From d8ecd9fc021db1e90521162f4656f67f57ea61ef Mon Sep 17 00:00:00 2001 From: Frank Loesche Date: Wed, 9 Sep 2026 11:57:14 -0400 Subject: [PATCH 1/3] Add per-neuron skeleton and mesh downloads to the neuroglancer view Closes #175. The "Neuron Visualization" header gets a download icon that opens a modal dialog. The dialog fetches one file per displayed neuron in the chosen format and saves them as a single zip archive, built in the browser with fflate. Neurons without a file are listed in missing_body_ids.txt inside the zip, and selections above 50 neurons ask for confirmation first. Formats come from a new `neuroglancer.download_formats` list in the dataset config (key, label, url_template with a `{body_id}` placeholder, kind). `kind: swc` stores the response verbatim; `kind: ngmesh` addresses the Neuroglancer legacy mesh manifest, fetches its fragments and converts them to Wavefront OBJ (vertices in nanometers) client-side. Entries are validated at load time (placeholder present, known kind, unique keys). The icon, dialog and scripts are only rendered when the list is non-empty, so datasets without configured formats are unchanged. The male CNS config offers coarse SWC, high-resolution SWC and OBJ mesh from the public flyem-male-cns bucket. The embedded viewer is a cross-origin iframe, so the page cannot read its current URL. Body IDs therefore default to the page's own neuroglancer state (type neurons plus ticked partners), which `initializeNeuroglancerLinks()` now exposes on `window`. As a fallback for selections changed inside the viewer, the dialog accepts a pasted Neuroglancer URL and takes the segments of the neuron layer, using the same layer lookup as the URL generator (`findMainSegmentationLayer`). Files are fetched through the GCS JSON API endpoint, since the plain storage.googleapis.com URLs send no CORS headers. --- README.md | 7 + config/README.md | 57 ++- config/config.cns.yaml | 17 + config/config.example.yaml | 17 + docs/developer-guide.md | 72 +++ docs/user-guide.md | 66 +++ src/neuview/config.py | 70 +++ .../services/neuroglancer_js_service.py | 18 + static/css/neuron-page.css | 109 +++++ static/images/neuroglancer-copy-url.png | Bin 0 -> 10003 bytes static/js/fflate.min.js | 2 + static/js/swc-download.js | 441 ++++++++++++++++++ templates/README.md.jinja | 6 + templates/help.html.jinja | 7 + templates/sections/neuroglancer.html.jinja | 39 ++ .../sections/neuron_page_scripts.html.jinja | 6 + .../js/neuroglancer-url-generator.js.jinja | 33 +- test/services/test_neuroglancer_js_service.py | 65 ++- test/test_config_download_formats.py | 74 +++ test/test_download_dialog_gating.py | 117 +++++ 20 files changed, 1217 insertions(+), 6 deletions(-) create mode 100644 static/images/neuroglancer-copy-url.png create mode 100644 static/js/fflate.min.js create mode 100644 static/js/swc-download.js create mode 100644 test/test_config_download_formats.py create mode 100644 test/test_download_dialog_gating.py diff --git a/README.md b/README.md index 5cbc9bb4..e2dee3c3 100644 --- a/README.md +++ b/README.md @@ -11,6 +11,7 @@ A modern Python CLI tool that generates beautiful HTML pages for neuron types us - **🎨 Beautiful Reports**: Clean, accessible HTML pages with interactive features - **🔍 Advanced Search**: Real-time filtering by cell count, neurotransmitter, brain regions - **📊 Rich Analytics**: Hemisphere balance, connectivity stats, ROI summaries +- **⬇️ Neuron Downloads**: One-click zip of SWC skeletons or OBJ meshes for the neurons shown in the 3D view (per-dataset, see `config/README.md`) ## 🚀 Quick Start @@ -136,6 +137,12 @@ We welcome contributions! Please see our comprehensive documentation: This project is licensed under the GPLv3 License - see the LICENSE file for details. +The generated website bundles third-party browser libraries from `static/js/`, +each under the MIT license with its notice kept in the file header: jQuery, +DataTables (with its export buttons and FileSaver), and fflate (zip creation +for the neuron download dialog). The written content of the generated site is +licensed under CC BY 4.0, see `static/LICENSE`. + ## 🆘 Support - **User Documentation**: [User Guide](docs/user-guide.md) for installation and usage diff --git a/config/README.md b/config/README.md index 0b28397d..9e2e6d90 100644 --- a/config/README.md +++ b/config/README.md @@ -2,7 +2,8 @@ Each `config..yaml` file configures one NeuPrint dataset (server, dataset name, output, discovery, neuroglancer template, HTML metadata, subsets). -This document describes the optional **`hide_features`** block. +This document describes the optional **`hide_features`** block and the optional +**`neuroglancer.download_formats`** list. ## `hide_features` @@ -96,3 +97,57 @@ hide_features: neuron: ["neuroglancer"] list: ["dimorphism", "hemilineage", "neuromere"] ``` + +## `neuroglancer.download_formats` + +Offer per-neuron file downloads (skeletons, meshes) from the neuron pages. When +the list has at least one entry, the "Neuron Visualization" header shows a +download icon that opens a dialog with one radio button per format. The dialog +fetches one file per displayed neuron and saves them as a single zip archive. +When the list is missing or empty, neither the icon nor the dialog is rendered. + +```yaml +neuroglancer: + base_url: "https://neuroglancer-demo.appspot.com/" + template: "neuroglancer-cns.js.jinja" + download_formats: + - key: swc + label: "SWC skeleton (coarse)" + kind: swc + url_template: "https://www.googleapis.com/storage/v1/b/flyem-male-cns/o/v1.0%2Fsegmentation%2Fskeletons-malecns%2Fskeletons-swc%2F{body_id}.swc?alt=media" + - key: obj + label: "OBJ mesh" + kind: ngmesh + url_template: "https://www.googleapis.com/storage/v1/b/flyem-male-cns/o/v1.0%2Fsegmentation%2Fsingle-res-meshes%2F{body_id}:0?alt=media" +``` + +| Field | Required | Meaning | +|---|---|---| +| `key` | yes | Unique identifier; also used in the zip file name (`_.zip`) | +| `label` | yes | Text of the radio button in the dialog | +| `url_template` | yes | URL with a `{body_id}` placeholder; one request per neuron | +| `kind` | no (default `swc`) | `swc` or `ngmesh`, see below | + +Kinds: + +| Kind | File in the zip | Behavior | +|---|---|---| +| `swc` | `.swc` | The response is stored verbatim. Works for any text or binary per-neuron file, not only SWC | +| `ngmesh` | `.obj` | `url_template` must address the Neuroglancer legacy mesh manifest `:0`. The fragments it lists are fetched from the same directory and converted to Wavefront OBJ in the browser (vertices in nanometers) | + +Requirements and notes: + +- The host must send CORS headers, because the browser fetches the files from + the neuView page's origin (or from `file://`). For Google Cloud Storage use + the JSON API form shown above; the plain + `https://storage.googleapis.com//` URL does not send them. + Object paths in the JSON API form are URL-encoded (`/` becomes `%2F`). +- Configuration loading fails with a clear error if `{body_id}` is missing, the + `kind` is unknown, or two entries share a `key`. +- The first entry is preselected. Order the list from cheapest to largest + download; mesh files are roughly a hundred times larger than coarse SWC files. +- Selections above 50 neurons ask the user for confirmation. Neurons without a + file are listed in `missing_body_ids.txt` inside the zip. +- The page only knows the neurons it sent to the viewer. Selections changed + inside Neuroglancer can be downloaded by pasting the viewer URL into the + dialog. diff --git a/config/config.cns.yaml b/config/config.cns.yaml index 687713d6..ed72e37e 100644 --- a/config/config.cns.yaml +++ b/config/config.cns.yaml @@ -9,6 +9,23 @@ output: neuroglancer: base_url: "https://neuroglancer-demo.appspot.com/" template: "neuroglancer-cns.js.jinja" + # Per-neuron downloads offered next to the Neuroglancer view. URLs go through + # the GCS JSON API so the browser gets CORS headers (the plain + # storage.googleapis.com URLs have none). SWC coordinates are 8 nm voxels, + # mesh vertices are nanometers. + download_formats: + - key: swc + label: "SWC skeleton (coarse, ~16 KB per neuron)" + kind: swc + url_template: "https://www.googleapis.com/storage/v1/b/flyem-male-cns/o/v1.0%2Fsegmentation%2Fskeletons-malecns%2Fskeletons-swc%2F{body_id}.swc?alt=media" + - key: swc-highres + label: "SWC skeleton (high resolution, ~300 KB per neuron)" + kind: swc + url_template: "https://www.googleapis.com/storage/v1/b/flyem-male-cns/o/v1.0%2Fsegmentation%2Fskeletons-malecns%2Fskeletons-highres-swc%2F{body_id}.swc?alt=media" + - key: obj + label: "OBJ mesh (converted from the Neuroglancer mesh, ~3 MB per neuron)" + kind: ngmesh + url_template: "https://www.googleapis.com/storage/v1/b/flyem-male-cns/o/v1.0%2Fsegmentation%2Fsingle-res-meshes%2F{body_id}:0?alt=media" # Auto-discovery settings for neuron types discovery: diff --git a/config/config.example.yaml b/config/config.example.yaml index fbc9fd19..554bce66 100644 --- a/config/config.example.yaml +++ b/config/config.example.yaml @@ -10,6 +10,23 @@ output: neuroglancer: base_url: "https://clio-ng.janelia.org/" template: "neuroglancer-cns.js.jinja" + # Optional: per-neuron file formats offered by a "Download" link next to the + # Neuroglancer view. Each entry needs a unique key, a label shown in the + # dialog, a url_template with a {body_id} placeholder, and a kind: + # swc the file is stored as-is (.swc) + # ngmesh Neuroglancer legacy mesh; url_template addresses the manifest + # ":0", the browser converts the fragments to OBJ + # The host must allow cross-origin requests (CORS). For Google Cloud Storage + # use the JSON API form shown here, not the storage.googleapis.com path. + # download_formats: + # - key: swc + # label: "SWC skeleton" + # kind: swc + # url_template: "https://www.googleapis.com/storage/v1/b//o/%2F{body_id}.swc?alt=media" + # - key: obj + # label: "OBJ mesh" + # kind: ngmesh + # url_template: "https://www.googleapis.com/storage/v1/b//o/%2F{body_id}:0?alt=media" html: title_prefix: "Neuron Type Report" diff --git a/docs/developer-guide.md b/docs/developer-guide.md index 12e509eb..56fafe5b 100644 --- a/docs/developer-guide.md +++ b/docs/developer-guide.md @@ -89,6 +89,16 @@ The project relies on several key Python packages defined in `pyproject.toml`. T **Code Quality (dev environment):** - `ruff>=0.12.11,<0.13` - Fast Python linter and formatter +**Vendored browser libraries (`static/js/`, copied into the generated site):** +- `jquery-3.7.1.min.js` - jQuery (MIT) +- `jquery.dataTables.min.js`, `dataTables.buttons.min.js`, `buttons.html5.min.js` - DataTables and its export buttons (MIT) +- `fflate.min.js` - fflate 0.8.2 (MIT), builds the zip archive for the neuron download dialog client-side + +These files are checked in rather than installed through a package manager so +that the generated site works from `file://` without a build step. To update +one, download the new UMD build, keep the one-line license header at the top +of the file, and mention the version bump in the commit message. + **Workflow Tools:** - `parallel>=20200322,<20250623` - GNU Parallel for batch processing - `python-lsp-server>=1.13.1,<2` - Python language server @@ -401,6 +411,14 @@ Templates are organized hierarchically with inheritance and includes. - `sections/header.html.jinja` - Page header with search - `sections/footer.html.jinja` - Page footer - `sections/connectivity_table.html.jinja` - Connectivity tables +- `sections/neuroglancer.html.jinja` - Embedded Neuroglancer viewer, theme toggle, and the "Download neurons" dialog (rendered only when `config.neuroglancer.download_formats` is non-empty) +- `sections/neuron_page_scripts.html.jinja` - Per-page script includes and the `neuroglancerData` bootstrap + +**Browser JavaScript:** +- `templates/static/js/neuroglancer-url-generator.js.jinja` - Rendered once per build into `static/js/neuroglancer-url-generator.js` with the Neuroglancer state template, ROI tables, and the `NEUROGLANCER_DOWNLOAD_FORMATS` list embedded +- `static/js/swc-download.js` - Neuron download dialog logic (body ID collection, fetching, OBJ conversion, zip) +- `static/js/neuron-page.js`, `static/js/responsive-nav.js`, `static/js/iframe-bridge.js` - Page behavior, navigation, and the bridge used when a neuView page itself is embedded in an iframe +- `static/js/fflate.min.js`, `static/js/jquery*.js`, `static/js/*dataTables*.js` - Vendored libraries (see Key Dependencies) ### Template Context @@ -774,6 +792,7 @@ Environment variable support for sensitive configuration: **Configuration Validation** (`src/neuview/config/config.py`): - Automatic validation with clear error messages using dataclass `__post_init__()` methods - Example: `NeuPrintConfig.__post_init__()` validates required server and dataset fields +- Example: `DownloadFormat.__post_init__()` (in `src/neuview/config.py`) requires the `{body_id}` placeholder in `url_template` and a known `kind`; `NeuroglancerConfig.__post_init__()` turns the YAML dicts into `DownloadFormat` objects and rejects duplicate keys - Validation occurs at configuration loading time with descriptive error messages ## API Reference @@ -1591,6 +1610,59 @@ Automatic template selection based on dataset: - FAFB datasets use specialized `neuroglancer-fafb.js.jinja` template - Other datasets use standard `neuroglancer.js.jinja` template +### Neuron Downloads (Skeletons and Meshes) + +The "Download neurons" link next to the embedded Neuroglancer view lets users +save one file per displayed neuron as a single zip archive (issue #175). The +feature is entirely client-side and only appears when the dataset config lists +at least one entry in `neuroglancer.download_formats`. + +**Data flow:** + +1. `config/config..yaml` lists formats; `NeuroglancerConfig` (`src/neuview/config.py`) parses them into validated `DownloadFormat` objects (`key`, `label`, `url_template`, `kind`, derived `extension`). +2. `NeuroglancerJSService._download_formats()` serialises the list and the JS template embeds it as `const NEUROGLANCER_DOWNLOAD_FORMATS = [...]` in the generated `static/js/neuroglancer-url-generator.js`. +3. `templates/sections/neuroglancer.html.jinja` renders the header icon and a native `` with one radio button per format. `templates/sections/neuron_page_scripts.html.jinja` includes `fflate.min.js` and `swc-download.js` under the same condition. +4. `static/js/swc-download.js` collects body IDs, fetches the files with a small concurrency pool, converts meshes, zips everything with fflate, and triggers the download through a Blob URL. + +**Body ID sources.** The embedded viewer is a cross-origin iframe, so the page +cannot read its current URL or DOM. `initializeNeuroglancerLinks()` therefore +exposes the page's own state as `window.neuviewNeuroglancerPageData`; its +`visibleNeurons` array is the default source (type neurons plus ticked +partners). As a fallback for selections changed inside the viewer, the dialog +accepts a pasted Neuroglancer URL: the `#!` fragment is decoded, parsed as +JSON, and the segments of the neuron layer are taken. The layer is found with +`findMainSegmentationLayer()` (shared with URL generation, matches `cns-seg` and +`flywire-fafb:v783b`), falling back to the first segmentation layer with +segments. Hidden segments (leading `!`) and ROI layers are skipped. + +**Formats.** `kind: swc` stores the response verbatim. `kind: ngmesh` treats +the URL as the Neuroglancer legacy mesh manifest (`:0`, a JSON list of +fragment names), derives fragment URLs by replacing `{body_id}:0` in the +template, parses each fragment (uint32 vertex count, float32 x/y/z per vertex +in nanometers, uint32 triangle indices), and writes a Wavefront OBJ with +1-based, offset-corrected face indices. Adding a new kind means extending +`DOWNLOAD_FORMAT_KINDS` in `config.py` (kind to file extension) and adding a +branch in `fetchNeuron()` in `swc-download.js`. + +**CORS.** Browsers only allow `fetch()` across origins when the host sends +`Access-Control-Allow-Origin`. The plain `storage.googleapis.com//...` +URLs of the FlyEM buckets do not, but the GCS JSON API endpoint +(`https://www.googleapis.com/storage/v1/b//o/?alt=media`) +does, including for the `null` origin of `file://` pages. Configure that form. +Neuroglancer itself is unaffected because it reads through the JSON API too. + +**Safeguards.** Selections above 50 neurons ask for confirmation. Missing files +(HTTP 404) are skipped and listed in `missing_body_ids.txt` inside the zip. +Mesh zips use a lower compression level because the OBJ text is large (about +6 MB per neuron before compression). The whole archive is assembled in memory. + +**Tests.