3 files changed, 523 insertions, 35 deletions

diff --git a/analysis/masks/overview.png b/analysis/masks/overview.png
new file mode 100644
index 0000000..73882a0
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diff --git a/analysis/masks/overview.svg b/analysis/masks/overview.svg
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index 0000000..6d1dd81
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+         x="78.666039"
+         y="99.283508">...</tspan></text>
+    <rect
+       style="fill:none;stroke:#656565;stroke-width:0.265;stroke-linejoin:round;stroke-dasharray:0.794998, 0.794998;stroke-dashoffset:0;stroke-opacity:1"
+       id="rect4-2-8"
+       width="178.15976"
+       height="122.76373"
+       x="16.438864"
+       y="38.056854" />
+    <text
+       xml:space="preserve"
+       style="font-size:3.52777px;font-family:'PT Sans';-inkscape-font-specification:'PT Sans';text-align:start;letter-spacing:0px;writing-mode:lr-tb;direction:ltr;text-anchor:start;fill:none;stroke:#666666;stroke-width:0.264999;stroke-linejoin:round;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+       x="21.589336"
+       y="43.408104"
+       id="text4-5-6"><tspan
+         sodipodi:role="line"
+         id="tspan4-4-3"
+         style="fill:#656565;fill-opacity:1;stroke:none;stroke-width:0.265;stroke-dasharray:none"
+         x="21.589336"
+         y="43.408104">One &quot;collection&quot;</tspan></text>
+    <text
+       xml:space="preserve"
+       style="font-size:3.52777px;font-family:'PT Sans';-inkscape-font-specification:'PT Sans';text-align:start;letter-spacing:0px;writing-mode:lr-tb;direction:ltr;text-anchor:start;fill:none;stroke:#666666;stroke-width:0.264999;stroke-linejoin:round;stroke-dasharray:none;stroke-dashoffset:0;stroke-opacity:1"
+       x="19.83744"
+       y="158.64517"
+       id="text4-5-6-1"><tspan
+         sodipodi:role="line"
+         id="tspan4-4-3-5"
+         style="fill:#656565;fill-opacity:1;stroke:none;stroke-width:0.265;stroke-dasharray:none"
+         x="19.83744"
+         y="158.64517">A collection like &quot;1000x100&quot; contains 1000 runs each with 100 executions.</tspan></text>
+  </g>
+</svg>
diff --git a/analysis/masks/visualize.ipynb b/analysis/masks/visualize.ipynb
index 39fa3df..08a7ee3 100644
--- a/analysis/masks/visualize.ipynb
+++ b/analysis/masks/visualize.ipynb
@@ -5,7 +5,12 @@
    "id": "5d6ed43a-3baf-4da1-a40e-c11a646df6d6",
    "metadata": {},
    "source": [
-    "### Masks"
+    "# Masks\n",
+    "In the following notebook we analyze random masks extracted from several smartcards performing elliptic curve crypto. We extracted the masks using the \"Test n + \\epsilon\" from the [ECTester paper](https://pyecsca.org/_static/ectester_ches25.pdf).\n",
+    "\n",
+    "See the overview of the data collection below.\n",
+    "\n",
+    "![](overview.svg)"
    ]
   },
   {
@@ -50,34 +55,44 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "def load_run(run_path):\n",
-    "    run = []\n",
-    "    files = [file for file in os.listdir(run_path) if file.endswith(\".txt\")]\n",
-    "    files = sorted(files,key = lambda x: int(x[:-4].split(\"_\")[-1]))\n",
+    "def load_collection(collection_path):\n",
+    "    collection = []\n",
+    "    run_files = [file for file in os.listdir(run_path) if file.endswith(\".txt\")]\n",
+    "    run_files = sorted(run_files, key = lambda x: int(x[:-4].split(\"_\")[-1]))\n",
     "    sizes = set()\n",
-    "    for file in files:\n",
-    "        masks = get_masks(os.path.join(run_path,file))\n",
-    "        \n",
-    "        run.append(masks)\n",
-    "    \n",
-    "    return run\n",
-    "    \n",
+    "    for file in run_files:\n",
+    "        masks = get_masks(os.path.join(collection_path,file))\n",
+    "        collection.append(masks)\n",
+    "    return collection\n",
     "\n",
-    "def load_runs(card,protocol):\n",
+    "def load_collections(card, protocol):\n",
     "    path = f\"results/{card}/testdn/\"\n",
-    "    runs = []\n",
+    "    collections = []\n",
     "    counter = 0\n",
-    "    for run_dir in os.listdir(path):\n",
