rebuild documentation

docs/html/.buildinfo

@@ -1,4 +1,4 @@
 # Sphinx build info version 1
 # This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: 5e52e2615b12b741b566a6519af889f6
+config: b60e509b812427f0a4a6ca47ff039bfe
 tags: 645f666f9bcd5a90fca523b33c5a78b7

docs/html/_sources/index.rst.txt

@@ -11,12 +11,12 @@ SPARCSpy is a scalable toolkit to analyse single-cell image datasets. This Pytho
 Installation
 =============
 
-Check out the installation instructions :ref:`here<installation>`. You can validate your installation by running one of the example notebooks `here <https://github.com/MannLabs/SPARCSpy/tree/main/docs_source/pages/notebooks>`_.
+Check out the installation instructions :ref:`here<installation>`. You can validate your installation by running one of the example notebooks `here <https://github.com/MannLabs/SPARCSspatial/tree/main/docs_source/pages/notebooks>`_.
 
 Getting Started
 ===============
 
-You can check out our :ref:`quickstart<quickstart>` guide to get started with SPARCSpy. For more detailed information on the package, we have written an in depth :ref:`computational workflow <pipeline>` guide. In the github repository you can also find some `tutorial notebooks <https://github.com/MannLabs/SPARCSpy/tree/main/docs_source/pages/notebooks>`_ as well as `small example datasets <https://github.com/MannLabs/SPARCSpy/tree/main/example_data>`_ to get started with. If you encounter issues feel free to `open up a git issue <https://github.com/MannLabs/SPARCSpy/issues>`_.
+You can check out our :ref:`quickstart<quickstart>` guide to get started with SPARCSpy. For more detailed information on the package, we have written an in depth :ref:`computational workflow <pipeline>` guide. In the github repository you can also find some `tutorial notebooks <https://github.com/MannLabs/SPARCSspatial/tree/main/docs_source/pages/notebooks>`_ as well as `small example datasets <https://github.com/MannLabs/SPARCSspatial/tree/main/example_data>`_ to get started with. If you encounter issues feel free to `open up a git issue <https://github.com/MannLabs/SPARCSspatial/issues>`_.
 
 Citing our Work
 ================

docs/html/_sources/pages/module.rst.txt

@@ -6,4 +6,5 @@ Module Documentation
 
    module/processing 
    module/pipeline
-   module/ml
+   module/ml
+   module/utils

docs/html/_sources/pages/module/processing.rst.txt

@@ -15,4 +15,9 @@ preprocessing
 segmentation
 ############
 .. automodule:: sparcscore.processing.segmentation
+    :members:
+
+filtering
+#########
+.. automodule:: sparcscore.processing.filtering
     :members:

docs/html/_sources/pages/module/utils.rst.txt

@@ -0,0 +1,12 @@
+*******************
+utils
+*******************
+
+.. toctree::
+   :maxdepth: 3
+
+vis
+########
+
+.. automodule:: sparcscore.utils.vis
+    :members:

docs/html/_sources/pages/quickstart/installation.rst.txt

@@ -14,7 +14,7 @@ We recommend installing the dependencies with mamba or conda before installing S
 
 .. code::
 
-   git clone https://github.com/MannLabs/SPARCSpy
+   git clone https://github.com/MannLabs/SPARCSspatial
    cd SPARCSpy
 
    conda create -n "SPARCSpy"
@@ -59,7 +59,7 @@ Currently SPARCSpy depends on a developer version of alphabase so please install
 SPARCSpy also depends on the `py-lmd <https://github.com/MannLabs/py-lmd>`_ library. Before proceeding please install the py-lmd libray into the same conda environment following the installation instructions `here <https://mannlabs.github.io/py-lmd/html/pages/quickstart.html#installation-from-github>`_.
 Once these steps are completed you can proceed to install the SPARCSpy package.
 
