twhy 0.2.0__tar.gz

twhy-0.2.0/LICENSE

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twhy-0.2.0/MANIFEST.in

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+include environment.yml
+recursive-include docs *.md
+recursive-include examples *.py
+recursive-include tests *.py

twhy-0.2.0/PKG-INFO

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+Metadata-Version: 2.4
+Name: twhy
+Version: 0.2.0
+Summary: Zoomable microscopy, image and PDF previews in a text terminal
+Author: Jason L Weirather
+License-Expression: Apache-2.0
+Project-URL: Repository, https://github.com/jason-weirather/twhy
+Project-URL: Issues, https://github.com/jason-weirather/twhy/issues
+Requires-Python: >=3.11
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: click<9,>=8.1
+Requires-Dist: coolname<6,>=2.2
+Requires-Dist: numpy<3,>=1.26.4
+Requires-Dist: scipy<2,>=1.14
+Requires-Dist: omeify>=0.22.1
+Requires-Dist: pillow<13,>=11.3
+Requires-Dist: pypdfium2<6,>=4.30
+Requires-Dist: prompt-toolkit<4,>=3.0.52
+Requires-Dist: wcwidth>=0.2.13
+Provides-Extra: s3
+Requires-Dist: omeify[s3]>=0.22.1; extra == "s3"
+Provides-Extra: dev
+Requires-Dist: pytest<10,>=8; extra == "dev"
+Requires-Dist: pytest-asyncio>=0.24; extra == "dev"
+Requires-Dist: pytest-cov>=5; extra == "dev"
+Requires-Dist: pexpect>=4.9; sys_platform != "win32" and extra == "dev"
+Requires-Dist: ruff>=0.12; extra == "dev"
+Requires-Dist: build>=1.2; extra == "dev"
+Dynamic: license-file
+
+# twhy
+
+**Whole-slide microscopy, ordinary images, and scientific PDFs, right in your terminal.**
+
+`twhy` is a zoomable, full-screen image viewer made of *actual terminal characters*. Open an OME-TIFF, SVS, or OME-Zarr slide, explore multichannel fluorescence, inspect a PNG, or page through a PDF. No browser, image server, X11, graphics protocol, or GPU required.
+
+I had a use case for this on a remote cluster with thousands of images. Sometimes
+I just needed the tissue's shape, a rough count of regions of interest, or to tell
+a big chunk of tissue from a few tiny core needle biopsies. An ASCII-art
+representation of a preview from the image pyramid seemed like it would do the job.
+
+Then working in tmux, switching the active area of the terminal with either the
+mouse or keyboard, got me wondering... just how far can we push a text-based image
+viewer? And thus began `twhy`. I've been having a little fun with AI slop along
+the way, and now it opens PDFs and lets me draw polygons on pathology images.
+It's ridiculous, but I'm actually going to use it.
+
+<p align="center">
+  <a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/pathology.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/pathology.gif" width="900" alt="Real recording of twhy zooming through multiplex immunofluorescence and revealing CD8 signal in cyan on blue DAPI nuclei"></a>
+</p>
+<p align="center"><em>Real terminal footage: 59-channel multiplex microscopy, DAPI and CD8. Channel selection and zoom, no mock interface.</em></p>
+
+## See it in action
+
+These are short, automatically looping recordings of `twhy` itself. Click any clip to view it at full GIF size.