** `test/test_config_download_formats.py` (config parsing and +validation), `test/services/test_neuroglancer_js_service.py` (embedding in the +generated JS), and `test/test_download_dialog_gating.py` (the link, dialog and +scripts render only with formats configured). The OBJ converter has no +automated test; it was verified against an independent Python parse of a real +mesh fragment. + ### Dataset Detection Patterns Centralized dataset type detection: diff --git a/docs/user-guide.md b/docs/user-guide.md index ff92eb04..724bc529 100644 --- a/docs/user-guide.md +++ b/docs/user-guide.md @@ -464,6 +464,15 @@ neuprint: dataset: hemibrain:v1.2.1 # or cns:v1.0, optic-lobe:v1.0 ``` +**Neuron downloads (male CNS only):** +`config/config.cns.yaml` configures three download formats for the "Download +neurons" dialog: coarse SWC skeleton, high-resolution SWC skeleton, and OBJ +mesh, all served from the public `flyem-male-cns` bucket. The hemibrain, +optic-lobe, FAFB and wasp configs define no formats, so their pages show no +download link. See [Neuroglancer Integration](#neuroglancer-integration) for +the user-facing behavior and [Configuration Reference](#configuration-reference) +for the config format. + ### Dataset Detection The system automatically detects dataset type and adjusts: @@ -534,6 +543,28 @@ The system automatically detects dataset type and adjusts: - Multiple selection → Build complex views - URL updates automatically +**Downloading skeletons and meshes:** + +When the dataset config lists `neuroglancer.download_formats`, the Neuron +Visualization header shows a download link next to the "open in new window" +link. It opens a dialog with one radio button per configured format (for the +male CNS: coarse SWC skeleton, high resolution SWC skeleton, OBJ mesh). The +"Download" button fetches one file per neuron the page currently sends to the +viewer (the type's neurons plus ticked partners) and saves them as a single +zip file. Neurons without a file are listed in `missing_body_ids.txt` inside +the zip. Selections above 50 neurons ask for confirmation first. Progress and +errors are shown in the dialog. + +Format notes: SWC coordinates are in 8 nm voxels, OBJ vertices are in +nanometers. OBJ files are converted in the browser from Neuroglancer's legacy +mesh format and are large (about 3 MB per neuron before compression). + +The page cannot see selection changes made inside the embedded viewer (the +viewer runs on a different origin). To download exactly what is selected in +Neuroglancer, open the viewer in a new window, copy its URL, and paste it into +the URL field of the dialog. The page parses the state in the URL and +downloads the visible segments of the neuron layer. + **Tips:** - Start with just the main neuron - Add partners one at a time @@ -708,6 +739,21 @@ output: directory: "output" clean_before_build: false +neuroglancer: + base_url: "https://neuroglancer-demo.appspot.com/" + template: "neuroglancer-cns.js.jinja" + # Optional: per-neuron downloads offered in the "Download neurons" dialog. + # Leave out (or empty) to hide the download link. + download_formats: + - key: swc + label: "SWC skeleton (coarse)" + kind: swc + url_template: "https://www.googleapis.com/storage/v1/b//o/%2F{body_id}.swc?alt=media" + - key: obj + label: "OBJ mesh" + kind: ngmesh + url_template: "https://www.googleapis.com/storage/v1/b//o/%2F{body_id}:0?alt=media" + performance: max_workers: 4 cache_enabled: true @@ -738,6 +784,18 @@ subsets: - The analytics script is automatically included on all generated pages when configured - No additional setup required - just uncomment and set your site ID +**Neuron Downloads** (`neuroglancer.download_formats`): +- Each entry needs a unique `key`, a `label` shown as a radio button, a + `url_template` containing `{body_id}`, and a `kind` +- `kind: swc` stores the fetched file as `.swc` +- `kind: ngmesh` expects the template to address the Neuroglancer legacy mesh + manifest (`:0`); the browser fetches the fragments and converts them + to `.obj` +- The file host must send CORS headers. For Google Cloud Storage use the JSON + API form shown above; the plain `storage.googleapis.com` URL does not send them +- The first entry is preselected in the dialog; an empty or missing list hides + the download link entirely + ### Command Reference neuView provides a comprehensive command-line interface. All commands are run with the `pixi run neuview` prefix. @@ -851,3 +909,11 @@ A: Same data, different formats. JSON for web servers/APIs, JS for local file ac **Q: Why do some neurons have L/R pages and others don't?** A: Automatically determined by soma distribution. Bilateral neurons get separate pages. + +**Q: How do I download the skeletons or meshes of the neurons I see?** +A: Click the download icon next to the "open in new window" icon above the +Neuroglancer view, pick a format, and press "Download". You get one zip file +with one file per neuron. The page only knows the neurons it sent to the +viewer; if you changed the selection inside Neuroglancer, copy the viewer URL +and paste it into the dialog's URL field first. The link is only present when +the dataset config defines `neuroglancer.download_formats`. diff --git a/src/neuview/config.py b/src/neuview/config.py index 2967a512..442ee0b8 100644 --- a/src/neuview/config.py +++ b/src/neuview/config.py @@ -38,12 +38,82 @@ class DiscoveryConfig: randomize: bool = True +# Supported kinds of per-neuron download formats and the file extension the +# browser writes for each. ``swc`` is stored verbatim; ``ngmesh`` (Neuroglancer +# legacy single-resolution mesh, addressed by its ``:0`` manifest) is +# converted to Wavefront OBJ in the browser. +DOWNLOAD_FORMAT_KINDS = {"swc": "swc", "ngmesh": "obj"} + + +@dataclass +class DownloadFormat: + """One per-neuron file format offered in the "Download" dialog. + + ``url_template`` must contain the ``{body_id}`` placeholder. The host has to + send CORS headers; for Google Cloud Storage that means the JSON API endpoint + (``https://www.googleapis.com/storage/v1/b//o/?alt=media``), + not the plain ``storage.googleapis.com`` path. For ``kind: ngmesh`` the + template addresses the mesh manifest (``...