From 3be3f85119d4180eef88d8945f3d1554129ac9aa Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Wed, 28 Feb 2024 19:03:20 +0800
Subject: [PATCH 1/9] remove `self._set_prop`

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 bundle/python_bundle_workflow/scripts/inference.py | 6 +-----
 bundle/python_bundle_workflow/scripts/train.py     | 6 +-----
 2 files changed, 2 insertions(+), 10 deletions(-)

diff --git a/bundle/python_bundle_workflow/scripts/inference.py b/bundle/python_bundle_workflow/scripts/inference.py
index 24810a0dfb..fab321b009 100644
--- a/bundle/python_bundle_workflow/scripts/inference.py
+++ b/bundle/python_bundle_workflow/scripts/inference.py
@@ -63,7 +63,6 @@ def __init__(self, dataset_dir: str = "."):
             nib.save(n, os.path.join(dataset_dir, f"seg{i:d}.nii.gz"))
 
         self._props = {}
-        self._set_props = {}
         self.dataset_dir = dataset_dir
 
     def initialize(self):
@@ -76,7 +75,7 @@ def finalize(self):
         pass
 
     def _set_property(self, name, property, value):
-        self._set_props[name] = value
+        self._props[name] = value
 
     def _get_property(self, name, property):
         """
@@ -90,9 +89,6 @@ def _get_property(self, name, property):
         value = None
         if name in self._props:
             value = self._props[name]
-        elif name in self._set_props:
-            value = self._set_props[name]
-            self._props[name] = value
         else:
             try:
                 value = getattr(self, f"get_{name}")()
diff --git a/bundle/python_bundle_workflow/scripts/train.py b/bundle/python_bundle_workflow/scripts/train.py
index ccd409e969..56fc36056a 100644
--- a/bundle/python_bundle_workflow/scripts/train.py
+++ b/bundle/python_bundle_workflow/scripts/train.py
@@ -72,7 +72,6 @@ def __init__(self, dataset_dir: str = "."):
 
         # define buckets to store the generated properties and set properties
         self._props = {}
-        self._set_props = {}
         self.dataset_dir = dataset_dir
 
         # besides the predefined properties, this bundle workflow can also provide `network`, `loss`, `optimizer`
@@ -91,7 +90,7 @@ def finalize(self):
         set_determinism(None)
 
     def _set_property(self, name, property, value):
-        self._set_props[name] = value
+        self._props[name] = value
 
     def _get_property(self, name, property):
         """
@@ -105,9 +104,6 @@ def _get_property(self, name, property):
         value = None
         if name in self._props:
             value = self._props[name]
-        elif name in self._set_props:
-            value = self._set_props[name]
-            self._props[name] = value
         else:
             try:
                 value = getattr(self, f"get_{name}")()

From 013a8bfef3a63bb110ffcb61bbf227a33777d180 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Thu, 29 Feb 2024 10:26:59 +0800
Subject: [PATCH 2/9] remove self._probs in initialize

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 bundle/python_bundle_workflow/scripts/inference.py | 2 +-
 bundle/python_bundle_workflow/scripts/train.py     | 1 -
 2 files changed, 1 insertion(+), 2 deletions(-)

diff --git a/bundle/python_bundle_workflow/scripts/inference.py b/bundle/python_bundle_workflow/scripts/inference.py
index fab321b009..19f9aa21ee 100644
--- a/bundle/python_bundle_workflow/scripts/inference.py
+++ b/bundle/python_bundle_workflow/scripts/inference.py
@@ -66,7 +66,7 @@ def __init__(self, dataset_dir: str = "."):
         self.dataset_dir = dataset_dir
 
     def initialize(self):
-        self.props = {}
+        pass
 
     def run(self):
         self.evaluator.run()
diff --git a/bundle/python_bundle_workflow/scripts/train.py b/bundle/python_bundle_workflow/scripts/train.py
index 56fc36056a..bc8a47afa6 100644
--- a/bundle/python_bundle_workflow/scripts/train.py
+++ b/bundle/python_bundle_workflow/scripts/train.py
@@ -81,7 +81,6 @@ def __init__(self, dataset_dir: str = "."):
 
     def initialize(self):
         set_determinism(0)
-        self.props = {}
 
     def run(self):
         self.trainer.run()

