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Merge pull request #133 from BodenmillerGroup/develop
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Updated XLSX to CSV download
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@nilseling
nilseling committed May 31, 2023
2 parents 2609835 + 0b75cdb commit d0eaecd
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Showing 4 changed files with 138 additions and 147 deletions.
3 changes: 2 additions & 1 deletion .gitignore
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/.vscode/
/analysis/
/raw/
sample_metadata.xlsx
sample_metadata.csv


# Byte-compiled / optimized / DLL files
__pycache__/
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131 changes: 63 additions & 68 deletions scripts/download_examples.ipynb
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},
{
"cell_type": "code",
"execution_count": 2,
"execution_count": 4,
"id": "83673a33",
"metadata": {},
"outputs": [],
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" request.urlretrieve(\"https://zenodo.org/record/6449127/files/IMCWorkflow.ilp\", ilastik_project)\n",
" \n",
"# Sample metadata\n",
"sample_metadata = Path(\"..\") / \"sample_metadata.xlsx\"\n",
"sample_metadata = Path(\"..\") / \"sample_metadata.csv\"\n",
"if not sample_metadata.exists():\n",
" request.urlretrieve(\"https://zenodo.org/record/7575859/files/sample_metadata.csv\", sample_metadata)"
]
},
{
"cell_type": "code",
"execution_count": 3,
"execution_count": 5,
"id": "5cebbf89",
"metadata": {},
"outputs": [
Expand All @@ -81,145 +81,140 @@
"# packages in environment at /Users/nils/opt/anaconda3/envs/imcsegpipe:\n",
"#\n",
"# Name Version Build Channel\n",
"aiofiles 22.1.0 pyhd8ed1ab_0 conda-forge\n",
"aiosqlite 0.18.0 pyhd8ed1ab_0 conda-forge\n",
"anyio 3.6.2 pyhd8ed1ab_0 conda-forge\n",
"appnope 0.1.3 pyhd8ed1ab_0 conda-forge\n",
"argon2-cffi 21.3.0 pyhd8ed1ab_0 conda-forge\n",
"argon2-cffi-bindings 21.2.0 py39ha30fb19_3 conda-forge\n",
"asttokens 2.2.1 pyhd8ed1ab_0 conda-forge\n",
"attrs 22.2.0 pyh71513ae_0 conda-forge\n",
"async-lru 2.0.2 pyhd8ed1ab_0 conda-forge\n",
"attrs 23.1.0 pyh71513ae_1 conda-forge\n",
"babel 2.12.1 pyhd8ed1ab_1 conda-forge\n",
"backcall 0.2.0 pyh9f0ad1d_0 conda-forge\n",
"backports 1.0 pyhd8ed1ab_3 conda-forge\n",
"backports.functools_lru_cache 1.6.4 pyhd8ed1ab_0 conda-forge\n",
"beautifulsoup4 4.11.2 pyha770c72_0 conda-forge\n",
"beautifulsoup4 4.12.2 pyha770c72_0 conda-forge\n",
"bleach 6.0.0 pyhd8ed1ab_0 conda-forge\n",
"brotlipy 0.7.0 py39ha30fb19_1005 conda-forge\n",
"brotli 1.0.9 hb7f2c08_8 conda-forge\n",
"brotli-bin 1.0.9 hb7f2c08_8 conda-forge\n",
"bzip2 1.0.8 h0d85af4_4 conda-forge\n",
"ca-certificates 2022.12.7 h033912b_0 conda-forge\n",
"certifi 2022.12.7 pyhd8ed1ab_0 conda-forge\n",
"ca-certificates 2023.5.7 h8857fd0_0 conda-forge\n",
"certifi 2023.5.7 pyhd8ed1ab_0 conda-forge\n",
"cffi 1.15.1 py39h131948b_3 conda-forge\n",
