cell-data-loader 0.0.3__tar.gz → 0.0.5__tar.gz

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (20) hide show
  1. cell_data_loader-0.0.5/.gitattributes +491 -0
  2. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/PKG-INFO +35 -12
  3. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/README.md +33 -10
  4. cell_data_loader-0.0.5/example_numpy.py +72 -0
  5. cell_data_loader-0.0.5/example_torch.py +88 -0
  6. cell_data_loader-0.0.5/github_push.sh +9 -0
  7. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/pyproject.toml +1 -1
  8. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/src/cell_data_loader/cell_data_loader.py +21 -2
  9. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/tests/unit_tests.py +15 -14
  10. cell_data_loader-0.0.3/example_numpy.py +0 -60
  11. cell_data_loader-0.0.3/example_torch.py +0 -60
  12. cell_data_loader-0.0.3/github_push.sh +0 -9
  13. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/__init__.py +0 -0
  14. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/pypi_push.sh +0 -0
  15. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/requirements.txt +0 -0
  16. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/setup.py +0 -0
  17. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/src/cell_data_loader/__init__.py +0 -0
  18. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/src/cell_data_loader/base_dataset.py +0 -0
  19. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/src/cell_data_loader/util.py +0 -0
  20. {cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/tests/__init__.py +0 -0
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{cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/PKG-INFO RENAMED
@@ -1,6 +1,6 @@
1
- Metadata-Version: 2.1
1
+ Metadata-Version: 2.3
2
2
  Name: cell_data_loader
3
- Version: 0.0.3
3
+ Version: 0.0.5
4
4
  Summary: Converts general images of cells into formats and labels for deep learning pipelines
5
5
  Project-URL: Homepage, https://github.com/mleming/CellDataLoader
6
6
  Author-email: Matt Leming <mleming@mgh.harvard.edu>
@@ -23,6 +23,8 @@ Cell Data Loader
23
23
 
24
24
  Cell Data Loader is a simple AI support tool in Python that can take in images of cells (or other image types) and output them with minimal effort to formats that can be read by Pytorch (Tensor) or Tensorflow (Numpy) format. With Cell Data Loader, users have the option to output their cell images as whole images, sliced images, or, with the support of [CellPose](https://github.com/MouseLand/cellpose), segment their images by cell and output those individually.
25
25
 
26
+ It can also be used for normal computer vision research, which is why CellPose is not a strict dependency.
27
+
26
28
  To install Cell Data Loader, simply type into a standard UNIX terminal
27
29
 
28
30
  pip install cell-data-loader
@@ -72,7 +74,12 @@ for label,image in dataloader:
72
74
  Alternatively, if you have one folder or file list with images that have different naming conventions, a regex match is supported:
73
75
 
74
76
  ~~~python
75
- imfiles = ['/path/to/CANCER_image1.png','/path/to/CANCER_image2.png','/path/to/CANCER_image3.png','/path/to/HEALTHY_image1.png','/path/to/HEALTHY_image2.png','/path/to/HEALTHY_image3.png']
77
+ imfiles = ['/path/to/CANCER_image1.png',
78
+ '/path/to/CANCER_image2.png',
79
+ '/path/to/CANCER_image3.png',
80
+ '/path/to/HEALTHY_image1.png',
81
+ '/path/to/HEALTHY_image2.png',
82
+ '/path/to/HEALTHY_image3.png']
76
83
 
77
84
  dataloader = CellDataloader(imfiles,label_regex = ["CANCER","HEALTHY"])
78
85
  for label,image in dataloader:
@@ -91,11 +98,26 @@ imfolder = '/path/to/folder'
91
98
 
92
99
  dataloader = CellDataloader(imfolder,
93
100
  dim = (64,64),
94
- batch_size = 32,
95
- dtype = "numpy", # Can also be "torch"
101
+ batch_size = 64,
102
+ dtype = "torch", # Can also be "numpy"
96
103
  label_regex = None,
97
- n_channels = 3, # This is detected in the first read image by default, if not provided; it re-samples all images to force this number of channels
98
- match_labels = False, # Outputs proportional amounts of each label in the dataset
104
+ verbose = True,
105
+ segment_image = "whole", # "whole" outputs the whole image, resized
106
+ # to dim; "sliced" cuts the image checkerboard pattern into
107
+ # dim-shaped outputs, so it's suitable for large images; "cell"
108
+ # segments cells from the image using CellPose, though it throws
109
+ # an error if CellPose is not installed properly. CellPose is
110
+ # not included by default in the dependencies and needs to be
111
+ # installed separately by the user.
112
+ n_channels = 3, # Detected in first image by default; re-samples all
113
+ # images to force this number of channels
114
+ augment_image = True, # Augments the output image in the standard
115
+ # ways -- rotation, color jiggling, etc.
116
+ label_balance = True, # Outputs proportional amounts of each label
117
+ # in the dataset
118
+ gpu_ids = None, # GPUs that the outputs are read to, if present.
119
+ channels_first = True # Places channels either first, before the
120
+ # batch dimension, or last
99
121
  )
100
122
  ~~~
101
123
 