From cf7448877d53908cb1949a3f9c179039902e0c2a Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 1 Mar 2024 10:44:40 +0800
Subject: [PATCH 3/9] Revert "remove `self._set_prop`"

This reverts commit 3be3f85119d4180eef88d8945f3d1554129ac9aa.
---
 bundle/python_bundle_workflow/scripts/inference.py | 6 +++++-
 bundle/python_bundle_workflow/scripts/train.py     | 6 +++++-
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/bundle/python_bundle_workflow/scripts/inference.py b/bundle/python_bundle_workflow/scripts/inference.py
index 19f9aa21ee..06ce1aff5f 100644
--- a/bundle/python_bundle_workflow/scripts/inference.py
+++ b/bundle/python_bundle_workflow/scripts/inference.py
@@ -63,6 +63,7 @@ def __init__(self, dataset_dir: str = "."):
             nib.save(n, os.path.join(dataset_dir, f"seg{i:d}.nii.gz"))
 
         self._props = {}
+        self._set_props = {}
         self.dataset_dir = dataset_dir
 
     def initialize(self):
@@ -75,7 +76,7 @@ def finalize(self):
         pass
 
     def _set_property(self, name, property, value):
-        self._props[name] = value
+        self._set_props[name] = value
 
     def _get_property(self, name, property):
         """
@@ -89,6 +90,9 @@ def _get_property(self, name, property):
         value = None
         if name in self._props:
             value = self._props[name]
+        elif name in self._set_props:
+            value = self._set_props[name]
+            self._props[name] = value
         else:
             try:
                 value = getattr(self, f"get_{name}")()
diff --git a/bundle/python_bundle_workflow/scripts/train.py b/bundle/python_bundle_workflow/scripts/train.py
index bc8a47afa6..16fa85b324 100644
--- a/bundle/python_bundle_workflow/scripts/train.py
+++ b/bundle/python_bundle_workflow/scripts/train.py
@@ -72,6 +72,7 @@ def __init__(self, dataset_dir: str = "."):
 
         # define buckets to store the generated properties and set properties
         self._props = {}
+        self._set_props = {}
         self.dataset_dir = dataset_dir
 
         # besides the predefined properties, this bundle workflow can also provide `network`, `loss`, `optimizer`
@@ -89,7 +90,7 @@ def finalize(self):
         set_determinism(None)
 
     def _set_property(self, name, property, value):
-        self._props[name] = value
+        self._set_props[name] = value
 
     def _get_property(self, name, property):
         """
@@ -103,6 +104,9 @@ def _get_property(self, name, property):
         value = None
         if name in self._props:
             value = self._props[name]
+        elif name in self._set_props:
+            value = self._set_props[name]
+            self._props[name] = value
         else:
             try:
                 value = getattr(self, f"get_{name}")()

From 84e76292e0977c3787733d88cd8ad4a6d258257f Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 1 Mar 2024 10:47:37 +0800
Subject: [PATCH 4/9] Revert "remove self._probs in initialize"

This reverts commit 013a8bfef3a63bb110ffcb61bbf227a33777d180.
---
 bundle/python_bundle_workflow/scripts/inference.py | 2 +-
 bundle/python_bundle_workflow/scripts/train.py     | 1 +
 2 files changed, 2 insertions(+), 1 deletion(-)

diff --git a/bundle/python_bundle_workflow/scripts/inference.py b/bundle/python_bundle_workflow/scripts/inference.py
index 06ce1aff5f..24810a0dfb 100644
--- a/bundle/python_bundle_workflow/scripts/inference.py
+++ b/bundle/python_bundle_workflow/scripts/inference.py
@@ -67,7 +67,7 @@ def __init__(self, dataset_dir: str = "."):
         self.dataset_dir = dataset_dir
 
     def initialize(self):
-        pass
+        self.props = {}
 
     def run(self):
         self.evaluator.run()
diff --git a/bundle/python_bundle_workflow/scripts/train.py b/bundle/python_bundle_workflow/scripts/train.py
index 16fa85b324..ccd409e969 100644
--- a/bundle/python_bundle_workflow/scripts/train.py
+++ b/bundle/python_bundle_workflow/scripts/train.py
@@ -82,6 +82,7 @@ def __init__(self, dataset_dir: str = "."):
 
     def initialize(self):
         set_determinism(0)
+        self.props = {}
 
     def run(self):
         self.trainer.run()

