Add jupyterlab to requirements.txt

This reverts commit f335d96c4f.

.gitignore

@@ -6,3 +6,4 @@ fab
 venv
 gerber
 gerber.zip
+.ipynb_checkpoints

.gitmodules

@@ -1,7 +1,7 @@
 [submodule "fw/upstream/PyCortexMDebug"]
-	path = fw/upstream/PyCortexMDebug
+	path = firmware/upstream/PyCortexMDebug
 	url = https://github.com/bnahill/PyCortexMDebug
 [submodule "fw/upstream/stm32square"]
-	path = fw/upstream/stm32square
+	path = firmware/upstream/stm32square
 	url = https://gitlab.com/neinseg/stm32square
 	branch = release

LICENSE.txt

@@ -0,0 +1,170 @@
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README.rst

@@ -0,0 +1,207 @@
+
+High Fidelity Security Mesh Monitoring using Low-Cost, Embedded Time Domain Reflectometry
+=========================================================================================
+
+This repository contains all sources for our paper "High Fidelity Security Mesh Monitoring using Low-Cost, Embedded Time
+Domain Reflectometry" to be published in CHES 2026/1 (`preprint on eprint <https://eprint.iacr.org/2025/1962>`__). You
+can find a brief overview of the project `on Jan's blog <https://jaseg.de/blog/paper-sampling-mesh-monitor/>`__.
+
+The canonical hosting location for this repo is https://git.jaseg.de/sampling-mesh-monitor.git . For comments or
+questions, please reach out to Jan via `email <mailto:research@jaseg.de>`__ or `on mastodon
+<https://chaos.social/@jaseg>`__.
+
+.. figure:: paper/pic_board_setup_2_small.jpg
+    :align: center
+    :width: 400px
+    :alt: A PCB with several chips sitting on a table with another PCB with only traces on it plugged in through a
+          board-edge connector. The first PCB looks not very complex.
+
+    The final setup. On the right is the measurement board, and on the left is the mesh test specimen plugged in. In a
+    real application, you would integrate both into your target circuit.
+
+Paper abstract
+--------------
+
+    Security Meshes are patterns of sensing traces covering an area that are used in Hardware Security Modules (HSMs)
+    and other systems to detect attempts to physically intrude into the device's protective shell. State-of-the-art
+    solutions manufacture meshes in bespoke processes from carefully chosen materials, which is expensive and makes
+    replication challenging. Additionally, state-of-the-art monitoring circuits sacrifice either monitoring precision or
+    cost efficiency. In this paper, we present an embeddable security mesh monitoring circuit constructed from low-cost,
+    standard components that utilizes Time Domain Reflectometry (TDR) to create a unique fingerprint of a mesh. Our
+    approach is both low-cost and precise, and enables the use of inexpensive standard Printed Circuit Boards (PCBs) as
+    security mesh material. We demonstrate a working prototype of our TDR circuit costing less than 10 € in components
+    that achieves both time resolution and rise time better than 200 ps—a 25 × improvement over previous work. We
+    demonstrate a simple classifier that detects several types of advanced attacks such as probing using an oscilloscope
+    probe or micro-soldering attacks with no false negatives.
+
+Repo structure
+--------------
+
+``main_pcb``
+    KiCad design files, exports and manufacturing files for the main circuit board. This board contains the measurement
+    circuit, and has a connector for test coupons to be inserted. Data is read out throught the SWD interface using an
+    SWD adapter. The board is a 6-layer PCB. The circuit is described in detail in the paper. It is based around a
+    ``STM32G474RE`` ARM microcontroller.
+
+``test_coupons``
+    KiCad design files, exports and manufacturing files for the test coupon PCBs. The coupons are four-layer boards.
+    Each coupon contains four test meshes, two on each side, that can be connected through four SFP form factor board
+    edge connectors at the coupon's corners.
+
+``firmware``
+    Source code for the board firmware as well as tooling for running the experiments. The firmware is written in C, and
+    you'll need a standard ARM GCC/binutils toolchain to build it. The experiment tool is a python script that connects
+    to the board through GDB and exposes a local web server for controlling the board, monitoring the measurements in
+    real time, and capturing data.
+
+``analysis``
+    All raw data, as well as the Jupyter notebooks used for analysis and plotting. By running these notebooks, you can
