docs(notebook): add show4dstem_colab.ipynb for one-click Colab workshop
Browse files- notebooks/show4dstem_colab.ipynb +145 -0
notebooks/show4dstem_colab.ipynb
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{
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"cells": [
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{
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"cell_type": "markdown",
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"id": "b5f2091f",
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"metadata": {},
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"source": [
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"# Workshop: Show4DSTEM from Hugging Face via `Dataset4dstem.from_tensor` (no local install needed)\n",
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"\n",
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"This notebook runs in **Google Colab** (or any Jupyter with internet + Chrome). You need\n",
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"only `quantem.widget` (TestPyPI rc) and `quantem` (dev fork; the `from_tensor`\n",
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"constructor lives on the `dataset-support-torch` branch). No CUDA, no h5, no\n",
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"`quantem.live`.\n",
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"\n",
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"[Open in Colab](https://colab.research.google.com/?url=https%3A%2F%2Fhuggingface.co%2Fdatasets%2Fbobleesj%2Fquantem-data%2Fresolve%2Fmain%2Fnotebooks%2Fshow4dstem_colab.ipynb)\n",
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"\n",
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"Flow: download a pre-binned NumPy 4D-STEM dataset from Hugging Face -> wrap it as a\n",
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"torch tensor -> `Dataset4dstem.from_tensor` carries the sampling -> `Show4DSTEM` renders\n",
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"in your browser via WebGPU. Drag the scan cursor; the diffraction pattern updates live."
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d9055753",
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"metadata": {},
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"outputs": [],
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"source": [
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"# quantem.widget rc from TestPyPI; quantem from the dev fork branch that\n",
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"# carries Dataset4dstem.from_tensor (the torch-native constructor).\n",
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"!pip install -q --pre --extra-index-url https://test.pypi.org/simple/ quantem.widget huggingface_hub\n",
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"!pip install -q git+https://github.com/bobleesj/quantem.git@dataset-support-torch"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "95dc87e5",
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"metadata": {},
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"outputs": [],
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"source": [
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"import quantem, quantem.widget\n",
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"print(\"quantem \", quantem.__version__)\n",
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"print(\"quantem.widget \", quantem.widget.__version__)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "590f83f1",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Download the pre-binned NumPy 4D-STEM dataset from Hugging Face. Public,\n",
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"# cached locally after the first run. ~302 MB; takes 5-30 s on Colab.\n",
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"import os, json\n",
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"import numpy as np\n",
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"from huggingface_hub import snapshot_download\n",
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"\n",
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"ASSET = \"gold_512_npy_bin8\" # or \"gold_512_npy_bin4\" for the larger 1.2 GB version\n",
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"folder = snapshot_download(\n",
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" \"bobleesj/quantem-data\",\n",
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" repo_type=\"dataset\",\n",
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" allow_patterns=[f\"4dstem/{ASSET}/*\"],\n",
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")\n",
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"asset_dir = os.path.join(folder, \"4dstem\", ASSET)\n",
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"data = np.load(os.path.join(asset_dir, \"data.npy\")) # (512, 512, 24, 24) uint16\n",
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"meta = json.load(open(os.path.join(asset_dir, \"meta.json\"))) # sampling + units + optics\n",
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"\n",
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"print(\"shape:\", data.shape, \"dtype:\", data.dtype)\n",
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"print(\"sampling:\", meta[\"sampling\"], meta[\"units\"])\n",
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"print(\"optics: voltage=%s kV, probe=%s mrad, CL=%s mm\" % (\n",
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" meta.get(\"voltage_kV\"), meta.get(\"probe_semiangle_mrad\"), meta.get(\"camera_length_mm\"),\n",
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"))"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "1e14a283",
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"metadata": {},
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"outputs": [],
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"source": [
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"# numpy -> torch tensor -> Dataset4dstem.from_tensor. The dataset carries\n",
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"# `sampling` + `units` so the widget paints the scale bar and axis labels.\n",
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"import torch\n",
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"from quantem.core.datastructures import Dataset4dstem\n",
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"\n",
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"dset = Dataset4dstem.from_tensor(\n",
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" torch.from_numpy(data),\n",
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" sampling=meta[\"sampling\"],\n",
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" units=meta[\"units\"],\n",
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" name=meta[\"name\"],\n",
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")\n",
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"print(\"dataset:\", type(dset).__name__, \"shape:\", dset.shape, \"sampling:\", dset.sampling)"
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]
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},
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{
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"cell_type": "code",
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"execution_count": null,
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"id": "d99029a3",
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"metadata": {},
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"outputs": [],
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"source": [
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"# Render in your browser via WebGPU. Drag the cursor in the real-space image on the\n",
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| 106 |
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"# left; the CBED on the right updates in real time.\n",
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"from quantem.widget import Show4DSTEM\n",
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"\n",
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"Show4DSTEM(dset)"
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]
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| 111 |
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},
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| 112 |
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{
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"cell_type": "markdown",
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| 114 |
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"id": "c1d194fd",
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| 115 |
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"metadata": {},
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| 116 |
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"source": [
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| 117 |
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"## What just happened\n",
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| 118 |
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"\n",
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| 119 |
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"1. Two `pip install` lines: `quantem.widget` (rc from TestPyPI) + `quantem` (dev fork\n",
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| 120 |
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" branch with the torch-native `Dataset4dstem.from_tensor`).\n",
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| 121 |
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"2. `snapshot_download` pulled a pre-binned NumPy file (~302 MB) from `bobleesj/quantem-data`.\n",
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| 122 |
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"3. `np.load` parsed it directly - no custom decompression, no h5 parser.\n",
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| 123 |
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"4. `Dataset4dstem.from_tensor` wrapped the torch tensor with sampling + units.\n",
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| 124 |
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"5. `Show4DSTEM` rendered it in your browser via WebGPU.\n",
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| 125 |
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"\n",
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| 126 |
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"No CUDA on Colab. No quantem.live. No private repos.\n",
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| 127 |
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"\n",
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| 128 |
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"## Try next\n",
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| 129 |
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"\n",
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| 130 |
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"- Swap `ASSET` to `\"gold_512_npy_bin4\"` for the sharper (larger, 1.2 GB) version.\n",
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| 131 |
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"- Try `gold_haadf_npy` with `Show2D` (a 2D HAADF image; same pattern, different widget).\n",
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| 132 |
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"- Bring your own 4D-STEM data: save as `(scan_row, scan_col, k_row, k_col)` NumPy +\n",
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| 133 |
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" a `meta.json` carrying sampling + units, and pass through the same pipeline."
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]
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| 135 |
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}
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],
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"metadata": {
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| 138 |
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"kernelspec": {
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| 139 |
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"display_name": "Python 3",
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| 140 |
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"name": "python3"
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}
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},
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"nbformat": 4,
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"nbformat_minor": 5
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}
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