From bc610f13cd8763a9a76d4a4b5f319d60e8f3a9af Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 1 Mar 2024 11:24:55 +0800
Subject: [PATCH 5/9] address comments

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 .../scripts/inference.py                      | 15 ++++------
 .../python_bundle_workflow/scripts/train.py   | 30 +++++++++++--------
 2 files changed, 23 insertions(+), 22 deletions(-)

diff --git a/bundle/python_bundle_workflow/scripts/inference.py b/bundle/python_bundle_workflow/scripts/inference.py
index 24810a0dfb..99e092e737 100644
--- a/bundle/python_bundle_workflow/scripts/inference.py
+++ b/bundle/python_bundle_workflow/scripts/inference.py
@@ -38,6 +38,7 @@
     ScaleIntensityd,
 )
 from monai.utils import BundleProperty
+from scripts.train import prepare_data
 
 
 class InferenceWorkflow(BundleWorkflow):
@@ -46,7 +47,7 @@ class InferenceWorkflow(BundleWorkflow):
 
     """
 
-    def __init__(self, dataset_dir: str = "."):
+    def __init__(self, dataset_dir: str = "./infer"):
         super().__init__(workflow="inference")
         print_config()
         # set root log level to INFO and init a evaluation logger, will be used in `StatsHandler`
@@ -54,20 +55,14 @@ def __init__(self, dataset_dir: str = "."):
         get_logger("eval_log")
 
         # create a temporary directory and 40 random image, mask pairs
-        print(f"generating synthetic data to {dataset_dir} (this may take a while)")
-        for i in range(5):
-            im, seg = create_test_image_3d(128, 128, 128, num_seg_classes=1, channel_dim=-1)
-            n = nib.Nifti1Image(im, np.eye(4))
-            nib.save(n, os.path.join(dataset_dir, f"img{i:d}.nii.gz"))
-            n = nib.Nifti1Image(seg, np.eye(4))
-            nib.save(n, os.path.join(dataset_dir, f"seg{i:d}.nii.gz"))
+        prepare_data(dataset_dir=dataset_dir)
 
         self._props = {}
         self._set_props = {}
         self.dataset_dir = dataset_dir
 
     def initialize(self):
-        self.props = {}
+        self._props = {}
 
     def run(self):
         self.evaluator.run()
@@ -112,7 +107,7 @@ def get_device(self):
         return torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
     def get_dataset_dir(self):
-        return "."
+        return "./infer"
 
     def get_network_def(self):
         return UNet(
diff --git a/bundle/python_bundle_workflow/scripts/train.py b/bundle/python_bundle_workflow/scripts/train.py
index ccd409e969..575df30503 100644
--- a/bundle/python_bundle_workflow/scripts/train.py
+++ b/bundle/python_bundle_workflow/scripts/train.py
@@ -12,6 +12,7 @@
 import logging
 import os
 import sys
+from pathlib import Path
 from glob import glob
 
 import nibabel as nib
@@ -48,32 +49,36 @@
 from monai.utils import BundleProperty, set_determinism
 
 
+def prepare_data(dataset_dir):
+    Path(dataset_dir).mkdir(exist_ok=True)
+    print(f"generating synthetic data to {dataset_dir} (this may take a while)")
+    for i in range(40):
+        im, seg = create_test_image_3d(128, 128, 128, num_seg_classes=1, channel_dim=-1)
+        n = nib.Nifti1Image(im, np.eye(4))
+        nib.save(n, os.path.join(dataset_dir, f"img{i:d}.nii.gz"))
+        n = nib.Nifti1Image(seg, np.eye(4))
+        nib.save(n, os.path.join(dataset_dir, f"seg{i:d}.nii.gz"))
+
+
 class TrainWorkflow(BundleWorkflow):
     """
     Test class simulates the bundle training workflow defined by Python script directly.
 