+    re-run the analysis, and re-export all plots in the paper. The raw data is contained in JSON files, one per
+    measurement series. Each JSON file contains some metadata describing the experiment and the settings used during the
+    experiment, a set of calibration runs with the target specimen disconnected using the board's routing switches, and
+    a full set of 12 measurement arrays consisting of a mean and standard deviation for each data point. To save space,
+    batches of these JSON files are aggregated into zip archives. The analysis Jupyter notebooks will automatically load
+    and decode the data from these zip archives when run.
+
+``paper``
+    The source of the paper, as well as exports of all plots.
+
+Running the analysis
+--------------------
+
+To re-run the analysis, first install `Jupyter Lab <https://jupyter.org/>`__ and the `numpy <https://numpy.org/>`__ and
+`scipy <https://scipy.org/>`__ python packages. If you're running in a virtualenv or on a weird platform like Windows or
+MacOS, make sure that jupyter and pip agree where your python lives and the packages get installed in the right place.
+
+Afterwards, just run ``jupyter lab`` in the ``analysis/jupyter_notebooks`` directory. You can then open any of the
+notebooks through the left side panel and re-run the analysis within. Make sure you run all of the setup code at the top
+of the notebook once before trying to run the analaysis code in the cells below. The analysis code only uses standard
+scientific python packages that you probably already have installed. If you get an ``ImportError``, make sure the
+packages listed in the file ``analysis/jupyter_notebooks/requirements.txt`` are installed.
+
+The notebooks will display the plots and results inside Jupyter Lab and will also automatically export the plots to the
+``paper`` directory of your clone of the git repository.
+
+PCB Designs
+-----------
+
+This repo includes both the raw CAD files of the PCBs, as well as exported manufacturing data for easier viewing if you
+don't have KiCad installed. The schematics are included as PDF exports.
+
+The PCB designs were prepared in the open source KiCad_ EDA tool. Note that for some files you might need to download a
+KiCad nightly build depending on how new your KiCad version is.
+
+PCB design folder structure
+...........................
+
+``foobar.{kicad_pro,kicad_sch,kicad_pcb,etc.}``
+    The KiCad source files of the PCB. Open the ``.kicad_pro`` file in KiCad, then you can open the schematics and board
+    layout from there.
+
+``fab/gerbers.zip``
+    Gerber exports of the board layouts. You can open these in any Gerber viewer such as gerbv_. These files are
+    essentially vector graphics exports of the board layout. They show what copper, silkscreen etc. you see on the
+    board, but they don't include any semantic information such as component values. You can send this zip directly to a
+    PCB manufacturer and they will be able to manufacture these boards for you. The order parameters are included in the
+    gerber files on the ``User.Comments`` layer.
+
+``fab/{bom.csv,pos.csv}``
+    Bill of materials and component placement coordinate files for board manufacturing. If you want a contract
+    manufacturer to solder these boards for you, you need to give them these two files in addition to the gerbers. The
+    BOM tells them what exact parts and how many of them you need, the position file tells them where to put them on the
+    board. We had JLCPCB make the PCBs, and we also had them solder most of the parts. Some parts we soldered after the
+    fact by hand because JLC didn't have them in stock, and getting them to order and solder them for us would have been
+    pretty expensive.
+
+    If you want to solder the main PCB yourself, you need some prior experience in fine SMD work and a decently setup
+    electronics lab with a microscope, a hot air reworks station, etc.
+
+    Note: **The PCB revision here does not have a functional driver IC!** For our lab experiments we microsoldered
+    the four different driver ICs by hand to avoid having to spin multiple copies of this expensive PCB. For some basic
+    measurements, you can just omit the driver IC included in the design and bridge it. This will drive the mesh
+    directly from the ``74LVC2G157`` gates, which is enough for some basic measurements.
+
+``schematics/*.pdf``
+    PDF export of the schematics of the board.
+
+Firmware
+--------
+
+The firmware and associated scripts are contained in the ``firmware`` directory.
