dsa-helpers 1.1.5.dev3__tar.gz → 1.1.5.dev5__tar.gz

{dsa_helpers-1.1.5.dev3/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.dev3
+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.dev3 → 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.dev3"
+__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.dev3 → dsa_helpers-1.1.5.dev5}/dsa_helpers/ml/datasets/SegFormerSegmentationDataset.py

@@ -19,7 +19,7 @@ class SegFormerSegmentationDataset(Dataset):
         """
         self.image_files = df["fp"].tolist()
         self.mask_files = df["mask_fp"].tolist()
-        self.df = df.copy()  # store potential metadata
+        self.df = df  # store potential metadata
 
     def __len__(self):
         return len(self.image_files)

{dsa_helpers-1.1.5.dev3 → dsa_helpers-1.1.5.dev5}/dsa_helpers/ml/datasets/utils.py

@@ -28,8 +28,6 @@ def create_segformer_segmentation_dataset(
     """
     if isinstance(df, str):
         df = pd.read_csv(df, low_memory=low_memory)
-    else:
-        df = df.copy()
 
     dataset = SegFormerSegmentationDataset(df)
 

{dsa_helpers-1.1.5.dev3 → 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.
@@ -71,6 +71,7 @@ def train_segformer_semantic_segmentation_model(
             will be used. Defaults to None. Note that there is a bug
             that this value must be kept short otherwise a cuda memory
             error will occur.
+
         random_state (int, optional): Random state for the validation
             split. Defaults to 42.
         tile_size (int, optional): Size of the tiles to use for the model.
@@ -240,15 +241,9 @@ def train_segformer_semantic_segmentation_model(
     # For each of the datasets provided, get the metrics.
     model = trainer.model
 
-    del train_dataset
-    del val_dataset
-
-    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,
@@ -256,12 +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,
@@ -272,12 +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.dev3 → 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.dev3
+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.dev3 → 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.dev3"
+version = "v1.1.5.dev5"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"