@@ -103,6 +125,12 @@ dataloader = CellDataloader(imfolder,
103
125
  Dependencies
104
126
  ------------
105
127
 
128
+ Note that the strict dependencies are automatically downloaded just with
129
+
130
+ pip install cell-data-loader
131
+
132
+ However, to get support with cell-segmentation-specific images (i.e., segment="cell"), [CellPose](https://github.com/MouseLand/cellpose) needs to be installed. GPU integration with CellPose would also need to be handled separately.
133
+
106
134
  Strict dependencies:
107
135
 
108
136
  numpy
@@ -119,8 +147,3 @@ Soft dependencies:
119
147
  CellPose # For cell segmentation support
120
148
  Tensorflow
121
149
 
122
- Note that some of the dependencies are not strict and vary depending on usage. Numpy is a hard requirement, but Tensorflow is not if the user only uses the Torch capabilities. If the user attempts to load cell images in "cell" mode without a working Cellpose installation, CellDataLoader will throw an error. Cellpose needs be be installed separately to use "cell" mode:
123
-
124
- pip install cellpose
125
-
126
- And GPU integration is a separate matter.
{cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/README.md RENAMED
@@ -3,6 +3,8 @@ Cell Data Loader
3
3
 
4
4
  Cell Data Loader is a simple AI support tool in Python that can take in images of cells (or other image types) and output them with minimal effort to formats that can be read by Pytorch (Tensor) or Tensorflow (Numpy) format. With Cell Data Loader, users have the option to output their cell images as whole images, sliced images, or, with the support of [CellPose](https://github.com/MouseLand/cellpose), segment their images by cell and output those individually.
5
5
 
6
+ It can also be used for normal computer vision research, which is why CellPose is not a strict dependency.
7
+
6
8
  To install Cell Data Loader, simply type into a standard UNIX terminal
7
9
 
8
10
  pip install cell-data-loader
@@ -52,7 +54,12 @@ for label,image in dataloader:
52
54
  Alternatively, if you have one folder or file list with images that have different naming conventions, a regex match is supported:
53
55
 