{body_id}:0``); fragment URLs are + derived from it by replacing ``{body_id}:0`` with the fragment name. + """ + + key: str + label: str + url_template: str + kind: str = "swc" + + def __post_init__(self): + if not self.key or not str(self.key).strip(): + raise ValueError("download format needs a non-empty 'key'") + self.key = str(self.key).strip() + self.label = str(self.label or self.key).strip() + self.url_template = str(self.url_template or "").strip() + if "{body_id}" not in self.url_template: + raise ValueError( + f"download format '{self.key}': url_template must contain {{body_id}}" + ) + if self.kind not in DOWNLOAD_FORMAT_KINDS: + raise ValueError( + f"download format '{self.key}': unknown kind '{self.kind}' " + f"(expected one of {sorted(DOWNLOAD_FORMAT_KINDS)})" + ) + + @property + def extension(self) -> str: + return DOWNLOAD_FORMAT_KINDS[self.kind] + + def to_dict(self) -> dict: + return { + "key": self.key, + "label": self.label, + "url_template": self.url_template, + "kind": self.kind, + "extension": self.extension, + } + + @dataclass class NeuroglancerConfig: """Neuroglancer configuration.""" base_url: str = "https://clio-ng.janelia.org/" template: str = "neuroglancer.js.jinja" + # Per-neuron file formats offered by the "Download" link next to the + # Neuroglancer view (see ``DownloadFormat``). Empty hides the link. + download_formats: list = field(default_factory=list) + + def __post_init__(self): + formats = [] + seen = set() + for entry in self.download_formats or []: + fmt = ( + entry if isinstance(entry, DownloadFormat) else DownloadFormat(**entry) + ) + if fmt.key in seen: + raise ValueError(f"duplicate download format key '{fmt.key}'") + seen.add(fmt.key) + formats.append(fmt) + self.download_formats = formats @dataclass diff --git a/src/neuview/services/neuroglancer_js_service.py b/src/neuview/services/neuroglancer_js_service.py index 21269879..a767e591 100644 --- a/src/neuview/services/neuroglancer_js_service.py +++ b/src/neuview/services/neuroglancer_js_service.py @@ -83,6 +83,7 @@ def generate_neuroglancer_js(self, output_dir: Path) -> bool: "neuroglancer_json": neuroglancer_json, "dataset_name": self.config.neuprint.dataset, "neuroglancer_base_url": self.config.neuroglancer.base_url.rstrip("/"), + "neuroglancer_download_formats": self._download_formats(), } # Add ROI data from environment globals if they exist @@ -117,6 +118,23 @@ def generate_neuroglancer_js(self, output_dir: Path) -> bool: logger.debug(f"Traceback: {traceback.format_exc()}") return False + def _download_formats(self) -> list: + """Return the configured download formats as JSON-serialisable dicts. + + Tolerates configs without the attribute (older configs, mocks) so the + generated JavaScript always has a list constant to work with. + """ + formats = getattr(self.config.neuroglancer, "download_formats", None) + if not isinstance(formats, (list, tuple)): + return [] + result = [] + for fmt in formats: + if hasattr(fmt, "to_dict"): + result.append(fmt.to_dict()) + elif isinstance(fmt, dict): + result.append(dict(fmt)) + return result + def get_neuroglancer_template_name(self) -> str: """ Get the name of the neuroglancer template that would be used. diff --git a/static/css/neuron-page.css b/static/css/neuron-page.css index 74a86f16..f3b36596 100644 --- a/static/css/neuron-page.css +++ b/static/css/neuron-page.css @@ -3235,3 +3235,112 @@ table.dataTable#roi-table tbody > tr > td:first-child { color: #666; margin-top: 2px; } + +/* SWC skeleton download dialog (opened from the Neuroglancer header) */ +.swc-download-dialog { + width: min(40rem, calc(100vw - 2rem)); + max-height: calc(100vh - 2rem); + padding: 1.25rem 1.5rem; + border: 1px solid rgba(127, 127, 127, 0.4); + border-radius: 6px; + background: #fff; + color: var(--pm-app-text-color, #333); + font-size: 0.95rem; + box-shadow: 0 12px 40px rgba(0, 0, 0, 0.3); +} +.swc-download-dialog::backdrop { + background: rgba(0, 0, 0, 0.5); +} +.swc-download-dialog-header { + display: flex; + align-items: flex-start; + justify-content: space-between; + gap: 1rem; + margin-bottom: 0.75rem; +} +.swc-download-dialog h3 { + margin: 0; + font-size: 1.4rem; +} +.swc-download-close { + flex: 0 0 auto; + min-width: unset; + min-height: unset; + width: 2rem; + height: 2rem; + margin: 0; + padding: 0; + border: none; + background: transparent; + font-size: 1.5rem; + line-height: 1; + cursor: pointer; + color: inherit; +} +.swc-download-dialog p { + margin: 0 0 0.75rem; + font-family: var(--pm-font-family-primary); +} +.swc-download-formats { + width: auto; + margin: 0 0 0.75rem; + padding: 0.5rem 0.75rem 0.25rem; +} +.swc-download-formats legend { + padding: 0 0.4rem; + font-weight: 600; +} +.swc-download-format { + display: flex; + align-items: center; + gap: 0.25rem; + margin: 0 0 0.35rem; + font-weight: normal; + cursor: pointer; +} +.swc-download-format input[type="radio"] { + flex: 0 0 auto; + margin: 0 0.5rem 0 0; +} +/* Screenshot of Neuroglancer's "copy URL" button, floated beside the hint text */ +#swc-download-hint-image { + float: right; + width: 12rem; + max-width: 45%; + height: auto; + margin: 0 0 0.5rem 1rem; + border: 1px solid rgba(127, 127, 127, 0.4); + border-radius: 4px; +} +/* Contain the float so the URL field below starts on its own line */ +.swc-download-dialog p:has(#swc-download-hint-image) { + display: flow-root; +} +.swc-download-label { + margin-bottom: 0.25rem; + font-weight: 600; +} +.swc-download-dialog input[type="text"] { + width: 100%; 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NEUROGLANCER_DOWNLOAD_FORMATS.filter((f) => f && f.url_template) + : []; + } + + function selectedFormat() { + const all = formats(); + const checked = document.querySelector('input[name="swc-download-format"]:checked'); + if (checked) { + const match = all.find((f) => f.key === checked.value); + if (match) return match; + } + return all[0]; + } + + function fileUrl(fmt, bodyId) { + return fmt.url_template.replace("{body_id}", encodeURIComponent(String(bodyId))); + } + + /** URL of one mesh fragment, derived from the manifest URL template. */ + function fragmentUrl(fmt, bodyId, fragment) { + const encoded = encodeURIComponent(String(fragment)); + if (fmt.url_template.includes("{body_id}:0")) { + return fmt.url_template.replace("{body_id}:0", encoded); + } + return fmt.url_template.replace("{body_id}", encoded); + } + + function setStatus(text, isError) { + const el = document.getElementById("swc-download-status"); + if (!el) return; + el.textContent = text || ""; + el.classList.toggle("is-error", Boolean(isError)); + } + + function dialogElement() { + return document.getElementById("swc-download-dialog"); + } + + function openDialog(event) { + if (event) event.preventDefault(); + const dialog = dialogElement(); + if (!dialog) return; + if (!running) setStatus(""); + if (typeof dialog.showModal === "function") { + if (!dialog.open) dialog.showModal(); + } else { + dialog.setAttribute("open", ""); + } + const input = document.getElementById("swc-url-input"); + if (input) input.focus(); + } + + function closeDialog(event) { + if (event) event.preventDefault(); + const dialog = dialogElement(); + if (!dialog) return; + if (typeof dialog.close === "function") { + if (dialog.open) dialog.close(); + } else { + dialog.removeAttribute("open"); + } + } + + function setBusy(busy) { + running = busy; + const link = document.getElementById("swc-download-link"); + const button = document.getElementById("swc-download-button"); + if (link) link.classList.toggle("is-busy", busy); + if (button) button.disabled = busy; + } + + /** + * Normalise a neuroglancer segments list to an array of unique, visible + * body ID strings. Hidden segments are stored with a leading "!". + */ + function normaliseSegments(segments) { + const ids = []; + const seen = new Set(); + (Array.isArray(segments) ? segments : []).forEach((seg) => { + if (seg === null || seg === undefined) return; + const str = String(seg).trim(); + if (!str || str.startsWith("!")) return; + if (!/^\d+$/.test(str)) return; + if (!seen.has(str)) { + seen.add(str); + ids.push(str); + } + }); + return ids; + } + + /** + * Extract the neuron body IDs from a Neuroglancer URL. + * @param {string} url + * @returns {{bodyIds: string[], error?: string}} + */ + function parseNeuroglancerUrl(url) { + const text = String(url || "").trim(); + const idx = text.indexOf("#!"); + if (idx === -1) { + return { bodyIds: [], error: "No Neuroglancer state found in the URL (expected \"#!\" followed by JSON)." }; + } + const fragment = text.slice(idx + 2); + if (/^(https?:|gs:|s3:)/i.test(fragment)) { + return { + bodyIds: [], + error: "This URL points to a state stored on a server. Open it in Neuroglancer, then copy the URL again once the JSON state is shown in the address bar.", + }; + } + let state; + try { + state = JSON.parse(decodeURIComponent(fragment)); + } catch (e1) { + try { + state = JSON.parse(fragment); + } catch (e2) { + return { bodyIds: [], error: "Could not parse the Neuroglancer state in the URL." }; + } + } + const layers = state && Array.isArray(state.layers) ? state.layers : []; + let layer = + typeof window.findMainSegmentationLayer === "function" + ? window.findMainSegmentationLayer(layers) + : undefined; + if (!layer) { + // Fallback for renamed layers: first segmentation layer with segments. + layer = layers.find( + (l) => l && l.type === "segmentation" && Array.isArray(l.segments) && l.segments.length > 0, + ); + } + if (!layer) { + return { bodyIds: [], error: "No segmentation layer with selected neurons found in the URL." }; + } + return { bodyIds: normaliseSegments(layer.segments) }; + } + + /** + * Determine which body IDs to download. + * @returns {{bodyIds: string[], source: "url"|"page", error?: string}} + */ + function collectBodyIds() { + const input = document.getElementById("swc-url-input"); + const pasted = input ? input.value.trim() : ""; + if (pasted) { + const parsed = parseNeuroglancerUrl(pasted); + return { bodyIds: parsed.bodyIds, source: "url", error: parsed.error }; + } + const pageData = window.neuviewNeuroglancerPageData || {}; + return { bodyIds: normaliseSegments(pageData.visibleNeurons), source: "page" }; + } + + async function fetchBytes(url) { + const response = await fetch(url, { mode: "cors" }); + if (!response.ok) { + const err = new Error(`HTTP ${response.status}`); + err.status = response.status; + throw err; + } + return new Uint8Array(await response.arrayBuffer()); + } + + /** + * Convert Neuroglancer legacy mesh fragments to Wavefront OBJ text. + * Fragment layout: uint32 vertex count, float32 x/y/z per vertex (nm), + * then uint32 triangle indices until the end of the buffer. + */ + function ngmeshToObj(fragments, bodyId) { + const lines = [ + `# body ID ${bodyId}`, + "# converted from Neuroglancer legacy mesh; vertex units: nanometers", + ]; + const faces = []; + let offset = 0; + fragments.forEach((bytes) => { + if (bytes.byteLength < 4) return; + const view = new DataView(bytes.buffer, bytes.byteOffset, bytes.byteLength); + const