| --- |
| license: mit |
| tags: |
| - electron-microscopy |
| - 4D-STEM |
| - materials-science |
| - quantem |
| pretty_name: quantem-data |
| --- |
| |
| # quantem-data |
|
|
| This repo is currently used primarily by |
| **[quantem.widget](https://github.com/electronmicroscopy/quantem.widget)** |
| (tutorial notebooks and `quantem.widget.datasets`). Other QuantEM packages |
| may use it later. Keys, the checker, and these instructions can grow as |
| we take more Community pull requests. Use the current required keys for |
| new PRs. |
|
|
| Public electron-microscopy data. MIT license. Downloads need no token. |
| This page is the upload and download protocol. |
|
|
| ## Download |
|
|
| ```python |
| from quantem.widget.datasets import show4dstem_gold |
| |
| ds = show4dstem_gold(size="small") |
| ``` |
|
|
| Notebook: [Example Data](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/tutorials/download_data.ipynb). |
|
|
| ## Add data (Hugging Face pull request) |
|
|
| Anyone with a Hugging Face account can add data. We follow a pull request |
| process. Do not use `quantem.widget.io.upload`. |
|
|
| Downloads need no token. Opening a pull request does. Create an account, |
| then a token at |
| [huggingface.co/settings/tokens](https://huggingface.co/settings/tokens). |
| Use a **Write** token (classic). A **Read** token can download; it cannot |
| open a PR. A fine-grained token also works if `--create-pr` is allowed on |
| a public dataset. You do not need collaborator access to this repo. |
|
|
| ```bash |
| pip install huggingface_hub # skip if `hf` is already on PATH |
| hf auth login |
| ``` |
|
|
| Paste the token. The prompt hides it. When asked `Add token as git |
| credential? [y/N]`, answer `n`. `hf upload` reads |
| `~/.cache/huggingface/token`. You do not need a git credential helper. |
| Ignore any hint to run `git config --global credential.helper store`. |
|
|
| ```bash |
| hf auth whoami |
| ``` |
|
|
| That should print your username. If you already logged in with a Read |
| token, run `hf auth login --force` and paste a Write token. If |
| `--create-pr` returns 403 after a valid login, the token is Read or the |
| fine-grained scopes omit Community PRs; make a Write token and login |
| again. On SSH (no browser on that machine), paste a token. Do not use the |
| browser login unless the browser and `hf` run on the same machine. Do not |
| commit the token. |
|
|
| A PR is the data file(s) plus one `meta.json`. Example already on the hub |
| (2 files): |
|
|
| ```text |
| widget-tutorials/show4dstem/gold-512-bin4/full/data.npy |
| widget-tutorials/show4dstem/gold-512-bin4/full/meta.json |
| ``` |
|
|
| One EMD: `gold_haadf.emd` + `meta.json` (2 files). A session folder: the |
| `.emd` files + `meta.json`. |
|
|
| Copy this `meta.json`. Required: `name`, `source`, `date`, `sample`, |
| `shape`, `dtype`, `permission`. Optional: `sampling`, `units`, optics. |
| Omit a key if unknown. Do not invent a number. |
|
|
| `shape` is `[row, col]` for an image, `[frame, row, col]` for a stack, or |
| `[scan_row, scan_col, det_row, det_col]` for 4D-STEM. `dtype` is the NumPy |
| name of the stored array (or of the EMD image). Examples already on this |
| repo: |
|
|
|
|
| | Data | `shape` | `dtype` | |
| | ------------------------- | -------------------- | -------- | |
| | 2D HAADF (`gold-haadf`) | `[4096, 4096]` | `uint16` | |
| | 4D-STEM (`gold-512-bin4`) | `[512, 512, 48, 48]` | `uint16` | |
| | One EMD HAADF | `[4096, 4096]` | `uint16` | |
|
|
|
|
| Processed float data uses `"float32"`. Read both values from the file |
| (`arr.shape`, `arr.dtype`, or the EMD image) and copy them into |
| `meta.json`. |
|
|
| Replace every placeholder in this example: |
|
|
| ```json |
| { |
| "name": "<public dataset name>", |
| "source": "<public-facing microscope, facility, and acquisition description>", |