54
56
  ~~~python
55
- imfiles = ['/path/to/CANCER_image1.png','/path/to/CANCER_image2.png','/path/to/CANCER_image3.png','/path/to/HEALTHY_image1.png','/path/to/HEALTHY_image2.png','/path/to/HEALTHY_image3.png']
57
+ imfiles = ['/path/to/CANCER_image1.png',
58
+ '/path/to/CANCER_image2.png',
59
+ '/path/to/CANCER_image3.png',
60
+ '/path/to/HEALTHY_image1.png',
61
+ '/path/to/HEALTHY_image2.png',
62
+ '/path/to/HEALTHY_image3.png']
56
63
 
57
64
  dataloader = CellDataloader(imfiles,label_regex = ["CANCER","HEALTHY"])
58
65
  for label,image in dataloader:
@@ -71,11 +78,26 @@ imfolder = '/path/to/folder'
71
78
 
72
79
  dataloader = CellDataloader(imfolder,
73
80
  dim = (64,64),
74
- batch_size = 32,
75
- dtype = "numpy", # Can also be "torch"
81
+ batch_size = 64,
82
+ dtype = "torch", # Can also be "numpy"
76
83
  label_regex = None,
77
- n_channels = 3, # This is detected in the first read image by default, if not provided; it re-samples all images to force this number of channels
78
- match_labels = False, # Outputs proportional amounts of each label in the dataset
84
+ verbose = True,
85
+ segment_image = "whole", # "whole" outputs the whole image, resized
86
+ # to dim; "sliced" cuts the image checkerboard pattern into
87
+ # dim-shaped outputs, so it's suitable for large images; "cell"
88
+ # segments cells from the image using CellPose, though it throws
89
+ # an error if CellPose is not installed properly. CellPose is
90
+ # not included by default in the dependencies and needs to be
91
+ # installed separately by the user.
92
+ n_channels = 3, # Detected in first image by default; re-samples all
93
+ # images to force this number of channels
94
+ augment_image = True, # Augments the output image in the standard
95
+ # ways -- rotation, color jiggling, etc.
96
+ label_balance = True, # Outputs proportional amounts of each label
97
+ # in the dataset
98
+ gpu_ids = None, # GPUs that the outputs are read to, if present.
99
+ channels_first = True # Places channels either first, before the
100
+ # batch dimension, or last
79
101
  )
80
102
  ~~~
81
103
 
@@ -83,6 +105,12 @@ dataloader = CellDataloader(imfolder,
83
105
  Dependencies
84
106
  ------------
85
107
 
108
+ Note that the strict dependencies are automatically downloaded just with
109
+
110
+ pip install cell-data-loader
111
+
112
+ However, to get support with cell-segmentation-specific images (i.e., segment="cell"), [CellPose](https://github.com/MouseLand/cellpose) needs to be installed. GPU integration with CellPose would also need to be handled separately.
113
+
86
114
  Strict dependencies:
87
115
 
88
116
  numpy
@@ -99,8 +127,3 @@ Soft dependencies:
99
127
  CellPose # For cell segmentation support
100
128
  Tensorflow
101
129
 
