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BMM-within

Research code and manuscript material for fine-scale 3D/4D reconstruction of bird migration from weather radar.

The project is organized around manuscript evidence blocks:

  • 01_forward_model/: radar beam geometry, sparse forward operator, and Section 2 appendix.
  • 02_preprocessing/: reference layers, beam blockage, refraction, and cleaning diagnostics.
  • 03_simulator_fit/: selected scans, cleaned case-study data, covariance fits, VP models, and transforms.
  • 04_static_synthetic/: static synthetic single-radar reconstruction benchmark.
  • 05_advection_synthetic/: moving synthetic single-radar reconstruction benchmark.
  • 06_simple_mosaic/: controlled synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 07_regional_synthetic/: regional synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 08_us_synthetic/: full-US synthetic scalability benchmark.
  • 09_key_west/: real-data Florida Keys single-radar reconstruction.
  • 10_cape_may/: real-data Cape May reconstruction kept for future manuscript use.
  • 11_midwest_mosaic/: real-data Midwest multi-radar reconstruction.

Shared code lives in functions/. Large raw, reference, derived, and cache data live in data/. Manuscript text and submission material live in manuscript/.

Synthetic data products are split by ownership:

  • data/derived/simulator/: shared fitted simulator inputs produced by 03_simulator_fit/
  • 04_static_synthetic/data/, 05_advection_synthetic/data/, 06_simple_mosaic/data/, 07_regional_synthetic/data/: generated cases and inversions for each analysis

Run active MATLAB scripts from their folder or section-by-section after calling:

project_root = setup_paths();

Shared MATLAB Contracts

The current first-party reconstruction pipeline uses these shared names consistently:

  • radar_scans: cleaned radar scans returned by read_rd(...)
  • elevation_kernels: precomputed elevation-specific forward kernels returned by load_F_elev(...)
  • g: Cartesian analysis grid returned by create_grid(...)
  • F: sparse forward operator returned by construct_F(...)
  • obs_matrix: sparse observation matrix saved in data/derived/simulator/scans_data.mat
  • info.obs_grid_size: observation reshape size used with reshape(full(obs_matrix(:, i_t)), info.obs_grid_size)
  • info.obs_block_offset: observation block offsets inside the stacked sparse system

Key function signatures:

[elevation_kernels, radar_scans] = load_F_elev(filepath, radar_scans);
g = create_grid(elevation_kernels, radar_scans, ...);
[F, obs_matrix, info] = construct_F(radar_scans, elevation_kernels, g);
density_field = compute_scan(F, obs_matrix(:, i_t), g, ...);
[obs_values, nonzero_obs_idx, azimuth_deg, elevation_deg, range_m, beam_height_m] = ...
format_data(obs_matrix(:, i_t), elevation_kernels, info);

Derived Data Note

Some saved .mat products are generated artifacts, not stable interfaces.

  • After changing the shared forward-model code, regenerate data/derived/simulator/scans_data.mat and related downstream products.
  • data/derived/F_elev/*.mat kernels now use the variable name elevation_kernel.
  • Older derived files that only store the legacy variable dfe are considered stale and should be regenerated or updated before rerunning the workflows.

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, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
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}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
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try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

