girder-large-image 1.23.3.dev31__tar.gz → 1.23.3.dev59__tar.gz

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: girder-large-image
-Version: 1.23.3.dev31
+Version: 1.23.3.dev59
 Summary: A Girder plugin to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/girder_large_image/rest/tiles.py

@@ -15,6 +15,7 @@
 #############################################################################
 
 import hashlib
+import io
 import math
 import os
 import pathlib
@@ -33,6 +34,7 @@ from girder.constants import AccessType, TokenScope
 from girder.exceptions import RestException
 from girder.models.file import File
 from girder.models.item import Item
+from girder.models.upload import Upload
 from girder.utility.progress import setResponseTimeLimit
 from large_image.cache_util import strhash
 from large_image.constants import TileInputUnits, TileOutputMimeTypes
@@ -150,6 +152,7 @@ class TilesItemResource(ItemResource):
         apiRoot.item.route('GET', (':itemId', 'tiles', 'thumbnail'), self.getTilesThumbnail)
         apiRoot.item.route('GET', (':itemId', 'tiles', 'thumbnails'), self.listTilesThumbnails)
         apiRoot.item.route('DELETE', (':itemId', 'tiles', 'thumbnails'), self.deleteTilesThumbnails)
+        apiRoot.item.route('POST', (':itemId', 'tiles', 'thumbnails'), self.addTilesThumbnails)
         apiRoot.item.route('GET', (':itemId', 'tiles', 'region'), self.getTilesRegion)
         apiRoot.item.route('GET', (':itemId', 'tiles', 'tile_frames'), self.tileFrames)
         apiRoot.item.route('GET', (':itemId', 'tiles', 'tile_frames', 'quad_info'),
@@ -1429,11 +1432,74 @@ class TilesItemResource(ItemResource):
     @autoDescribeRoute(
         Description('Delete thumbnail and data files associated with a large_image item.')
         .modelParam('itemId', model=Item, level=AccessType.READ)
-        .param('keep', 'Number of thumbnails to keep.', dataType='integer',
-               required=False, default=10000)
+        .param('keep', 'Number of thumbnails to keep.  Ignored if a key is '
+               'specified.', dataType='integer', required=False,
+               default=10000)
+        .param('key', 'A specific key to delete', required=False)
+        .param('thumbnail', 'If a key is specified, true if the key is a '
+               'thumbnail; false if the key is a data record',
+               dataType='boolean', required=False)
         .errorResponse('ID was invalid.')
         .errorResponse('Read access was denied for the item.', 403)
     )
     @access.admin(scope=TokenScope.DATA_WRITE)
-    def deleteTilesThumbnails(self, item, keep):
-        return self.imageItemModel.removeThumbnailFiles(item, keep=keep or 0)
+    def deleteTilesThumbnails(self, item, keep, key=None, thumbnail=True):
+        if not key:
+            return self.imageItemModel.removeThumbnailFiles(item, keep=keep or 0)
+        thumbnail = str(thumbnail).lower() != 'false'
+        query = {
+            'attachedToType': 'item',
+            'attachedToId': item['_id'],
+            'isLargeImageThumbnail' if thumbnail is not False else 'isLargeImageData': True,
+            'thumbnailKey': key,
+        }
+        file = File().findOne(query)
+        if file:
+            File().remove(file)
+        return [file]
+
+    @autoDescribeRoute(
+        Description('Associate or replace a thumbnail or data file with a large_image items.')
+        .responseClass('File')
+        .modelParam('itemId', model=Item, level=AccessType.WRITE)
+        .param('key', 'A specific key to delete', required=True)
+        .param('thumbnail', 'If a key is specified, true if the key is a '
+               'thumbnail; false if the key is a data record',
+               dataType='boolean', required=False)
+        .param('mimeType', 'The MIME type of the file.', required=False)
+        .param('data', 'An image or data block to associated with the large_image item.',
+               paramType='body', dataType='binary')
+        .consumes('application/octet-stream')
+        .errorResponse('ID was invalid.')
+        .errorResponse('Read access was denied for the item.', 403)
+    )
+    @access.user(scope=TokenScope.DATA_WRITE)
+    def addTilesThumbnails(self, item, key, mimeType, thumbnail=False, data=None):
+        user = self.getCurrentUser()
+        thumbnail = str(thumbnail).lower() != 'false'
+        query = {
+            'attachedToType': 'item',
+            'attachedToId': item['_id'],
+            'isLargeImageThumbnail' if thumbnail is not False else 'isLargeImageData': True,
+            'thumbnailKey': key,
+        }
+        file = File().findOne(query)
+        if file:
+            File().remove(file)
+        data = cherrypy.request.body.read()
+        try:
+            import magic
+            mimeType = magic.from_buffer(data, mime=True) or mimeType
+        except Exception:
+            pass
+        mimeType = mimeType or 'application/octet-stream'
+        datafile = Upload().uploadFromFile(
+            io.BytesIO(data), size=len(data),
+            name='_largeImageThumbnail', parentType='item', parent=item,
+            user=user, mimeType=mimeType, attachParent=True)
+        datafile.update({
+            'isLargeImageThumbnail' if thumbnail is not False else 'isLargeImageData': True,
+            'thumbnailKey': key,
+        })
+        datafile = File().save(datafile)
+        return datafile