-    "        if not run_dir.startswith(protocol):\n",
+    "    for collection_dir in os.listdir(path):\n",
+    "        if not collection_dir.startswith(protocol):\n",
     "            continue\n",
-    "        run_path = os.path.join(path,run_dir)\n",
-    "        run = load_run(run_path)\n",
-    "        runs.append(run)\n",
-    "        sizes = set([len(masks) for masks in run])\n",
+    "        collection_path = os.path.join(path, collection_dir)\n",
+    "        collection = load_collection(collection_path)\n",
+    "        collections.append(collection)\n",
+    "        sizes = set([len(masks) for masks in collection])\n",
     "        assert len(sizes)==1\n",
-    "        print(f\"({counter}) Loading {len(run)}x{sizes.pop()} masks from {run_path}\")\n",
+    "        print(f\"({counter}) Loading collection with {len(collection)}x{sizes.pop()} masks from {collection_path}\")\n",
     "        counter+=1\n",
-    "    return runs"
+    "    return collections"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "32ff43b3-fe9f-4301-9653-87cf401a9153",
+   "metadata": {},
+   "source": [
+    "## Loading measured masks\n",
+    "See the structure of the results directory for an overview of what collections are available.\n",
+    "\n",
+    "The \"rk\" or \"rpk\" in the protocol name signifies what is done during a reset:\n",
+    " - \"rk\" -> Resets only the key parameters (S,W)\n",
+    " - \"rpk\" -> Resets the key parameters and the curve parameters (FP,A,B,G,R,K)"
    ]
   },
   {
@@ -96,12 +111,10 @@
     }
    ],
    "source": [
-    "## Loading measured masks\n",
-    "\n",
-    "# runs = load_runs(\"N1\",\"ecdsa_rpk\")\n",
-    "# runs = load_runs(\"N8\",\"ecdsa_rpk\")\n",
-    "# runs = load_runs(\"N2\",\"ecdsa_rpk\")\n",
-    "runs = load_runs(\"N9\",\"ecdsa_rk\")"
+    "# collections = load_collections(\"N1\",\"ecdsa_rpk\")\n",
+    "# collections = load_collections(\"N8\",\"ecdsa_rpk\")\n",
+    "# collections = load_collections(\"N2\",\"ecdsa_rpk\")\n",
+    "collections = load_collections(\"N9\",\"ecdsa_rk\")"
    ]
   },
   {
@@ -109,7 +122,9 @@
    "id": "d7011abd-5461-4e3e-a615-8fa1f12391e6",
    "metadata": {},
    "source": [
-    "### MSB bias"
+    "## MSB bias\n",
+    "We see behavior in which each run has some bias in the MSB. The reset at the start of the run \"chooses\" some distribution from a family of distributions and then all masks from that run have the bias.\n",
+    "Below, we visualize 20 runs from the first collection. Each run has 100 executions only, as we were focusing on the overall behavior and not on the details of the distribution."
    ]
   },
   {
@@ -130,7 +145,7 @@
     }
    ],
    "source": [
-    "masks_multiple = runs[0][:20]\n",
+    "masks_multiple = collections[0][:20]\n",
     "\n",
     "num = len(masks_multiple)\n",
     "ncols = 4\n",
@@ -153,7 +168,8 @@
    "id": "cbb76c0d-c428-4655-8681-fa699643ff1e",
    "metadata": {},
    "source": [
-    "### Residue bias"
+    "## Residue bias\n",
+    "Furthermore, when we look at the same 20 runs we see that there is also bias in the residue classes modulo small primes. These plots show on the x-axis the prime and on the y-axis the number of residue classes that the masks \"hit\" for that run. The expected number of hits is marked in red."
    ]
   },
   {
@@ -215,7 +231,8 @@
    "id": "154e0b4d-6552-4b54-8ae4-131658b22c96",
    "metadata": {},
    "source": [
-    "### Simulated bias for a\\*r1+b\\*r2+c"
+    "### Simulated bias for a\\*r1+b\\*r2+c\n",
+    "We had a hypothesis that the masks are of the form $ a*r_1+b*r_2+c $ where each run has a fixed $a, b, c$ but random $r_1$ and $r_2$ for each execution. The simulated results are shown below."
    ]
   },
   {
@@ -283,9 +300,9 @@
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "env",
+   "display_name": "Python 3 (ipykernel)",
    "language": "python",
-   "name": "env"
+   "name": "python3"
   },
   "language_info": {
    "codemirror_mode": {
@@ -297,7 +314,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.12.3"
+   "version": "3.13.7"
   }
  },
  "nbformat": 4,