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Repository files navigation
BMM-within
Research code and manuscript material for fine-scale 3D/4D reconstruction of bird migration from weather radar.
The project is organized around manuscript evidence blocks:
  • 01_forward_model/: radar beam geometry, sparse forward operator, and Section 2 appendix.
  • 02_preprocessing/: reference layers, beam blockage, refraction, and cleaning diagnostics.
  • 03_simulator_fit/: selected scans, cleaned case-study data, covariance fits, VP models, and transforms.
  • 04_static_synthetic/: static synthetic single-radar reconstruction benchmark.
  • 05_advection_synthetic/: moving synthetic single-radar reconstruction benchmark.
  • 06_simple_mosaic/: controlled synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 07_regional_synthetic/: regional synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 08_us_synthetic/: full-US synthetic scalability benchmark.
  • 09_key_west/: real-data Florida Keys single-radar reconstruction.
  • 10_cape_may/: real-data Cape May reconstruction kept for future manuscript use.
  • 11_midwest_mosaic/: real-data Midwest multi-radar reconstruction.
Shared code lives in functions/. Large raw, reference, derived, and cache data live in data/. Manuscript text and submission material live in manuscript/.
Synthetic data products are split by ownership:
  • data/derived/simulator/: shared fitted simulator inputs produced by 03_simulator_fit/
  • 04_static_synthetic/data/, 05_advection_synthetic/data/, 06_simple_mosaic/data/, 07_regional_synthetic/data/: generated cases and inversions for each analysis
Run active MATLAB scripts from their folder or section-by-section after calling:
project_root = setup_paths();
Shared MATLAB Contracts
The current first-party reconstruction pipeline uses these shared names consistently:
  • radar_scans: cleaned radar scans returned by read_rd(...)
  • elevation_kernels: precomputed elevation-specific forward kernels returned by load_F_elev(...)
  • g: Cartesian analysis grid returned by create_grid(...)
  • F: sparse forward operator returned by construct_F(...)
  • obs_matrix: sparse observation matrix saved in data/derived/simulator/scans_data.mat
  • info.obs_grid_size: observation reshape size used with reshape(full(obs_matrix(:, i_t)), info.obs_grid_size)
  • info.obs_block_offset: observation block offsets inside the stacked sparse system
Key function signatures:
[elevation_kernels, radar_scans] = load_F_elev(filepath, radar_scans);
g = create_grid(elevation_kernels, radar_scans, ...);
[F, obs_matrix, info] = construct_F(radar_scans, elevation_kernels, g);
density_field = compute_scan(F, obs_matrix(:, i_t), g, ...);
[obs_values, nonzero_obs_idx, azimuth_deg, elevation_deg, range_m, beam_height_m] = ...
format_data(obs_matrix(:, i_t), elevation_kernels, info);
Derived Data Note
Some saved .mat products are generated artifacts, not stable interfaces.
  • After changing the shared forward-model code, regenerate data/derived/simulator/scans_data.mat and related downstream products.
  • data/derived/F_elev/*.mat kernels now use the variable name elevation_kernel.
  • Older derived files that only store the legacy variable dfe are considered stale and should be regenerated or updated before rerunning the workflows.
About
No description, website, or topics provided.
Resources
Readme
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1 watching
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injectUserscript("// Force GitHub README to respect dark mode\n(function() {\n var style = document.createElement('style');\n style.textContent = '\n .markdown-body {\n color-scheme: dark light;\n }\n .markdown-body pre { background: #161b22 !important; }\n .markdown-body code { background: rgba(110, 118, 129, 0.4) !important; }\n .markdown-body table th, .markdown-body table td { border-color: #30363d !important; }\n .markdown-body img { background: #0d1117; }\n .markdown-body blockquote { border-left-color: #8b949e; }\n .markdown-body hr { border-color: #30363d; }\n ';\n document.head.appendChild(style);\n})();", "GitHub Dark Mode README Fix");
}
} catch(__e) { console.warn('[Userscript:GitHub Dark Mode README Fix]', __e); }
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setup_paths.m
singular_log.txt
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Repository files navigation
BMM-within
Research code and manuscript material for fine-scale 3D/4D reconstruction of bird migration from weather radar.
The project is organized around manuscript evidence blocks:
  • 01_forward_model/: radar beam geometry, sparse forward operator, and Section 2 appendix.
  • 02_preprocessing/: reference layers, beam blockage, refraction, and cleaning diagnostics.
  • 03_simulator_fit/: selected scans, cleaned case-study data, covariance fits, VP models, and transforms.
  • 04_static_synthetic/: static synthetic single-radar reconstruction benchmark.
  • 05_advection_synthetic/: moving synthetic single-radar reconstruction benchmark.
  • 06_simple_mosaic/: controlled synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 07_regional_synthetic/: regional synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 08_us_synthetic/: full-US synthetic scalability benchmark.
  • 09_key_west/: real-data Florida Keys single-radar reconstruction.
  • 10_cape_may/: real-data Cape May reconstruction kept for future manuscript use.
  • 11_midwest_mosaic/: real-data Midwest multi-radar reconstruction.
Shared code lives in functions/. Large raw, reference, derived, and cache data live in data/. Manuscript text and submission material live in manuscript/.
Synthetic data products are split by ownership:
  • data/derived/simulator/: shared fitted simulator inputs produced by 03_simulator_fit/
  • 04_static_synthetic/data/, 05_advection_synthetic/data/, 06_simple_mosaic/data/, 07_regional_synthetic/data/: generated cases and inversions for each analysis
Run active MATLAB scripts from their folder or section-by-section after calling:
project_root = setup_paths();
Shared MATLAB Contracts
The current first-party reconstruction pipeline uses these shared names consistently:
  • radar_scans: cleaned radar scans returned by read_rd(...)
  • elevation_kernels: precomputed elevation-specific forward kernels returned by load_F_elev(...)
  • g: Cartesian analysis grid returned by create_grid(...)
  • F: sparse forward operator returned by construct_F(...)
  • obs_matrix: sparse observation matrix saved in data/derived/simulator/scans_data.mat
  • info.obs_grid_size: observation reshape size used with reshape(full(obs_matrix(:, i_t)), info.obs_grid_size)
  • info.obs_block_offset: observation block offsets inside the stacked sparse system
Key function signatures:
[elevation_kernels, radar_scans] = load_F_elev(filepath, radar_scans);
g = create_grid(elevation_kernels, radar_scans, ...);
[F, obs_matrix, info] = construct_F(radar_scans, elevation_kernels, g);
density_field = compute_scan(F, obs_matrix(:, i_t), g, ...);
[obs_values, nonzero_obs_idx, azimuth_deg, elevation_deg, range_m, beam_height_m] = ...
format_data(obs_matrix(:, i_t), elevation_kernels, info);
Derived Data Note
Some saved .mat products are generated artifacts, not stable interfaces.
  • After changing the shared forward-model code, regenerate data/derived/simulator/scans_data.mat and related downstream products.
  • data/derived/F_elev/*.mat kernels now use the variable name elevation_kernel.
  • Older derived files that only store the legacy variable dfe are considered stale and should be regenerated or updated before rerunning the workflows.
About
No description, website, or topics provided.
Resources
Readme
Activity
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Stars
0 stars
Watchers
1 watching
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0 forks
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if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Highlight search terms from Google/DuckDuckGo/Bing referrer\n(function() {\n var ref = document.referrer;\n var terms = [];\n \n if (ref.includes('google.com') || ref.includes('duckduckgo.com') || ref.includes('bing.com')) {\n var url = new URL(ref);\n var q = url.searchParams.get('q') || url.searchParams.get('p');\n if (q) {\n terms = q.split(/\\s+/).filter(function(t) { return t.length > 2; });\n }\n }\n \n if (terms.length === 0) return;\n \n var style = document.createElement('style');\n style.textContent = '.userscript-highlight { background: #fbbf24; color: #1a1a2e; padding: 1px 3px; border-radius: 2px; }';\n document.head.appendChild(style);\n \n function highlight(node) {\n if (node.nodeType === 3) { // text node\n var text = node.textContent;\n var found = false;\n terms.forEach(function(term) {\n var regex = new RegExp('(' + term.replace(/[.*+?^${}()|[\\]\\\\]/g, '\\\\') + ')', 'gi');\n if (regex.test(text)) {\n found = true;\n var frag = document.createDocumentFragment();\n var parts = text.split(regex);\n parts.forEach(function(part, i) {\n if (i % 2 === 0) {\n frag.appendChild(document.createTextNode(part));\n } else {\n var span = document.createElement('span');\n span.className = 'userscript-highlight';\n span.textContent = part;\n frag.appendChild(span);\n }\n });\n node.parentNode.replaceChild(frag, node);\n }\n });\n } else if (node.nodeType === 1 && node.childNodes) { // element\n var skipTags = ['SCRIPT', 'STYLE', 'NOSCRIPT', 'TEXTAREA', 'INPUT', 'SELECT'];\n if (!skipTags.includes(node.tagName)) {\n Array.from(node.childNodes).forEach(highlight);\n }\n }\n }\n \n highlight(document.body);\n \n // Re-highlight on dynamic content\n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1 || node.nodeType === 3) highlight(node);\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Highlight Search Terms");