+
+<table>
+<tr>
+<td width="50%" valign="top">
+<strong>Whole-slide H&amp;E SVS</strong><br>
+<a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/he.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/he.gif" width="440" alt="twhy zooming from an SVS whole-slide tissue overview to individual nuclei in a real H&E image"></a><br>
+<small>Zoom from whole-slide tissue context into individual nuclei.</small>
+</td>
+<td width="50%" valign="top">
+<strong>An ordinary PNG. Featuring a cat.</strong><br>
+<a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/cat.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/cat.gif" width="440" alt="twhy zooming into an orange-and-white cat in a sunlit windowsill illustration"></a><br>
+<small>PNG, JPEG, WebP: zoom and pan familiar images, too.</small>
+</td>
+</tr>
+<tr>
+<td width="50%" valign="top">
+<strong>A scientific PDF</strong><br>
+<a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/pdf.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/pdf.gif" width="440" alt="twhy switching pages in a scientific PDF and zooming into a transformer architecture diagram"></a><br>
+<small>Turn pages, then zoom into figures. PDF support is standard.</small>
+</td>
+<td width="50%" valign="top">
+<strong>Polygon selections</strong><br>
+<a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/selection.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/selection.gif" width="440" alt="twhy drawing a yellow polygon selection around a tissue core and preparing it for GeoJSON export"></a><br>
+<small>Select rectangles or polygons; export GeoJSON, text, ANSI art, or PNG.</small>
+</td>
+</tr>
+</table>
+
+## Install
+
+Python **3.11+**. The **PyPI distribution**, terminal command, and Python import all share the name `twhy`.
+
+Install the standalone command without changing packages in a scientific Python environment:
+
+```bash
+uv tool install twhy
+# or: pipx install twhy
+# or: python -m pip install twhy
+```
+
+From a cloned checkout, for development:
+
+```bash
+python -m pip install -e '.[dev]'
+```
+
+PDF support is **included** in the standard install. No special extra or system PDF converter is needed.
+
+## Quickstart
+
+```bash
+twhy photo.png                         # PNG, JPEG, WebP, and more
+twhy paper.pdf                         # page navigation and progressive detail
+twhy slide.svs                         # Aperio whole-slide RGB
+twhy slide.ome.tif                     # OME-TIFF, grayscale or multichannel
+twhy /data/sample.ome.zarr             # local OME-Zarr
+
+# Compose two fluorescence channels with chosen colors:
+twhy slide.ome.tif --channel 0 --channel 2 \
+  --channel-color 0 blue --channel-color 2 cyan
+```
+
+The initial view fits the image. Wheel zoom is anchored to the pointer; pan with the mouse or arrow keys. The terminal sidebar keeps channels, colors, and contrast controls at hand.
+
+## Why a terminal viewer?
+
+- **Whole-slide without whole-slide RAM use:** regional TIFF/SVS reads and pyramids, with bounded previews and useful zoomed-out overviews.
+- **Multichannel, not just RGB:** select channels, change pseudocolors, and adjust each marker's display window and gamma without modifying source pixels.
+- **PDFs and everyday images:** ordinary images use in-memory pyramids; PDFs refine progressively from a quick preview to higher-detail pages.
+- **Real characters:** colored `▀` half-blocks, Braille detail, shape-oriented Unicode art, and portable ASCII modes.
+- **Selection and export:** copy/save terminal text, colored ANSI, shareable PNGs, and GeoJSON polygons/rectangles.
+- **Reusable Python library:** sampling, intensity normalization, composition, and rendering are available without opening the interactive terminal UI.
+
+`twhy` works over ordinary terminal sessions, including environments where a desktop image viewer is inconvenient. It is an exploratory display, **not a color-managed diagnostic viewer** and not a substitute for measuring the original pixels.
+
+## The keys you'll actually use
+
+| Action | Key or gesture |
+|---|---|
+| Zoom; pan; fit image | Wheel or `+`/`-`; arrows or drag; `r`/Home |
+| Next/previous PDF page or OME series | `]` / `[` or PageDown / PageUp; `p` to jump |
+| Toggle a channel; focus another | Click channel/Space; `,` and `.` |
+| Adjust channel color or contrast | `h` (hue); `l`/`u` (limits); `g` (gamma); `a` (auto window) |
+| Switch artwork / strict ASCII | `m` / `M`; `t` toggles artwork color; `f` toggles fullscreen |
+| Select region | `s` rectangle; `v` polygon |
+| Export a selection | `y/Y` text, `i/I` PNG, `t/T` ANSI, `j/J` GeoJSON (copy/save) |
+| Help or quit | `?` / `q` |
+
+## From terminal annotations to full-resolution ROIs
+
+The useful part of the joke: draw regions in `twhy`, save their coordinates as
+GeoJSON, and let [Omeify](https://github.com/jason-weirather/omeify) extract them
+from the original image. This example uses a calibrated OME-TIFF, series 0.
