andreped albertvillanova HF staff commited on
Commit
b429893
1 Parent(s): bc53ced

Download data from Hub (#5)

Browse files

- Move data to data dir (dec3021e71af4c43fed5f3b09e815f21b293ad99)
- Update script to download data from the Hub (db9ed1017f7752a08dbce2c5d01ad4982b63be11)
- Fix style (39fc043dd7eec650f180a7bec89278ab0273d146)


Co-authored-by: Albert Villanova <[email protected]>

This view is limited to 50 files because it contains too many changes.   See raw diff
Files changed (50) hide show
  1. AeroPath.py +29 -123
  2. {1 → data/1}/1_CT_HR.nii.gz +0 -0
  3. {1 → data/1}/1_CT_HR_label_airways.nii.gz +0 -0
  4. {1 → data/1}/1_CT_HR_label_lungs.nii.gz +0 -0
  5. {10 → data/10}/10_CT_HR.nii.gz +0 -0
  6. {10 → data/10}/10_CT_HR_label_airways.nii.gz +0 -0
  7. {10 → data/10}/10_CT_HR_label_lungs.nii.gz +0 -0
  8. {11 → data/11}/11_CT_HR.nii.gz +0 -0
  9. {11 → data/11}/11_CT_HR_label_airways.nii.gz +0 -0
  10. {11 → data/11}/11_CT_HR_label_lungs.nii.gz +0 -0
  11. {12 → data/12}/12_CT_HR.nii.gz +0 -0
  12. {12 → data/12}/12_CT_HR_label_airways.nii.gz +0 -0
  13. {12 → data/12}/12_CT_HR_label_lungs.nii.gz +0 -0
  14. {13 → data/13}/13_CT_HR.nii.gz +0 -0
  15. {13 → data/13}/13_CT_HR_label_airways.nii.gz +0 -0
  16. {13 → data/13}/13_CT_HR_label_lungs.nii.gz +0 -0
  17. {14 → data/14}/14_CT_HR.nii.gz +0 -0
  18. {14 → data/14}/14_CT_HR_label_airways.nii.gz +0 -0
  19. {14 → data/14}/14_CT_HR_label_lungs.nii.gz +0 -0
  20. {15 → data/15}/15_CT_HR.nii.gz +0 -0
  21. {15 → data/15}/15_CT_HR_label_airways.nii.gz +0 -0
  22. {15 → data/15}/15_CT_HR_label_lungs.nii.gz +0 -0
  23. {16 → data/16}/16_CT_HR.nii.gz +0 -0
  24. {16 → data/16}/16_CT_HR_label_airways.nii.gz +0 -0
  25. {16 → data/16}/16_CT_HR_label_lungs.nii.gz +0 -0
  26. {17 → data/17}/17_CT_HR.nii.gz +0 -0
  27. {17 → data/17}/17_CT_HR_label_airways.nii.gz +0 -0
  28. {17 → data/17}/17_CT_HR_label_lungs.nii.gz +0 -0
  29. {18 → data/18}/18_CT_HR.nii.gz +0 -0
  30. {18 → data/18}/18_CT_HR_label_airways.nii.gz +0 -0
  31. {18 → data/18}/18_CT_HR_label_lungs.nii.gz +0 -0
  32. {19 → data/19}/19_CT_HR.nii.gz +0 -0
  33. {19 → data/19}/19_CT_HR_label_airways.nii.gz +0 -0
  34. {19 → data/19}/19_CT_HR_label_lungs.nii.gz +0 -0
  35. {2 → data/2}/2_CT_HR.nii.gz +0 -0
  36. {2 → data/2}/2_CT_HR_label_airways.nii.gz +0 -0
  37. {2 → data/2}/2_CT_HR_label_lungs.nii.gz +0 -0
  38. {20 → data/20}/20_CT_HR.nii.gz +0 -0
  39. {20 → data/20}/20_CT_HR_label_airways.nii.gz +0 -0
  40. {20 → data/20}/20_CT_HR_label_lungs.nii.gz +0 -0
  41. {21 → data/21}/21_CT_HR.nii.gz +0 -0
  42. {21 → data/21}/21_CT_HR_label_airways.nii.gz +0 -0
  43. {21 → data/21}/21_CT_HR_label_lungs.nii.gz +0 -0
  44. {22 → data/22}/22_CT_HR.nii.gz +0 -0
  45. {22 → data/22}/22_CT_HR_label_airways.nii.gz +0 -0
  46. {22 → data/22}/22_CT_HR_label_lungs.nii.gz +0 -0
  47. {23 → data/23}/23_CT_HR.nii.gz +0 -0
  48. {23 → data/23}/23_CT_HR_label_airways.nii.gz +0 -0
  49. {23 → data/23}/23_CT_HR_label_lungs.nii.gz +0 -0
  50. {24 → data/24}/24_CT_HR.nii.gz +0 -0
AeroPath.py CHANGED
@@ -1,29 +1,16 @@
1
- # Copyright 2020 The HuggingFace Datasets Authors and the current dataset script contributor.
2
- #
3
- # Licensed under the Apache License, Version 2.0 (the "License");
4
- # you may not use this file except in compliance with the License.
5
- # You may obtain a copy of the License at
6
- #
7
- # http://www.apache.org/licenses/LICENSE-2.0
8
- #
9
- # Unless required by applicable law or agreed to in writing, software
10
- # distributed under the License is distributed on an "AS IS" BASIS,
11
- # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
12
- # See the License for the specific language governing permissions and
13
- # limitations under the License.
14
- # TODO: Address all TODOs and remove all explanatory comments
15
- """TODO: Add a description here."""
16
 
17
 
18
- import csv
19
- import json
20
- import os
21
-
22
  import datasets
23
 
 
 
 
 
 
 
 
24
 
25
- # TODO: Add BibTeX citation
26
- # Find for instance the citation on arxiv or on the dataset repo/website
27
  _CITATION = """\
28
  @misc{støverud2023aeropath,
29
  title={AeroPath: An airway segmentation benchmark dataset with challenging pathology},
@@ -35,130 +22,49 @@ primaryClass={cs.CV}
35
  }
36
  """
37
 
38
- # TODO: Add description of the dataset here
39
- # You can copy an official description
40
- _DESCRIPTION = """\
41
- AeroPath: An airway segmentation benchmark dataset with challenging pathology.
42
- """
43
-
44
- # TODO: Add a link to an official homepage for the dataset here
45
- _HOMEPAGE = "https://github.com/raidionics/AeroPath"
46
-
47
- # TODO: Add the licence for the dataset here if you can find it
48
- _LICENSE = "MIT"
49
-
50
- # TODO: Add link to the official dataset URLs here
51
- # The HuggingFace Datasets library doesn't host the datasets but only points to the original files.
52
- # This can be an arbitrary nested dict/list of URLs (see below in `_split_generators` method)
53
- _URLS = {
54
- #"first_domain": "https://huggingface.co/great-new-dataset-first_domain.zip",
55
- #"second_domain": "https://huggingface.co/great-new-dataset-second_domain.zip",
56
- "zenodo": "https://zenodo.org/records/10069289/files/AeroPath.zip?download=1"
57
- }
58
 
59
 
60
- # TODO: Name of the dataset usually matches the script name with CamelCase instead of snake_case
61
  class AeroPath(datasets.GeneratorBasedBuilder):
62
  """An airway segmentation benchmark dataset with challenging pathology."""
63
 
64
  VERSION = datasets.Version("1.0.0")
65
 
66
- # This is an example of a dataset with multiple configurations.
67
- # If you don't want/need to define several sub-sets in your dataset,
68
- # just remove the BUILDER_CONFIG_CLASS and the BUILDER_CONFIGS attributes.
69
-
70
- # If you need to make complex sub-parts in the datasets with configurable options
71
- # You can create your own builder configuration class to store attribute, inheriting from datasets.BuilderConfig
72
- # BUILDER_CONFIG_CLASS = MyBuilderConfig
73
-
74
- # You will be able to load one or the other configurations in the following list with
75
- # data = datasets.load_dataset('my_dataset', 'first_domain')
76
- # data = datasets.load_dataset('my_dataset', 'second_domain')
77
- BUILDER_CONFIGS = [
78
- #datasets.BuilderConfig(name="first_domain", version=VERSION, description="This part of my dataset covers a first domain"),
79
- #datasets.BuilderConfig(name="second_domain", version=VERSION, description="This part of my dataset covers a second domain"),
80
- datasets.BuilderConfig(name="zenodo", version=VERSION, description="This includes all 27 CTs stored as a single zip on Zenodo"),
81
- ]
82
-
83
- DEFAULT_CONFIG_NAME = "zenodo" # It's not mandatory to have a default configuration. Just use one if it make sense.
84
-
85
- def __init__(self, **kwargs):
86
- super().__init__(**kwargs)
87
- self.DATA_DIR = None
88
-
89
- def get_patient(self, patient_id):
90
- if (patient_id < 1) or (patiend_id > 27):
91
- raise ValueError("patient_id should be an integer in range [1, 27].")
92
-
93
  def _info(self):
94
- # TODO: This method specifies the datasets.DatasetInfo object which contains informations and typings for the dataset
95
- if self.config.name == "zenodo": # This is the name of the configuration selected in BUILDER_CONFIGS above
96
- features = datasets.Features(
97
- {
98
- "ct": datasets.Value("string"),
99
- "airways": datasets.Value("string"),
100
- "lungs": datasets.Value("string")
101
- # These are the features of your dataset like images, labels ...
102
- }
103
- )
104
- else:
105
- raise ValueError("Only 'zenodo' is supported.")# This is an example to show how to have different features for "first_domain" and "second_domain"
106
-
107
  return datasets.DatasetInfo(
108
- # This is the description that will appear on the datasets page.
109
  description=_DESCRIPTION,
110
- # This defines the different columns of the dataset and their types
111
- features=features, # Here we define them above because they are different between the two configurations
112
- # If there's a common (input, target) tuple from the features, uncomment supervised_keys line below and
113
- # specify them. They'll be used if as_supervised=True in builder.as_dataset.
114
- # supervised_keys=("sentence", "label"),
115
- # Homepage of the dataset for documentation
116
  homepage=_HOMEPAGE,
117
- # License for the dataset if available
118
  license=_LICENSE,
119
- # Citation for the dataset
120
  citation=_CITATION,
121
  )
122
 
123
- def get_data_dir(self):
124
- return self.DATA_DIR
125
-
126
  def _split_generators(self, dl_manager):
127
- # TODO: This method is tasked with downloading/extracting the data and defining the splits depending on the configuration
128
- # If several configurations are possible (listed in BUILDER_CONFIGS), the configuration selected by the user is in self.config.name
129
-
130
- # dl_manager is a datasets.download.DownloadManager that can be used to download and extract URLS
131
- # It can accept any type or nested list/dict and will give back the same structure with the url replaced with path to local files.
132
- # By default the archives will be extracted and a path to a cached folder where they are extracted is returned instead of the archive
133
- urls = _URLS[self.config.name]
134
- self.DATA_DIR = dl_manager.download_and_extract(urls)
135
-
136
- # append AeroPath
137
- self.DATA_DIR = os.path.join(self.DATA_DIR, "AeroPath")
138
-
139
- print("data is downloaded to:", self.DATA_DIR)
140
-
141
  return [
142
  datasets.SplitGenerator(
143
  name=datasets.Split.TEST,
144
  # These kwargs will be passed to _generate_examples
145
  gen_kwargs={
146
- "split": "test",
147
  },
148
  ),
149
  ]
150
 
151
- # method parameters are unpacked from `gen_kwargs` as given in `_split_generators`
152
- def _generate_examples(self, split):
153
- # TODO: This method handles input defined in _split_generators to yield (key, example) tuples from the dataset.
154
- # The `key` is for legacy reasons (tfds) and is not important in itself, but must be unique for each example.
155
- for patient_id in os.listdir(self.DATA_DIR):
156
- curr_path = os.path.join(self.DATA_DIR, patient_id)
157
- if patient_id in ["README.md", "license.md"]:
158
- continue
159
- yield patient_id, {
160
- "ct": os.path.join(curr_path, patient_id + "_CT_HR.nii.gz"),
161
- "airways": os.path.join(curr_path, patient_id + "_CT_HR_label_airways.nii.gz"),
162
- "lungs": os.path.join(curr_path, patient_id + "_CT_HR_label_lungs.nii.gz"),
163
- }
164
-
 
1
+ """AeroPath: An airway segmentation benchmark dataset with challenging pathology."""
 
 
 
 
 
 
 
 
 
 
 
 
 
 
2
 
3
 
 
 
 
 
4
  import datasets
5
 
6
+ _DESCRIPTION = """\
7
+ AeroPath: An airway segmentation benchmark dataset with challenging pathology.
8
+ """
9
+
10
+ _HOMEPAGE = "https://github.com/raidionics/AeroPath"
11
+
12
+ _LICENSE = "MIT"
13
 
 
 
14
  _CITATION = """\
15
  @misc{støverud2023aeropath,
16
  title={AeroPath: An airway segmentation benchmark dataset with challenging pathology},
 
22
  }
23
  """
24
 
25
+ _URLS = [
26
+ {
27
+ "ct": f"data/{i}/{i}_CT_HR.nii.gz",
28
+ "airways": f"data/{i}/{i}_CT_HR_label_airways.nii.gz",
29
+ "lungs": f"data/{i}/{i}_CT_HR_label_lungs.nii.gz",
30
+ }
31
+ for i in range(1, 28)
32
+ ]
 
 
 
 
 
 
 
 
 
 
 
 
33
 
34
 
 
35
  class AeroPath(datasets.GeneratorBasedBuilder):
36
  """An airway segmentation benchmark dataset with challenging pathology."""
37
 
38
  VERSION = datasets.Version("1.0.0")
39
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
40
  def _info(self):
41
+ features = datasets.Features(
42
+ {
43
+ "ct": datasets.Value("string"),
44
+ "airways": datasets.Value("string"),
45
+ "lungs": datasets.Value("string"),
46
+ }
47
+ )
 
 
 
 
 
