Merge pull request #1 from mj-will/address-referee-reports

Address referee reports

experiments/analytic_results.ipynb

@@ -14,7 +14,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "import os\n",
@@ -42,18 +44,22 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
-    "path = './outdir/'\n",
+    "path = './outdir_rerun/'\n",
     "gaussian_path = os.path.join(path, f'ins_gaussian_*d', '')\n",
     "gmm_path = os.path.join(path, f'ins_gmm_paper_*d', '')"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "gaussian_results = load_all_results(gaussian_path)"
@@ -62,7 +68,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "gmm_results = load_all_results(gmm_path)"
@@ -71,7 +79,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "possible_dims = np.arange(2, 34, 2)\n",
@@ -81,7 +91,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "figsize = ((10 / 13) * default_figsize[0], default_figsize[1] * (1.8 / 5))\n",
@@ -127,7 +139,7 @@
     "    \n",
     "# h, l = fig.axes[0].get_legend_handles_labels()\n",
     "# fig.legend(h, l, frameon=False, ncol=2, loc='lower center', bbox_to_anchor=(0.6, -0.05))\n",
-    "fig.savefig('figures/resampling.pdf')"
+    "fig.savefig('figures_rerun/resampling.pdf')"
    ]
   },
   {
@@ -140,7 +152,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "gaussian_baseline_path = './outdir/baseline_gaussian_*d/'\n",
@@ -152,7 +166,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "gmm_baseline_path = './outdir/baseline_gmm_paper_*'\n",
@@ -164,17 +180,21 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
-    "rosenbrock_path = './outdir/ins_rosenbrock_*d/'\n",
+    "rosenbrock_path = './outdir_rerun/ins_rosenbrock_*d/'\n",
     "rosenbrock_results = load_all_results(rosenbrock_path, file=\"summary.json\")"
    ]
   },
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "rosenbrock_baseline_path = './outdir/baseline_rosenbrock_*d/'\n",
@@ -184,7 +204,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "all_results = [gaussian_results, gmm_results, rosenbrock_results]\n",
@@ -194,7 +216,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "references = [\"gaussian\", \"gaussian\", \"ins\"]\n",
@@ -317,7 +341,7 @@
     "\n",
     "# plt.tight_layout()\n",
     "\n",
-    "fig.savefig(\"figures/comparison_all.pdf\")\n",
+    "fig.savefig(\"figures_rerun/comparison_all.pdf\")\n",
     "\n"
    ]
   },
@@ -331,7 +355,9 @@
   {
    "cell_type": "code",
    "execution_count": null,
-   "metadata": {},
+   "metadata": {
+    "tags": []
+   },
    "outputs": [],
    "source": [
     "fig, axs = plt.subplots(1, 2, sharey=True)\n",
@@ -372,7 +398,7 @@
     "\n",
     "handles, labels = axs[0].get_legend_handles_labels()\n",
     "fig.legend(handles, labels, title=\"Dimensions\", ncols=5, loc=\"lower center\", bbox_to_anchor=(0.5, -0.05))\n",
-    "fig.savefig(\"figures/uncertainty_pp_plots.pdf\")\n",
+    "fig.savefig(\"figures_rerun/uncertainty_pp_plots.pdf\")\n",
     "plt.show()"
    ]
   },

experiments/config.mk

@@ -1,5 +1,5 @@
 # General config
-OUTDIR=outdir/
+OUTDIR=outdir_rerun/
 # Random seed
 SEED=1234
 # Analytic likelihoods config

experiments/nlive_comparison_results.ipynb

@@ -38,7 +38,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "path = \"outdir/ins_nlive_gaussian_16d_nlive*\""
+    "path = \"outdir_rerun/ins_nlive_gaussian_16d_nlive*\""
    ]
   },
   {
@@ -141,7 +141,7 @@
     "plt.tight_layout()\n",
     "# plt.subplots_adjust(hspace=0.15)\n",
     "\n",
-    "fig.savefig(\"figures/scaling.pdf\", bbox_inches=\"tight\")\n",
+    "fig.savefig(\"figures_rerun/scaling.pdf\", bbox_inches=\"tight\")\n",
     "plt.show()"
    ]
   },

gw/bbh_parallelisation/parallelisation.ipynb

@@ -21,7 +21,9 @@
     "sys.path.append(basedir)\n",
     "from utils import configure_plotting, load_json\n",
     "\n",
-    "configure_plotting(basedir)"
+    "configure_plotting(basedir)\n",
+    "\n",
+    "os.environ[\"PATH\"] = os.pathsep.join((\"/usr/local/texlive/2022/bin/x86_64-linux\", os.environ[\"PATH\"]))"
    ]
   },
   {
@@ -310,7 +312,7 @@
     "    \n",
     "plt.tight_layout()\n",
     "plt.legend(handles=handles, labels=labels, loc=\"upper right\", ncol=2)\n",
-    "fig.savefig(\"figures/parallelisation.pdf\", bbox_inches=\"tight\")\n",
+    "fig.savefig(\"figures_rerun/parallelisation.pdf\", bbox_inches=\"tight\")\n",
     "# plt.show()"
    ]
   },

gw/bbh_pp_test/inessai.ini

@@ -1,7 +1,7 @@
 accounting = ligo.dev.o4.cbc.pe.bilby
 
 label = inessai
-outdir = outdir_inessai
+outdir = outdir_inessai_rerun
 
 request-memory=20.0
 
@@ -16,6 +16,8 @@ phase-marginalization=True
 distance-marginalization=True
 time-marginalization=True
 
+transfer-files = True
+
 injection-file = precessing_injections.json
 gaussian-noise = True
 generation-seed = 12345