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/girder_large_image/web_client/views/imageViewerSelectWidget.js

@@ -47,7 +47,12 @@ var ImageViewerSelectWidget = View.extend({
         this.itemId = settings.imageModel.id;
         this.model = settings.imageModel;
         this.currentViewer = null;
-        largeImageConfig.getSettings(() => this.render());
+        largeImageConfig.getSettings(() => {
+            largeImageConfig.getConfigFile(this.model.get('folderId')).done((config) => {
+                this._liConfig = config || {};
+                this.render();
+            });
+        });
     },
 
     render: function () {
@@ -73,7 +78,8 @@ var ImageViewerSelectWidget = View.extend({
             propsData: {
                 itemId: this.itemId,
                 imageMetadata: imageMetadata,
-                frameUpdate: frameUpdate
+                frameUpdate: frameUpdate,
+                liConfig: this._liConfig
             }
         });
         this.vueApp = vm;

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/girder_large_image/web_client/vue/components/CompositeLayers.vue

@@ -66,7 +66,6 @@ export default {
                     enabled: true,
                     min: undefined,
                     max: undefined,
-                    custom: false,
                     autoRange: undefined
                 }
             })
@@ -102,36 +101,45 @@ export default {
         },
         initializeStateFromStyle() {
             this.enabledLayers = []
-            const styleArray = this.currentStyle.bands
-            this.layers.forEach((layerName) => {
-                const layerInfo = this.compositeLayerInfo[layerName]
-                const currentLayerStyle = styleArray.find((s) => s.framedelta === layerInfo.framedelta && s.band === layerInfo.band)
+            this.layers.forEach((layer) => {
+                const layerInfo = this.compositeLayerInfo[layer]
+                const currentLayerStyle = this.currentStyle.bands.find(
+                    (s) => s.framedelta === layerInfo.framedelta
+                        && s.band === layerInfo.band
+                )
                 if (currentLayerStyle) {
-                    this.enabledLayers.push(layerName)
+                    this.enabledLayers.push(layer)
+                    this.compositeLayerInfo[layer].enabled = true;
+                    this.compositeLayerInfo[layer].palette = currentLayerStyle.palette;
                     if (
                         currentLayerStyle.min && currentLayerStyle.max
-                        && currentLayerStyle.min.includes("min:")
-                        && currentLayerStyle.max.includes("max:")
+                        && currentLayerStyle.min.toString().includes("min:")
+                        && currentLayerStyle.max.toString().includes("max:")
                     ) {
-                        currentLayerStyle.autoRange = parseFloat(
-                            currentLayerStyle.min.replace("min:", '')
+                        this.compositeLayerInfo[layer].autoRange = parseFloat(
+                            currentLayerStyle.min.toString().replace("min:", '')
                         ) * 100
-                        currentLayerStyle.min = undefined
-                        currentLayerStyle.max = undefined
+                        this.compositeLayerInfo[layer].min = undefined
+                        this.compositeLayerInfo[layer].max = undefined
+                    } else {
+                        this.compositeLayerInfo[layer].autoRange = undefined
                     }
                 }
-                this.compositeLayerInfo[layerName] = Object.assign(
-                    {}, layerInfo, currentLayerStyle
-                )
-            })
-            this.layers.forEach((layer) => {
-                this.compositeLayerInfo[layer].enabled = this.enabledLayers.includes(layer);
+                else {
+                    this.compositeLayerInfo[layer].enabled = false;
+                    this.compositeLayerInfo[layer].autoRange = undefined;
+                    this.compositeLayerInfo[layer].min = undefined;
+                    this.compositeLayerInfo[layer].max = undefined;
+                }
             })
+
             const autoRanges = Object.entries(this.compositeLayerInfo)
+                .filter(([index, info]) => info.enabled)
                 .map(([index, info]) => info.autoRange)
-                .filter((a) => a !== undefined)
             if (autoRanges.every((v) => v === autoRanges[0])) {
                 this.autoRangeForAll = autoRanges[0]
+            } else {
+                this.autoRangeForAll = undefined
             }
         },
         fetchCurrentFrameHistogram() {
@@ -285,7 +293,9 @@ export default {
             }
         },
         currentStyle() {
-            this.initializeStateFromStyle()
+            if(this.currentStyle.preset) {
+                this.initializeStateFromStyle()
+            }
         }
     }
 }