+You also need the `omeify` command on your PATH; with isolated tool installs,
+install it separately using `uv tool install omeify`.
+
+```bash
+# Open the source and choose where to save the annotations.
+twhy slide.ome.tif --series 0 --output-geojson-clip regions.geojson
+```
+
+Zoom to the view you need, then press **`s`** for a rectangle or **`v`** for a
+polygon and draw. Close a polygon with **Enter**; **`a`** adds another region in
+the same view. Press **Shift+J** to save all the regions before quitting.
+
+```bash
+# Export one full-resolution image per region, with lossless compression.
+omeify crop slide.ome.tif --series 0 \
+  --geojson regions.geojson -o regions.ome.tif \
+  --shatter by_index --compression Deflate --no-overwrite
+```
+
+This writes `regions-01.ome.tif`, `regions-02.ome.tif`, and so on, retaining all
+channels from the selected series. Omit `--shatter by_index` to put the regions
+into separate image series in one OME-TIFF instead.
+
+**Full-resolution pixels, not a screenshot:** Omeify reads the original image,
+not the terminal preview. Polygon crops use their **bounding rectangles**, not
+polygon masks; keep the GeoJSON for the outlines. Use the same source image,
+series, and orientation in both steps. Annotation placement follows the terminal
+grid, so zoom in before drawing for finer boundaries.
+[More crop options](https://github.com/jason-weirather/omeify/blob/main/docs/regions.md).
+
+## Supported files
+
+| Format | What twhy does |
+|---|---|
+| OME-TIFF | Regional, pyramidal microscopy viewing and channel composition |
+| Aperio SVS | RGB whole-slide viewing using available stored levels |
+| OME-Zarr | Local and HTTP(S) stores, regional chunk reads, supported NGFF multiscales |
+| PNG, JPEG, WebP, BMP, TGA, PPM | Ordinary raster viewing with zoom and pan |
+| GIF, APNG, animated WebP | View a selected frame (not animation playback) |
+| PDF | Navigate pages; progressively improve raster detail; copy embedded text from a rectangular selection |
+
+For advanced flags, channel/series semantics, color modes, cache limits, clipboard behavior, and format caveats, use the **[full reference](https://github.com/jason-weirather/twhy/blob/main/docs/reference.md)**. Architecture notes are in [docs/architecture.md](https://github.com/jason-weirather/twhy/blob/main/docs/architecture.md).
+
+## Try a synthetic microscopy example
+
+The repo includes a deterministic fixture generator that creates public-safe, synthetic tissue-like RGB and multichannel OME-TIFFs. It is a renderer demonstration, not a biological simulation.
+
+```bash
+python examples/make_demo.py --output-directory /tmp/twhy-demo
+twhy /tmp/twhy-demo/synthetic-mif.ome.tif --channel 0 --channel 2
+```
+
+## Python API
+
+```python
+import numpy as np
+from twhy import TextRenderer
+
+pixels = np.linspace(0, 1, 256**2).reshape(256, 256)
+frame = TextRenderer(mode="detail", color=False).render(pixels, columns=80)
+print(frame.to_text())
+```
+
+## Optional remote sources
+
+Local files are the main workflow. `twhy` also supports HTTP(S) images/PDFs (bounded download) and HTTP(S) OME-Zarr (regional chunk reads). For native S3 or S3-compatible stores, install `twhy[s3]` and use your normal AWS credentials or an endpoint override. No S3 setup is needed for local images, slides, or PDFs. [Remote input reference](https://github.com/jason-weirather/twhy/blob/main/docs/reference.md#local-and-remote-inputs).
