-trt conversion!"
+    )
+    def test_onnx_trt_export(self, convert_precision, input_shape, dynamic_batch):
+        tests_dir = Path(__file__).resolve().parent
+        meta_file = os.path.join(tests_dir, "testing_data", "metadata.json")
+        config_file = os.path.join(tests_dir, "testing_data", "inference.json")
+        with tempfile.TemporaryDirectory() as tempdir:
+            def_args = {"meta_file": "will be replaced by `meta_file` arg"}
+            def_args_file = os.path.join(tempdir, "def_args.yaml")
+
+            ckpt_file = os.path.join(tempdir, "model.pt")
+            ts_file = os.path.join(tempdir, f"model_trt_{convert_precision}.ts")
+
+            parser = ConfigParser()
+            parser.export_config_file(config=def_args, filepath=def_args_file)
+            parser.read_config(config_file)
+            net = parser.get_parsed_content("network_def")
+            save_state(src=net, path=ckpt_file)
+
+            cmd = ["python", "-m", "monai.bundle", "trt_export", "network_def", "--filepath", ts_file]
+            cmd += ["--meta_file", meta_file, "--config_file", f"['{config_file}','{def_args_file}']", "--ckpt_file"]
+            cmd += [ckpt_file, "--args_file", def_args_file, "--precision", convert_precision]
+            cmd += ["--use_onnx", "True"]
+            if input_shape:
+                cmd += ["--input_shape", str(input_shape)]
+            if dynamic_batch:
+                cmd += ["--dynamic_batch", str(dynamic_batch)]
+            command_line_tests(cmd)
+            self.assertTrue(os.path.exists(ts_file))
+
+            _, metadata, extra_files = load_net_with_metadata(
+                ts_file, more_extra_files=["inference.json", "def_args.json"]
+            )
+            self.assertIn("schema", metadata)
+            self.assertIn("meta_file", json.loads(extra_files["def_args.json"]))
+            self.assertIn("network_def", json.loads(extra_files["inference.json"]))
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/bundle/test_bundle_utils.py

@@ -0,0 +1,149 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import os
+import shutil
+import tempfile
+import unittest
+
+import torch
+
+from monai.bundle import update_kwargs
+from monai.bundle.utils import load_bundle_config
+from monai.networks.nets import UNet
+from monai.utils import pprint_edges
+from tests.test_utils import command_line_tests, skip_if_windows
+
+metadata = """
+{
+    "test_value": 1,
+    "test_list": [2,3]
+}
+"""
+
+test_json = """
+{
+    "test_dict": {
+        "a": 3,
+        "b": "c"
+    },
+    "network_def": {
+        "_target_": "UNet",
+        "spatial_dims": 2,
+        "in_channels": 1,
+        "out_channels": 1,
+        "channels": [4,8],
+        "strides": [2]
+    }
+}
+"""
+
+
+@skip_if_windows
+class TestLoadBundleConfig(unittest.TestCase):
+    def setUp(self):
+        self.bundle_dir = tempfile.TemporaryDirectory()
+        self.dir_name = os.path.join(self.bundle_dir.name, "TestBundle")
+        self.configs_name = os.path.join(self.dir_name, "configs")
+        self.models_name = os.path.join(self.dir_name, "models")
+        self.metadata_name = os.path.join(self.configs_name, "metadata.json")
+        self.test_name = os.path.join(self.configs_name, "test.json")
+        self.modelpt_name = os.path.join(self.models_name, "model.pt")
+
+        self.zip_file = os.path.join(self.bundle_dir.name, "TestBundle.zip")
+        self.ts_file = os.path.join(self.bundle_dir.name, "TestBundle.ts")
+
+        # create the directories for the bundle
+        os.mkdir(self.dir_name)
+        os.mkdir(self.configs_name)
+        os.mkdir(self.models_name)
+
+        # fill bundle configs
+
+        with open(self.metadata_name, "w") as o:
+            o.write(metadata)
+
+        with open(self.test_name, "w") as o:
