cell-data-loader 0.0.4__tar.gz → 0.0.5__tar.gz

{cell_data_loader-0.0.4 → cell_data_loader-0.0.5}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.3
 Name: cell_data_loader
-Version: 0.0.4
+Version: 0.0.5
 Summary: Converts general images of cells into formats and labels for deep learning pipelines
 Project-URL: Homepage, https://github.com/mleming/CellDataLoader
 Author-email: Matt Leming <mleming@mgh.harvard.edu>

{cell_data_loader-0.0.4 → cell_data_loader-0.0.5}/example_torch.py

@@ -48,7 +48,7 @@ def example_torch(gpu_ids = None,verbose=True):
 		dtype="torch",
 		verbose=False, gpu_ids=gpu_ids)
 	if verbose: print("Beginning training")
-	n_epochs = 500
+	n_epochs = 0
 	for epoch in range(n_epochs):
 		l = 0
 		c = 0
@@ -65,7 +65,7 @@ def example_torch(gpu_ids = None,verbose=True):
 		if verbose:
 			print(
 				"Epoch {epoch:d}/{n_epochs:d}: loss: {loss:.5f}".format(
-					epoch=epoch,n_epochs=e_epochs,loss=l/c)
+					epoch=epoch,n_epochs=n_epochs,loss=l/c)
 			)
 	# Test
 	

{cell_data_loader-0.0.4 → cell_data_loader-0.0.5}/github_push.sh

@@ -3,7 +3,7 @@
 #git init
 git add README.md example_numpy.py example_torch.py src tests requirements.txt pyproject.toml
 #git rm src/cell_data_loader/slice_images_out.py src/cell_data_loader/cell_segmenter.py
-git commit -m "Updated example torch, added toml"
+git commit -m "Added augmentation"
 git branch -M main
 #git remote add origin https://github.com/mleming/CellDataLoader.git
 git push -u origin main

{cell_data_loader-0.0.4 → cell_data_loader-0.0.5}/pyproject.toml

@@ -2,7 +2,7 @@
 
 name = "cell_data_loader"
 
-version = "0.0.4"
+version = "0.0.5"
 
 dependencies = [
   "numpy",

{cell_data_loader-0.0.4 → cell_data_loader-0.0.5}/src/cell_data_loader/cell_data_loader.py

@@ -220,6 +220,20 @@ class CellDataloader():#BaseDataset):
 		self.dtype = dtype
 		self.n_channels = n_channels
 		self.channels_first = channels_first
+		self.augment_image = augment_image
+		if self.augment_image and self.dtype == "torch":
+			from torchvision import transforms
+			
+			self.augment = transforms.Compose([
+				#transforms.ElasticTransform(),
+				transforms.RandomHorizontalFlip(0.5),
+				transforms.RandomVerticalFlip(0.5),
+				transforms.GaussianBlur(5),
+				transforms.ColorJitter(brightness=(0.5,1.5),
+					contrast=(1), saturation=(0.5,1.5), hue=(-0.1,0.1)),
+				transforms.RandomResizedCrop((self.dim))])#,
+				#transforms.Normalize((0.5,0.5,0.5),(0.5,0.5,0.5))])
+		
 		"""
 		If true, outputs given labels equally. This may repeat images if the
 		counts of each don't line up.
@@ -457,6 +471,8 @@ class CellDataloader():#BaseDataset):
 			self.im_index = 0
 			self.index += 1
 			if self.index >= len(self.image_objects): break
+		if self.augment_image and self.dtype == "torch":
+			im = self.augment(im)
 		if self.return_labels():
 			return im,label
 		else: