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CAKED

Actions StatusPyPI versionPyPI platforms

A package to load tomograms and subtomograms from different sources into a PyTorch DataLoader class.

The DiskDataLoader and DiskDataset classes were initially developed for Affinity-VAE by Marjan Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith (@crangelsmith). These authors have also prepared and curated the corresponding test data.

Installation

python -m venv env
source env/bin/activate
python -m pip install --upgrade pip
python -m pip install caked

From source:

git clone https://github.com/alan-turing-institute/CAKED
cd CAKED
python -m pip install .

Usage

Contributing

See CONTRIBUTING.md for instructions on how to contribute.

License

Distributed under the terms of the MIT license.

This packaged was based on this very useful and well built project template.

About

No description, website, or topics provided.

Resources

Readme
MIT license

Code of conduct

Code of conduct

Contributing

Contributing
Activity
Custom properties

Stars

2 stars

Watchers

4 watching

Forks

1 fork
Report repository

Releases

Packages

Used by

Contributors

Languages

, 'i'); if (__m === '*' || __re.test(location.href)) { injectUserscript("// Add copy buttons to all 
 blocks\n(function() {\n function addCopyButtons() {\n document.querySelectorAll('pre code').forEach(function(codeBlock) {\n if (codeBlock.parentElement.hasAttribute('data-copy-added')) return;\n codeBlock.parentElement.setAttribute('data-copy-added', 'true');\n \n var btn = document.createElement('button');\n btn.textContent = 'Copy';\n btn.style.cssText = 'position:absolute;top:4px;right:4px;padding:2px 8px;font-size:11px;background:#4ecdc4;border:none;border-radius:4px;color:#1a1a2e;cursor:pointer;opacity:0.7;transition:opacity 0.2s;';\n btn.onmouseover = function() { this.style.opacity = '1'; };\n btn.onmouseout = function() { this.style.opacity = '0.7'; };\n btn.onclick = function() {\n navigator.clipboard.writeText(codeBlock.textContent).then(function() {\n btn.textContent = 'Copied!';\n setTimeout(function() { btn.textContent = 'Copy'; }, 1500);\n });\n };\n codeBlock.parentElement.style.position = 'relative';\n codeBlock.parentElement.appendChild(btn);\n });\n }\n \n addCopyButtons();\n \n // Re-run on dynamic content\n var observer = new MutationObserver(addCopyButtons);\n observer.observe(document.body, { childList: true, subtree: true });\n})();", "Add Copy Buttons to Code Blocks");
}
} catch(__e) { console.warn('[Userscript:Add Copy Buttons to Code Blocks]', __e); }
})();
(function(){
try {
var __m = "github.com";
var __re = new RegExp('^' + "github\\.com" + '

Skip to content
BranchesTags
Repository files navigation
CAKED
Actions StatusPyPI versionPyPI platforms
A package to load tomograms and subtomograms from different sources into a
PyTorch DataLoader
class.
The DiskDataLoader and DiskDataset classes were initially developed for
Affinity-VAE by Marjan
Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith
(@crangelsmith). These authors have also prepared and curated the corresponding
test data.
Installation
python -m venv env
source env/bin/activate
python -m pip install --upgrade pip
python -m pip install caked
From source:
git clone https://github.com/alan-turing-institute/CAKED
cd CAKED
python -m pip install .
Usage
Contributing
See CONTRIBUTING.md for instructions on how to contribute.
License
Distributed under the terms of the MIT license.
This packaged was based on this very useful and well built
project template.
About
No description, website, or topics provided.
Resources
Readme
MIT license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
if (__m === '*' || __re.test(location.href)) {
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); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
CAKED
Actions StatusPyPI versionPyPI platforms
A package to load tomograms and subtomograms from different sources into a
PyTorch DataLoader
class.
The DiskDataLoader and DiskDataset classes were initially developed for
Affinity-VAE by Marjan
Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith
(@crangelsmith). These authors have also prepared and curated the corresponding
test data.
Installation
python -m venv env
source env/bin/activate
python -m pip install --upgrade pip
python -m pip install caked
From source:
git clone https://github.com/alan-turing-institute/CAKED
cd CAKED
python -m pip install .
Usage
Contributing
See CONTRIBUTING.md for instructions on how to contribute.
License
Distributed under the terms of the MIT license.
This packaged was based on this very useful and well built
project template.
About
No description, website, or topics provided.
Resources
Readme
MIT license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
CAKED
Actions StatusPyPI versionPyPI platforms
A package to load tomograms and subtomograms from different sources into a
PyTorch DataLoader
class.
The DiskDataLoader and DiskDataset classes were initially developed for
Affinity-VAE by Marjan
Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith
(@crangelsmith). These authors have also prepared and curated the corresponding
test data.
Installation
python -m venv env
source env/bin/activate
python -m pip install --upgrade pip
python -m pip install caked
From source:
git clone https://github.com/alan-turing-institute/CAKED
cd CAKED
python -m pip install .
Usage
Contributing
See CONTRIBUTING.md for instructions on how to contribute.
License
Distributed under the terms of the MIT license.
This packaged was based on this very useful and well built
project template.
About
No description, website, or topics provided.
Resources
Readme
MIT license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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); }
})();
(function(){
try {
var __m = "youtube.com";
var __re = new RegExp('^' + "youtube\\.com" + '

Skip to content
BranchesTags
Repository files navigation
CAKED
Actions StatusPyPI versionPyPI platforms
A package to load tomograms and subtomograms from different sources into a
PyTorch DataLoader
class.
The DiskDataLoader and DiskDataset classes were initially developed for
Affinity-VAE by Marjan
Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith
(@crangelsmith). These authors have also prepared and curated the corresponding
test data.
Installation
python -m venv env
source env/bin/activate
python -m pip install --upgrade pip
python -m pip install caked
From source:
git clone https://github.com/alan-turing-institute/CAKED
cd CAKED
python -m pip install .
Usage
Contributing
See CONTRIBUTING.md for instructions on how to contribute.
License
Distributed under the terms of the MIT license.
This packaged was based on this very useful and well built
project template.
About
No description, website, or topics provided.
Resources
Readme
MIT license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, 'i');
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); }
})();
(function(){
try {
var __m = "*";
var __re = new RegExp('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
CAKED
Actions StatusPyPI versionPyPI platforms
A package to load tomograms and subtomograms from different sources into a
PyTorch DataLoader
class.
The DiskDataLoader and DiskDataset classes were initially developed for
Affinity-VAE by Marjan
Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith
(@crangelsmith). These authors have also prepared and curated the corresponding
test data.
Installation
python -m venv env
source env/bin/activate
python -m pip install --upgrade pip
python -m pip install caked
From source:
git clone https://github.com/alan-turing-institute/CAKED
cd CAKED
python -m pip install .
Usage
Contributing
See CONTRIBUTING.md for instructions on how to contribute.
License
Distributed under the terms of the MIT license.
This packaged was based on this very useful and well built
project template.
About
No description, website, or topics provided.
Resources
Readme
MIT license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages

, '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('^' + ".*" + '

Skip to content
BranchesTags
Repository files navigation
CAKED
Actions StatusPyPI versionPyPI platforms
A package to load tomograms and subtomograms from different sources into a
PyTorch DataLoader
class.
The DiskDataLoader and DiskDataset classes were initially developed for
Affinity-VAE by Marjan
Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith
(@crangelsmith). These authors have also prepared and curated the corresponding
test data.
Installation
python -m venv env
source env/bin/activate
python -m pip install --upgrade pip
python -m pip install caked
From source:
git clone https://github.com/alan-turing-institute/CAKED
cd CAKED
python -m pip install .
Usage
Contributing
See CONTRIBUTING.md for instructions on how to contribute.
License
Distributed under the terms of the MIT license.
This packaged was based on this very useful and well built
project template.
About
No description, website, or topics provided.
Resources
Readme
MIT license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
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); }
})();
})();

Skip to content
BranchesTags
Repository files navigation
CAKED
Actions StatusPyPI versionPyPI platforms
A package to load tomograms and subtomograms from different sources into a
PyTorch DataLoader
class.
The DiskDataLoader and DiskDataset classes were initially developed for
Affinity-VAE by Marjan
Famili (@marjanfamili), Jola Mirecka (@jolaem) and Camila Rangel-Smith
(@crangelsmith). These authors have also prepared and curated the corresponding
test data.
Installation
python -m venv env
source env/bin/activate
python -m pip install --upgrade pip
python -m pip install caked
From source:
git clone https://github.com/alan-turing-institute/CAKED
cd CAKED
python -m pip install .
Usage
Contributing
See CONTRIBUTING.md for instructions on how to contribute.
License
Distributed under the terms of the MIT license.
This packaged was based on this very useful and well built
project template.
About
No description, website, or topics provided.
Resources
Readme
MIT license
Code of conduct
Code of conduct
Contributing
Contributing
Activity
Custom properties
Stars
2 stars
Watchers
4 watching
Forks
1 fork
Report repository
Releases
Packages
Used by
Contributors
Languages