docs(README): lead with TestPyPI quantem.widget + Colab; document npy_bin variants
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README.md
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# quantem-data
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Reference electron-microscopy datasets for [quantem.
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Two buckets:
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- **`4dstem/`** — 4D-STEM acquisitions
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- **`haadf/`** — HAADF survey images
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##
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```python
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from quantem.live import io
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from quantem.widget import Show4DSTEM
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import torch
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Show4DSTEM(torch.from_dlpack(data.data))
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# HAADF image
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Show2D(io.read_image(io.download("gold_haadf"))) # -> haadf/gold_haadf.emd
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```
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## Memory (VRAM)
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The
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loaded array**, set by `det_bin` (bins the detector on the fly):
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| det_bin | detector | loaded | peak VRAM | fits 16 GB? |
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| **2** |
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Show4DSTEM keeps the data on the GPU; cursor interaction is ~0.03 ms/frame.
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##
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- `4dstem/`: gold_512, gold_30mrad1.3mx04, gold_30mrad1.3mx06, gold_30mrad1.3mx07, gold_30mrad1.3mx09
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- `haadf/`: gold_haadf
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# quantem-data
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Reference electron-microscopy datasets for browsing and learning. Open them in your browser via [quantem.widget](https://github.com/bobleesj/quantem.widget) — **no quantem.live install needed**.
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Two buckets, that's it:
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- **`4dstem/`** — 4D-STEM acquisitions. `_npy_bin*` variants are pre-binned NumPy files for fast workshop / Colab demos; the originals are full Arina h5 bundles.
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- **`haadf/`** — HAADF survey images.
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## Quick start — Show4DSTEM in Google Colab (or any Jupyter)
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Workshop path: just `quantem.widget` from TestPyPI + `huggingface_hub`. No CUDA, no h5, no quantem.live.
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```python
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!pip install -q --pre --extra-index-url https://test.pypi.org/simple/ quantem.widget huggingface_hub
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import os, json, numpy as np, torch
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from huggingface_hub import snapshot_download
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from quantem.widget import Show4DSTEM
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# Pre-binned NumPy bundle — fast download, no decompression needed.
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folder = snapshot_download(
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"bobleesj/quantem-data",
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repo_type="dataset",
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allow_patterns=["4dstem/gold_512_npy_bin8/*"],
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)
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asset = os.path.join(folder, "4dstem", "gold_512_npy_bin8")
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data = np.load(os.path.join(asset, "data.npy")) # (512, 512, 24, 24) uint16, ~300 MB
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meta = json.load(open(os.path.join(asset, "meta.json"))) # sampling + units
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Show4DSTEM(torch.from_numpy(data), sampling=meta["sampling"], units=meta["units"])
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```
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Drag the scan cursor in the real-space image; the CBED updates in real time. Chrome works best (WebGPU).
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For HAADF use `Show2D` with `quantem.live.io.read_image` (or load the `.emd` directly with `hyperspy`).
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## Datasets
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| name | kind | shape | dtype | size | use |
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|---|---|---|---|---|---|
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| `4dstem/gold_512_npy_bin8/` | NumPy bundle | (512, 512, 24, 24) | uint16 | ~302 MB | workshop / Colab demo |
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| `4dstem/gold_512_npy_bin4/` | NumPy bundle | (512, 512, 48, 48) | uint16 | ~1.2 GB | sharper version |
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| `4dstem/gold_512/` | Arina h5 (full) | (512, 512, 192, 192) | uint16 | ~5 GB | power user, full data |
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| `4dstem/gold_30mrad1.3mx04` …`09` | Arina h5 (full) | smaller scans | uint16 | ~5 GB each | series demo |
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| `haadf/gold_haadf.emd` | Velox EMD | (4096, 4096) | float32 | a few MB | Show2D |
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Each `_npy_*` bundle ships a `meta.json` next to `data.npy`: `shape`, `dtype`, `sampling`, `units`, `bin_factor`, original source.
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## Power-user path (full data, GPU decompression)
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If you have an NVIDIA GPU and want the full uncooked h5 path, install `quantem.live` (private):
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```python
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from quantem.live import io
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from quantem.widget import Show4DSTEM
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import torch
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folder = io.download("gold_512") # → 4dstem/gold_512/
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result = io.load(io.discover_masters(folder)[0], det_bin=2) # GPU decompression
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Show4DSTEM(torch.from_dlpack(result.data))
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```
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Same data, full Arina h5, decompressed on the GPU. Faster + full resolution.
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## Memory (VRAM) for the full h5
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The Arina h5 sets are 512×512×192×192. Peak VRAM is about 1.4× the loaded array; control with `det_bin`:
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| `det_bin` | detector | loaded | peak VRAM | fits 16 GB? |
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| 1 | 192×192 | 18 GB | ~25 GB | no |
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| **2** | 96×96 | 4.5 GB | **~6.9 GB** | **yes** |
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| 4 | 48×48 | 1.1 GB | ~2.2 GB | yes |
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| 8 | 24×24 | 0.3 GB | ~0.5 GB | yes (good for flipping through many) |
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Show4DSTEM keeps the data on the GPU; cursor interaction is ~0.03 ms/frame.
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## Licence
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CC-BY-4.0. Cite quantem.live / quantem.widget if you use these in a publication.
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