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/girder_large_image/web_client/vue/components/FrameSelector.vue

@@ -5,7 +5,7 @@ import DualInput from './DualInput.vue';
 import PresetsMenu from './PresetsMenu.vue';
 
 export default Vue.extend({
-    props: ['itemId', 'imageMetadata', 'frameUpdate'],
+    props: ['itemId', 'imageMetadata', 'frameUpdate', 'liConfig'],
     components: { CompositeLayers, DualInput, PresetsMenu },
     data() {
         return {
@@ -75,7 +75,8 @@ export default Vue.extend({
                 }
             });
             this.currentFrame = frame
-            let style = this.currentModeId > 1 ? this.style[this.currentModeId] : undefined
+            let style = this.currentModeId > 1 ? Object.assign({}, this.style[this.currentModeId]) : undefined
+            if(style && style.preset) delete style.preset
             this.frameUpdate(frame, style);
         },
         fillMetadata() {
@@ -200,6 +201,9 @@ export default Vue.extend({
             </select>
             <presets-menu
                 :itemId="itemId"
+                :liConfig="liConfig"
+                :imageMetadata="imageMetadata"
+                :availableModes="sliderModes.map((m) => m.id)"
                 :currentMode="sliderModes.find((m) => m.id === currentModeId)"
                 :currentFrame="currentFrame"
                 :currentStyle="style[currentModeId]"

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/girder_large_image/web_client/vue/components/PresetsMenu.vue

@@ -2,11 +2,12 @@
 import { restRequest } from '@girder/core/rest';
 
