From cf331d8951b823c536ca53596ad6c52eba33cdc7 Mon Sep 17 00:00:00 2001
From: TibbersHao <ghao@lbl.gov>
Date: Fri, 8 Mar 2024 16:14:12 -0800
Subject: [PATCH 1/3] added temporary code to save single mask case

---
 src/seg_utils.py | 6 ++++++
 1 file changed, 6 insertions(+)

diff --git a/src/seg_utils.py b/src/seg_utils.py
index 8702c6b..ef10815 100644
--- a/src/seg_utils.py
+++ b/src/seg_utils.py
@@ -258,6 +258,12 @@ def train_segmentation(
                 live.next_step()
 
             print(f'Epoch: {epoch}')
+            
+            # Note: This is a very temporary solution to address the single frame mask case.
+            if validationloader is None:
+                F1_val_micro = None
+                F1_val_macro = None
+                
             table = save_loss(
                 validationloader,
                 savepath,

From 114a3380acff05dfac7496c9aaa027c22d59be7f Mon Sep 17 00:00:00 2001
From: TibbersHao <ghao@lbl.gov>
Date: Fri, 8 Mar 2024 16:15:01 -0800
Subject: [PATCH 2/3] added functionality to validate seg_tiled_uri containers
 and create new if not existed

---
 src/utils.py | 22 +++++++++++++++++++++-
 1 file changed, 21 insertions(+), 1 deletion(-)

diff --git a/src/utils.py b/src/utils.py
index c574448..8ea37e1 100644
--- a/src/utils.py
+++ b/src/utils.py
@@ -2,6 +2,7 @@
 from tiled.client import from_uri
 from tiled.structures.array import ArrayStructure
 import numpy as np
+from urllib.parse import urlparse
 
 # Create directory
 def create_directory(path):
@@ -11,6 +12,21 @@ def create_directory(path):
     else:
         print(f"Local directory '{path}' already exsists.")
 
+def ensure_parent_containers(tiled_uri, tiled_api_key):
+    parsed_url = urlparse(tiled_uri)
+    path = parsed_url.path
+    # Splitting path into parts
+    path_parts = path.split('/')[1:]  # Split and remove the first empty element
+    tiled_root = f'{parsed_url.scheme}://{parsed_url.netloc}/{path_parts[0]}/{path_parts[1]}/{path_parts[2]}'
+    last_container = from_uri(tiled_root, api_key=tiled_api_key)
+
+    for part in path_parts:
+        if part in last_container.keys():
+            last_container = last_container[part]
+        else:
+            last_container = last_container.create_container(key=part)
+    return last_container
+
 
 # Tiled Saving
 def allocate_array_space(
@@ -22,7 +38,11 @@ def allocate_array_space(
                       array_name,
                       ):
     
-    last_container = from_uri(seg_tiled_uri, api_key=seg_tiled_api_key)
+    
+    last_container = ensure_parent_containers(seg_tiled_uri, seg_tiled_api_key)
+    
+    assert uid not in last_container.keys(), f'uid_save: {uid} already existed in Tiled Server'
+
     last_container = last_container.create_container(key=uid)
     array_shape = tiled_dataset.mask_client.shape if tiled_dataset.mask_client else tiled_dataset.data_client.shape
     structure = ArrayStructure.from_array(np.zeros(array_shape,dtype=np.int8))

From 3af17ede2b40eae92cee74074470ba74b0b559e8 Mon Sep 17 00:00:00 2001
From: TibbersHao <ghao@lbl.gov>
Date: Fri, 8 Mar 2024 17:14:49 -0800
Subject: [PATCH 3/3] changed to urlunparse for url stitching

---
 src/utils.py | 7 +++++--
 1 file changed, 5 insertions(+), 2 deletions(-)

diff --git a/src/utils.py b/src/utils.py
index 8ea37e1..adfa151 100644
--- a/src/utils.py
+++ b/src/utils.py
@@ -2,7 +2,7 @@
 from tiled.client import from_uri
 from tiled.structures.array import ArrayStructure
 import numpy as np
-from urllib.parse import urlparse
+from urllib.parse import urlparse, urlunparse
 
 # Create directory
 def create_directory(path):
@@ -17,7 +17,10 @@ def ensure_parent_containers(tiled_uri, tiled_api_key):
     path = parsed_url.path
     # Splitting path into parts
     path_parts = path.split('/')[1:]  # Split and remove the first empty element
-    tiled_root = f'{parsed_url.scheme}://{parsed_url.netloc}/{path_parts[0]}/{path_parts[1]}/{path_parts[2]}'
+    root_path = '/'.join(path_parts[:3])
+    tiled_root = urlunparse((parsed_url.scheme, parsed_url.netloc, root_path, 
+                             parsed_url.params, parsed_url.query, parsed_url.fragment))
+    
     last_container = from_uri(tiled_root, api_key=tiled_api_key)
 
     for part in path_parts: