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ahahah biotech go brrrrrrrrr

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  1. .envrc +1 -0
  2. .gitattributes +54 -0
  3. .gitignore +163 -0
  4. README.md +3 -0
  5. flake.lock +61 -0
  6. flake.nix +19 -0
  7. nct-crc-he.py +102 -0
  8. test.py +7 -0
.envrc ADDED
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+ use flake
.gitattributes ADDED
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+ *.7z filter=lfs diff=lfs merge=lfs -text
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+ *.arrow filter=lfs diff=lfs merge=lfs -text
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+ *.bin filter=lfs diff=lfs merge=lfs -text
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+ *.bz2 filter=lfs diff=lfs merge=lfs -text
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+ *.ckpt filter=lfs diff=lfs merge=lfs -text
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+ *.ftz filter=lfs diff=lfs merge=lfs -text
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+ *.gz filter=lfs diff=lfs merge=lfs -text
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+ *.h5 filter=lfs diff=lfs merge=lfs -text
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+ *.joblib filter=lfs diff=lfs merge=lfs -text
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+ *.lfs.* filter=lfs diff=lfs merge=lfs -text
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+ *.lz4 filter=lfs diff=lfs merge=lfs -text
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+ *.mlmodel filter=lfs diff=lfs merge=lfs -text
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+ *.model filter=lfs diff=lfs merge=lfs -text
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+ *.msgpack filter=lfs diff=lfs merge=lfs -text
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+ *.npy filter=lfs diff=lfs merge=lfs -text
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+ *.npz filter=lfs diff=lfs merge=lfs -text
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+ *.onnx filter=lfs diff=lfs merge=lfs -text
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+ *.ot filter=lfs diff=lfs merge=lfs -text
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+ *.parquet filter=lfs diff=lfs merge=lfs -text
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+ *.pb filter=lfs diff=lfs merge=lfs -text
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+ *.pickle filter=lfs diff=lfs merge=lfs -text
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+ *.pkl filter=lfs diff=lfs merge=lfs -text
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+ *.pt filter=lfs diff=lfs merge=lfs -text
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+ *.pth filter=lfs diff=lfs merge=lfs -text
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+ *.rar filter=lfs diff=lfs merge=lfs -text
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+ *.safetensors filter=lfs diff=lfs merge=lfs -text
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+ saved_model/**/* filter=lfs diff=lfs merge=lfs -text
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+ *.tar.* filter=lfs diff=lfs merge=lfs -text
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+ *.tflite filter=lfs diff=lfs merge=lfs -text
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+ *.tgz filter=lfs diff=lfs merge=lfs -text
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+ *.wasm filter=lfs diff=lfs merge=lfs -text
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+ *.xz filter=lfs diff=lfs merge=lfs -text
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+ *.zip filter=lfs diff=lfs merge=lfs -text
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+ *.zst filter=lfs diff=lfs merge=lfs -text
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+ *tfevents* filter=lfs diff=lfs merge=lfs -text
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+ # Audio files - uncompressed
37
+ *.pcm filter=lfs diff=lfs merge=lfs -text
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+ *.sam filter=lfs diff=lfs merge=lfs -text
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+ *.raw filter=lfs diff=lfs merge=lfs -text
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+ # Audio files - compressed
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+ *.aac filter=lfs diff=lfs merge=lfs -text
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+ *.flac filter=lfs diff=lfs merge=lfs -text
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+ *.mp3 filter=lfs diff=lfs merge=lfs -text
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+ *.ogg filter=lfs diff=lfs merge=lfs -text
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+ *.wav filter=lfs diff=lfs merge=lfs -text
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+ # Image files - uncompressed
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+ *.bmp filter=lfs diff=lfs merge=lfs -text
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+ *.gif filter=lfs diff=lfs merge=lfs -text
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+ *.png filter=lfs diff=lfs merge=lfs -text
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+ *.tiff filter=lfs diff=lfs merge=lfs -text
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+ # Image files - compressed
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+ *.jpg filter=lfs diff=lfs merge=lfs -text
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+ *.jpeg filter=lfs diff=lfs merge=lfs -text
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+ *.webp filter=lfs diff=lfs merge=lfs -text
.gitignore ADDED
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+ .direnv
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+
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+ # https://github.com/github/gitignore/blob/main/Python.gitignore
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+ # Byte-compiled / optimized / DLL files
5
+ __pycache__/
6
+ *.py[cod]
7
+ *$py.class
8
+
9
+ # C extensions
10
+ *.so
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+
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+ # Distribution / packaging
13
+ .Python
14
+ build/
15
+ develop-eggs/
16
+ dist/
17
+ downloads/
18
+ eggs/
19
+ .eggs/
20
+ lib/
21
+ lib64/
22
+ parts/
23
+ sdist/
24
+ var/
25
+ wheels/
26
+ share/python-wheels/
27
+ *.egg-info/
28
+ .installed.cfg
29
+ *.egg
30
+ MANIFEST
31
+
32
+ # PyInstaller
33
+ # Usually these files are written by a python script from a template
34
+ # before PyInstaller builds the exe, so as to inject date/other infos into it.
35
+ *.manifest
36
+ *.spec
37
+
38
+ # Installer logs
39
+ pip-log.txt
40
+ pip-delete-this-directory.txt
41
+
42
+ # Unit test / coverage reports
43
+ htmlcov/
44
+ .tox/
45
+ .nox/
46
+ .coverage
47
+ .coverage.*
48
+ .cache
49
+ nosetests.xml
50
+ coverage.xml
51
+ *.cover
52
+ *.py,cover
53
+ .hypothesis/
54
+ .pytest_cache/
55
+ cover/
56
+
57
+ # Translations
58
+ *.mo
59
+ *.pot
60
+
61
+ # Django stuff:
62
+ *.log
63
+ local_settings.py
64
+ db.sqlite3
65
+ db.sqlite3-journal
66
+
67
+ # Flask stuff:
68
+ instance/
69
+ .webassets-cache
70
+
71
+ # Scrapy stuff:
72
+ .scrapy
73
+
74
+ # Sphinx documentation
75
+ docs/_build/
76
+
77
+ # PyBuilder
78
+ .pybuilder/
79
+ target/
80
+
81
+ # Jupyter Notebook
82
+ .ipynb_checkpoints
83
+
84
+ # IPython
85
+ profile_default/
86
+ ipython_config.py
87
+
88
+ # pyenv
89
+ # For a library or package, you might want to ignore these files since the code is
90
+ # intended to run in multiple environments; otherwise, check them in:
91
+ # .python-version
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+
93
+ # pipenv
94
+ # According to pypa/pipenv#598, it is recommended to include Pipfile.lock in version control.
95
+ # However, in case of collaboration, if having platform-specific dependencies or dependencies
96
+ # having no cross-platform support, pipenv may install dependencies that don't work, or not
97
+ # install all needed dependencies.
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+ #Pipfile.lock
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+
100
+ # poetry
101
+ # Similar to Pipfile.lock, it is generally recommended to include poetry.lock in version control.
102
+ # This is especially recommended for binary packages to ensure reproducibility, and is more
103
+ # commonly ignored for libraries.
104
+ # https://python-poetry.org/docs/basic-usage/#commit-your-poetrylock-file-to-version-control
105
+ #poetry.lock
106
+
107
+ # pdm
108
+ # Similar to Pipfile.lock, it is generally recommended to include pdm.lock in version control.
109
+ #pdm.lock
110
+ # pdm stores project-wide configurations in .pdm.toml, but it is recommended to not include it
111
+ # in version control.
112
+ # https://pdm.fming.dev/#use-with-ide
113
+ .pdm.toml
114
+
115
+ # PEP 582; used by e.g. github.com/David-OConnor/pyflow and github.com/pdm-project/pdm
116
+ __pypackages__/
117
+
118
+ # Celery stuff
119
+ celerybeat-schedule
120
+ celerybeat.pid
121
+
122
+ # SageMath parsed files
123
+ *.sage.py
124
+
125
+ # Environments
126
+ .env
127
+ .venv
128
+ env/
129
+ venv/
130
+ ENV/
131
+ env.bak/
132
+ venv.bak/
133
+
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+ # Spyder project settings
135
+ .spyderproject
136
+ .spyproject
137
+
138
+ # Rope project settings
139
+ .ropeproject
140
+
141
+ # mkdocs documentation
142
+ /site
143
+
144
+ # mypy
145
+ .mypy_cache/
146
+ .dmypy.json
147
+ dmypy.json
148
+
149
+ # Pyre type checker
150
+ .pyre/
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+
152
+ # pytype static type analyzer
153
+ .pytype/
154
+
155
+ # Cython debug symbols
156
+ cython_debug/
157
+
158
+ # PyCharm
159
+ # JetBrains specific template is maintained in a separate JetBrains.gitignore that can
160
+ # be found at https://github.com/github/gitignore/blob/main/Global/JetBrains.gitignore
161
+ # and can be added to the global gitignore or merged into this file. For a more nuclear
162
+ # option (not recommended) you can uncomment the following to ignore the entire idea folder.
163
+ #.idea/
README.md ADDED
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1
+ ---
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+ license: cc-by-4.0
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+ ---
flake.lock ADDED
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1
+ {
2
+ "nodes": {
3
+ "flake-utils": {
4
+ "inputs": {
5
+ "systems": "systems"
6
+ },
7
+ "locked": {
8
+ "lastModified": 1694529238,
9
+ "narHash": "sha256-zsNZZGTGnMOf9YpHKJqMSsa0dXbfmxeoJ7xHlrt+xmY=",
10
+ "owner": "numtide",
11
+ "repo": "flake-utils",
12
+ "rev": "ff7b65b44d01cf9ba6a71320833626af21126384",
13
+ "type": "github"
14
+ },
15
+ "original": {
16
+ "owner": "numtide",
17
+ "repo": "flake-utils",
18
+ "type": "github"
19
+ }
20
+ },
21
+ "nixpkgs": {
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+ "locked": {
23
+ "lastModified": 1694767346,
24
+ "narHash": "sha256-5uH27SiVFUwsTsqC5rs3kS7pBoNhtoy9QfTP9BmknGk=",
25
+ "owner": "NixOS",
26
+ "repo": "nixpkgs",
27
+ "rev": "ace5093e36ab1e95cb9463863491bee90d5a4183",
28
+ "type": "github"
29
+ },
30
+ "original": {
31
+ "owner": "NixOS",
32
+ "ref": "nixos-unstable",
33
+ "repo": "nixpkgs",
34
+ "type": "github"
35
+ }
36
+ },
37
+ "root": {
38
+ "inputs": {
39
+ "flake-utils": "flake-utils",
40
+ "nixpkgs": "nixpkgs"
41
+ }
42
+ },
43
+ "systems": {
44
+ "locked": {
45
+ "lastModified": 1681028828,
46
+ "narHash": "sha256-Vy1rq5AaRuLzOxct8nz4T6wlgyUR7zLU309k9mBC768=",
47
+ "owner": "nix-systems",
48
+ "repo": "default",
49
+ "rev": "da67096a3b9bf56a91d16901293e51ba5b49a27e",
50
+ "type": "github"
51
+ },
52
+ "original": {
53
+ "owner": "nix-systems",
54
+ "repo": "default",
55
+ "type": "github"
56
+ }
57
+ }
58
+ },
59
+ "root": "root",
60
+ "version": 7
61
+ }
flake.nix ADDED
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1
+ {
2
+ inputs = {
3
+ nixpkgs.url = "github:NixOS/nixpkgs/nixos-unstable";
4
+ flake-utils.url = "github:numtide/flake-utils";
5
+ };
6
+
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+ outputs = { self, nixpkgs, flake-utils }:
8
+ flake-utils.lib.eachDefaultSystem (system:
9
+ let pkgs = nixpkgs.legacyPackages.${system};
10
+ in {
11
+ devShell = pkgs.mkShell {
12
+ buildInputs = with pkgs; [
13
+ python311
14
+ python311Packages.datasets
15
+ python311Packages.pillow
16
+ ];
17
+ };
18
+ });
19
+ }
nct-crc-he.py ADDED
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1
+ import pathlib
2
+ import datasets
3
+
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+ _DL_URL = "https://zenodo.org/record/1214456/files/"
5
+
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+ _BASE_URLS = {
7
+ "CRC_VAL_HE_7K": f"{_DL_URL}/CRC-VAL-HE-7K.zip",
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+ "NCT_CRC_HE_100K": f"{_DL_URL}/NCT-CRC-HE-100K.zip",
9
+ "NCT_CRC_HE_100K_NONORM": f"{_DL_URL}/NCT-CRC-HE-100K-NONORM.zip",
10
+ }
11
+
12
+ # _MD5_CHECKSUMS = {
13
+ # "CRC_VAL_HE_7K": "2fd1651b4f94ebd818ebf90ad2b6ce06",
14
+ # "NCT_CRC_HE_100K": "035777cf327776a71a05c95da6d6325f",
15
+ # "NCT_CRC_HE_100K_NONORM": "6fd702d11df6292bc054397ae038a464",
16
+ # }
17
+
18
+ _HOMEPAGE = "https://zenodo.org/record/1214456"
19
+
20
+ _DESCRIPTION = """
21
+ This is a set of non-overlapping image patches from hematoxylin & eosin (H&E) stained histological images of human colorectal cancer (CRC) and normal tissue.