"charset-normalizer 2.1.1 pyhd8ed1ab_0 conda-forge\n",
"comm 0.1.2 pyhd8ed1ab_0 conda-forge\n",
"cryptography 39.0.2 py39hbeae22c_0 conda-forge\n",
"debugpy 1.6.6 py39h7a8716b_0 conda-forge\n",
"charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge\n",
"comm 0.1.3 pyhd8ed1ab_0 conda-forge\n",
"debugpy 1.6.7 py39h7a8716b_0 conda-forge\n",
"decorator 5.1.1 pyhd8ed1ab_0 conda-forge\n",
"defusedxml 0.7.1 pyhd8ed1ab_0 conda-forge\n",
"entrypoints 0.4 pyhd8ed1ab_0 conda-forge\n",
"executing 1.2.0 pyhd8ed1ab_0 conda-forge\n",
"flit-core 3.8.0 pyhd8ed1ab_0 conda-forge\n",
"flit-core 3.9.0 pyhd8ed1ab_0 conda-forge\n",
"idna 3.4 pyhd8ed1ab_0 conda-forge\n",
"imageio 2.26.0 pypi_0 pypi\n",
"imageio 2.30.0 pypi_0 pypi\n",
"imcsegpipe 1.0.0 pypi_0 pypi\n",
"importlib-metadata 6.0.0 pyha770c72_0 conda-forge\n",
"importlib_metadata 6.0.0 hd8ed1ab_0 conda-forge\n",
"importlib-metadata 6.6.0 pyha770c72_0 conda-forge\n",
"importlib_metadata 6.6.0 hd8ed1ab_0 conda-forge\n",
"importlib_resources 5.12.0 pyhd8ed1ab_0 conda-forge\n",
"ipykernel 6.21.2 pyh736e0ef_0 conda-forge\n",
"ipython 8.11.0 pyhd1c38e8_0 conda-forge\n",
"ipython_genutils 0.2.0 py_1 conda-forge\n",
"ipykernel 6.23.1 pyh736e0ef_0 conda-forge\n",
"ipython 8.13.2 pyhd1c38e8_0 conda-forge\n",
"jedi 0.18.2 pyhd8ed1ab_0 conda-forge\n",
"jinja2 3.1.2 pyhd8ed1ab_1 conda-forge\n",
"json5 0.9.5 pyh9f0ad1d_0 conda-forge\n",
"jsonschema 4.17.3 pyhd8ed1ab_0 conda-forge\n",
"jupyter_client 8.0.3 pyhd8ed1ab_0 conda-forge\n",
"jupyter_core 5.2.0 py39h6e9494a_0 conda-forge\n",
"jupyter-lsp 2.1.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_client 8.2.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_core 5.3.0 py39h6e9494a_0 conda-forge\n",
"jupyter_events 0.6.3 pyhd8ed1ab_0 conda-forge\n",
"jupyter_server 2.4.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_server_fileid 0.8.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_server 2.6.0 pyhd8ed1ab_0 conda-forge\n",
"jupyter_server_terminals 0.4.4 pyhd8ed1ab_1 conda-forge\n",
"jupyter_server_ydoc 0.6.1 pyhd8ed1ab_0 conda-forge\n",
"jupyter_ydoc 0.2.2 pyhd8ed1ab_0 conda-forge\n",
"jupyterlab 3.6.1 pyhd8ed1ab_0 conda-forge\n",
"jupyterlab 4.0.0 pyhd8ed1ab_1 conda-forge\n",
"jupyterlab_pygments 0.2.2 pyhd8ed1ab_0 conda-forge\n",
"jupyterlab_server 2.20.0 pyhd8ed1ab_0 conda-forge\n",
"jupyterlab_server 2.22.1 pyhd8ed1ab_0 conda-forge\n",
"jupytext 1.14.5 pyhcff175f_0 conda-forge\n",
"libcxx 15.0.7 h71dddab_0 conda-forge\n",
"libbrotlicommon 1.0.9 hb7f2c08_8 conda-forge\n",
"libbrotlidec 1.0.9 hb7f2c08_8 conda-forge\n",
"libbrotlienc 1.0.9 hb7f2c08_8 conda-forge\n",
"libcxx 16.0.4 hd57cbcb_0 conda-forge\n",
"libffi 3.4.2 h0d85af4_5 conda-forge\n",
"libsodium 1.0.18 hbcb3906_1 conda-forge\n",
"libsqlite 3.40.0 ha978bb4_0 conda-forge\n",
"libsqlite 3.42.0 h58db7d2_0 conda-forge\n",
"libzlib 1.2.13 hfd90126_4 conda-forge\n",
"markdown-it-py 2.2.0 pyhd8ed1ab_0 conda-forge\n",