-Clone the `Github repository <https://github.com/MannLabs/sparcspy>`_ and use pip to install the library in your current environment. Please make sure that the package is installed editable (with the `-e` flag). Otherwise pretrained models might not be available:
+Clone the `Github repository <https://github.com/MannLabs/SPARCSspatial>`_ and use pip to install the library in your current environment. Please make sure that the package is installed editable (with the `-e` flag). Otherwise pretrained models might not be available:
 
 .. code:: 
 

docs/html/_static/_sphinx_javascript_frameworks_compat.js

@@ -0,0 +1,123 @@
+/* Compatability shim for jQuery and underscores.js.
+ *
+ * Copyright Sphinx contributors
+ * Released under the two clause BSD licence
+ */
+
+/**
+ * small helper function to urldecode strings
+ *
+ * See https://developer.mozilla.org/en-US/docs/Web/JavaScript/Reference/Global_Objects/decodeURIComponent#Decoding_query_parameters_from_a_URL
+ */
+jQuery.urldecode = function(x) {
+    if (!x) {
+        return x
+    }
+    return decodeURIComponent(x.replace(/\+/g, ' '));
+};
+
+/**
+ * small helper function to urlencode strings
+ */
+jQuery.urlencode = encodeURIComponent;
+
+/**
+ * This function returns the parsed url parameters of the
+ * current request. Multiple values per key are supported,
+ * it will always return arrays of strings for the value parts.
+ */
+jQuery.getQueryParameters = function(s) {
+    if (typeof s === 'undefined')
+        s = document.location.search;
+    var parts = s.substr(s.indexOf('?') + 1).split('&');
+    var result = {};
+    for (var i = 0; i < parts.length; i++) {
+        var tmp = parts[i].split('=', 2);
+        var key = jQuery.urldecode(tmp[0]);
+        var value = jQuery.urldecode(tmp[1]);
+        if (key in result)
+            result[key].push(value);
+        else
+            result[key] = [value];
+    }
+    return result;
+};
+
+/**
+ * highlight a given string on a jquery object by wrapping it in
+ * span elements with the given class name.
+ */
+jQuery.fn.highlightText = function(text, className) {
+    function highlight(node, addItems) {
+        if (node.nodeType === 3) {
+            var val = node.nodeValue;
+            var pos = val.toLowerCase().indexOf(text);
+            if (pos >= 0 &&
+                !jQuery(node.parentNode).hasClass(className) &&
+                !jQuery(node.parentNode).hasClass("nohighlight")) {
+                var span;
+                var isInSVG = jQuery(node).closest("body, svg, foreignObject").is("svg");
+                if (isInSVG) {
+                    span = document.createElementNS("http://www.w3.org/2000/svg", "tspan");
+                } else {
+                    span = document.createElement("span");
+                    span.className = className;
+                }
+                span.appendChild(document.createTextNode(val.substr(pos, text.length)));
+                node.parentNode.insertBefore(span, node.parentNode.insertBefore(
+                    document.createTextNode(val.substr(pos + text.length)),
+                    node.nextSibling));
+                node.nodeValue = val.substr(0, pos);
+                if (isInSVG) {
+                    var rect = document.createElementNS("http://www.w3.org/2000/svg", "rect");
+                    var bbox = node.parentElement.getBBox();
+                    rect.x.baseVal.value = bbox.x;
+                    rect.y.baseVal.value = bbox.y;
+                    rect.width.baseVal.value = bbox.width;
+                    rect.height.baseVal.value = bbox.height;
+                    rect.setAttribute('class', className);
+                    addItems.push({
+                        "parent": node.parentNode,
+                        "target": rect});
+                }
+            }
+        }
+        else if (!jQuery(node).is("button, select, textarea")) {
+            jQuery.each(node.childNodes, function() {
+                highlight(this, addItems);
+            });
+        }
+    }
+    var addItems = [];
+    var result = this.each(function() {
+        highlight(this, addItems);
+    });
+    for (var i = 0; i < addItems.length; ++i) {
+        jQuery(addItems[i].parent).before(addItems[i].target);
+    }
+    return result;
+};
+
+/*
+ * backward compatibility for jQuery.browser
+ * This will be supported until firefox bug is fixed.
+ */
+if (!jQuery.browser) {
+    jQuery.uaMatch = function(ua) {
+        ua = ua.toLowerCase();
+
+        var match = /(chrome)[ \/]([\w.]+)/.exec(ua) ||
+            /(webkit)[ \/]([\w.]+)/.exec(ua) ||
+            /(opera)(?:.*version|)[ \/]([\w.]+)/.exec(ua) ||
+            /(msie) ([\w.]+)/.exec(ua) ||
+            ua.indexOf("compatible") < 0 && /(mozilla)(?:.*? rv:([\w.]+)|)/.exec(ua) ||
+            [];
+
+        return {
+            browser: match[ 1 ] || "",
+            version: match[ 2 ] || "0"
+        };
+    };
+    jQuery.browser = {};
+    jQuery.browser[jQuery.uaMatch(navigator.userAgent).browser] = true;
+}