     """
 
-    def __init__(self, dataset_dir: str = "."):
+    def __init__(self, dataset_dir: str = "./train"):
         super().__init__(workflow="train")
         print_config()
         # set root log level to INFO and init a train logger, will be used in `StatsHandler`
         logging.basicConfig(stream=sys.stdout, level=logging.INFO)
         get_logger("train_log")
-
+        
         # create a temporary directory and 40 random image, mask pairs
-        print(f"generating synthetic data to {dataset_dir} (this may take a while)")
-        for i in range(40):
-            im, seg = create_test_image_3d(128, 128, 128, num_seg_classes=1, channel_dim=-1)
-            n = nib.Nifti1Image(im, np.eye(4))
-            nib.save(n, os.path.join(dataset_dir, f"img{i:d}.nii.gz"))
-            n = nib.Nifti1Image(seg, np.eye(4))
-            nib.save(n, os.path.join(dataset_dir, f"seg{i:d}.nii.gz"))
+        prepare_data(dataset_dir=dataset_dir)
 
         # define buckets to store the generated properties and set properties
         self._props = {}
         self._set_props = {}
-        self.dataset_dir = dataset_dir
 
         # besides the predefined properties, this bundle workflow can also provide `network`, `loss`, `optimizer`
         self.add_property(name="network", required=True, desc="network for the training.")
@@ -82,7 +87,7 @@ def __init__(self, dataset_dir: str = "."):
 
     def initialize(self):
         set_determinism(0)
-        self.props = {}
+        self._props = {}
 
     def run(self):
         self.trainer.run()
@@ -91,6 +96,7 @@ def finalize(self):
         set_determinism(None)
 
     def _set_property(self, name, property, value):
+        # stores user-reset initialized objects that should not be re-initialized.
         self._set_props[name] = value
 
     def _get_property(self, name, property):
@@ -127,7 +133,7 @@ def get_device(self):
         return torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
     def get_dataset_dir(self):
-        return "."
+        return "./train"
 
     def get_network(self):
         return UNet(

From 5bc6ffe53993176949223a55fe036132a1a259ea Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 1 Mar 2024 03:25:55 +0000
Subject: [PATCH 6/9] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 bundle/python_bundle_workflow/scripts/train.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/bundle/python_bundle_workflow/scripts/train.py b/bundle/python_bundle_workflow/scripts/train.py
index 575df30503..7eb19cb177 100644
--- a/bundle/python_bundle_workflow/scripts/train.py
+++ b/bundle/python_bundle_workflow/scripts/train.py
@@ -72,7 +72,7 @@ def __init__(self, dataset_dir: str = "./train"):
         # set root log level to INFO and init a train logger, will be used in `StatsHandler`
         logging.basicConfig(stream=sys.stdout, level=logging.INFO)
         get_logger("train_log")
-        
+
         # create a temporary directory and 40 random image, mask pairs
         prepare_data(dataset_dir=dataset_dir)
 

From e0eb904268bc1fac2977588d41bbb7888b2f5318 Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Fri, 1 Mar 2024 11:26:21 +0800
Subject: [PATCH 7/9] DCO Remediation Commit for YunLiu
 <55491388+KumoLiu@users.noreply.github.com>

I, YunLiu <55491388+KumoLiu@users.noreply.github.com>, hereby add my Signed-off-by to this commit: cf7448877d53908cb1949a3f9c179039902e0c2a
I, YunLiu <55491388+KumoLiu@users.noreply.github.com>, hereby add my Signed-off-by to this commit: 84e76292e0977c3787733d88cd8ad4a6d258257f

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 bundle/python_bundle_workflow/scripts/inference.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/bundle/python_bundle_workflow/scripts/inference.py b/bundle/python_bundle_workflow/scripts/inference.py
index 99e092e737..93ddad7847 100644
--- a/bundle/python_bundle_workflow/scripts/inference.py
+++ b/bundle/python_bundle_workflow/scripts/inference.py
@@ -71,6 +71,7 @@ def finalize(self):
         pass
 
     def _set_property(self, name, property, value):
+        # stores user-reset initialized objects that should not be re-initialized.
         self._set_props[name] = value
 
     def _get_property(self, name, property):