"markupsafe 2.1.2 py39ha30fb19_0 conda-forge\n",
"matplotlib-inline 0.1.6 pyhd8ed1ab_0 conda-forge\n",
"mdit-py-plugins 0.3.5 pyhd8ed1ab_0 conda-forge\n",
"mdurl 0.1.0 pyhd8ed1ab_0 conda-forge\n",
"mistune 2.0.5 pyhd8ed1ab_0 conda-forge\n",
"nbclassic 0.5.3 pyhb4ecaf3_3 conda-forge\n",
"nbclient 0.7.2 pyhd8ed1ab_0 conda-forge\n",
"nbconvert 7.2.9 pyhd8ed1ab_0 conda-forge\n",
"nbconvert-core 7.2.9 pyhd8ed1ab_0 conda-forge\n",
"nbconvert-pandoc 7.2.9 pyhd8ed1ab_0 conda-forge\n",
"nbformat 5.7.3 pyhd8ed1ab_0 conda-forge\n",
"nbclient 0.8.0 pyhd8ed1ab_0 conda-forge\n",
"nbconvert-core 7.4.0 pyhd8ed1ab_0 conda-forge\n",
"nbformat 5.8.0 pyhd8ed1ab_0 conda-forge\n",
"ncurses 6.3 h96cf925_1 conda-forge\n",
"nest-asyncio 1.5.6 pyhd8ed1ab_0 conda-forge\n",
"notebook 6.5.3 pyha770c72_0 conda-forge\n",
"notebook-shim 0.2.2 pyhd8ed1ab_0 conda-forge\n",
"numpy 1.24.2 pypi_0 pypi\n",
"openssl 3.0.8 hfd90126_0 conda-forge\n",
"packaging 23.0 pyhd8ed1ab_0 conda-forge\n",
"pandas 1.5.3 pypi_0 pypi\n",
"pandoc 2.19.2 h694c41f_2 conda-forge\n",
"notebook-shim 0.2.3 pyhd8ed1ab_0 conda-forge\n",
"numpy 1.24.3 pypi_0 pypi\n",
"openssl 3.1.0 h8a1eda9_3 conda-forge\n",
"overrides 7.3.1 pyhd8ed1ab_0 conda-forge\n",
"packaging 23.1 pyhd8ed1ab_0 conda-forge\n",
"pandas 2.0.2 pypi_0 pypi\n",
"pandocfilters 1.5.0 pyhd8ed1ab_0 conda-forge\n",
"parso 0.8.3 pyhd8ed1ab_0 conda-forge\n",
"pexpect 4.8.0 pyh1a96a4e_2 conda-forge\n",
"pickleshare 0.7.5 py_1003 conda-forge\n",
"pillow 9.4.0 pypi_0 pypi\n",
"pip 23.0.1 pyhd8ed1ab_0 conda-forge\n",
"pillow 9.5.0 pypi_0 pypi\n",
"pip 23.1.2 pyhd8ed1ab_0 conda-forge\n",
"pkgutil-resolve-name 1.3.10 pyhd8ed1ab_0 conda-forge\n",
"platformdirs 3.1.0 pyhd8ed1ab_0 conda-forge\n",
"prometheus_client 0.16.0 pyhd8ed1ab_0 conda-forge\n",
"platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge\n",
"prometheus_client 0.17.0 pyhd8ed1ab_0 conda-forge\n",
"prompt-toolkit 3.0.38 pyha770c72_0 conda-forge\n",
"prompt_toolkit 3.0.38 hd8ed1ab_0 conda-forge\n",
"psutil 5.9.4 py39ha30fb19_0 conda-forge\n",
"psutil 5.9.5 py39ha30fb19_0 conda-forge\n",
"ptyprocess 0.7.0 pyhd3deb0d_0 conda-forge\n",
"pure_eval 0.2.2 pyhd8ed1ab_0 conda-forge\n",
"pycparser 2.21 pyhd8ed1ab_0 conda-forge\n",
"pygments 2.14.0 pyhd8ed1ab_0 conda-forge\n",
"pyopenssl 23.0.0 pyhd8ed1ab_0 conda-forge\n",
"pygments 2.15.1 pyhd8ed1ab_0 conda-forge\n",
"pyobjc-core 9.1.1 py39h0504f80_0 conda-forge\n",
"pyobjc-framework-cocoa 9.1.1 py39h0504f80_0 conda-forge\n",
"pyrsistent 0.19.3 py39ha30fb19_0 conda-forge\n",
"pysocks 1.7.1 pyha2e5f31_6 conda-forge\n",
"python 3.9.16 h709bd14_0_cpython conda-forge\n",
"python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge\n",
"python-fastjsonschema 2.16.3 pyhd8ed1ab_0 conda-forge\n",
"python-fastjsonschema 2.17.1 pyhd8ed1ab_0 conda-forge\n",
"python-json-logger 2.0.7 pyhd8ed1ab_0 conda-forge\n",
"python_abi 3.9 3_cp39 conda-forge\n",