}
} catch(__e) { console.warn('[Userscript:Highlight Search Terms]', __e); }
})();
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try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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Repository files navigation
BMM-within
Research code and manuscript material for fine-scale 3D/4D reconstruction of bird migration from weather radar.
The project is organized around manuscript evidence blocks:
  • 01_forward_model/: radar beam geometry, sparse forward operator, and Section 2 appendix.
  • 02_preprocessing/: reference layers, beam blockage, refraction, and cleaning diagnostics.
  • 03_simulator_fit/: selected scans, cleaned case-study data, covariance fits, VP models, and transforms.
  • 04_static_synthetic/: static synthetic single-radar reconstruction benchmark.
  • 05_advection_synthetic/: moving synthetic single-radar reconstruction benchmark.
  • 06_simple_mosaic/: controlled synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 07_regional_synthetic/: regional synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 08_us_synthetic/: full-US synthetic scalability benchmark.
  • 09_key_west/: real-data Florida Keys single-radar reconstruction.
  • 10_cape_may/: real-data Cape May reconstruction kept for future manuscript use.
  • 11_midwest_mosaic/: real-data Midwest multi-radar reconstruction.
Shared code lives in functions/. Large raw, reference, derived, and cache data live in data/. Manuscript text and submission material live in manuscript/.
Synthetic data products are split by ownership:
  • data/derived/simulator/: shared fitted simulator inputs produced by 03_simulator_fit/
  • 04_static_synthetic/data/, 05_advection_synthetic/data/, 06_simple_mosaic/data/, 07_regional_synthetic/data/: generated cases and inversions for each analysis
Run active MATLAB scripts from their folder or section-by-section after calling:
project_root = setup_paths();
Shared MATLAB Contracts
The current first-party reconstruction pipeline uses these shared names consistently:
  • radar_scans: cleaned radar scans returned by read_rd(...)
  • elevation_kernels: precomputed elevation-specific forward kernels returned by load_F_elev(...)
  • g: Cartesian analysis grid returned by create_grid(...)
  • F: sparse forward operator returned by construct_F(...)
  • obs_matrix: sparse observation matrix saved in data/derived/simulator/scans_data.mat
  • info.obs_grid_size: observation reshape size used with reshape(full(obs_matrix(:, i_t)), info.obs_grid_size)
  • info.obs_block_offset: observation block offsets inside the stacked sparse system
Key function signatures:
[elevation_kernels, radar_scans] = load_F_elev(filepath, radar_scans);
g = create_grid(elevation_kernels, radar_scans, ...);
[F, obs_matrix, info] = construct_F(radar_scans, elevation_kernels, g);
density_field = compute_scan(F, obs_matrix(:, i_t), g, ...);
[obs_values, nonzero_obs_idx, azimuth_deg, elevation_deg, range_m, beam_height_m] = ...
format_data(obs_matrix(:, i_t), elevation_kernels, info);
Derived Data Note
Some saved .mat products are generated artifacts, not stable interfaces.
  • After changing the shared forward-model code, regenerate data/derived/simulator/scans_data.mat and related downstream products.
  • data/derived/F_elev/*.mat kernels now use the variable name elevation_kernel.
  • Older derived files that only store the legacy variable dfe are considered stale and should be regenerated or updated before rerunning the workflows.
About
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Resources
Readme
Activity
Custom properties
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Watchers
1 watching
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if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Strip utm_, fbclid, gclid, etc. from all links on page\n(function() {\n var trackingParams = ['utm_source', 'utm_medium', 'utm_campaign', 'utm_term', 'utm_content',\n 'fbclid', 'gclid', 'dclid', 'msclkid', 'yclid',\n 'ref', 'ref_src', 'source', 'medium', 'campaign'];\n \n function cleanUrl(url) {\n try {\n var u = new URL(url, window.location.origin);\n var changed = false;\n trackingParams.forEach(function(p) {\n if (u.searchParams.has(p)) {\n u.searchParams.delete(p);\n changed = true;\n }\n });\n return changed ? u.toString() : url;\n } catch (e) {\n return url;\n }\n }\n \n function cleanLinks() {\n document.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n \n cleanLinks();\n \n var observer = new MutationObserver(function(mutations) {\n mutations.forEach(function(m) {\n m.addedNodes.forEach(function(node) {\n if (node.nodeType === 1) {\n if (node.tagName === 'A') cleanLinks();\n node.querySelectorAll('a[href]').forEach(function(a) {\n var clean = cleanUrl(a.href);\n if (clean !== a.href) a.href = clean;\n });\n }\n });\n });\n });\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Remove Tracking Parameters from Links");
}
} catch(__e) { console.warn('[Userscript:Remove Tracking Parameters from Links]', __e); }
})();
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try {
var __m = "youtube.com";
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Repository files navigation
BMM-within
Research code and manuscript material for fine-scale 3D/4D reconstruction of bird migration from weather radar.
The project is organized around manuscript evidence blocks:
  • 01_forward_model/: radar beam geometry, sparse forward operator, and Section 2 appendix.
  • 02_preprocessing/: reference layers, beam blockage, refraction, and cleaning diagnostics.
  • 03_simulator_fit/: selected scans, cleaned case-study data, covariance fits, VP models, and transforms.
  • 04_static_synthetic/: static synthetic single-radar reconstruction benchmark.
  • 05_advection_synthetic/: moving synthetic single-radar reconstruction benchmark.
  • 06_simple_mosaic/: controlled synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 07_regional_synthetic/: regional synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 08_us_synthetic/: full-US synthetic scalability benchmark.
  • 09_key_west/: real-data Florida Keys single-radar reconstruction.
  • 10_cape_may/: real-data Cape May reconstruction kept for future manuscript use.
  • 11_midwest_mosaic/: real-data Midwest multi-radar reconstruction.
Shared code lives in functions/. Large raw, reference, derived, and cache data live in data/. Manuscript text and submission material live in manuscript/.
Synthetic data products are split by ownership:
  • data/derived/simulator/: shared fitted simulator inputs produced by 03_simulator_fit/
  • 04_static_synthetic/data/, 05_advection_synthetic/data/, 06_simple_mosaic/data/, 07_regional_synthetic/data/: generated cases and inversions for each analysis
Run active MATLAB scripts from their folder or section-by-section after calling:
project_root = setup_paths();
Shared MATLAB Contracts
The current first-party reconstruction pipeline uses these shared names consistently:
  • radar_scans: cleaned radar scans returned by read_rd(...)
  • elevation_kernels: precomputed elevation-specific forward kernels returned by load_F_elev(...)
  • g: Cartesian analysis grid returned by create_grid(...)
  • F: sparse forward operator returned by construct_F(...)
  • obs_matrix: sparse observation matrix saved in data/derived/simulator/scans_data.mat
  • info.obs_grid_size: observation reshape size used with reshape(full(obs_matrix(:, i_t)), info.obs_grid_size)
  • info.obs_block_offset: observation block offsets inside the stacked sparse system
Key function signatures:
[elevation_kernels, radar_scans] = load_F_elev(filepath, radar_scans);
g = create_grid(elevation_kernels, radar_scans, ...);
[F, obs_matrix, info] = construct_F(radar_scans, elevation_kernels, g);
density_field = compute_scan(F, obs_matrix(:, i_t), g, ...);
[obs_values, nonzero_obs_idx, azimuth_deg, elevation_deg, range_m, beam_height_m] = ...
format_data(obs_matrix(:, i_t), elevation_kernels, info);
Derived Data Note
Some saved .mat products are generated artifacts, not stable interfaces.
  • After changing the shared forward-model code, regenerate data/derived/simulator/scans_data.mat and related downstream products.
  • data/derived/F_elev/*.mat kernels now use the variable name elevation_kernel.
  • Older derived files that only store the legacy variable dfe are considered stale and should be regenerated or updated before rerunning the workflows.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Contributors
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if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Auto-enable theater mode on YouTube\n(function() {\n function tryTheater() {\n var btn = document.querySelector('button[aria-label=\"Theater mode\"], ytd-player #player button[title=\"Theater mode\"]');\n if (btn && !btn.classList.contains('activated')) {\n btn.click();\n }\n }\n \n // Try immediately\n tryTheater();\n \n // Try after navigation (SPA)\n var lastUrl = location.href;\n setInterval(function() {\n if (location.href !== lastUrl) {\n lastUrl = location.href;\n setTimeout(tryTheater, 500);\n }\n }, 1000);\n \n // Also try on player load\n var observer = new MutationObserver(tryTheater);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "YouTube Theater Mode Default");
}
} catch(__e) { console.warn('[Userscript:YouTube Theater Mode Default]', __e); }
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setup_paths.m
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Repository files navigation
BMM-within
Research code and manuscript material for fine-scale 3D/4D reconstruction of bird migration from weather radar.
The project is organized around manuscript evidence blocks:
  • 01_forward_model/: radar beam geometry, sparse forward operator, and Section 2 appendix.
  • 02_preprocessing/: reference layers, beam blockage, refraction, and cleaning diagnostics.
  • 03_simulator_fit/: selected scans, cleaned case-study data, covariance fits, VP models, and transforms.
  • 04_static_synthetic/: static synthetic single-radar reconstruction benchmark.
  • 05_advection_synthetic/: moving synthetic single-radar reconstruction benchmark.
  • 06_simple_mosaic/: controlled synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 07_regional_synthetic/: regional synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 08_us_synthetic/: full-US synthetic scalability benchmark.
  • 09_key_west/: real-data Florida Keys single-radar reconstruction.
  • 10_cape_may/: real-data Cape May reconstruction kept for future manuscript use.
  • 11_midwest_mosaic/: real-data Midwest multi-radar reconstruction.
Shared code lives in functions/. Large raw, reference, derived, and cache data live in data/. Manuscript text and submission material live in manuscript/.
Synthetic data products are split by ownership:
  • data/derived/simulator/: shared fitted simulator inputs produced by 03_simulator_fit/
  • 04_static_synthetic/data/, 05_advection_synthetic/data/, 06_simple_mosaic/data/, 07_regional_synthetic/data/: generated cases and inversions for each analysis
Run active MATLAB scripts from their folder or section-by-section after calling:
project_root = setup_paths();
Shared MATLAB Contracts
The current first-party reconstruction pipeline uses these shared names consistently:
  • radar_scans: cleaned radar scans returned by read_rd(...)
  • elevation_kernels: precomputed elevation-specific forward kernels returned by load_F_elev(...)
  • g: Cartesian analysis grid returned by create_grid(...)
  • F: sparse forward operator returned by construct_F(...)
  • obs_matrix: sparse observation matrix saved in data/derived/simulator/scans_data.mat
  • info.obs_grid_size: observation reshape size used with reshape(full(obs_matrix(:, i_t)), info.obs_grid_size)
  • info.obs_block_offset: observation block offsets inside the stacked sparse system
Key function signatures:
[elevation_kernels, radar_scans] = load_F_elev(filepath, radar_scans);
g = create_grid(elevation_kernels, radar_scans, ...);
[F, obs_matrix, info] = construct_F(radar_scans, elevation_kernels, g);
density_field = compute_scan(F, obs_matrix(:, i_t), g, ...);
[obs_values, nonzero_obs_idx, azimuth_deg, elevation_deg, range_m, beam_height_m] = ...
format_data(obs_matrix(:, i_t), elevation_kernels, info);
Derived Data Note
Some saved .mat products are generated artifacts, not stable interfaces.
  • After changing the shared forward-model code, regenerate data/derived/simulator/scans_data.mat and related downstream products.
  • data/derived/F_elev/*.mat kernels now use the variable name elevation_kernel.
  • Older derived files that only store the legacy variable dfe are considered stale and should be regenerated or updated before rerunning the workflows.
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, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Remove or un-stick sticky/fixed headers that block content\n(function() {\n function unstick() {\n document.querySelectorAll('header, nav, [role=\"banner\"], .header, .navbar, .sticky, .fixed-top, [style*=\"position: fixed\"], [style*=\"position:sticky\"]').forEach(function(el) {\n if (el.style.position === 'fixed' || el.style.position === 'sticky' || \n getComputedStyle(el).position === 'fixed' || getComputedStyle(el).position === 'sticky') {\n el.style.position = 'static';\n el.style.top = 'auto';\n el.style.zIndex = 'auto';\n }\n });\n }\n \n unstick();\n \n var observer = new MutationObserver(unstick);\n observer.observe(document.body, { childList: true, subtree: true, attributes: true, attributeFilter: ['style', 'class'] });\n})();", "Kill Sticky Headers");
}
} catch(__e) { console.warn('[Userscript:Kill Sticky Headers]', __e); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