 export default {
-    props: ['itemId', 'currentMode', 'currentFrame', 'currentStyle'],
+    props: ['itemId', 'liConfig', 'imageMetadata', 'availableModes', 'currentMode', 'currentFrame', 'currentStyle'],
     emits: ['setCurrentMode', 'setCurrentFrame', 'updateStyle'],
     data() {
         return {
-            availablePresets: [],
+            itemPresets: [],
+            folderPresets: [],
             selectedPreset: undefined,
             showPresetCreation: false,
             newPresetName: undefined,
@@ -14,13 +15,36 @@ export default {
         }
     },
     methods: {
+        presetApplicable(preset) {
+            if (this.itemPresets.find((p) => p.name === preset.name)) {
+                // preset with this name already exists on the item,
+                // prefer the item preset; don't show both
+                return false
+            } else if (
+                parseInt(preset.frame) >= this.imageMetadata.frames.length
+                || !this.availableModes.includes(preset.mode.id)
+            ) {
+                return false
+            } else if (
+                preset.style && preset.style.bands
+                && this.imageMetadata.IndexRange.IndexC
+                && preset.style.bands.some((b) => b.framedelta > this.imageMetadata.IndexRange.IndexC)
+            ) {
+                return false
+            }
+
+            return true
+        },
         getPresets() {
             restRequest({
                 type: 'GET',
                 url: 'item/' + this.itemId + '/internal_metadata/presets',
             }).then((presets) => {
                 if (presets) {
-                    this.availablePresets = presets
+                    this.itemPresets = presets
+                }
+                if (this.liConfig.imageFramePresets) {
+                    this.folderPresets = this.liConfig.imageFramePresets.filter(this.presetApplicable)
                 }
             })
         },
@@ -35,8 +59,8 @@ export default {
             if (!overwrite && this.availablePresets.find((p) => p.name === newPreset.name)) {
                 this.errorMessage = `There is already a preset named "${newPreset.name}". Overwrite "${newPreset.name}"?`
             } else {
-                this.availablePresets = this.availablePresets.filter((p) => p.name !== newPreset.name)
-                this.availablePresets.push(newPreset)
+                this.itemPresets = this.itemPresets.filter((p) => p.name !== newPreset.name)
+                this.itemPresets.push(newPreset)
                 this.selectedPreset = newPreset.name
                 this.savePresetsList()
                 this.newPresetName = undefined
@@ -45,7 +69,7 @@ export default {
             }
         },
         deleteSelectedPreset() {
-            this.availablePresets = this.availablePresets.filter((p) => p.name !== this.selectedPreset)
+            this.itemPresets = this.itemPresets.filter((p) => p.name !== this.selectedPreset)
             this.selectedPreset = undefined
             this.savePresetsList()
         },
@@ -53,47 +77,48 @@ export default {
             restRequest({
                 type: 'PUT',
                 url: 'item/' + this.itemId + '/internal_metadata/presets',
-                data: JSON.stringify(this.availablePresets),
+                data: JSON.stringify(this.itemPresets),
                 contentType: 'application/json',
             })
         },
+        styleFromAutoRange(band) {
+            band = Object.assign({}, band)  // new reference
+            if (band.autoRange) {
+                band.min = `min:${band.autoRange / 100}`
+                band.max = `max:${band.autoRange / 100}`
+                delete band.autoRange
+            }
+            return band
+        },
         styleEqual(style1, style2) {
             if (style1 === style2) {
                 return true
             }
-            if (style1.bands.length !== style2.bands.length) {
+            if (style1.length !== style2.length) {
                 return false
             }
-            return style1.bands.every((b1) => {
-                b1 = Object.fromEntries(Object.entries(b1).filter(([k, v]) => v !== undefined))
-                return style2.bands.some((b2) => {
-                    b2 = Object.fromEntries(Object.entries(b2).filter(([k, v]) => v !== undefined))
+            return style1.every((b1) => {
+                b1 = this.styleFromAutoRange(b1)
+                let b2 = style2.find((b) => b.framedelta === b1.framedelta && b.band === b1.band)
+                if (b2) {
+                    b2 = this.styleFromAutoRange(b2)
                     return (
-                        Object.entries(b1).every(([k, v]) => b2[k] === v)
-                        && Object.entries(b2).every(([k, v]) => b1[k] === v)
+                        b1.min === b2.min
+                        && b1.max === b2.max
+                        && b1.palette === b2.palette
                     )
-                })
+                } else return false
             })
         },
         checkPresetMatch() {
-            const targetStyle = this.currentStyle && this.currentStyle.bands ? {
-                bands: this.currentStyle.bands.map((b) => {
-                    if (b.min && b.max && b.min.includes("min:") && b.max.includes("max:")) {
-                        b.autoRange = parseFloat(
-                            b.min.replace("min:", '')
-                        ) * 100
-                        b.min = undefined
-                        b.max = undefined
-                    }
-                    return b
-                })
-            } : this.currentStyle
-            const match = this.availablePresets.find((p) => (
-                p.mode.id === this.currentMode.id
-                && p.frame === this.currentFrame
-                && this.styleEqual(targetStyle, p.style)
-            ))
-            this.selectedPreset = match ? match.name : undefined
+            if (this.currentStyle) {
+                const match = this.availablePresets.find((p) => (
+                    p.mode.id === this.currentMode.id
+                    && p.frame === this.currentFrame
+                    && this.styleEqual(this.currentStyle.bands, p.style.bands)
+                ))
+                this.selectedPreset = match ? match.name : undefined
+            }
         }
     },
     computed: {
@@ -105,6 +130,9 @@ export default {
                 name = `${this.currentStyle.bands.length} bands`
             }
             return name;
+        },
+        availablePresets() {
+            return this.itemPresets.concat(this.folderPresets)
         }
     },
     watch: {
@@ -122,8 +150,21 @@ export default {
                 if (preset.frame !== undefined) {
                     this.$emit('setCurrentFrame', preset.frame)
                 }
-                if (preset.style && Object.keys(preset.style.bands).length) {
-                    this.$emit('updateStyle', preset.mode.id, preset.style)
+                if (preset.style && preset.style.bands.length) {
+                    const styleArray = []
+                    preset.style.bands.forEach((layer) => {
+                        const styleEntry = {
+                            min: layer.autoRange !== undefined ? `min:${layer.autoRange / 100}` : parseInt(layer.min),
+                            max: layer.autoRange !== undefined ? `max:${layer.autoRange / 100}` : parseInt(layer.max),
+                            palette: layer.palette,
+                            framedelta: layer.framedelta,
+                            band: layer.band,
+                        }
+                        if (!styleEntry.min) delete styleEntry.min
+                        if (!styleEntry.max) delete styleEntry.max
+                        styleArray.push(styleEntry);
+                    });
+                    this.$emit('updateStyle', preset.mode.id, {bands: styleArray, preset: true})
                 }
             }
         },