"pytz 2022.7.1 pyhd8ed1ab_0 conda-forge\n",
"pytz 2023.3 pyhd8ed1ab_0 conda-forge\n",
"pyyaml 6.0 py39ha30fb19_5 conda-forge\n",
"pyzmq 25.0.0 py39hed8f129_0 conda-forge\n",
"pyzmq 25.0.2 py39hed8f129_0 conda-forge\n",
"readimc 0.6.2 pypi_0 pypi\n",
"readline 8.1.2 h3899abd_0 conda-forge\n",
"requests 2.28.2 pyhd8ed1ab_0 conda-forge\n",
"readline 8.2 h9e318b2_1 conda-forge\n",
"requests 2.31.0 pyhd8ed1ab_0 conda-forge\n",
"rfc3339-validator 0.1.4 pyhd8ed1ab_0 conda-forge\n",
"rfc3986-validator 0.1.1 pyh9f0ad1d_0 conda-forge\n",
"scipy 1.10.1 pypi_0 pypi\n",
"send2trash 1.8.0 pyhd8ed1ab_0 conda-forge\n",
"setuptools 67.5.1 pyhd8ed1ab_0 conda-forge\n",
"send2trash 1.8.2 pyhd1c38e8_0 conda-forge\n",
"setuptools 67.7.2 pyhd8ed1ab_0 conda-forge\n",
"six 1.16.0 pyh6c4a22f_0 conda-forge\n",
"sniffio 1.3.0 pyhd8ed1ab_0 conda-forge\n",
"soupsieve 2.3.2.post1 pyhd8ed1ab_0 conda-forge\n",
"stack_data 0.6.2 pyhd8ed1ab_0 conda-forge\n",
"terminado 0.17.1 pyhd1c38e8_0 conda-forge\n",
"tifffile 2023.2.28 pypi_0 pypi\n",
"tifffile 2023.4.12 pypi_0 pypi\n",
"tinycss2 1.2.1 pyhd8ed1ab_0 conda-forge\n",
"tk 8.6.12 h5dbffcc_0 conda-forge\n",
"toml 0.10.2 pyhd8ed1ab_0 conda-forge\n",
"tomli 2.0.1 pyhd8ed1ab_0 conda-forge\n",
"tornado 6.2 py39ha30fb19_1 conda-forge\n",
"tornado 6.3.2 py39hdc70f33_0 conda-forge\n",
"traitlets 5.9.0 pyhd8ed1ab_0 conda-forge\n",
"typing-extensions 4.4.0 hd8ed1ab_0 conda-forge\n",
"typing_extensions 4.4.0 pyha770c72_0 conda-forge\n",
"tzdata 2022g h191b570_0 conda-forge\n",
"urllib3 1.26.14 pyhd8ed1ab_0 conda-forge\n",
"typing-extensions 4.6.2 hd8ed1ab_0 conda-forge\n",
"typing_extensions 4.6.2 pyha770c72_0 conda-forge\n",
"typing_utils 0.1.0 pyhd8ed1ab_0 conda-forge\n",
"tzdata 2023.3 pypi_0 pypi\n",
"urllib3 2.0.2 pyhd8ed1ab_0 conda-forge\n",
"wcwidth 0.2.6 pyhd8ed1ab_0 conda-forge\n",
"webencodings 0.5.1 py_1 conda-forge\n",
"websocket-client 1.5.1 pyhd8ed1ab_0 conda-forge\n",
"wheel 0.38.4 pyhd8ed1ab_0 conda-forge\n",
"websocket-client 1.5.2 pyhd8ed1ab_0 conda-forge\n",
"wheel 0.40.0 pyhd8ed1ab_0 conda-forge\n",
"xtiff 0.7.9 pypi_0 pypi\n",
"xz 5.2.6 h775f41a_0 conda-forge\n",
"y-py 0.5.9 py39hd4bc93a_0 conda-forge\n",
"yaml 0.2.5 h0d85af4_2 conda-forge\n",
"ypy-websocket 0.8.2 pyhd8ed1ab_0 conda-forge\n",
"zeromq 4.3.4 he49afe7_1 conda-forge\n",
"zipp 3.15.0 pyhd8ed1ab_0 conda-forge\n"
]
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2 changes: 1 addition & 1 deletion scripts/download_examples.py
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request.urlretrieve("https://zenodo.org/record/6449127/files/IMCWorkflow.ilp", ilastik_project)

# Sample metadata
sample_metadata = Path("..") / "sample_metadata.xlsx"
sample_metadata = Path("..") / "sample_metadata.csv"
if not sample_metadata.exists():
request.urlretrieve("https://zenodo.org/record/7575859/files/sample_metadata.csv", sample_metadata)

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