+            o.write(test_json)
+
+        # save network
+        net = UNet(2, 1, 1, [4, 8], [2])
+        torch.save(net.state_dict(), self.modelpt_name)
+
+    def tearDown(self):
+        self.bundle_dir.cleanup()
+
+    def test_load_config_dir(self):
+        p = load_bundle_config(self.dir_name, "test.json")
+
+        self.assertEqual(p["_meta_"]["test_value"], 1)
+
+        self.assertEqual(p["test_dict"]["b"], "c")
+
+    def test_load_config_zip(self):
+        # create a zip of the bundle
+        shutil.make_archive(self.zip_file[:-4], "zip", self.bundle_dir.name)
+
+        p = load_bundle_config(self.zip_file, "test.json")
+
+        self.assertEqual(p["_meta_"]["test_value"], 1)
+
+        self.assertEqual(p["test_dict"]["b"], "c")
+
+    def test_run(self):
+        command_line_tests(
+            [
+                "python",
+                "-m",
+                "monai.bundle",
+                "run",
+                "test",
+                "--test",
+                "$print('hello world')",
+                "--config_file",
+                self.test_name,
+                "--meta_file",
+                self.metadata_name,
+            ]
+        )
+
+    def test_load_config_ts(self):
+        # create a Torchscript zip of the bundle
+        cmd = ["python", "-m", "monai.bundle", "ckpt_export", "network_def", "--filepath", self.ts_file]
+        cmd += ["--meta_file", self.metadata_name]
+        cmd += ["--config_file", self.test_name]
+        cmd += ["--ckpt_file", self.modelpt_name]
+
+        command_line_tests(cmd)
+
+        p = load_bundle_config(self.ts_file, "test.json")
+
+        self.assertEqual(p["_meta_"]["test_value"], 1)
+
+        self.assertEqual(p["test_dict"]["b"], "c")
+
+
+class TestPPrintEdges(unittest.TestCase):
+    def test_str(self):
+        self.assertEqual(pprint_edges("", 0), "''")
+        self.assertEqual(pprint_edges({"a": 1, "b": 2}, 0), "{'a': 1, 'b': 2}")
+        self.assertEqual(
+            pprint_edges([{"a": 1, "b": 2}] * 20, 1),
+            "[{'a': 1, 'b': 2},\n\n ... omitted 18 line(s)\n\n {'a': 1, 'b': 2}]",
+        )
+        self.assertEqual(pprint_edges([{"a": 1, "b": 2}] * 8, 4), pprint_edges([{"a": 1, "b": 2}] * 8, 3))
+        self.assertEqual(update_kwargs({"a": 1}, a=2, b=3), {"a": 2, "b": 3})
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/bundle/test_bundle_verify_metadata.py

@@ -0,0 +1,66 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import json
+import os
+import tempfile
+import unittest
+from pathlib import Path
+
+from parameterized import parameterized
+
+from monai.bundle import ConfigParser, verify_metadata
+from tests.test_utils import command_line_tests, download_url_or_skip_test, skip_if_windows, testing_data_config
+
+TESTS_DIR = Path(__file__).parents[1]
+SCHEMA_FILE = os.path.join(TESTS_DIR, "testing_data", "schema.json")
+
+TEST_CASE_1 = [os.path.join(TESTS_DIR, "testing_data", "metadata.json"), SCHEMA_FILE]
+
+
+@skip_if_windows
+class TestVerifyMetaData(unittest.TestCase):
+    def setUp(self):
+        self.config = testing_data_config("configs", "test_meta_file")
+        download_url_or_skip_test(
+            url=self.config["url"],
+            filepath=SCHEMA_FILE,
+            hash_val=self.config.get("hash_val"),
+            hash_type=self.config.get("hash_type", "sha256"),
+        )
+
+    @parameterized.expand([TEST_CASE_1])
+    def test_verify(self, meta_file, schema_file):
+        with tempfile.TemporaryDirectory() as tempdir:
+            def_args = {"meta_file": "will be replaced by `meta_file` arg"}
+            def_args_file = os.path.join(tempdir, "def_args.json")
+            ConfigParser.export_config_file(config=def_args, filepath=def_args_file)
+
+            cmd = ["coverage", "run", "-m", "monai.bundle", "verify_metadata", "--meta_file", meta_file]
