Merge pull request #13 from mlexchange/create_seg_tiled_container

Create Seg Tiled Container

Author: dylanmcreynolds

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,

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, urlunparse
 
 # Create directory
 def create_directory(path):
@@ -11,6 +12,24 @@ 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
+    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:
+        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 +41,11 @@ 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))