dsa-helpers 1.1.5.dev7__tar.gz → 1.1.5.dev9__tar.gz

{dsa_helpers-1.1.5.dev7/dsa_helpers.egg-info → dsa_helpers-1.1.5.dev9}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.1.5.dev7
+Version: 1.1.5.dev9
 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.dev7 → dsa_helpers-1.1.5.dev9}/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.dev7"
+__version__ = "1.1.5.dev9"
 
 # To avoid slow downs, do not allow from dsa_helpers import * to import anything.
 __all__ = []

dsa_helpers-1.1.5.dev9/dsa_helpers/ml/segformer_semantic_segmentation/datasets.py

@@ -0,0 +1,55 @@
+from torch.utils.data import Dataset
+import pandas as pd
+from PIL import Image
+
+
+class SegFormerSegmentationDataset(Dataset):
+    """PyTorch dataset class for semantic segmentation using
+    HuggingFaces SegFormer model.
+
+    """
+
+    def __init__(
+        self, df: pd.DataFrame, extras: bool = False, group: str = "wsi_name"
+    ):
+        """Initiate an instance of the segmentation dataset.
+
+        Args:
+            df (pandas.DataFrame): Must have columns "fp" and "mask_fp".
+            extras (bool, optional): Whether to include additional
+                columns "x", "y" and "group" in the dataset. Default
+                is False.
+            group (str | None, optional): Additional column to add when
+                extras is True. Default is "wsi_name".
+
+        """
+        self.image_files = df["fp"].tolist()
+        self.mask_files = df["mask_fp"].tolist()
+        self.extras = extras
+
+        if extras:
+            self.x = df["x"].tolist()
+            self.y = df["y"].tolist()
+            self.group = df[group].tolist()
+
+    def __len__(self):
+        return len(self.image_files)
+
+    def __getitem__(self, idx):
+        # Get the filepath to the image and its mask.
+        image_path = self.image_files[idx]
+        mask_path = self.mask_files[idx]
+
+        if self.extras:
+            return {
+                "pixel_values": Image.open(image_path),
+                "label": Image.open(mask_path),
+                "x": self.x[idx],
+                "y": self.y[idx],
+                "group": self.group[idx],
+            }
+        else:
+            return {
+                "pixel_values": Image.open(image_path),
+                "label": Image.open(mask_path),
+            }

{dsa_helpers-1.1.5.dev7 → dsa_helpers-1.1.5.dev9}/dsa_helpers/ml/segformer_semantic_segmentation/evaluate.py

@@ -4,7 +4,7 @@ import numpy as np
 import torch
 
 from .transforms import val_transforms
-from .datasets import create_segformer_segmentation_dataset
+from .utils import create_segformer_segmentation_dataset
 
 
 def per_class_dice_on_dataset(

{dsa_helpers-1.1.5.dev7 → dsa_helpers-1.1.5.dev9}/dsa_helpers/ml/segformer_semantic_segmentation/train.py

@@ -10,7 +10,7 @@ from pathlib import Path
 import torch
 from torch import nn
 
-from .datasets import create_segformer_segmentation_dataset
+from .utils import create_segformer_segmentation_dataset
 from .transforms import train_transforms, val_transforms
 from .evaluate import per_class_dice_on_dataset
 from ..callbacks import MetricsLoggerCallback

dsa_helpers-1.1.5.dev7/dsa_helpers/ml/segformer_semantic_segmentation/datasets.py → dsa_helpers-1.1.5.dev9/dsa_helpers/ml/segformer_semantic_segmentation/utils.py

@@ -1,59 +1,6 @@
-from torch.utils.data import Dataset as TorchDataset
-import pandas as pd
-from PIL import Image
 from datasets import Dataset, Features, Image, Value
-
-
-class SegFormerSegmentationDataset(TorchDataset):
-    """PyTorch dataset class for semantic segmentation using
-    HuggingFaces SegFormer model.
-
-    """
-
-    def __init__(
-        self, df: pd.DataFrame, extras: bool = False, group: str = "wsi_name"
-    ):
-        """Initiate an instance of the segmentation dataset.
-
-        Args:
-            df (pandas.DataFrame): Must have columns "fp" and "mask_fp".
-            extras (bool, optional): Whether to include additional
-                columns "x", "y" and "group" in the dataset. Default
-                is False.
-            group (str | None, optional): Additional column to add when
-                extras is True. Default is "wsi_name".
-
-        """
-        self.image_files = df["fp"].tolist()
-        self.mask_files = df["mask_fp"].tolist()
-        self.extras = extras
-
-        if extras:
-            self.x = df["x"].tolist()
-            self.y = df["y"].tolist()
-            self.group = df[group].tolist()
-
-    def __len__(self):
-        return len(self.image_files)
-
-    def __getitem__(self, idx):
-        # Get the filepath to the image and its mask.
-        image_path = self.image_files[idx]
-        mask_path = self.mask_files[idx]
-
-        if self.extras:
-            return {
-                "pixel_values": Image.open(image_path),
-                "label": Image.open(mask_path),
-                "x": self.x[idx],
-                "y": self.y[idx],
-                "group": self.group[idx],
-            }
-        else:
-            return {
-                "pixel_values": Image.open(image_path),
-                "label": Image.open(mask_path),
-            }
+import pandas as pd
+from .datasets import SegFormerSegmentationDataset
 
 
 def dataset_generator(dataset):

{dsa_helpers-1.1.5.dev7 → dsa_helpers-1.1.5.dev9/dsa_helpers.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: dsa_helpers
-Version: 1.1.5.dev7
+Version: 1.1.5.dev9
 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.dev7 → dsa_helpers-1.1.5.dev9}/dsa_helpers.egg-info/SOURCES.txt

@@ -45,6 +45,7 @@ dsa_helpers/ml/segformer_semantic_segmentation/evaluate.py
 dsa_helpers/ml/segformer_semantic_segmentation/inference.py
 dsa_helpers/ml/segformer_semantic_segmentation/train.py
 dsa_helpers/ml/segformer_semantic_segmentation/transforms.py
+dsa_helpers/ml/segformer_semantic_segmentation/utils.py
 dsa_helpers/ml/transforms/__init__.py
 dsa_helpers/ml/transforms/segformer_transforms.py
 tests/docker-compose.yaml

{dsa_helpers-1.1.5.dev7 → dsa_helpers-1.1.5.dev9}/pyproject.toml

@@ -38,7 +38,7 @@ classifiers = [
     "License :: OSI Approved :: MIT License",
 ]
 keywords = ["dsa", "girder", "girder_client"]
-version = "v1.1.5.dev7"
+version = "v1.1.5.dev9"
 
 [project.urls]
 Repository = "https://github.com/Gutman-Lab/dsa-python-utils"