docs/html/_static/basic.css

@@ -4,7 +4,7 @@
  *
  * Sphinx stylesheet -- basic theme.
  *
- * :copyright: Copyright 2007-2022 by the Sphinx team, see AUTHORS.
+ * :copyright: Copyright 2007-2024 by the Sphinx team, see AUTHORS.
  * :license: BSD, see LICENSE for details.
  *
  */
@@ -222,7 +222,7 @@ table.modindextable td {
 /* -- general body styles --------------------------------------------------- */
 
 div.body {
-    min-width: 450px;
+    min-width: 360px;
     max-width: 800px;
 }
 
@@ -237,14 +237,8 @@ a.headerlink {
     visibility: hidden;
 }
 
-a.brackets:before,
-span.brackets > a:before{
-    content: "[";
-}
-
-a.brackets:after,
-span.brackets > a:after {
-    content: "]";
+a:visited {
+    color: #551A8B;
 }
 
 h1:hover > a.headerlink,
@@ -335,12 +329,16 @@ p.sidebar-title {
     font-weight: bold;
 }
 
+nav.contents,
+aside.topic,
 div.admonition, div.topic, blockquote {
     clear: left;
 }
 
 /* -- topics ---------------------------------------------------------------- */
 
+nav.contents,
+aside.topic,
 div.topic {
     border: 1px solid #ccc;
     padding: 7px;
@@ -379,13 +377,17 @@ div.body p.centered {
 
 div.sidebar > :last-child,
 aside.sidebar > :last-child,
+nav.contents > :last-child,
+aside.topic > :last-child,
 div.topic > :last-child,
 div.admonition > :last-child {
     margin-bottom: 0;
 }
 
 div.sidebar::after,
 aside.sidebar::after,
+nav.contents::after,
+aside.topic::after,
 div.topic::after,
 div.admonition::after,
 blockquote::after {
@@ -428,10 +430,6 @@ table.docutils td, table.docutils th {
     border-bottom: 1px solid #aaa;
 }
 
-table.footnote td, table.footnote th {
-    border: 0 !important;
-}
-
 th {
     text-align: left;
     padding-right: 5px;
@@ -615,19 +613,26 @@ ul.simple p {
     margin-bottom: 0;
 }
 
-dl.footnote > dt,
-dl.citation > dt {
+aside.footnote > span,
+div.citation > span {
     float: left;
-    margin-right: 0.5em;
 }
-
-dl.footnote > dd,
-dl.citation > dd {
+aside.footnote > span:last-of-type,
+div.citation > span:last-of-type {
+  padding-right: 0.5em;
+}
+aside.footnote > p {
+  margin-left: 2em;
+}
+div.citation > p {
+  margin-left: 4em;
+}
+aside.footnote > p:last-of-type,
+div.citation > p:last-of-type {
     margin-bottom: 0em;
 }
-
-dl.footnote > dd:after,
-dl.citation > dd:after {
+aside.footnote > p:last-of-type:after,
+div.citation > p:last-of-type:after {
     content: "";
     clear: both;
 }
@@ -644,10 +649,6 @@ dl.field-list > dt {
     padding-right: 5px;
 }
 
-dl.field-list > dt:after {
-    content: ":";
-}
-
 dl.field-list > dd {
     padding-left: 0.5em;
     margin-top: 0em;
@@ -673,6 +674,16 @@ dd {
     margin-left: 30px;
 }
 
+.sig dd {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
+.sig dl {
+    margin-top: 0px;
+    margin-bottom: 0px;
+}
+
 dl > dd:last-child,
 dl > dd:last-child > :last-child {
     margin-bottom: 0;
@@ -741,6 +752,14 @@ abbr, acronym {
     cursor: help;
 }
 
+.translated {
+    background-color: rgba(207, 255, 207, 0.2)
+}
+
+.untranslated {
+    background-color: rgba(255, 207, 207, 0.2)
+}
+
 /* -- code displays --------------------------------------------------------- */
 
 pre {