102
- Note that some of the dependencies are not strict and vary depending on usage. Numpy is a hard requirement, but Tensorflow is not if the user only uses the Torch capabilities. If the user attempts to load cell images in "cell" mode without a working Cellpose installation, CellDataLoader will throw an error. Cellpose needs be be installed separately to use "cell" mode:
103
-
104
- pip install cellpose
105
-
106
- And GPU integration is a separate matter.
cell_data_loader-0.0.5/example_numpy.py ADDED
@@ -0,0 +1,72 @@
1
+ #!/usr/bin/python3
2
+
3
+ from src.cell_data_loader import CellDataloader
4
+
5
+ try:
6
+ import tensorflow as tf
7
+ except:
8
+ try:
9
+ from keras import tensorflow as tf
10
+ except:
11
+ raise Exception("Need valid tensorflow")
12
+
13
+ import numpy
14
+ import os
15
+
16
+ def example_numpy(verbose=True):
17
+
18
+ """
19
+ Replace these folders with whatever folders of cells you may have. Note that
20
+ the test/train folders in this script are the same -- you would need to
21
+ have a separate train/test set in your own implementation
22
+ """
23
+ wd = os.path.dirname(os.path.realpath(__file__))
24
+ imfolder1 = os.path.join(wd,'data',
25
+ '3368914_4_non_tumor')
26
+ imfolder2 = os.path.join(wd,'data',
27
+ '4173633_5')
28
+
29
+ model = resnet50()
30
+ model = tf.keras.applications.resnet50.ResNet50(
31
+ include_top=True,
32
+ weights='imagenet',
33
+ input_tensor=None,
34
+ input_shape=None,
35
+ pooling=None,
36
+ classes=1000
37
+ )
38
+
39
+ # Train
40
+
41
+ dataloader_train = CellDataloader(imfolder1,imfolder2,
42
+ dtype="numpy",verbose=False)
43
+
44
+ z = None
45
+ for epoch in range(100):
46
+ for image,y in dataloader_train:
47
+ if z is None:
48
+ z_dim = list(y.shape)
49
+ z_dim[1] = 1000 - z_dim[1]
50
+ z = np.zeros(z_dim)
51
+ y = np.concatenate(y,z,axis=1)
52
+ model.fit(image,y)
53
+
54
+ # Test
55
+
56
+ model.eval()
57
+ dataloader_test = CellDataloader(imfolder1,imfolder2,dtype="torch",
58
+ verbose=False)
59
+ total_images = 0
60
+ sum_accuracy = 0
61
+ for image,y in dataloader_test:
62
+ total_images += image.shape[0]
63
+ y_pred = model(image)
64
+ y_pred = y_pred[:,:y.shape[1]]
65
+ sum_accuracy += torch.sum(torch.argmax(y_pred,axis=1) == \
66
+ torch.argmax(y,axis=1))
67
+
68
+ accuracy = sum_accuracy / total_images
69
+ if verbose: print("Final accuracy: %.4f" % sum_accuracy)
70
+
71
+ if __name__ == "__main__":
72
+ example_numpy()
cell_data_loader-0.0.5/example_torch.py ADDED
@@ -0,0 +1,88 @@
1
+ #!/usr/bin/python3
2
+
3
+ from cell_data_loader import CellDataloader
4
+ from torchvision.models import resnet50 #, ResNet50_Weights
5
+ import torch
6
+ import os
7
+ import glob
8
+
9
+ def example_torch(gpu_ids = None,verbose=True):
10
+
11
+ """
12
+ Replace these folders with whatever folders of cells you may have. Note that
13
+ the test/train folders in this script are the same -- you would need to
14
+ have a separate train/test set in your own implementation
15
+ """
16
+
17
+ wd = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
18
+ model_folder = os.path.join(wd,'checkpoints')
19
+ os.makedirs(model_folder,exist_ok=True)
20
+ model_file = os.path.join(model_folder,'torch_model.pt')
21
+
22
+ # Training data folders
23
+ imfolder1_train = os.path.join(wd,'data',
24
+ '3368914_4_non_tumor')
25
+ imfolder2_train = os.path.join(wd,'data',
26
+ '4173633_5')
27
+
28
+ # Test data folders
29
+ imfolder1_test = os.path.join(wd,'data','3368914_4_non_tumor')
30
+ imfolder2_test = os.path.join(wd,'data','4173633_5')
31
+
32
+ # Get a pretrained model from torchvision
33
+ if os.path.isfile(model_file):
34
+ if verbose: print("Loading %s" % model_file)
35
+ model = torch.load(model_file)
36
+ else:
37
+ model = resnet50(pretrained=True)
38
+
39
+ if gpu_ids is not None:
40
+ model.to(gpu_ids)
41
+
42
+ # Train
43
+
44
+ model.train()
45
+ loss_fn = torch.nn.MSELoss(reduction='sum')
46
+ optimizer = torch.optim.Adam(model.parameters(), lr=1e-5)
47
+ dataloader_train = CellDataloader(imfolder1_train,imfolder2_train,
48
+ dtype="torch",
49
+ verbose=False, gpu_ids=gpu_ids)
50
+ if verbose: print("Beginning training")
51
+ n_epochs = 0
52
+ for epoch in range(n_epochs):
53
+ l = 0
54
+ c = 0
55
+ for image,y in dataloader_train:
56
+ y_pred = model(image)
57
+ y_pred = y_pred[:,:y.size()[1]]
58
+ loss = loss_fn(y_pred, y)
59
+ l += float(loss)
60
+ c += 1
61
+ optimizer.zero_grad()
62
+ loss.backward()
63
+ optimizer.step()
64
+ torch.save(model,model_file)
65
+ if verbose:
66
+ print(
67
+ "Epoch {epoch:d}/{n_epochs:d}: loss: {loss:.5f}".format(
68
+ epoch=epoch,n_epochs=n_epochs,loss=l/c)
69
+ )
70
+ # Test
71
+
72
+ model.eval()
73
+
74
+ dataloader_test = CellDataloader(imfolder1_test,imfolder2_test,
75
+ dtype="torch",verbose=False, gpu_ids = gpu_ids)
76
+ total_images = 0
77
+ sum_accuracy = 0
78
+ for image,y in dataloader_test:
79
+ total_images += image.size()[0]
80
+ y_pred = model(image)
81
+ y_pred = y_pred[:,:y.size()[1]]
82
+ sum_accuracy += torch.sum(torch.argmax(y_pred,axis=1) == \
83
+ torch.argmax(y,axis=1))
84
+ accuracy = sum_accuracy / total_images
85
+ if verbose: print("Final accuracy: %.4f" % accuracy)
86
+
87
+ if __name__ == "__main__":
88
+ example_torch()
cell_data_loader-0.0.5/github_push.sh ADDED
@@ -0,0 +1,9 @@
1
+ #!/bin/bash
2
+
3
+ #git init
4
+ git add README.md example_numpy.py example_torch.py src tests requirements.txt pyproject.toml
5
+ #git rm src/cell_data_loader/slice_images_out.py src/cell_data_loader/cell_segmenter.py
6
+ git commit -m "Added augmentation"
7
+ git branch -M main
8
+ #git remote add origin https://github.com/mleming/CellDataLoader.git
9
+ git push -u origin main
{cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/pyproject.toml RENAMED
@@ -2,7 +2,7 @@
2
2
 