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BMM-within
Research code and manuscript material for fine-scale 3D/4D reconstruction of bird migration from weather radar.
The project is organized around manuscript evidence blocks:
  • 01_forward_model/: radar beam geometry, sparse forward operator, and Section 2 appendix.
  • 02_preprocessing/: reference layers, beam blockage, refraction, and cleaning diagnostics.
  • 03_simulator_fit/: selected scans, cleaned case-study data, covariance fits, VP models, and transforms.
  • 04_static_synthetic/: static synthetic single-radar reconstruction benchmark.
  • 05_advection_synthetic/: moving synthetic single-radar reconstruction benchmark.
  • 06_simple_mosaic/: controlled synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 07_regional_synthetic/: regional synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 08_us_synthetic/: full-US synthetic scalability benchmark.
  • 09_key_west/: real-data Florida Keys single-radar reconstruction.
  • 10_cape_may/: real-data Cape May reconstruction kept for future manuscript use.
  • 11_midwest_mosaic/: real-data Midwest multi-radar reconstruction.
Shared code lives in functions/. Large raw, reference, derived, and cache data live in data/. Manuscript text and submission material live in manuscript/.
Synthetic data products are split by ownership:
  • data/derived/simulator/: shared fitted simulator inputs produced by 03_simulator_fit/
  • 04_static_synthetic/data/, 05_advection_synthetic/data/, 06_simple_mosaic/data/, 07_regional_synthetic/data/: generated cases and inversions for each analysis
Run active MATLAB scripts from their folder or section-by-section after calling:
project_root = setup_paths();
Shared MATLAB Contracts
The current first-party reconstruction pipeline uses these shared names consistently:
  • radar_scans: cleaned radar scans returned by read_rd(...)
  • elevation_kernels: precomputed elevation-specific forward kernels returned by load_F_elev(...)
  • g: Cartesian analysis grid returned by create_grid(...)
  • F: sparse forward operator returned by construct_F(...)
  • obs_matrix: sparse observation matrix saved in data/derived/simulator/scans_data.mat
  • info.obs_grid_size: observation reshape size used with reshape(full(obs_matrix(:, i_t)), info.obs_grid_size)
  • info.obs_block_offset: observation block offsets inside the stacked sparse system
Key function signatures:
[elevation_kernels, radar_scans] = load_F_elev(filepath, radar_scans);
g = create_grid(elevation_kernels, radar_scans, ...);
[F, obs_matrix, info] = construct_F(radar_scans, elevation_kernels, g);
density_field = compute_scan(F, obs_matrix(:, i_t), g, ...);
[obs_values, nonzero_obs_idx, azimuth_deg, elevation_deg, range_m, beam_height_m] = ...
format_data(obs_matrix(:, i_t), elevation_kernels, info);
Derived Data Note
Some saved .mat products are generated artifacts, not stable interfaces.
  • After changing the shared forward-model code, regenerate data/derived/simulator/scans_data.mat and related downstream products.
  • data/derived/F_elev/*.mat kernels now use the variable name elevation_kernel.
  • Older derived files that only store the legacy variable dfe are considered stale and should be regenerated or updated before rerunning the workflows.
About
No description, website, or topics provided.
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Readme
Activity
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0 stars
Watchers
1 watching
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0 forks
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Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
injectUserscript("// Universal Dark Mode - works on any site\n(function() {\n var enabled = true;\n \n function applyDarkMode() {\n if (!enabled) return;\n \n // Create style element if it doesn't exist\n var style = document.getElementById('universal-dark-mode-style');\n if (!style) {\n style = document.createElement('style');\n style.id = 'universal-dark-mode-style';\n document.head.appendChild(style);\n }\n \n // Dark mode CSS - inverts colors but preserves images/video\n style.textContent = '\n /* Invert everything except media */\n html {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #1a1a2e !important;\n }\n \n /* Restore images, videos, iframes, canvas */\n img, video, iframe, canvas, svg, picture, [style*=\"background-image\"] {\n filter: invert(1) hue-rotate(180deg) !important;\n }\n \n /* Preserve specific elements that should not be inverted */\n .no-dark-mode, .no-dark-mode *,\n [data-theme=\"light\"], [data-theme=\"light\"],\n .ace_editor, .ace_editor *,\n .CodeMirror, .CodeMirror *,\n .monaco-editor, .monaco-editor *,\n .markdown-body pre, .markdown-body pre *,\n .highlight, .highlight *,\n pre code, pre code * {\n filter: none !important;\n }\n \n /* Fix common UI elements */\n .modal, .popup, .dropdown-menu, .tooltip, .popover {\n filter: invert(1) hue-rotate(180deg) !important;\n background: #2d2d44 !important;\n border-color: #444 !important;\n }\n \n /* Scrollbars */\n ::-webkit-scrollbar { background: #1a1a2e !important; }\n ::-webkit-scrollbar-thumb { background: #444 !important; }\n ::-webkit-scrollbar-thumb:hover { background: #555 !important; }\n \n /* Selection */\n ::selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ::-moz-selection { background: #4ecdc4 !important; color: #1a1a2e !important; }\n ';\n }\n \n function removeDarkMode() {\n var style = document.getElementById('universal-dark-mode-style');\n if (style) style.remove();\n }\n \n // Toggle with Alt+Shift+D\n document.addEventListener('keydown', function(e) {\n if (e.altKey && e.shiftKey && e.key === 'D') {\n e.preventDefault();\n enabled = !enabled;\n if (enabled) {\n applyDarkMode();\n console.log('[Universal Dark Mode] Enabled');\n } else {\n removeDarkMode();\n console.log('[Universal Dark Mode] Disabled');\n }\n }\n });\n \n // Apply on load\n applyDarkMode();\n \n // Re-apply on dynamic content\n var observer = new MutationObserver(function(mutations) {\n if (enabled && !document.getElementById('universal-dark-mode-style')) {\n applyDarkMode();\n }\n });\n observer.observe(document.head, { childList: true });\n \n console.log('[Universal Dark Mode] Loaded - Press Alt+Shift+D to toggle');\n})();", "Universal Dark Mode");
}
} catch(__e) { console.warn('[Userscript:Universal Dark Mode]', __e); }
})();
})();

