Merge pull request #1799 from girder/girder-5-update-20253101

Merge recent changes from `master` into `girder-5`

.pre-commit-config.yaml

@@ -46,12 +46,12 @@ repos:
         files: README.rst
         name: rst-linter of README.rst
   - repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.0
     hooks:
       - id: codespell
         args:
           - --ignore-words-list
-          - "hist,indext,pixelx,thex,subtile,slippy,fram"
+          - "hist,indext,pixelx,thex,subtile,slippy,fram,thet"
         exclude: '.*\.ipynb$'
   - repo: https://github.com/syntaqx/git-hooks
     rev: v0.0.18
@@ -61,19 +61,18 @@ repos:
     rev: v4.0.0
     hooks:
       - id: stylus-supremacy
-        language_version: "22.10.0"
         args:
           - '--options'
           - './girder/girder_large_image/web_client/package.json'
   - repo: https://github.com/asottile/pyupgrade
-    rev: v3.18.0
+    rev: v3.19.1
     hooks:
       - id: pyupgrade
         args:
           - --py38-plus
           - --keep-percent-format
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.9.2
     hooks:
       - id: ruff
         args:

CHANGELOG.md

@@ -1,10 +1,22 @@
 # Change Log
 
-## 1.30.7
+## 1.31.1
+
+### Improvements
+
+- Improve how we use vips to read lower tile levels ([#1794](../../pull/1794))
+- Be more specific in casting when converting images via vips ([#1795](../../pull/1795))
+
+### Bug Fixes
+
+- Fix an issue with lazy tiles that have non power of two scaling ([#1797](../../pull/1797))
+
+## 1.31.0
 
 ### Features
 
 - Add utility functions for converting between frame and axes ([#1778](../../pull/1778))
+- Jupyter frame selector ([#1738](../../pull/1738), [#1792](../../pull/1792), [#1793](../../pull/1793))
 
 ### Improvements
 
@@ -13,10 +25,16 @@
 - Don't read multiplane ndpi files with openslide ([#1772](../../pull/1772))
 - Harden sources based on more fuzz testing ([#1774](../../pull/1774))
 - Default to not caching source in notebooks ([#1776](../../pull/1776))
+- Automatically set the JUPYTER_PROXY value ([#1781](../../pull/1781))
+- Add a general channelNames property to tile sources ([#1783](../../pull/1783))
+- Speed up compositing styles ([#1784](../../pull/1784))
+- Better repr of large_image classes ([#1787](../../pull/1787))
+- Better detect multiframe images in PIL ([#1791](../../pull/1791))
 
 ### Changes
 
 - Allow umap-learn for graphing in girder annotations in python 3.13 ([#1780](../../pull/1780))
+- List a few more known extensions for different sources ([#1790](../../pull/1790))
 
 ### Bug Fixes
 
@@ -44,7 +62,7 @@
 ### Changes
 
 - Suppress a warning about nd2 files that we can't do anything about ([#1749](../../pull/1749))
-- Zero empty areas in tile frames ([#1752](../../pull/1752))
+- Zero empty areas in tile frames ([#1755](../../pull/1755))
 - Don't include cache libraries in [common] deployments ([#1758](../../pull/1758))
 - Specify empty_dir=yes when constructing vsicurl parameters ([#1760](../../pull/1760))
 - Update how some associated images are read in tiff files ([#1763](../../pull/1763))

docs/notebooks/large_image_examples.ipynb

@@ -46,7 +46,7 @@
     "\n",
     "# For maximum capabilities in Jupyter, also install ipyleaflet so you can\n",
     "# view zoomable images in the notebook\n",
-    "!pip install ipyleaflet\n",
+    "!pip install 'ipyleaflet>=0.19'\n",
     "\n",
     "# If you are accessing files on a Girder server, it is useful to install girder_client\n",
     "!pip install girder_client"
@@ -182,6 +182,10 @@
     "to an internal tile server that allows you to view the image in a zoomable viewer.  There are more options\n",
     "depending on your Jupyter configuration and whether it is running locally or remotely.  \n",
     "Some environments need different proxy options, like Google CoLab.\n",
+    "The system will attempt to determine the correct proxy values by default.\n",
+    "If you needed to, you could ask JupyterLab to locally proxy an internal tile server.  As an example:\n",
+    "\n",
+    "`large_image.tilesource.jupyter.IPyLeafletMixin.JUPYTER_PROXY = True`\n",
     "\n",
     "If ipyleaflet isn't installed, inspecting a tile source will just show the thumbnail."
    ]
@@ -208,15 +212,6 @@
     }
    ],
    "source": [
-    "# Ask JupyterLab to locally proxy an internal tile server\n",
-    "import importlib.util\n",
-    "\n",
-    "if importlib.util.find_spec('google') and importlib.util.find_spec('google.colab'):\n",
-    "    # colab intercepts localhost\n",
-    "    large_image.tilesource.jupyter.IPyLeafletMixin.JUPYTER_PROXY = 'https://localhost'\n",
-    "else:\n",
-    "    large_image.tilesource.jupyter.IPyLeafletMixin.JUPYTER_PROXY = True\n",
-    "\n",
     "# Look at our tile source\n",
     "ts"
    ]

docs/tilesource_options.rst

@@ -111,7 +111,7 @@ A band definition is an object which can contain the following keys:
 
     - ``band``: the band numpy image in a band stage.
 