+
+## Release media and provenance
+
+These GIFs are edited recordings of the real `twhy` terminal viewer. Showcase sources:
+
+- **mIF:** Tan, Y. & Kempchen, T. (2024), [*SPACEc demo dataset*](https://doi.org/10.5061/dryad.brv15dvj1), Dryad.
+- **H&E whole-slide demo:** `CMU-1.svs`, [OpenSlide test data](https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/), Carnegie Mellon University, CC0 1.0.
+- **PDF:** Vaswani, A. et al. (2017), [*Attention Is All You Need*](https://arxiv.org/abs/1706.03762), NeurIPS.
+- **Cat:** Illustration generated with ChatGPT (OpenAI).
+
+## License
+
+Apache-2.0. See [LICENSE](https://github.com/jason-weirather/twhy/blob/main/LICENSE).

twhy-0.2.0/README.md

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+# twhy
+
+**Whole-slide microscopy, ordinary images, and scientific PDFs, right in your terminal.**
+
+`twhy` is a zoomable, full-screen image viewer made of *actual terminal characters*. Open an OME-TIFF, SVS, or OME-Zarr slide, explore multichannel fluorescence, inspect a PNG, or page through a PDF. No browser, image server, X11, graphics protocol, or GPU required.
+
+I had a use case for this on a remote cluster with thousands of images. Sometimes
+I just needed the tissue's shape, a rough count of regions of interest, or to tell
+a big chunk of tissue from a few tiny core needle biopsies. An ASCII-art
+representation of a preview from the image pyramid seemed like it would do the job.
+
+Then working in tmux, switching the active area of the terminal with either the
+mouse or keyboard, got me wondering... just how far can we push a text-based image
+viewer? And thus began `twhy`. I've been having a little fun with AI slop along
+the way, and now it opens PDFs and lets me draw polygons on pathology images.
+It's ridiculous, but I'm actually going to use it.
+
+<p align="center">
+  <a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/pathology.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/pathology.gif" width="900" alt="Real recording of twhy zooming through multiplex immunofluorescence and revealing CD8 signal in cyan on blue DAPI nuclei"></a>
+</p>
+<p align="center"><em>Real terminal footage: 59-channel multiplex microscopy, DAPI and CD8. Channel selection and zoom, no mock interface.</em></p>
+
+## See it in action
+
+These are short, automatically looping recordings of `twhy` itself. Click any clip to view it at full GIF size.
+
+<table>
+<tr>
+<td width="50%" valign="top">
+<strong>Whole-slide H&amp;E SVS</strong><br>
+<a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/he.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/he.gif" width="440" alt="twhy zooming from an SVS whole-slide tissue overview to individual nuclei in a real H&E image"></a><br>
+<small>Zoom from whole-slide tissue context into individual nuclei.</small>
+</td>
+<td width="50%" valign="top">
+<strong>An ordinary PNG. Featuring a cat.</strong><br>
+<a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/cat.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/cat.gif" width="440" alt="twhy zooming into an orange-and-white cat in a sunlit windowsill illustration"></a><br>
+<small>PNG, JPEG, WebP: zoom and pan familiar images, too.</small>
+</td>
+</tr>
+<tr>
+<td width="50%" valign="top">
+<strong>A scientific PDF</strong><br>
+<a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/pdf.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/pdf.gif" width="440" alt="twhy switching pages in a scientific PDF and zooming into a transformer architecture diagram"></a><br>
+<small>Turn pages, then zoom into figures. PDF support is standard.</small>
+</td>
+<td width="50%" valign="top">
+<strong>Polygon selections</strong><br>
+<a href="https://github.com/jason-weirather/twhy/blob/main/docs/media/selection.gif"><img src="https://raw.githubusercontent.com/jason-weirather/twhy/main/docs/media/selection.gif" width="440" alt="twhy drawing a yellow polygon selection around a tissue core and preparing it for GeoJSON export"></a><br>
+<small>Select rectangles or polygons; export GeoJSON, text, ANSI art, or PNG.</small>
+</td>
+</tr>
+</table>
+
+## Install
+
+Python **3.11+**. The **PyPI distribution**, terminal command, and Python import all share the name `twhy`.