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functions
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README.md
README.md
setup_paths.m
setup_paths.m
singular_log.txt
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Repository files navigation
BMM-within
Research code and manuscript material for fine-scale 3D/4D reconstruction of bird migration from weather radar.
The project is organized around manuscript evidence blocks:
  • 01_forward_model/: radar beam geometry, sparse forward operator, and Section 2 appendix.
  • 02_preprocessing/: reference layers, beam blockage, refraction, and cleaning diagnostics.
  • 03_simulator_fit/: selected scans, cleaned case-study data, covariance fits, VP models, and transforms.
  • 04_static_synthetic/: static synthetic single-radar reconstruction benchmark.
  • 05_advection_synthetic/: moving synthetic single-radar reconstruction benchmark.
  • 06_simple_mosaic/: controlled synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 07_regional_synthetic/: regional synthetic multi-radar, multi-time mosaic reconstruction benchmark.
  • 08_us_synthetic/: full-US synthetic scalability benchmark.
  • 09_key_west/: real-data Florida Keys single-radar reconstruction.
  • 10_cape_may/: real-data Cape May reconstruction kept for future manuscript use.
  • 11_midwest_mosaic/: real-data Midwest multi-radar reconstruction.
Shared code lives in functions/. Large raw, reference, derived, and cache data live in data/. Manuscript text and submission material live in manuscript/.
Synthetic data products are split by ownership:
  • data/derived/simulator/: shared fitted simulator inputs produced by 03_simulator_fit/
  • 04_static_synthetic/data/, 05_advection_synthetic/data/, 06_simple_mosaic/data/, 07_regional_synthetic/data/: generated cases and inversions for each analysis
Run active MATLAB scripts from their folder or section-by-section after calling:
project_root = setup_paths();
Shared MATLAB Contracts
The current first-party reconstruction pipeline uses these shared names consistently:
  • radar_scans: cleaned radar scans returned by read_rd(...)
  • elevation_kernels: precomputed elevation-specific forward kernels returned by load_F_elev(...)
  • g: Cartesian analysis grid returned by create_grid(...)
  • F: sparse forward operator returned by construct_F(...)
  • obs_matrix: sparse observation matrix saved in data/derived/simulator/scans_data.mat
  • info.obs_grid_size: observation reshape size used with reshape(full(obs_matrix(:, i_t)), info.obs_grid_size)
  • info.obs_block_offset: observation block offsets inside the stacked sparse system
Key function signatures:
[elevation_kernels, radar_scans] = load_F_elev(filepath, radar_scans);
g = create_grid(elevation_kernels, radar_scans, ...);
[F, obs_matrix, info] = construct_F(radar_scans, elevation_kernels, g);
density_field = compute_scan(F, obs_matrix(:, i_t), g, ...);
[obs_values, nonzero_obs_idx, azimuth_deg, elevation_deg, range_m, beam_height_m] = ...
format_data(obs_matrix(:, i_t), elevation_kernels, info);
Derived Data Note
Some saved .mat products are generated artifacts, not stable interfaces.
  • After changing the shared forward-model code, regenerate data/derived/simulator/scans_data.mat and related downstream products.
  • data/derived/F_elev/*.mat kernels now use the variable name elevation_kernel.
  • Older derived files that only store the legacy variable dfe are considered stale and should be regenerated or updated before rerunning the workflows.
About
No description, website, or topics provided.
Resources
Readme
Activity
Custom properties
Stars
0 stars
Watchers
1 watching
Forks
0 forks
Report repository
Contributors
Languages