| "date": "<YYYY-MM-DD>", |
| "sample": "<sample description>", |
| "shape": [512, 512, 48, 48], |
| "dtype": "uint16", |
| "permission": { |
| "received": true, |
| "from": ["<person who granted permission>"], |
| "collectors": ["<data collector>"], |
| "date": "<YYYY-MM-DD>" |
| }, |
| "sampling": [0.5, 0.5, 1.84, 1.84], |
| "units": ["A", "A", "mrad", "mrad"], |
| "voltage_kV": 300, |
| "semiangle_mrad": 30, |
| "camera_length_mm": 91 |
| } |
| ``` |
|
|
| `source` is a public-facing microscope, facility, and acquisition description; |
| omit local paths and non-public filenames. `date` is the acquisition day |
| (`YYYY-MM-DD`). `permission.received` must be `true`. `from` is who granted |
| the share (one name or several). `collectors` is who used the instrument |
| (one name or several). `permission.date` is when that share was granted. |
|
|
| ```bash |
| python -m check_meta ./gold-512-bin4 |
| hf upload bobleesj/quantem-data ./gold-512-bin4 \ |
| widget-tutorials/show4dstem/gold-512-bin4/full \ |
| --repo-type dataset --create-pr |
| ``` |
|
|
| Run `python -m check_meta` from a checkout of this dataset so the |
| `check_meta/` package is importable. `./gold-512-bin4` is your local |
| folder (`data.npy` + `meta.json`). The last `hf upload` path is the |
| folder on this repo. The hub path is |
| `widget-tutorials/<widget>/<name>/<size>/`. For a new ShowBragg set that |
| would be `widget-tutorials/showbragg/<name>/full`. Size is `small`, |
| `medium`, `large`, or `full`. Use `widget-tutorials/shared/` only when |
| more than one widget will read the same files. |
|
|
| `python -m check_meta` must print `ok` or do not open the PR. Resume a stopped |
| upload with `--revision refs/pr/N` (do not pass `--create-pr` again). |
| Merge is on the |
| [Community tab](https://huggingface.co/datasets/bobleesj/quantem-data/discussions). |
|
|
| ### Coding agents |
|
|
| A coding agent can open the Community pull request. The human creates the |
| Write token and attests permission. The agent does not invent |
| `permission.*`, `sampling`, or optics. The agent does not run |
| `hf auth login` (that prompt is interactive). The agent does not write the |
| token into a repository file. |
|
|
| ```bash |
| # human already ran `hf auth login` or exported HF_TOKEN (Write) |
| hf auth whoami |
| hf download bobleesj/quantem-data --repo-type dataset \ |
| --include "check_meta/**" --include "templates/meta.json" \ |
| --local-dir ./quantem-data-tools |
| export PYTHONPATH="$PWD/quantem-data-tools${PYTHONPATH:+:$PYTHONPATH}" |
| python -m check_meta ./gold-512-bin4 |
| hf upload bobleesj/quantem-data ./gold-512-bin4 \ |
| widget-tutorials/show4dstem/gold-512-bin4/full \ |
| --repo-type dataset --create-pr \ |
| --commit-message "add show4dstem gold-512-bin4 full tutorial data" |
| ``` |
|
|
| `hf auth whoami` must print a username. If it fails or `--create-pr` |
| returns 403, stop and ask the human for a Write token (`export HF_TOKEN=...`). |
| If `python -m check_meta` is not `ok`, stop. After the upload, give the |
| human the Community URL. Do not merge. |
|
|
| Copy this prompt into your coding agent. Replace every placeholder before |
| submitting it. Do not paste a Hugging Face token into the prompt. |
|
|
| ```text |
| Add these files to the public Hugging Face dataset bobleesj/quantem-data |
| as a Community pull request. |
| |
| Local folder: |
| <path to a folder that already contains the data files and will get meta.json> |
| |
| Target hub path: |
| widget-tutorials/<widget-or-shared>/<name>/<size>/ |
| |
| Permission (required; do not invent): |
| - I collected this data myself: <yes/no> |
| - permission.from: <name or list> |
| - permission.collectors: <name or list> |
| - permission.date: <YYYY-MM-DD> |
| - I have written permission from the collector: <yes, or "I collected it"> |
| |
