dsa-helpers 1.1.5.dev4__tar.gz → 1.1.5.dev5__tar.gz

{dsa_helpers-1.1.5.dev4/dsa_helpers.egg-info → dsa_helpers-1.1.5.dev5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.1.5.dev4
+Version: 1.1.5.dev5
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

{dsa_helpers-1.1.5.dev4 → dsa_helpers-1.1.5.dev5}/dsa_helpers/__init__.py

@@ -3,7 +3,7 @@ from .imread import imread
 from .imwrite import imwrite
 
 # Version of the dsa-helpers package
-__version__ = "1.1.5.dev4"
+__version__ = "1.1.5.dev5"
 
 # To avoid slow downs, do not allow from dsa_helpers import * to import anything.
 __all__ = []

{dsa_helpers-1.1.5.dev4 → dsa_helpers-1.1.5.dev5}/dsa_helpers/ml/segformer_semantic_segmentation/train.py

@@ -41,7 +41,7 @@ def train_segformer_semantic_segmentation_model(
     Args:
         save_dir (str): Directory where model checkpoint directory will
             be saved to.
-        train_data (pd.DataFrame | str): Train data, should be a pandas
+        train_csv_fp (str): Train data, should be a pandas
             dataframe or a path to a csv file containing the train data.
             Must have the "fp" and "mask_fp" columns, which are the
             filepaths to the images and masks, respectively.
@@ -91,9 +91,6 @@ def train_segformer_semantic_segmentation_model(
     if test_data is not None and isinstance(test_data, str):
         test_data = pd.read_csv(test_data)
 
-    train_data_copy = train_data.copy()
-    val_data_copy = val_data.copy()
-
     if device is None:
         device = torch.device("cuda" if torch.cuda.is_available() else "cpu")
 
@@ -131,16 +128,14 @@ def train_segformer_semantic_segmentation_model(
 
     # Create datasets for the model.
     train_dataset = create_segformer_segmentation_dataset(
-        train_data_copy, transforms=train_transforms
+        train_data, transforms=train_transforms
     )
 
     val_dataset = create_segformer_segmentation_dataset(
         (
-            val_data_copy
+            val_data
             if max_val_size is None
-            else val_data_copy.sample(
-                n=max_val_size, random_state=random_state
-            )
+            else val_data.sample(n=max_val_size, random_state=random_state)
         ),
         transforms=val_transforms,
     )
@@ -246,12 +241,9 @@ def train_segformer_semantic_segmentation_model(
     # For each of the datasets provided, get the metrics.
     model = trainer.model
 
-    dataset = create_segformer_segmentation_dataset(
-        train_data, transforms=val_transforms
-    )
     results["train"]["metrics"] = per_class_dice_on_dataset(
         model,
-        dataset,
+        train_data,
         label2id,
         batch_size=batch_size,
         device=device,
@@ -259,12 +251,9 @@ def train_segformer_semantic_segmentation_model(
         tqdm_notebook=tqdm_notebook,
     )
 
-    dataset = create_segformer_segmentation_dataset(
-        val_data, transforms=val_transforms
-    )
     results["val"]["metrics"] = per_class_dice_on_dataset(
         model,
-        dataset,
+        val_data,
         label2id,
         batch_size=batch_size,
         device=device,
@@ -275,12 +264,9 @@ def train_segformer_semantic_segmentation_model(
     if test_data is not None:
         results["test"] = {}
 
-        dataset = create_segformer_segmentation_dataset(
-            test_data, transforms=val_transforms
-        )
         results["test"]["metrics"] = per_class_dice_on_dataset(
             model,
-            dataset,
+            test_data,
             label2id,
             batch_size=batch_size,
             device=device,

{dsa_helpers-1.1.5.dev4 → dsa_helpers-1.1.5.dev5/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.1.5.dev4
+Version: 1.1.5.dev5
 Summary: Utility functions for working with the DSA girder client.
 Author-email: "Juan C. Vizcarra" <jvizcar@emory.edu>
 Maintainer-email: "Juan C. Vizcarra" <jvizcar@emory.edu>

{dsa_helpers-1.1.5.dev4 → dsa_helpers-1.1.5.dev5}/pyproject.toml

@@ -37,7 +37,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v1.1.5.dev4"
+version = "v1.1.5.dev5"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"