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/girder_large_image.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: girder-large-image
-Version: 1.23.3.dev31
+Version: 1.23.3.dev59
 Summary: A Girder plugin to work with large, multiresolution images.
 Home-page: https://github.com/girder/large_image
 Author: Kitware, Inc.

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/girder_large_image.egg-info/requires.txt

@@ -1,10 +1,10 @@
 girder>=3.1.18
 girder-jobs>=3.0.3
-large_image>=1.23.3.dev31
+large_image>=1.23.3.dev59
 
 [:python_version < "3.8"]
 importlib-metadata<5
 
 [tasks]
-large-image-tasks[girder]>=1.23.3.dev31
+large-image-tasks[girder]>=1.23.3.dev59
 girder-worker[girder]>=0.6.0

{girder-large-image-1.23.3.dev31 → girder-large-image-1.23.3.dev59}/test_girder/test_tiles_rest.py

@@ -1499,3 +1499,30 @@ def testThumbnailMaintenance(server, admin, fsAssetstore):
     resp = server.request(path='/item/%s/tiles/thumbnails' % itemId, user=admin)
     assert utilities.respStatus(resp) == 200
     assert len(resp.json) == 0
+
+    # Get a thumbnail
+    resp = server.request(path='/item/%s/tiles/thumbnail' % itemId,
+                          user=admin, isJson=False)
+    assert utilities.respStatus(resp) == 200
+    thumb = utilities.getBody(resp, text=False)
+    resp = server.request(path='/item/%s/tiles/thumbnails' % itemId, user=admin)
+    assert utilities.respStatus(resp) == 200
+    # Ask to delete it specifically
+    key = resp.json[0]['thumbnailKey']
+    resp = server.request(
+        path='/item/%s/tiles/thumbnails' % itemId, method='DELETE', user=admin,
+        params={'key': key})
+    assert utilities.respStatus(resp) == 200
+    assert len(resp.json) == 1
+    # It should be gone
+    resp = server.request(path='/item/%s/tiles/thumbnails' % itemId, user=admin)
+    assert utilities.respStatus(resp) == 200
+    assert len(resp.json) == 0
+    # Add it back
+    resp = server.request(
+        path='/item/%s/tiles/thumbnails' % itemId, method='POST', user=admin,
+        params={'key': key}, body=thumb, type='application/octet-stream')
+
+    resp = server.request(path='/item/%s/tiles/thumbnails' % itemId, user=admin)
+    assert utilities.respStatus(resp) == 200
+    assert len(resp.json) == 1