| Follow the current Add data and Coding agents instructions on this dataset |
| card. Do not use quantem.widget.io.upload. Do not commit .npy or .emd into |
| electronmicroscopy/quantem.widget. |
| |
| 1. Confirm `hf auth whoami` prints a username. If it fails, stop and ask me |
| to create a Write token and run `hf auth login`, or export `HF_TOKEN`. |
| Do not run an interactive login yourself or write the token into a repo. |
| 2. Download the checker and template, then copy the template into the folder: |
| |
| hf download bobleesj/quantem-data --repo-type dataset \ |
| --include "check_meta/**" --include "templates/meta.json" \ |
| --local-dir ./quantem-data-tools |
| cp ./quantem-data-tools/templates/meta.json <folder>/meta.json |
| |
| 3. Fill every required field in `<folder>/meta.json` from the files and the |
| permission lines above. Read shape and dtype from the array or EMD. Omit |
| optional values when unknown; do not invent them. Do not put a local path |
| or credential in `meta.json`. Validate it: |
| |
| export PYTHONPATH="$PWD/quantem-data-tools${PYTHONPATH:+:$PYTHONPATH}" |
| python -m check_meta <folder> |
| |
| Stop unless validation prints `ok`. |
| 4. Open the Community pull request: |
| |
| hf upload bobleesj/quantem-data <folder> \ |
| widget-tutorials/<widget-or-shared>/<name>/<size>/ \ |
| --repo-type dataset --create-pr \ |
| --commit-message "add <widget> <name> <size> tutorial data" |
| 5. Give me the Community URL. Do not merge. Open a GitHub PR only if a named |
| loader is also needed in `quantem.widget.datasets`; that PR waits until |
| this Hugging Face PR merges. A new widget is discuss-first. |
| ``` |
|
|
| If a notebook should call `quantem.widget.datasets`, open a GitHub PR after |
| this one merges: |
| [Contribute tutorial data](https://github.com/electronmicroscopy/quantem.widget/blob/main/docs/tutorials/contribute_data.md). |
|
|
| Colab: [Show4DSTEM](https://colab.research.google.com/gist/bobleesj/54864ce5b2a6f0a4fd5ae1e5d5719b45/show4dstem_colab.ipynb) |
| · [Workshop v1](https://colab.research.google.com/gist/bobleesj/a05a90185c6cddbb331342cae6d7e9c1/berk_workshop_v1.ipynb) |
|
|
| ## Acquisition parameters |
|
|
| The 20260423 drift session optics are confirmed via the session HAADF EMD. |
| 4D-STEM `scan_sampling` is an operator pattern from a sibling SSB session. |
|
|
|
|
| | dataset | voltage | probe | CL | scan | scan sampling | det pitch | mag | |
| | -------------------------------- | -------- | --------- | ------- | ----------- | -------------- | ------------ | ----------- | |
| | `haadf/gold_haadf_npy` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 4096² image | 0.0186 nm/px | n/a | FOV 76.2 nm | |
| | `4dstem/gold_512_npy_bin8` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 3.68 mrad/px | unknown | |
| | `4dstem/gold_512_npy_bin4` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 1.84 mrad/px | unknown | |
| | `4dstem/gold_512` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 512² | 0.5 Å (op) | 0.46 mrad/px | unknown | |
| | `4dstem/gold_30mrad1.3mx04`…`09` | 300 kV | 30 mrad | 91 mm | smaller | (session yaml) | 0.46 mrad/px | 1.3 Mx | |
| | `haadf/gold_haadf.emd` | 300 kV ✓ | 30 mrad ✓ | 91 mm ✓ | 4096² image | 0.0186 nm/px | n/a | FOV 76.2 nm | |
|
|
|
|
| ✓ = confirmed via EMD/yaml. `(op)` = operator pattern, not file-certified. |
|
|
| ## License |
|
|
| Files on this repo are published under **MIT**. |
|
|
| **You must have explicit written permission from the person who collected |
| the data before you open a pull request**, unless you collected the data |
| yourself. Put that receipt in `meta.json` (`permission.received`, |
| `permission.from`, `permission.collectors`, `permission.date`). If you |
| collected it yourself, set `from` and `collectors` to your name. |
|
|
| Do not open a pull request without that permission. `python -m check_meta` |
| must print `ok`. |
|
|
