added integration test for write_starfile utility

paper/supplementary_figure_7.ipynb

@@ -0,0 +1,77 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# plotting functions for supplementary figure 7\n",
+    "Showing the results of 3DFlex training for the c3-c3b steered MD simulation"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# imports\n",
+    "import os\n",
+    "import mdtraj\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "metadata": {},
+   "outputs": [
+    {
+     "name": "stdout",
+     "output_type": "stream",
+     "text": [
+      "number of frames in trajectory: 8000\n"
+     ]
+    }
+   ],
+   "source": [
+    "# first test: load the trajectory and compare with the number of sampled states in the pdb-directory\n",
+    "trj_dir = \"/tudelft/mjoosten1/staff-umbrella/ajlab/MJ/projects/Roodmus/data/c3c3b/trj\"\n",
+    "\n",
+    "trj = mdtraj.load(\n",
+    "    os.path.join(trj_dir, \"c3_to_c3b_morph_attempt_2.nc\"),\n",
+    "    top=os.path.join(trj_dir, \"c3_to_c3b_morph_frame_1_MD.pdb\")\n",
+    ")\n",
+    "\n",
+    "print(f\"number of frames in trajectory: {trj.n_frames}\")\n",
+    "\n"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "roodmus",
+   "language": "python",
+   "name": "python3"
+  },
+  "language_info": {
+   "codemirror_mode": {
+    "name": "ipython",
+    "version": 3
+   },
+   "file_extension": ".py",
+   "mimetype": "text/x-python",
+   "name": "python",
+   "nbconvert_exporter": "python",
+   "pygments_lexer": "ipython3",
+   "version": "3.10.13"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 2
+}

tests/integration/simulation_test.py

@@ -348,3 +348,51 @@ def test_run_parakeet(self) -> None:
                 )
 
     # maybe should add filecmp for run_parakeet_output/ files????
+
+    def test_write_starfile(self) -> None:
+        """
+        Test that a correct .star file is generated
+        based on the input .csv dataframe file
+        """
+
+        # set up the args to pass to roodmus write_starfile
+        csv_file = os.path.join(
+            self.test_data,
+            "analysis_test_outputs",
+            "picking_star",
+            "label_truth",
+            "df_truth.csv",
+        )
+        output_dir = os.path.join(self.test_dir, "star_files")
+        os.makedirs(output_dir)
+
+        # run the write_starfile utility
+        system_cmd = (
+            "roodmus write_starfile"
+            + " --input_csv {}".format(csv_file)
+            + " --type coordinate_star"
+            + " --output_dir {}".format(output_dir)
+            + " --ugraph_dir {}".format(output_dir)
+            + " --pixel_size 1.0"
+        )
+        os.system(system_cmd)
+
+        # check that the groundtruth.star file has been generated
+        assert os.path.exists(
+            os.path.join(output_dir, "groundtruth.star")
+        ), "groundtruth.star not found in {}".format(output_dir)
+
+        # check that there are individual particle starfiles
+        # in the micrographs directory
+        assert os.path.exists(
+            os.path.join(output_dir, "micrographs")
+        ), "micrographs directory not found in {}".format(output_dir)
+        assert (
+            len(os.listdir(os.path.join(output_dir, "micrographs"))) > 0
+        ), "No files found in micrographs directory in {}".format(output_dir)
+
+        # a comparison with the contents of the groundtruth.star file
+        # is currently not possible, since the output directory is
+        # also used as the name for where to find the micrographs,
+        # and since this directory is created by the utility, the
+        # paths in the .star file will not match the reference file