22
+ All images are 224x224 pixels (px) at 0.5 microns per pixel (MPP). All images are color-normalized using Macenko's method (http://ieeexplore.ieee.org/abstract/document/5193250/, DOI 10.1109/ISBI.2009.5193250).
23
+ Tissue classes are: Adipose (ADI), background (BACK), debris (DEB), lymphocytes (LYM), mucus (MUC), smooth muscle (MUS), normal colon mucosa (NORM), cancer-associated stroma (STR), colorectal adenocarcinoma epithelium (TUM).
24
+ These images were manually extracted from N=86 H&E stained human cancer tissue slides from formalin-fixed paraffin-embedded (FFPE) samples from the NCT Biobank (National Center for Tumor Diseases, Heidelberg, Germany) and the UMM pathology archive (University Medical Center Mannheim, Mannheim, Germany). Tissue samples contained CRC primary tumor slides and tumor tissue from CRC liver metastases; normal tissue classes were augmented with non-tumorous regions from gastrectomy specimen to increase variability.
25
+ """
26
+
27
+ _LICENSE = "CC BY 4.0"
28
+
29
+ _VERSION = datasets.Version("0.1.0")
30
+
31
+ _CITATION = """
32
+ @dataset{kather_jakob_nikolas_2018_1214456,
33
+ author = {Kather, Jakob Nikolas and Halama, Niels and Marx, Alexander},
34
+ title = {{100,000 histological images of human colorectal cancer and healthy tissue}},
35
+ month = apr,
36
+ year = 2018,
37
+ publisher = {Zenodo},
38
+ version = {v0.1},
39
+ doi = {10.5281/zenodo.1214456},
40
+ url = {https://doi.org/10.5281/zenodo.1214456}
41
+ }
42
+ """
43
+
44
+ _NAMES = [
45
+ "ADI", # Adipose
46
+ "BACK", # Background
47
+ "DEB", # Debris
48
+ "LYM", # Lymphocytes
49
+ "MUC", # Mucus
50
+ "MUS", # Smooth muscle
51
+ "NORM", # Normal colon mucosa
52
+ "STR", # Cancer-associated stroma
53
+ "TUM", # Colorectal adenocarcinoma epithelium
54
+ ]
55
+
56
+ class NCT_CRC_HE(datasets.GeneratorBasedBuilder):
57
+ """NCT-CRC-HE (7k, 100k, 100k_nonorm) dataset."""
58
+
59
+ def _info(self):
60
+ return datasets.DatasetInfo(
61
+ homepage=_HOMEPAGE,
62
+ description=_DESCRIPTION,
63
+ citation=_CITATION,
64
+ license=_LICENSE,
65
+ version=_VERSION,
66
+ features=datasets.Features(
67
+ {
68
+ "image": datasets.Image(),
69
+ "label": datasets.ClassLabel(names=_NAMES),
70
+ }
71
+ ),
72
+ supervised_keys=(
73
+ "image",
74
+ "label",
75
+ ),
76
+ task_templates=[
77
+ datasets.tasks.ImageClassification(
78
+ image_column="image",
79
+ label_column="label",
80
+ ),
81
+ ],
82
+ )
83
+
84
+ def _split_generators(self, dl_manager):
85
+ return [
86
+ datasets.SplitGenerator(
87
+ name=datasets.NamedSplit(name),
88
+ gen_kwargs={
89
+ "data_dir": pathlib.Path(dl_manager.download_and_extract(url))
90
+ },
91
+ )
92
+ for name, url in _BASE_URLS.items()
93
+ ]
94
+
95
+ def _generate_examples(self, data_dir):
96
+ """Generate images and labels for splits."""
97
+ tif_images = pathlib.Path(data_dir).rglob("*.tif")
98
+ for index, filepath in enumerate(tif_images):
99
+ yield index, {
100
+ "image": str(filepath),
101
+ "label": filepath.parent.name,
102
+ }
test.py ADDED
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1
+ import datasets
2
+
3
+ ds = datasets.load_dataset('./nct-crc-he.py')
4
+
5
+ print(ds)
6
+
7
+ print(ds['CRC_VAL_HE_7K'][0])