3
3
  name = "cell_data_loader"
4
4
 
5
- version = "0.0.3"
5
+ version = "0.0.5"
6
6
 
7
7
  dependencies = [
8
8
  "numpy",
{cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/src/cell_data_loader/cell_data_loader.py RENAMED
@@ -202,7 +202,6 @@ class CellDataloader():#BaseDataset):
202
202
  label_balance = True,
203
203
  cell_box_regex = None,
204
204
  cell_box_filelist = None,
205
- filelists = None,
206
205
  n_channels = None,
207
206
  channels_first = True,
208
207
  match_labels=False):
@@ -221,6 +220,20 @@ class CellDataloader():#BaseDataset):
221
220
  self.dtype = dtype
222
221
  self.n_channels = n_channels
223
222
  self.channels_first = channels_first
223
+ self.augment_image = augment_image
224
+ if self.augment_image and self.dtype == "torch":
225
+ from torchvision import transforms
226
+
227
+ self.augment = transforms.Compose([
228
+ #transforms.ElasticTransform(),
229
+ transforms.RandomHorizontalFlip(0.5),
230
+ transforms.RandomVerticalFlip(0.5),
231
+ transforms.GaussianBlur(5),
232
+ transforms.ColorJitter(brightness=(0.5,1.5),
233
+ contrast=(1), saturation=(0.5,1.5), hue=(-0.1,0.1)),
234
+ transforms.RandomResizedCrop((self.dim))])#,
235
+ #transforms.Normalize((0.5,0.5,0.5),(0.5,0.5,0.5))])
236
+
224
237
  """
225
238
  If true, outputs given labels equally. This may repeat images if the
226
239
  counts of each don't line up.
@@ -359,7 +372,7 @@ class CellDataloader():#BaseDataset):
359
372
  if self.dtype == "numpy":
360
373
  self.label_batch = np.zeros((self.batch_size,self.n_labels))
361
374
  elif self.dtype == "torch":
362
- self.label_batch = torch.zeros(self.batch_size,self.n_labels,
375
+ self.label_batch = torch.zeros((self.batch_size,self.n_labels),
363
376
  device = self.gpu_ids)
364
377
  sample = self.image_objects[0]
365
378
  if n_channels is None:
@@ -458,6 +471,8 @@ class CellDataloader():#BaseDataset):
458
471
  self.im_index = 0
459
472
  self.index += 1
460
473
  if self.index >= len(self.image_objects): break
474
+ if self.augment_image and self.dtype == "torch":
475
+ im = self.augment(im)
461
476
  if self.return_labels():
462
477
  return im,label
463
478
  else:
@@ -486,12 +501,16 @@ class CellDataloader():#BaseDataset):
486
501
  im = self.next_im()
487
502
  assert(not isinstance(im,int))
488
503
  if self.dtype == "torch":
504
+ if len(im.size()) == 2 and self.n_channels == 1:
505
+ im = torch.unsqueeze(im,2)
489
506
  self.batch[i,...] = torch.unsqueeze(im,0)
490
507
  if self.channels_first:
491
508
  b = torch.moveaxis(self.batch,-1,1)
492
509
  else:
493
510
  b = self.batch
494
511
  elif self.dtype == "numpy":
512
+ if len(im.shape) == 2 and self.n_channels == 1:
513
+ im = np.expand_dims(im,axis=2)
495
514
  self.batch[i,...] = np.expand_dims(im,axis=0)
496
515
  if self.channels_first:
497
516
  b = np.moveaxis(self.batch,-1,1)
{cell_data_loader-0.0.3 → cell_data_loader-0.0.5}/tests/unit_tests.py RENAMED
@@ -8,7 +8,7 @@ import numpy as np
8
8
  import torch
9
9
 
