add vista2d (#618)

Fixes # .

### Description
A few sentences describing the changes proposed in this pull request.

### Status
**Ready/Work in progress/Hold**

### Please ensure all the checkboxes:
<!--- Put an `x` in all the boxes that apply, and remove the not
applicable items -->
- [x] Codeformat tests passed locally by running `./runtests.sh
--codeformat`.
- [ ] In-line docstrings updated.
- [ ] Update `version` and `changelog` in `metadata.json` if changing an
existing bundle.
- [ ] Please ensure the naming rules in config files meet our
requirements (please refer to: `CONTRIBUTING.md`).
- [ ] Ensure versions of packages such as `monai`, `pytorch` and `numpy`
are correct in `metadata.json`.
- [ ] Descriptions should be consistent with the content, such as
`eval_metrics` of the provided weights and TorchScript modules.
- [ ] Files larger than 25MB are excluded and replaced by providing
download links in `large_file.yml`.
- [ ] Avoid using path that contains personal information within config
files (such as use `/home/your_name/` for `"bundle_root"`).

---------

Signed-off-by: Yiheng Wang <[email protected]>
Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: yiheng-wang-nv

ci/bundle_custom_data.py

@@ -39,6 +39,7 @@
     "brats_mri_axial_slices_generative_diffusion",
     "vista3d",
     "maisi_ct_generative",
+    "vista2d",
 ]
 
 # This list is used for our CI tests to determine whether a bundle needs to be tested after downloading

ci/unit_tests/test_vista2d.py

@@ -0,0 +1,125 @@
+# 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.
+
+import os
+import shutil
+import sys
+import tempfile
+import unittest
+
+import matplotlib.pyplot as plt
+import numpy as np
+from monai.bundle import create_workflow
+from parameterized import parameterized
+from utils import check_workflow
+
+TEST_CASE_TRAIN = [{"bundle_root": "models/vista2d", "mode": "train", "train#trainer#max_epochs": 1}]
+
+TEST_CASE_INFER = [{"bundle_root": "models/vista2d", "mode": "infer"}]
+
+
+def test_order(test_name1, test_name2):
+    def get_order(name):
+        if "train" in name:
+            return 1
+        if "infer" in name:
+            return 2
+        return 3
+
+    return get_order(test_name1) - get_order(test_name2)
+
+
+class TestVista2d(unittest.TestCase):
+    def setUp(self):
+        self.dataset_dir = tempfile.mkdtemp()
+        self.tmp_output_dir = os.path.join(self.dataset_dir, "output")
+        os.makedirs(self.tmp_output_dir, exist_ok=True)
+        self.dataset_size = 5
+        input_shape = (256, 256)
+        for s in range(self.dataset_size):
+            test_image = np.random.randint(low=0, high=2, size=input_shape).astype(np.int8)
+            test_label = np.random.randint(low=0, high=2, size=input_shape).astype(np.int8)
+            image_filename = os.path.join(self.dataset_dir, f"image_{s}.png")
+            label_filename = os.path.join(self.dataset_dir, f"label_{s}.png")
+            plt.imsave(image_filename, test_image, cmap="gray")
+            plt.imsave(label_filename, test_label, cmap="gray")
+
+        self.bundle_root = "models/vista2d"
+        sys.path = [self.bundle_root] + sys.path
+        from scripts.workflow import VistaCell
+
+        self.workflow = VistaCell
+
+    def tearDown(self):
+        shutil.rmtree(self.dataset_dir)
+
+    @parameterized.expand([TEST_CASE_INFER])
+    def test_infer_config(self, override):
+        # update override with dataset dir
+        override["dataset#data"] = [
+            {
+                "image": os.path.join(self.dataset_dir, f"image_{s}.png"),
+                "label": os.path.join(self.dataset_dir, f"label_{s}.png"),
+            }
+            for s in range(self.dataset_size)
+        ]
+        override["output_dir"] = self.tmp_output_dir
+        workflow = create_workflow(
+            workflow_name=self.workflow,
+            config_file=os.path.join(self.bundle_root, "configs/hyper_parameters.yaml"),
+            meta_file=os.path.join(self.bundle_root, "configs/metadata.json"),
+            **override,
+        )
+
+        # check_properties=False, need to add monai service properties later
+        check_workflow(workflow, check_properties=False)
+
+        expected_output_file = os.path.join(self.tmp_output_dir, f"image_{self.dataset_size-1}.tif")
+        self.assertTrue(os.path.isfile(expected_output_file))
+
+    @parameterized.expand([TEST_CASE_TRAIN])
+    def test_train_config(self, override):
+        # update override with dataset dir
+        override["train#dataset#data"] = [
+            {
+                "image": os.path.join(self.dataset_dir, f"image_{s}.png"),
+                "label": os.path.join(self.dataset_dir, f"label_{s}.png"),
+            }
+            for s in range(self.dataset_size)
+        ]
+        override["dataset#data"] = override["train#dataset#data"]
+
+        workflow = create_workflow(
+            workflow_name=self.workflow,
+            config_file=os.path.join(self.bundle_root, "configs/hyper_parameters.yaml"),
+            meta_file=os.path.join(self.bundle_root, "configs/metadata.json"),
+            **override,
+        )
+
+        # check_properties=False, need to add monai service properties later
+        check_workflow(workflow, check_properties=False)
+
+        # follow up to use trained weights and test eval
+        override["mode"] = "eval"
+        override["pretrained_ckpt_name"] = "model.pt"
+        workflow = create_workflow(
+            workflow_name=self.workflow,
+            config_file=os.path.join(self.bundle_root, "configs/hyper_parameters.yaml"),
+            meta_file=os.path.join(self.bundle_root, "configs/metadata.json"),
+            **override,
+        )
+        check_workflow(workflow, check_properties=False)
+
+
+if __name__ == "__main__":
+    loader = unittest.TestLoader()
+    loader.sortTestMethodsUsing = test_order
+    unittest.main(testLoader=loader)