nVerts = view.getUint32(0, true); + const vertBytes = nVerts * 12; + if (4 + vertBytes > bytes.byteLength) { + throw new Error("truncated mesh fragment"); + } + for (let i = 0; i < nVerts; i++) { + const b = 4 + i * 12; + lines.push( + `v ${view.getFloat32(b, true).toFixed(2)} ${view.getFloat32(b + 4, true).toFixed(2)} ${view.getFloat32(b + 8, true).toFixed(2)}`, + ); + } + const triStart = 4 + vertBytes; + const nIdx = Math.floor((bytes.byteLength - triStart) / 4); + for (let i = 0; i + 2 < nIdx; i += 3) { + const b = triStart + i * 4; + faces.push( + `f ${view.getUint32(b, true) + offset + 1} ${view.getUint32(b + 4, true) + offset + 1} ${view.getUint32(b + 8, true) + offset + 1}`, + ); + } + offset += nVerts; + }); + return lines.concat(faces).join("\n") + "\n"; + } + + async function fetchNgmesh(fmt, bodyId) { + const manifest = JSON.parse( + new TextDecoder().decode(await fetchBytes(fileUrl(fmt, bodyId))), + ); + const names = Array.isArray(manifest.fragments) ? manifest.fragments : []; + if (names.length === 0) throw new Error("mesh manifest lists no fragments"); + const fragments = []; + for (const name of names) { + fragments.push(await fetchBytes(fragmentUrl(fmt, bodyId, name))); + } + return fflate.strToU8(ngmeshToObj(fragments, bodyId)); + } + + /** Fetch one neuron in the given format. Never throws; data is null on failure. */ + async function fetchNeuron(fmt, bodyId) { + try { + const data = + fmt.kind === "ngmesh" + ? await fetchNgmesh(fmt, bodyId) + : await fetchBytes(fileUrl(fmt, bodyId)); + return { bodyId, data }; + } catch (err) { + if (err && err.status !== 404) console.warn("[download] failed for", bodyId, err); + return { bodyId, data: null }; + } + } + + async function runPool(items, worker, limit, onProgress) { + const results = new Array(items.length); + let next = 0; + let done = 0; + async function lane() { + while (next < items.length) { + const i = next++; + results[i] = await worker(items[i]); + done += 1; + if (onProgress) onProgress(done, items.length); + } + } + const lanes = []; + for (let i = 0; i < Math.min(limit, items.length); i++) lanes.push(lane()); + await Promise.all(lanes); + return results; + } + + function safeFileName(name) { + return String(name || "neurons") + .replace(/[^A-Za-z0-9._-]+/g, "_") + .replace(/^_+|_+$/g, "") || "neurons"; + } + + function zipFileName(fmt) { + const pageData = window.neuviewNeuroglancerPageData || {}; + const base = pageData.currentNeuronType || pageData.websiteTitle || document.title; + return `${safeFileName(base)}_${safeFileName(fmt.key)}.zip`; + } + + function saveBlob(bytes, fileName) { + const blob = new Blob([bytes], { type: "application/zip" }); + const url = URL.createObjectURL(blob); + const a = document.createElement("a"); + a.href = url; + a.download = fileName; + document.body.appendChild(a); + a.click(); + a.remove(); + setTimeout(() => URL.revokeObjectURL(url), 10000); + } + + async function downloadSwc(event) { + if (event) event.preventDefault(); + if (running) return; + const fmt = selectedFormat(); + if (!fmt) { + setStatus("Downloads are not configured for this dataset.", true); + return; + } + if (typeof fflate === "undefined") { + setStatus("The zip library (fflate) did not load.", true); + return; + } + + const { bodyIds, source, error } = collectBodyIds(); + if (error) { + setStatus(error, true); + return; + } + if (bodyIds.length === 0) { + setStatus( + source === "url" + ? "The pasted Neuroglancer URL has no visible neurons selected." + : "No neurons are currently displayed.", + true, + ); + return; + } + if (bodyIds.length > MAX_FILES_WITHOUT_CONFIRM) { + const ok = window.confirm( + `This will fetch ${bodyIds.length} files (${fmt.label}) and pack them into one zip file. Continue?`, + ); + if (!ok) { + setStatus("Download cancelled.", false); + return; + } + } + + setBusy(true); + const origin = source === "url" ? "pasted URL" : "this page"; + const ext = fmt.extension || (fmt.kind === "ngmesh" ? "obj" : "swc"); + setStatus(`Fetching 0 of ${bodyIds.length} ${fmt.label} files (neurons from ${origin})...`); + try { + const results = await runPool( + bodyIds, + (id) => fetchNeuron(fmt, id), + CONCURRENCY, + (done, total) => { + setStatus(`Fetching ${done} of ${total} ${fmt.label} files (neurons from ${origin})...`); + }, + ); + + const files = {}; + const missing = []; + results.forEach((r) => { + if (r.data) { + files[`${r.bodyId}.${ext}`] = r.data; + } else { + missing.push(r.bodyId); + } + }); + + const found = Object.keys(files).length; + if (found === 0) { + setStatus( + `None of the ${bodyIds.length} neurons has a ${fmt.label} file at the configured location.`, + true, + ); + return; + } + if (missing.length > 0) { + files["missing_body_ids.txt"] = fflate.strToU8( + `Body IDs without a ${fmt.label} file:\n` + missing.join("\n") + "\n", + ); + } + + setStatus(`Packing ${found} files into a zip archive...`); + // Meshes are large text files; trade compression for speed there. + const level = fmt.kind === "ngmesh" ? 3 : 6; + const zipped = fflate.zipSync(files, { level }); + saveBlob(zipped, zipFileName(fmt)); + + const skipped = + missing.length > 0 + ? `, ${missing.length} without a file (listed in missing_body_ids.txt)` + : ""; + setStatus(`Downloaded ${found} file${found === 1 ? "" : "s"}${skipped}.