Merge pull request #115 from alan-turing-institute/install

Install GRACE from conda environment

README.md

@@ -60,9 +60,36 @@ The `grace` workflow consists of the following steps:
 For local development, clone the repo and install in editable mode:
 
 ```sh
+# clone the grace GitHub repository
+
 git clone https://github.com/alan-turing-institute/grace.git
 cd ./grace
+
+# create a conda playground from environment.yaml
+conda env create -f environment.yaml
+
+# To activate this environment, use
+#
+#     $ conda activate grace-environment
+#
+# To deactivate an active environment, use
+#
+#     $ conda deactivate
+
+conda activate grace-environment
+
+# install grace from local folder (not on pypi yet)
+
 pip install -e ".[dev]"
+
+# install pre-commit separately
+
+conda install -c conda-forge pre_commit
+
+# follow the hooks from .pre-commit-config.yaml
+
+pre-commit install
+
 ```
 
 ---

environment.yaml

@@ -0,0 +1,103 @@
+name: grace_env
+channels:
+  - conda-forge
+  - defaults
+dependencies:
+  - brotli-python=1.0.9
+  - bzip2=1.0.8
+  - ca-certificates=2023.5.7
+  - certifi=2023.5.7
+  - charset-normalizer=3.2.0
+  - idna=3.4
+  - joblib=1.3.0
+  - libblas=3.9.0
+  - libcblas=3.9.0
+  - libcxx=16.0.6
+  - libexpat=2.5.0
+  - libffi=3.4.2
+  - libgfortran=5.0.0
+  - libgfortran5=12.2.0
+  - liblapack=3.9.0
+  - libopenblas=0.3.23
+  - libsqlite=3.42.0
+  - libzlib=1.2.13
+  - llvm-openmp=16.0.6
+  - ncurses=6.4
+  - numpy=1.25.1
+  - openssl=3.1.1
+  - packaging=23.1
+  - pip=23.1.2
+  - platformdirs=3.8.1
+  - pooch=1.7.0
+  - pysocks=1.7.1
+  - python=3.11.4
+  - python_abi=3.11
+  - readline=8.2
+  - requests=2.31.0
+  - scikit-learn=1.3.0
+  - scipy=1.11.1
+  - setuptools=68.0.0
+  - threadpoolctl=3.1.0
+  - tk=8.6.12
+  - typing-extensions
+  - typing_extensions
+  - wheel=0.40.0
+  - xz=5.2.6
+  - pip:
+      - absl-py==1.4.0
+      - cachetools==5.3.1
+      - click==8.1.6
+      - contourpy==1.1.0
+      - cvxopt==1.3.1
+      - cycler==0.11.0
+      - filelock==3.12.2
+      - fonttools==4.40.0
+      - google-auth==2.21.0
+      - google-auth-oauthlib==1.0.0
+      - grpcio==1.56.0
+      - imageio==2.31.1
+      - iniconfig==2.0.0
+      - jinja2==3.1.2
+      - kiwisolver==1.4.4
+      - lazy-loader==0.3
+      - magicgui==0.7.2
+      - markdown==3.4.3
+      - markupsafe==2.1.3
+      - matplotlib==3.7.2
+      - mpmath==1.3.0
+      - mrcfile==1.4.3
+      - networkx==3.1
+      - oauthlib==3.2.2
+      - opencv-python==4.8.0.74
+      - pandas==2.0.3
+      - pillow==10.0.0
+      - pluggy==1.2.0
+      - protobuf==4.23.4
+      - psutil==5.9.5
+      - pyarrow==12.0.1
+      - pyasn1==0.5.0
+      - pyasn1-modules==0.3.0
+      - pyparsing==3.0.9
+      - pytest==7.4.0
+      - python-dateutil==2.8.2
+      - pytz==2023.3
+      - pywavelets==1.4.1
+      - pyyaml==6.0
+      - qtpy==2.3.1
+      - requests-oauthlib==1.3.1
+      - rsa==4.9
+      - scikit-image==0.21.0
+      - seaborn==0.12.2
+      - six==1.16.0
+      - starfile==0.4.12
+      - sympy==1.12
+      - tensorboard==2.13.0
+      - tensorboard-data-server==0.7.1
+      - tifffile==2023.7.10
+      - torch==2.0.1
+      - torch-geometric==2.3.1
+      - torchvision==0.15.2
+      - tqdm==4.65.0
+      - tzdata==2023.3
+      - urllib3==1.26.16
+      - werkzeug==2.3.6

examples/show_data.py

@@ -9,17 +9,21 @@
 
 
 DATA_PATH = Path(
-    "/Users/csoelistyo/Documents/grace_files/notebook_test/image_files"
+    # "/Users/csoelistyo/Documents/grace_files/notebook_test/image_files"
+    "/Users/kulicna/Desktop/classifier/data_fake/infer/padded"
 )
-IMAGE_PATH = (
-    DATA_PATH
-    / "FoilHole_24680421_Data_24671727_24671728_20181024_2216-78563_noDW.mrc"
+IMAGE_FILE = (
+    # "FoilHole_24680421_Data_24671727_24671728_20181024_2216-78563_noDW"
+    "MRC_Synthetic_File_000"
 )
-NODES_PATH = DATA_PATH / "data.h5"
+IMAGE_PATH = DATA_PATH / f"{IMAGE_FILE}.mrc"
+NODES_PATH = DATA_PATH / f"{IMAGE_FILE}.h5"
 
 
 with mrcfile.open(IMAGE_PATH, "r") as mrc:
-    image_data = mrc.data.astype(int)
+    # image_data = mrc.data.astype(int)
+    image_data = mrc.data
+
 nodes_data = pd.read_hdf(NODES_PATH)
 points = np.asarray(nodes_data.loc[:, [GraphAttrs.NODE_Y, GraphAttrs.NODE_X]])
 # features = {

notebooks/run.ipynb

@@ -67,6 +67,11 @@
     "json.dump(config.__dict__, open(CONFIG_FILE, 'w'))"
    ]
   },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
+  },
   {
    "cell_type": "markdown",
    "metadata": {},