10
10
  wd = os.path.dirname(os.path.dirname(os.path.realpath(__file__)))
11
- im_root = os.path.join(os.path.dirname(wd),'cell_data_loader_data')
11
+ im_root = os.path.join(wd,'data')
12
12
  #imfile_svs = os.path.join(im_root,'10447627_1.svs')
13
13
  imfolder1 = os.path.join(im_root,'4173633_5')
14
14
  imfolder2 = os.path.join(im_root,'3368914_4_non_tumor')
@@ -159,21 +159,22 @@ class TestSimple(unittest.TestCase):
159
159
  if not torch.cuda.is_available():
160
160
  print("No available GPU for torch -- skipping")
161
161
  continue
162
- device = torch.cuda.current_device()
162
+ devices = [torch.cuda.device(i) for i in range(torch.cuda.device_count())]
163
163
  elif dtype == "numpy":
164
164
  continue
165
- dataset = CellDataloader(imfolder1,imfolder2,imfolder3,dim=dim,
166
- batch_size=batch_size,dtype=dtype,match_labels=True,
167
- gpu_ids = device)
168
- for x,y in dataset:
169
- if dtype == "torch":
170
- self.assertEquals(device,x.device.index)
171
- self.assertEquals(device,y.device.index)
172
- break
173
- elif dtype == "numpy":
174
- break
175
- else:
176
- break
165
+ for device in devices:
166
+ dataset = CellDataloader(imfolder1,imfolder2,imfolder3,dim=dim,
167
+ batch_size=batch_size,dtype=dtype,match_labels=True,
168
+ gpu_ids = device.idx)
169
+ for x,y in dataset:
170
+ if dtype == "torch":
171
+ self.assertEqual(device.idx,x.device.index)
172
+ self.assertEqual(device.idx,y.device.index)
173
+ break
174
+ elif dtype == "numpy":
175
+ break
176
+ else:
177
+ break
177
178
 