+            cmd += ["--filepath", schema_file, "--hash_val", self.config["hash_val"], "--args_file", def_args_file]
+            command_line_tests(cmd)
+
+    def test_verify_error(self):
+        with tempfile.TemporaryDirectory() as tempdir:
+            filepath = os.path.join(tempdir, "schema.json")
+            metafile = os.path.join(tempdir, "metadata.json")
+            meta_dict = {"schema": self.config["url"], "wrong_meta": "wrong content"}
+            with open(metafile, "w") as f:
+                json.dump(meta_dict, f)
+
+            with self.assertRaises(ValueError):
+                verify_metadata(meta_file=metafile, filepath=filepath)
+
+
+if __name__ == "__main__":
+    unittest.main()

tests/bundle/test_bundle_verify_net.py

@@ -0,0 +1,76 @@
+# Copyright (c) MONAI Consortium
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#     http://www.apache.org/licenses/LICENSE-2.0
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from __future__ import annotations
+
+import os
+import tempfile
+import unittest
+from pathlib import Path
+
+from parameterized import parameterized
+
+from monai.bundle import ConfigParser, verify_net_in_out
+from tests.test_utils import command_line_tests, skip_if_no_cuda, skip_if_windows
+
+TESTS_PATH = Path(__file__).parents[1].as_posix()
+
+TEST_CASE_1 = [
+    os.path.join(TESTS_PATH, "testing_data", "metadata.json"),
+    os.path.join(TESTS_PATH, "testing_data", "inference.json"),
+]
+
+
+@skip_if_windows
+class TestVerifyNetwork(unittest.TestCase):
+    @parameterized.expand([TEST_CASE_1])
+    def test_verify(self, meta_file, config_file):
+        with tempfile.TemporaryDirectory() as tempdir:
+            def_args = {"meta_file": "will be replaced by `meta_file` arg", "p": 2}
+            def_args_file = os.path.join(tempdir, "def_args.json")
+            ConfigParser.export_config_file(config=def_args, filepath=def_args_file)
+
+            cmd = ["coverage", "run", "-m", "monai.bundle", "verify_net_in_out", "network_def", "--meta_file"]
+            cmd += [meta_file, "--config_file", config_file, "-n", "4", "--any", "16", "--args_file", def_args_file]
+            cmd += ["--device", "cpu", "--_meta_::network_data_format::inputs#image#spatial_shape", "[16,'*','2**p*n']"]
+            command_line_tests(cmd)
+
+    @parameterized.expand([TEST_CASE_1])
+    @skip_if_no_cuda
+    def test_verify_fp16(self, meta_file, config_file):
+        with tempfile.TemporaryDirectory() as tempdir:
+            def_args = {"meta_file": "will be replaced by `meta_file` arg", "p": 2}
+            def_args_file = os.path.join(tempdir, "def_args.json")
+            ConfigParser.export_config_file(config=def_args, filepath=def_args_file)
+
+            cmd = ["coverage", "run", "-m", "monai.bundle", "verify_net_in_out", "network_def", "--meta_file"]
+            cmd += [meta_file, "--config_file", config_file, "-n", "4", "--any", "16", "--args_file", def_args_file]
+            cmd += ["--device", "cuda", "--_meta_#network_data_format#inputs#image#spatial_shape", "[16,'*','2**p*n']"]
+            cmd += ["--_meta_#network_data_format#inputs#image#dtype", "float16"]
+            cmd += ["--_meta_::network_data_format::outputs::pred::dtype", "float16"]
+            command_line_tests(cmd)
+
+    @parameterized.expand([TEST_CASE_1])
+    @skip_if_no_cuda
+    def test_verify_fp16_extra_forward_args(self, meta_file, config_file):
+        verify_net_in_out(
+            net_id="network_def",
+            meta_file=meta_file,
+            config_file=config_file,
+            n=4,
+            any=16,
+            extra_forward_args={"extra_arg1": 1, "extra_arg2": 2},
+            **{"network_def#_target_": "tests.testing_data.bundle_test_network.TestMultiInputUNet"},
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()