+
+Install the standalone command without changing packages in a scientific Python environment:
+
+```bash
+uv tool install twhy
+# or: pipx install twhy
+# or: python -m pip install twhy
+```
+
+From a cloned checkout, for development:
+
+```bash
+python -m pip install -e '.[dev]'
+```
+
+PDF support is **included** in the standard install. No special extra or system PDF converter is needed.
+
+## Quickstart
+
+```bash
+twhy photo.png                         # PNG, JPEG, WebP, and more
+twhy paper.pdf                         # page navigation and progressive detail
+twhy slide.svs                         # Aperio whole-slide RGB
+twhy slide.ome.tif                     # OME-TIFF, grayscale or multichannel
+twhy /data/sample.ome.zarr             # local OME-Zarr
+
+# Compose two fluorescence channels with chosen colors:
+twhy slide.ome.tif --channel 0 --channel 2 \
+  --channel-color 0 blue --channel-color 2 cyan
+```
+
+The initial view fits the image. Wheel zoom is anchored to the pointer; pan with the mouse or arrow keys. The terminal sidebar keeps channels, colors, and contrast controls at hand.
+
+## Why a terminal viewer?
+
+- **Whole-slide without whole-slide RAM use:** regional TIFF/SVS reads and pyramids, with bounded previews and useful zoomed-out overviews.
+- **Multichannel, not just RGB:** select channels, change pseudocolors, and adjust each marker's display window and gamma without modifying source pixels.
+- **PDFs and everyday images:** ordinary images use in-memory pyramids; PDFs refine progressively from a quick preview to higher-detail pages.
+- **Real characters:** colored `▀` half-blocks, Braille detail, shape-oriented Unicode art, and portable ASCII modes.
+- **Selection and export:** copy/save terminal text, colored ANSI, shareable PNGs, and GeoJSON polygons/rectangles.
+- **Reusable Python library:** sampling, intensity normalization, composition, and rendering are available without opening the interactive terminal UI.
+
+`twhy` works over ordinary terminal sessions, including environments where a desktop image viewer is inconvenient. It is an exploratory display, **not a color-managed diagnostic viewer** and not a substitute for measuring the original pixels.
+
+## The keys you'll actually use
+
+| Action | Key or gesture |
+|---|---|
+| Zoom; pan; fit image | Wheel or `+`/`-`; arrows or drag; `r`/Home |
+| Next/previous PDF page or OME series | `]` / `[` or PageDown / PageUp; `p` to jump |
+| Toggle a channel; focus another | Click channel/Space; `,` and `.` |
+| Adjust channel color or contrast | `h` (hue); `l`/`u` (limits); `g` (gamma); `a` (auto window) |
+| Switch artwork / strict ASCII | `m` / `M`; `t` toggles artwork color; `f` toggles fullscreen |
+| Select region | `s` rectangle; `v` polygon |
+| Export a selection | `y/Y` text, `i/I` PNG, `t/T` ANSI, `j/J` GeoJSON (copy/save) |
+| Help or quit | `?` / `q` |
+
+## From terminal annotations to full-resolution ROIs
+
+The useful part of the joke: draw regions in `twhy`, save their coordinates as
+GeoJSON, and let [Omeify](https://github.com/jason-weirather/omeify) extract them
+from the original image. This example uses a calibrated OME-TIFF, series 0.
+You also need the `omeify` command on your PATH; with isolated tool installs,
+install it separately using `uv tool install omeify`.
+
+```bash
+# Open the source and choose where to save the annotations.
+twhy slide.ome.tif --series 0 --output-geojson-clip regions.geojson
+```
+
+Zoom to the view you need, then press **`s`** for a rectangle or **`v`** for a
+polygon and draw. Close a polygon with **Enter**; **`a`** adds another region in
+the same view. Press **Shift+J** to save all the regions before quitting.
