Notebook showing how to use LinearSimulator to generate particle images from a given volume

.dockerignore

@@ -9,4 +9,4 @@
 !simSPI/**
 !notebooks/**
 !tests/**
-!docker/**
+!docker/**

.gitignore

@@ -2,4 +2,5 @@
 *__pycache__*
 temp_workspace/*
 data/pdb_files/*
-notebooks/.ipynb_checkpoints
+notebooks/.ipynb_checkpoints
+.ipynb_checkpoints/

docker/Dockerfile

@@ -31,6 +31,7 @@ RUN wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh &
 
 # Copy the code and generate the environment
 COPY . /work/
+
 RUN . /opt/anaconda/etc/profile.d/conda.sh && conda update -c conda-forge conda
 RUN . /opt/anaconda/etc/profile.d/conda.sh && \
     conda env update --name base --file environment.yml && \
@@ -41,4 +42,4 @@ RUN . /opt/anaconda/etc/profile.d/conda.sh && \
 # Copy and add the entrypoint script
 ADD docker/entrypoint.sh /opt/entrypoint.sh
 RUN chmod +x /opt/entrypoint.sh
-ENTRYPOINT ["/opt/entrypoint.sh"]
+ENTRYPOINT ["/opt/entrypoint.sh"]

notebooks/path_config.yaml

@@ -3,5 +3,4 @@
   metadata_params_file: './notebooks/metadata_fields.yaml'
   mrc_keyword: '_randomrot'
   output_dir: './notebooks/'
-  local_sim_dir: '/work/TEM-simulator_1.3/src/TEM-simulator'
-
+  local_sim_dir: './TEM-simulator_1.3/src/TEM-simulator'

notebooks/sim_tutorial.ipynb

@@ -108,14 +108,25 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 35,
-   "metadata": {},
+   "execution_count": null,
+   "metadata": {
+    "tags": [
+     "parameters"
+    ]
+   },
    "outputs": [],
    "source": [
     "root_dir = \"/work/\"  # change this to your desired path.\n",
     "sim_config = f\"{root_dir}notebooks/sim_config.yaml\"\n",
-    "path_config = f\"{root_dir}notebooks/path_config.yaml\"\n",
-    "\n",
+    "path_config = f\"{root_dir}notebooks/path_config.yaml\""
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
     "os.chdir(root_dir)"
    ]
   },

notebooks/tem_tutorial.ipynb

@@ -67,7 +67,7 @@
      "name": "stdout",
      "output_type": "stream",
      "text": [
-      "This is the root: /Users/callumhepworth/Developer/ENPH-459/compSPI\n"
+      "This is the root: /Users/bogdan/Work/cryoem/compspi\n"
      ]
     }
    ],
@@ -97,7 +97,7 @@
      "name": "stderr",
      "output_type": "stream",
      "text": [
-      "/Users/callumhepworth/anaconda3/envs/simSPI/lib/python3.9/site-packages/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
+      "/opt/anaconda3/envs/simspi/lib/python3.9/site-packages/tqdm/auto.py:22: TqdmWarning: IProgress not found. Please update jupyter and ipywidgets. See https://ipywidgets.readthedocs.io/en/stable/user_install.html\n",
       "  from .autonotebook import tqdm as notebook_tqdm\n"
      ]
     }
@@ -502,7 +502,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.9.7"
+   "version": "3.9.12"
   }
  },
  "nbformat": 4,

tests/test_notebooks.py

@@ -0,0 +1,108 @@
+"""Unit tests for demo notebooks."""
+import os
+import subprocess
+import tempfile
+from pathlib import Path
+
+import pytest
+
+
+@pytest.fixture
+def test_resources_tem_sim():
+    """Return resources for testing the sim_tutorial and the tem_tutorial notebooks."""
+    test_files_path = "/work/tests/test_files/tem"
+    notebooks_path = "/work/notebooks/"
+    cwd = os.getcwd()
+    resources = {
+        "notebook_path": str(Path(cwd, notebooks_path)),
+        "arg_paths": {
+            "path_config": str(Path(cwd, test_files_path, "path_config.yaml")),
+            "sim_config": str(Path(cwd, test_files_path, "sim_config.yaml")),
+            "sim_yaml_clean": str(Path(cwd, test_files_path, "sim_config_clean.yaml")),
+        },
+    }
+
+    return resources
+
+
+@pytest.fixture
+def test_resources_linsim():
+    """Return resources for testing the linearsimulator_tutorial notebook."""
+    test_data_path = "/work/tests/data/"
+    notebooks_path = "/work/notebooks/"
+    cwd = os.getcwd()
+    resources = {
+        "notebook_path": str(Path(cwd, notebooks_path)),
+        "arg_paths": {
+            "vol_path": str(Path(cwd, test_data_path, "linear_simulator_vol.mrc")),
+            "data_path": str(Path(cwd, test_data_path, "linear_simulator_data.npy")),
+        },
+    }
+
+    return resources
+
+
+def _exec_notebook(path, arg_paths):
+    """Execute notebook on path using papermill to fill config paths.
+
+    Parameters
+    ----------
+    path : String
+        The full path of the notebook to test.
+
+    arg_paths: dict[String, String]
+        Dictionary containing the path to the config files passed to papermill
+        for running the current notebook, e.g. arg_paths["path_config"] = /work/...
+    """
+    file_name = tempfile.NamedTemporaryFile(suffix=".ipynb").name
+    args = [
+        "papermill",
+        path,
+        file_name,
+        "--execution-timeout",
+        "360",
+    ]
+
+    for arg_name, arg_val in arg_paths.items():
+        args.extend(["-p", arg_name, arg_val])
+
+    subprocess.check_call(args)
+
+
+def test_tem_tutorial(test_resources_tem_sim):
+    """Test execution of tem_tutorial.ipynb notebook."""
+    notebook_name = "/tem_tutorial.ipynb"
+    notebook_path = test_resources_tem_sim["notebook_path"]
+
+    try:
+        _exec_notebook(
+            notebook_path + notebook_name, test_resources_tem_sim["arg_paths"]
+        )
+    except subprocess.CalledProcessError as exc:
+        assert False, f"{notebook_name} raised exception: {exc}"
+
+
+def test_sim_tutorial(test_resources_tem_sim):
+    """Test execution of sim_tutorial.ipynb notebook."""
+    notebook_name = "/sim_tutorial.ipynb"
+    notebook_path = test_resources_tem_sim["notebook_path"]
+
+    try:
+        _exec_notebook(
+            notebook_path + notebook_name, test_resources_tem_sim["arg_paths"]
+        )
+    except subprocess.CalledProcessError as exc:
+        assert False, f"{notebook_name} raised exception: {exc}"
+
+
+def test_linearsimulator_tutorial(test_resources_linsim):
+    """Test execution of the linearsimulator_tutorial.ipynb notebook."""
+    notebook_name = "/linearsimulator_tutorial.ipynb"
+    notebook_path = test_resources_linsim["notebook_path"]
+
+    try:
+        _exec_notebook(
+            notebook_path + notebook_name, test_resources_linsim["arg_paths"]
+        )
+    except subprocess.CalledProcessError as exc:
+        assert False, f"{notebook_name} raised exception: {exc}"