-    - ``mask``: a mask numpy image to use when applying the band.
+    - ``mask``: a mask numpy image to use when applying the band.  None for no mask (this is the equivalent of the mask being all True).
 
     - ``palette``: the normalized palette for a band.
 

girder/girder_large_image/web_client/package.json

@@ -60,7 +60,8 @@
             "promise/no-return-in-finally": "error",
             "promise/no-return-wrap": "error",
             "vue/require-prop-types": "off",
-            "vue/multiline-html-element-content-newline": "off"
+            "vue/multiline-html-element-content-newline": "off",
+            "vue/html-self-closing": "off"
         },
         "ignorePatterns": ["dist/**"],
         "root": true,

girder/girder_large_image/web_client/views/imageViewerSelectWidget.js

@@ -1,16 +1,25 @@
+import Vue from 'vue';
+
 import largeImageConfig from './configView';
 import * as viewers from './imageViewerWidget';
 
 import imageViewerSelectWidget from '../templates/imageViewerSelectWidget.pug';
 import '../stylesheets/imageViewerSelectWidget.styl';
-import FrameSelector from '../vue/components/FrameSelector.vue';
+
+import FrameSelector from '../widgets/FrameSelector.vue';
+import DualInput from '../widgets/DualInput.vue';
+import CompositeLayers from '../widgets/CompositeLayers.vue';
+import HistogramEditor from '../widgets/HistogramEditor.vue';
+import colors from '../widgets/colors.json';
+import PresetsMenu from '../vue/components/PresetsMenu.vue';
 
 const $ = girder.$;
 const _ = girder._;
 const {wrap} = girder.utilities.PluginUtils;
 const eventStream = girder.utilities.EventStream;
 const ItemView = girder.views.body.ItemView;
 const View = girder.views.View;
+const {restRequest} = girder.rest;
 
 wrap(ItemView, 'render', function (render) {
     // ItemView is a special case in which rendering is done asynchronously,
@@ -72,13 +81,33 @@ var ImageViewerSelectWidget = View.extend({
 
     _createVue(imageMetadata, frameUpdate) {
         const el = this.$('#vue-container').get(0);
-        const vm = new FrameSelector({
+        const getFrameHistogram = (params) => {
+            params = Object.assign({}, params);
+            restRequest({
+                type: 'GET',
+                url: 'item/' + this.itemId + '/tiles/histogram',
+                data: params
+            }).then((response) => {
+                const frameHistograms = this.vueApp._props.frameHistograms || {};
+                frameHistograms[params.frame] = response;
+                this.vueApp._props.frameHistograms = Object.assign({}, frameHistograms);
+                return undefined;
+            });
+        };
+        CompositeLayers.components = {HistogramEditor};
+        FrameSelector.components = {DualInput, CompositeLayers, HistogramEditor, PresetsMenu};
+        const Component = Vue.extend(FrameSelector);
+        const vm = new Component({
             el,
             propsData: {
+                currentFrame: 0,
                 itemId: this.itemId,
                 imageMetadata: imageMetadata,
-                frameUpdate: frameUpdate,
-                liConfig: this._liConfig
+                frameUpdate,
+                liConfig: this._liConfig,
+                frameHistograms: undefined,
+                getFrameHistogram,
+                colors
             }
         });
         this.vueApp = vm;

girder/girder_large_image/web_client/views/imageViewerWidget/geojs.js

@@ -137,7 +137,7 @@ var GeojsImageViewerWidget = ImageViewerWidget.extend({
     _postRender: function () {
     },
 
-    frameUpdate: function (frame, style) {
+    frameUpdate: function ({frame, style}) {
         if (this._frame === undefined) {
             // don't set up layers until the we access the first non-zero frame
             if (frame === 0 && style === undefined) {
@@ -225,8 +225,8 @@ var GeojsImageViewerWidget = ImageViewerWidget.extend({
                     this._layer2 = ltemp;
                     this._updating = false;
                     this.trigger('g:imageFrameChanged', this, frame);
-                    if (frame !== this._nextframe || style !== this._nextstyle) {
-                        this.frameUpdate(this._nextframe, this._nextstyle);
+                    if (frame !== this._nextframe || JSON.stringify(style) !== JSON.stringify(this._nextstyle)) {
+                        this.frameUpdate({frame: this._nextframe, style: this._nextstyle});
                     }
                 });
             });

girder/girder_large_image/web_client/vue/components/PresetsMenu.vue

@@ -153,7 +153,7 @@ export default {
         },
         styleToAutoRange(band) {
             band = Object.assign({}, band); // new reference
-            if (band.min && band.min.includes('min:')) {
+            if (band.min && band.min.toString().includes('min:')) {
                 band.autoRange = parseFloat(band.min.replace('min:', '')) * 100;
                 delete band.min;
                 delete band.max;

girder/girder_large_image/web_client/vue/index.js

@@ -1,7 +1,7 @@
-import CompositeLayers from './components/CompositeLayers.vue';
-import DualInput from './components/DualInput.vue';
-import FrameSelector from './components/FrameSelector.vue';
-import HistogramEditor from './components/HistogramEditor.vue';
+import CompositeLayers from '../widgets/CompositeLayers.vue';
+import DualInput from '../widgets/DualInput.vue';
+import FrameSelector from '../widgets/FrameSelector.vue';
+import HistogramEditor from '../widgets/HistogramEditor.vue';
 import PresetsMenu from './components/PresetsMenu.vue';
 
 export {