From e94cf15a35e68afa9e32ce46b3443551e4f493ed Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Mon, 4 Mar 2024 14:51:37 +0800
Subject: [PATCH 8/9] address comments

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 bundle/python_bundle_workflow/scripts/inference.py | 6 +++---
 bundle/python_bundle_workflow/scripts/train.py     | 6 +++---
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/bundle/python_bundle_workflow/scripts/inference.py b/bundle/python_bundle_workflow/scripts/inference.py
index 93ddad7847..9d05c1218b 100644
--- a/bundle/python_bundle_workflow/scripts/inference.py
+++ b/bundle/python_bundle_workflow/scripts/inference.py
@@ -84,11 +84,11 @@ def _get_property(self, name, property):
 
         """
         value = None
-        if name in self._props:
-            value = self._props[name]
-        elif name in self._set_props:
+        if name in self._set_props:
             value = self._set_props[name]
             self._props[name] = value
+        elif name in self._props:
+            value = self._props[name]
         else:
             try:
                 value = getattr(self, f"get_{name}")()
diff --git a/bundle/python_bundle_workflow/scripts/train.py b/bundle/python_bundle_workflow/scripts/train.py
index 7eb19cb177..d1282daf6e 100644
--- a/bundle/python_bundle_workflow/scripts/train.py
+++ b/bundle/python_bundle_workflow/scripts/train.py
@@ -109,11 +109,11 @@ def _get_property(self, name, property):
 
         """
         value = None
-        if name in self._props:
-            value = self._props[name]
-        elif name in self._set_props:
+        if name in self._set_props:
             value = self._set_props[name]
             self._props[name] = value
+        elif name in self._props:
+            value = self._props[name]
         else:
             try:
                 value = getattr(self, f"get_{name}")()

From 5a4d80c17c1d93ddf9a3142e0a68171893c4759b Mon Sep 17 00:00:00 2001
From: YunLiu <55491388+KumoLiu@users.noreply.github.com>
Date: Mon, 4 Mar 2024 15:06:40 +0800
Subject: [PATCH 9/9] address comments

Signed-off-by: YunLiu <55491388+KumoLiu@users.noreply.github.com>
---
 bundle/python_bundle_workflow/scripts/inference.py | 2 +-
 bundle/python_bundle_workflow/scripts/train.py     | 3 ++-
 2 files changed, 3 insertions(+), 2 deletions(-)

diff --git a/bundle/python_bundle_workflow/scripts/inference.py b/bundle/python_bundle_workflow/scripts/inference.py
index 9d05c1218b..a98b47bb64 100644
--- a/bundle/python_bundle_workflow/scripts/inference.py
+++ b/bundle/python_bundle_workflow/scripts/inference.py
@@ -108,7 +108,7 @@ def get_device(self):
         return torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
     def get_dataset_dir(self):
-        return "./infer"
+        return self.dataset_dir
 
     def get_network_def(self):
         return UNet(
diff --git a/bundle/python_bundle_workflow/scripts/train.py b/bundle/python_bundle_workflow/scripts/train.py
index d1282daf6e..29a53b46a1 100644
--- a/bundle/python_bundle_workflow/scripts/train.py
+++ b/bundle/python_bundle_workflow/scripts/train.py
@@ -79,6 +79,7 @@ def __init__(self, dataset_dir: str = "./train"):
         # define buckets to store the generated properties and set properties
         self._props = {}
         self._set_props = {}
+        self.dataset_dir = dataset_dir
 
         # besides the predefined properties, this bundle workflow can also provide `network`, `loss`, `optimizer`
         self.add_property(name="network", required=True, desc="network for the training.")
@@ -133,7 +134,7 @@ def get_device(self):
         return torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
     def get_dataset_dir(self):
-        return "./train"
+        return self.dataset_dir
 
     def get_network(self):
         return UNet(