 
48
  return datasets.DatasetInfo(
 
49
  description=_DESCRIPTION,
50
+ features=features,
 
 
 
 
 
51
  homepage=_HOMEPAGE,
 
52
  license=_LICENSE,
 
53
  citation=_CITATION,
54
  )
55
 
 
 
 
56
  def _split_generators(self, dl_manager):
57
+ data_dirs = dl_manager.download(_URLS)
 
 
 
 
 
 
 
 
 
 
 
 
 
58
  return [
59
  datasets.SplitGenerator(
60
  name=datasets.Split.TEST,
61
  # These kwargs will be passed to _generate_examples
62
  gen_kwargs={
63
+ "data_dirs": data_dirs,
64
  },
65
  ),
66
  ]
67
 
68
+ def _generate_examples(self, data_dirs):
69
+ for key, patient in enumerate(data_dirs):
70
+ yield key, patient
 
 
 
 
 
 
 
 
 
 
 
{1 → data/1}/1_CT_HR.nii.gz RENAMED
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{1 → data/1}/1_CT_HR_label_airways.nii.gz RENAMED
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{1 → data/1}/1_CT_HR_label_lungs.nii.gz RENAMED
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{10 → data/10}/10_CT_HR.nii.gz RENAMED
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{10 → data/10}/10_CT_HR_label_airways.nii.gz RENAMED
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{10 → data/10}/10_CT_HR_label_lungs.nii.gz RENAMED
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{11 → data/11}/11_CT_HR.nii.gz RENAMED
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{11 → data/11}/11_CT_HR_label_airways.nii.gz RENAMED
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{11 → data/11}/11_CT_HR_label_lungs.nii.gz RENAMED
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{12 → data/12}/12_CT_HR.nii.gz RENAMED
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{12 → data/12}/12_CT_HR_label_airways.nii.gz RENAMED
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{12 → data/12}/12_CT_HR_label_lungs.nii.gz RENAMED
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{13 → data/13}/13_CT_HR.nii.gz RENAMED
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{13 → data/13}/13_CT_HR_label_airways.nii.gz RENAMED
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{13 → data/13}/13_CT_HR_label_lungs.nii.gz RENAMED
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{14 → data/14}/14_CT_HR.nii.gz RENAMED
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{14 → data/14}/14_CT_HR_label_lungs.nii.gz RENAMED
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{15 → data/15}/15_CT_HR.nii.gz RENAMED
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{15 → data/15}/15_CT_HR_label_airways.nii.gz RENAMED
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{15 → data/15}/15_CT_HR_label_lungs.nii.gz RENAMED
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{16 → data/16}/16_CT_HR.nii.gz RENAMED
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{16 → data/16}/16_CT_HR_label_airways.nii.gz RENAMED
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{16 → data/16}/16_CT_HR_label_lungs.nii.gz RENAMED
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{17 → data/17}/17_CT_HR.nii.gz RENAMED
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{17 → data/17}/17_CT_HR_label_airways.nii.gz RENAMED
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{17 → data/17}/17_CT_HR_label_lungs.nii.gz RENAMED
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{18 → data/18}/18_CT_HR.nii.gz RENAMED
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{18 → data/18}/18_CT_HR_label_airways.nii.gz RENAMED
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{18 → data/18}/18_CT_HR_label_lungs.nii.gz RENAMED
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{19 → data/19}/19_CT_HR.nii.gz RENAMED
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{19 → data/19}/19_CT_HR_label_airways.nii.gz RENAMED
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{19 → data/19}/19_CT_HR_label_lungs.nii.gz RENAMED
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{2 → data/2}/2_CT_HR.nii.gz RENAMED
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{2 → data/2}/2_CT_HR_label_airways.nii.gz RENAMED
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{2 → data/2}/2_CT_HR_label_lungs.nii.gz RENAMED
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{20 → data/20}/20_CT_HR.nii.gz RENAMED
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{20 → data/20}/20_CT_HR_label_airways.nii.gz RENAMED
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{20 → data/20}/20_CT_HR_label_lungs.nii.gz RENAMED
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{21 → data/21}/21_CT_HR.nii.gz RENAMED
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{21 → data/21}/21_CT_HR_label_airways.nii.gz RENAMED
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{21 → data/21}/21_CT_HR_label_lungs.nii.gz RENAMED
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{22 → data/22}/22_CT_HR.nii.gz RENAMED
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{22 → data/22}/22_CT_HR_label_airways.nii.gz RENAMED
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{22 → data/22}/22_CT_HR_label_lungs.nii.gz RENAMED
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{23 → data/23}/23_CT_HR.nii.gz RENAMED
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{23 → data/23}/23_CT_HR_label_airways.nii.gz RENAMED
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{23 → data/23}/23_CT_HR_label_lungs.nii.gz RENAMED
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{24 → data/24}/24_CT_HR.nii.gz RENAMED
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