+
+Building the firmware
+.....................
+
+If you have an ARM GCC toolchain installed, you can build the firmware by running ``make`` in this directory. During
+build, the makefile exports some diagnostic information about the build artifacts. For that to work, you have to have
+the `cxxfilt python package <https://pypi.org/project/cxxfilt/>`__ installed. If the package can't be found, the
+firmware will still be built, but you will get a crash in the makefile during the analysis step that runs after the
+build was successful.
+
+Running experiments
+...................
+
+To run an experiment, you need a measurement board and a test coupon. You also need the following software installed on
+your machine:
+
+* ``openocd``
+* ``arm-none-eabi-gdb`` (another ABI arm gdb should work too)
+* The python packages listed in ``firmware/requirements.txt``
+
+To build the firmware, you additionally need a ARM toolchain installed. By default, the makefile assumes gcc/gnu
+binutils, but you can override that if you prefer to use LLVM.
+
+To run an experiment, connect the board to power via USB, and to your computer through an SWD debug adapter. We used
+cheap STLinkV2 clones, if you have a different adapter you'll have to modify the ``.gdbinit`` script accordingly. After
+connecting the board, open three terminal windows running the following three commands one per window, in this order.
+
+1. ``openocd -f openocd.cfg``
+2. ``arm-none-eabi-gdb build/main.elf``
+3. ``python adc_serve.py``
+
+This will connect to the board and start the realtime control and measurement web interface. You can open the web
+interface at the location printed by ``adc_serve.py`` on startup.
+
+If you're cheap like us and use a STLinkV2 clone SWD adapter, it may be that openocd takes a few (maybe up to five or
+so) attempts to start up and connect to the microcontroller. After starting, the GDB terminal should start printing a
+few lines of output every 30 seconds or so when it saves a measurement series. If GDB starts to hang, it might be that
+you bumped a cable or accidentially shorted something on the board. To re-start, you first kill gdb (Ctrl+C, then
+Ctrl+D, then Ctrl+D again), then you stop openocd (Ctrl+C, kill it if it doesn't stop in a few seconds), then you
+restart them in the order above. You don't have to restart the web interface, just adjust any of the knobs to overwrite
+the default control settings again.
+
+Firmware Folder Structure
+.........................
+
+``src/main.c``
+    The source code of the mainboard firmware. This firmware captures data into internal buffers, which are read out
+    from the host through SWD.
+
+``openocd.cfg``
+    OpenOCD script for connecting to the debug adapter. We used cheap STLinkV2 clones from aliexpress. If you use a
+    different debug adapter, you will have to modify this file accordingly to tell OpenOCD how to connect to the board.
+    The port numbers given here and in the ``.gdbinit`` must match up.
+
+``.gdbinit``
+    GDB script running the data extraction. This script will continuously dump the measurement data into ``/tmp`` every
+    time a measurement series has been completed. Note that this file will be hidden on unixes. Also note that you will
+    have to explicitly allowlist this file's absolute path on your computer in your ``$HOME/.gdbinit`` the first time
+    you run it because gdb refuses to run unknown ``.gdbinit`` files for security.
+
+``adc_serve.py``
+    Real-time monitoring and data capture tool. Before running this, first make sure you have gdb attached to the board
+    using the ``.gdbinit``. The tool communicates with the gdb script through files in ``/tmp``. It exposes a web
+    interface that displays the captured data in real time, allows you to change the board's measurement settings, and
+    allows you to export measurement series.
+
+``make_barcodes.py``
+    This is a helper script we used to create barcode labels for all ~120 test specimens to simplify the measurement
+    workflow. We had a barcode reader hooked up to the computer running the measurements, so you could just scan a
+    specimen's barcode to capture a data series registered to that board in the web interface.
+    
+other files:
+    Build files for the firmware. These are mostly generic to this type of microcontroller and are included here so the
+    firmware source is self-contained.
+
+.. _KiCad: https://www.kicad.org/
+.. _gerbv: https://gerbv.github.io/