178
179
  if __name__ == "__main__":
179
180
  unittest.main()
cell_data_loader-0.0.3/example_numpy.py DELETED
@@ -1,60 +0,0 @@
1
- #!/usr/bin/python3
2
-
3
- from src.cell_data_loader import CellDataloader
4
- from keras import tensorflow as tf
5
- import numpy
6
- import os
7
-
8
- def example_numpy():
9
-
10
- """
11
- Replace whese with folders locally on your computer -- script will not work
12
- without new folders.
13
- """
14
- wd = os.path.dirname(os.path.realpath(__file__))
15
- imfolder_test = os.path.join(os.path.dirname(wd),'cell_data_loader_data',
16
- '3368914_4_non_tumor')
17
- imfolder_train = os.path.join(os.path.dirname(wd),'cell_data_loader_data',
18
- '4173633_5')
19
-
20
- model = resnet50()
21
- model = tf.keras.applications.resnet50.ResNet50(
22
- include_top=True,
23
- weights='imagenet',
24
- input_tensor=None,
25
- input_shape=None,
26
- pooling=None,
27
- classes=1000
28
- )
29
-
30
- # Train
31
-
32
- dataloader_train = CellDataloader(imfolder_train,imfolder_test,
33
- dtype="numpy",verbose=False)
34
-
35
- for epoch in range(5):
36
- for image,y in dataloader_train:
37
- #print("image.size(): %s" % str(image.shape))
38
- #print("y.size(): %s" % str(y.shape))
39
- y_pred = y_pred[:,:2]
40
- #print("y_pred.size(): %s" % str(y_pred.shape))
41
- model.fit(y_pred,y)
42
-
43
- # Test
44
-
45
- model.eval()
46
- dataloader_test = CellDataloader(imfolder_test,imfolder_train,dtype="torch",
47
- verbose=False)
48
- total_images = 0
49
- sum_accuracy = 0
50
- for image,y in dataloader_test:
51
- total_images += image.shape[0]
52
- y_pred = model(image)
53
- sum_accuracy += torch.sum(torch.argmax(y_pred,axis=1) == \
54
- torch.argmax(y,axis=1))
55
-
56
- accuracy = sum_accuracy / total_images
57
- #print("Final accuracy: %.4f" % sum_accuracy)
58
-
59
- if __name__ == "__main__":
60
- example_numpy()
cell_data_loader-0.0.3/example_torch.py DELETED
@@ -1,60 +0,0 @@
1
- #!/usr/bin/python3
2
-
3
- from src.cell_data_loader import CellDataloader
4
- from torchvision.models import resnet50
5
- import torch
6
- import os
7
-
8
- def example_torch():
9
-
10
- """
11
- Replace whese with folders locally on your computer -- script will not work
12
- without new folders.
13
- """
14
- wd = os.path.dirname(os.path.realpath(__file__))
15
- imfolder_test = os.path.join(os.path.dirname(wd),'cell_data_loader_data',
16
- '3368914_4_non_tumor')
17
- imfolder_train = os.path.join(os.path.dirname(wd),'cell_data_loader_data',
18
- '4173633_5')
19
- model = resnet50()
20
-
21
- # Train
22
-
23
- model.train()
24
- loss_fn = torch.nn.MSELoss(reduction='sum')
25
- optimizer = torch.optim.Adam(model.parameters(), lr=1e-5)
26
- dataloader_train = CellDataloader(imfolder_train,imfolder_test,
27
- dtype="torch",
28
- verbose=False)
29
-
30
- for epoch in range(5):
31
- for image,y in dataloader_train:
32
- #print("image.size(): %s" % str(image.size()))
33
- #print("y.size(): %s" % str(y.size()))
34
- y_pred = model(image)
35
- y_pred = y_pred[:,:2]
36
- #print("y_pred.size(): %s" % str(y_pred.size()))
37
- loss = loss_fn(y_pred, y)
38
- optimizer.zero_grad()
39
- loss.backward()
40
- optimizer.step()
41
-
42
- # Test
43
-
44
- model.eval()
45
-
46
- dataloader_test = CellDataloader(imfolder_test,imfolder_train,dtype="torch",
47
- verbose=False)
48
- total_images = 0
49
- sum_accuracy = 0
50
- for image,y in dataloader_test:
51
- total_images += image.size()[0]
52
- y_pred = model(image)
53
- sum_accuracy += torch.sum(torch.argmax(y_pred,axis=1) == \
54
- torch.argmax(y,axis=1))
55
-
56
- accuracy = sum_accuracy / total_images
57
- #print("Final accuracy: %.4f" % sum_accuracy)
58
-
59
- if __name__ == "__main__":
60
- example_torch()
cell_data_loader-0.0.3/github_push.sh DELETED
@@ -1,9 +0,0 @@
1
- #!/bin/bash
2
-
3
- #git init
4
- git add README.md example_numpy.py example_torch.py src tests requirements.txt
5
- git rm src/cell_data_loader/slice_images_out.py src/cell_data_loader/cell_segmenter.py
6
- git commit -m "First commit"
7
- git branch -M main
8
- git remote add origin https://github.com/mleming/CellDataLoader.git
9
- git push -u origin main