`); + } catch (err) { + console.error("[download] failed", err); + setStatus(`Download failed: ${err && err.message ? err.message : err}`, true); + } finally { + setBusy(false); + } + } + + function init() { + const link = document.getElementById("swc-download-link"); + const dialog = dialogElement(); + const button = document.getElementById("swc-download-button"); + const closeButtons = [ + document.getElementById("swc-download-close"), + document.getElementById("swc-download-cancel"), + ]; + const input = document.getElementById("swc-url-input"); + + // The header link opens the dialog; the download starts from its button. + if (link) link.addEventListener("click", openDialog); + if (button) button.addEventListener("click", downloadSwc); + closeButtons.forEach((b) => b && b.addEventListener("click", closeDialog)); + if (dialog) { + // Click on the backdrop (outside the dialog box) closes it. + dialog.addEventListener("click", (e) => { + if (e.target === dialog) closeDialog(); + }); + } + if (input) { + input.addEventListener("keydown", (e) => { + if (e.key === "Enter") downloadSwc(e); + }); + input.addEventListener("input", () => setStatus("")); + } + } + + if (document.readyState === "loading") { + document.addEventListener("DOMContentLoaded", init); + } else { + init(); + } + + // Expose for debugging and tests. + window.neuviewSwcDownload = { + parseNeuroglancerUrl, + collectBodyIds, + selectedFormat, + ngmeshToObj, + downloadSwc, + openDialog, + closeDialog, + }; +})(); diff --git a/templates/README.md.jinja b/templates/README.md.jinja index 1729e97a..ed8ec081 100644 --- a/templates/README.md.jinja +++ b/templates/README.md.jinja @@ -97,6 +97,9 @@ Each neuron type in the index table links to a comprehensive analysis page conta - **Direct links** to explore neuron reconstructions in 3D space - **Zoom, rotate, and navigate** through the brain volume - **View neuron reconstructions** in their anatomical context +{% if config.neuroglancer.download_formats %} +- **Download neurons** as one zip file with one file per displayed neuron. Available formats: {{ config.neuroglancer.download_formats | map(attribute='label') | join(', ') }}. Paste a Neuroglancer URL into the dialog to download exactly the neurons selected in the viewer +{% endif %} ### Layer Analysis - **Detailed breakdown** of neuron presence across brain regions: Lamina (LA), Medulla (ME), Lobula (LO), Lobula Plate (LOP), Accessory Medulla (AME), and Central Brain (CB) @@ -180,6 +183,9 @@ Neurotransmitter assignments are computational predictions based on: - **Printable pages** - Browser print function works with all pages - **Bookmarkable URLs** - Save direct links to specific neuron types - **Shareable content** - URLs can be shared with colleagues +{% if config.neuroglancer.download_formats %} +- **Neuron files** - The download icon above the 3D view saves skeletons or meshes of the displayed neurons ({{ config.neuroglancer.download_formats | map(attribute='label') | join(', ') }}) as a zip archive +{% endif %} ## Dataset Information diff --git a/templates/help.html.jinja b/templates/help.html.jinja index 59333fe3..06d9067f 100644 --- a/templates/help.html.jinja +++ b/templates/help.html.jinja @@ -444,6 +444,13 @@

  • Select: Click on neurons to highlight and inspect
  • Layers: Toggle reference layers on/off (as available). For example, the video below shows how you can use the "synapses" layer to view the synapses of the visible neurons.
    • + {% if config is defined and config.neuroglancer.download_formats %} +
  • Download neurons: The link in the + section header opens a dialog that downloads one file per displayed neuron as a single zip file, in the + chosen format ({{ config.neuroglancer.download_formats | map(attribute='label') | join(', ') }}). + Changes made inside the viewer are not visible to the page; to download exactly the neurons selected in + Neuroglancer, open the viewer in a new window, copy its URL and paste it into the URL field of the dialog.
    • + {% endif %} How to toggle reference layers in neuroglancer view. diff --git a/templates/sections/neuroglancer.html.jinja b/templates/sections/neuroglancer.html.jinja index 7da9c663..daa53ecb 100644 --- a/templates/sections/neuroglancer.html.jinja +++ b/templates/sections/neuroglancer.html.jinja @@ -5,6 +5,9 @@

    Neuron Visualization ⧉ + {% if config is defined and config.neuroglancer.download_formats %} + ⤓ + {% endif %} {% if youtube_url and (features is not defined or features.nav_visible('youtube')) %} @@ -58,6 +61,42 @@ + {% if config is defined and config.neuroglancer.download_formats %} + +
    +

    Download neurons

    + +
    +

    + Downloads one file per neuron that this page sends to the viewer (the neurons of this type plus any + partners ticked in the tables below), packed into a single zip file. Neurons without a file are listed in + missing_body_ids.txt inside the zip. +

    +
    + Format + {% for fmt in config.neuroglancer.download_formats %} + + {% endfor %} +
    +

    + screenshot of the 'copy URL' button in Neuroglancer + Changes made inside Neuroglancer are invisible to the Cell Type Explorer. To download exactly the neurons selected + in Neuroglancer, copy the URL from Neuroglancer and paste it here: +

    + + +

    +
    + + +
    + + {% endif %} + {{ iframe_embed("about:blank", title="Neuroglancer Visualization", extra_class="neuroglancer-iframe") }} diff --git a/templates/sections/neuron_page_scripts.html.jinja b/templates/sections/neuron_page_scripts.html.jinja index 556b2648..c8be03aa 100644 --- a/templates/sections/neuron_page_scripts.html.jinja +++ b/templates/sections/neuron_page_scripts.html.jinja @@ -7,6 +7,12 @@ {# -- Iframe communication bridge for cross-origin parent-child communication -- #} +{# -- Skeleton / mesh download (zip built client-side with fflate), only when configured -- #} +{% if config.neuroglancer.download_formats and features.neuron_visible('neuroglancer') %} + + +{% endif %} +