+
+```bash
+# Export one full-resolution image per region, with lossless compression.
+omeify crop slide.ome.tif --series 0 \
+  --geojson regions.geojson -o regions.ome.tif \
+  --shatter by_index --compression Deflate --no-overwrite
+```
+
+This writes `regions-01.ome.tif`, `regions-02.ome.tif`, and so on, retaining all
+channels from the selected series. Omit `--shatter by_index` to put the regions
+into separate image series in one OME-TIFF instead.
+
+**Full-resolution pixels, not a screenshot:** Omeify reads the original image,
+not the terminal preview. Polygon crops use their **bounding rectangles**, not
+polygon masks; keep the GeoJSON for the outlines. Use the same source image,
+series, and orientation in both steps. Annotation placement follows the terminal
+grid, so zoom in before drawing for finer boundaries.
+[More crop options](https://github.com/jason-weirather/omeify/blob/main/docs/regions.md).
+
+## Supported files
+
+| Format | What twhy does |
+|---|---|
+| OME-TIFF | Regional, pyramidal microscopy viewing and channel composition |
+| Aperio SVS | RGB whole-slide viewing using available stored levels |
+| OME-Zarr | Local and HTTP(S) stores, regional chunk reads, supported NGFF multiscales |
+| PNG, JPEG, WebP, BMP, TGA, PPM | Ordinary raster viewing with zoom and pan |
+| GIF, APNG, animated WebP | View a selected frame (not animation playback) |
+| PDF | Navigate pages; progressively improve raster detail; copy embedded text from a rectangular selection |
+
+For advanced flags, channel/series semantics, color modes, cache limits, clipboard behavior, and format caveats, use the **[full reference](https://github.com/jason-weirather/twhy/blob/main/docs/reference.md)**. Architecture notes are in [docs/architecture.md](https://github.com/jason-weirather/twhy/blob/main/docs/architecture.md).
+
+## Try a synthetic microscopy example
+
+The repo includes a deterministic fixture generator that creates public-safe, synthetic tissue-like RGB and multichannel OME-TIFFs. It is a renderer demonstration, not a biological simulation.
+
+```bash
+python examples/make_demo.py --output-directory /tmp/twhy-demo
+twhy /tmp/twhy-demo/synthetic-mif.ome.tif --channel 0 --channel 2
+```
+
+## Python API
+
+```python
+import numpy as np
+from twhy import TextRenderer
+
+pixels = np.linspace(0, 1, 256**2).reshape(256, 256)
+frame = TextRenderer(mode="detail", color=False).render(pixels, columns=80)
+print(frame.to_text())
+```
+
+## Optional remote sources
+
+Local files are the main workflow. `twhy` also supports HTTP(S) images/PDFs (bounded download) and HTTP(S) OME-Zarr (regional chunk reads). For native S3 or S3-compatible stores, install `twhy[s3]` and use your normal AWS credentials or an endpoint override. No S3 setup is needed for local images, slides, or PDFs. [Remote input reference](https://github.com/jason-weirather/twhy/blob/main/docs/reference.md#local-and-remote-inputs).
+
+## Release media and provenance
+
+These GIFs are edited recordings of the real `twhy` terminal viewer. Showcase sources:
+
+- **mIF:** Tan, Y. & Kempchen, T. (2024), [*SPACEc demo dataset*](https://doi.org/10.5061/dryad.brv15dvj1), Dryad.
+- **H&E whole-slide demo:** `CMU-1.svs`, [OpenSlide test data](https://openslide.cs.cmu.edu/download/openslide-testdata/Aperio/), Carnegie Mellon University, CC0 1.0.
+- **PDF:** Vaswani, A. et al. (2017), [*Attention Is All You Need*](https://arxiv.org/abs/1706.03762), NeurIPS.
+- **Cat:** Illustration generated with ChatGPT (OpenAI).
+
+## License
+
+Apache-2.0. See [LICENSE](https://github.com/jason-weirather/twhy/blob/main/LICENSE).