ci/unit_tests/test_vista2d_dist.py

@@ -0,0 +1,70 @@
+# 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.
+
+import os
+import shutil
+import sys
+import tempfile
+import unittest
+
+import matplotlib.pyplot as plt
+import numpy as np
+import torch
+from parameterized import parameterized
+from utils import export_config_and_run_mgpu_cmd
+
+TEST_CASE_TRAIN_MGPU = [{"bundle_root": "models/vista2d", "workflow_type": "train", "train#trainer#max_epochs": 2}]
+
+
+class TestVista2d(unittest.TestCase):
+    def setUp(self):
+        self.dataset_dir = tempfile.mkdtemp()
+        self.dataset_size = 5
+        input_shape = (256, 256)
+        for s in range(self.dataset_size):
+            test_image = np.random.randint(low=0, high=2, size=input_shape).astype(np.int8)
+            test_label = np.random.randint(low=0, high=2, size=input_shape).astype(np.int8)
+            image_filename = os.path.join(self.dataset_dir, f"image_{s}.png")
+            label_filename = os.path.join(self.dataset_dir, f"label_{s}.png")
+            plt.imsave(image_filename, test_image, cmap="gray")
+            plt.imsave(label_filename, test_label, cmap="gray")
+
+        self.bundle_root = "models/vista2d"
+        sys.path = [self.bundle_root] + sys.path
+
+    def tearDown(self):
+        shutil.rmtree(self.dataset_dir)
+
+    @parameterized.expand([TEST_CASE_TRAIN_MGPU])
+    def test_train_mgpu_config(self, override):
+        override["train#dataset#data"] = [
+            {
+                "image": os.path.join(self.dataset_dir, f"image_{s}.png"),
+                "label": os.path.join(self.dataset_dir, f"label_{s}.png"),
+            }
+            for s in range(self.dataset_size)
+        ]
+        override["dataset#data"] = override["train#dataset#data"]
+
+        output_path = os.path.join(self.bundle_root, "configs/train_override.json")
+        n_gpu = torch.cuda.device_count()
+        export_config_and_run_mgpu_cmd(
+            config_file=os.path.join(self.bundle_root, "configs/hyper_parameters.yaml"),
+            meta_file=os.path.join(self.bundle_root, "configs/metadata.json"),
+            custom_workflow="scripts.workflow.VistaCell",
+            override_dict=override,
+            output_path=output_path,
+            ngpu=n_gpu,
+        )
+
+
+if __name__ == "__main__":
+    unittest.main()

ci/unit_tests/utils.py

@@ -23,7 +23,7 @@ def export_overrided_config(config_file, override_dict, output_path):
     ConfigParser.export_config_file(parser.config, output_path, indent=4)
 
 
-def produce_mgpu_cmd(config_file, meta_file, logging_file, nnodes=1, nproc_per_node=2):
+def produce_mgpu_cmd(config_file, meta_file, logging_file=None, nnodes=1, nproc_per_node=2):
     cmd = [
         "torchrun",
         "--standalone",
@@ -34,20 +34,43 @@ def produce_mgpu_cmd(config_file, meta_file, logging_file, nnodes=1, nproc_per_n
         "run",
         "--config_file",
         config_file,
-        "--logging_file",
-        logging_file,
         "--meta_file",
         meta_file,
     ]
+    if logging_file is not None:
+        cmd.extend(["--logging_file", logging_file])
+    return cmd
+
+
+def produce_custom_workflow_mgpu_cmd(
+    custom_workflow, config_file, meta_file, logging_file=None, nnodes=1, nproc_per_node=2
+):
+    cmd = [
+        "torchrun",
+        "--standalone",
+        f"--nnodes={nnodes}",
+        f"--nproc_per_node={nproc_per_node}",
+        "-m",
+        "monai.bundle",
+        "run_workflow",
+        custom_workflow,
+        "--config_file",
+        config_file,
+        "--meta_file",
+        meta_file,
+    ]
+    if logging_file is not None:
+        cmd.extend(["--logging_file", logging_file])
     return cmd
 
 
 def export_config_and_run_mgpu_cmd(
     config_file,
     meta_file,
-    logging_file,
     override_dict,
     output_path,
+    custom_workflow=None,
+    logging_file=None,
     workflow_type="train",
     nnode=1,
     ngpu=2,
@@ -68,9 +91,19 @@ def export_config_and_run_mgpu_cmd(
         check_result = engine.check_properties()
         if check_result is not None and len(check_result) > 0:
             raise ValueError(f"check properties for overrided mgpu configs failed: {check_result}")
-    cmd = produce_mgpu_cmd(
-        config_file=output_path, meta_file=meta_file, logging_file=logging_file, nnodes=nnode, nproc_per_node=ngpu
-    )
+    if custom_workflow is None:
+        cmd = produce_mgpu_cmd(
+            config_file=output_path, meta_file=meta_file, logging_file=logging_file, nnodes=nnode, nproc_per_node=ngpu
+        )
+    else:
+        cmd = produce_custom_workflow_mgpu_cmd(
+            custom_workflow=custom_workflow,
+            config_file=output_path,
+            meta_file=meta_file,
+            logging_file=logging_file,
+            nnodes=nnode,
+            nproc_per_node=ngpu,
+        )
     env = os.environ.copy()
     # ensure customized library can be loaded in subprocess
     env["PYTHONPATH"] = override_dict.get("bundle_root", ".")