Merge pull request #1726 from girder/edit-views-class-name

Add a distinct class name to controls in the item list

CHANGELOG.md

@@ -8,6 +8,7 @@
 - Guard dtype types ([#1711](../../pull/1711), [#1714](../../pull/1714), [#1716](../../pull/1716))
 - Better handle IndicaLabs tiff files ([#1717](../../pull/1717))
 - Better detect files with geotransform data that aren't geospatial ([#1718](../../pull/1718))
+- Better scale float-valued tiles ([#1725](../../pull/1725))
 
 ### Changes
 
@@ -16,6 +17,7 @@
 ### Bug Fixes
 
 - Fix an issue searching for annotation metadata on items that a user doesn't have permissions to view ([#1723](../../pull/1723))
+- Fix a typo in a column header ([#1727](../../pull/1727))
 
 ## 1.30.2
 

girder/girder_large_image/__init__.py

@@ -541,7 +541,7 @@ def addSettingsToConfig(config, user, name=None):
                 columns.append({'type': 'image', 'value': value, 'title': value.title()})
 
     columns.append({'type': 'record', 'value': 'name', 'title': 'Name'})
-    columns.append({'type': 'record', 'value': 'controls', 'title': 'Contols'})
+    columns.append({'type': 'record', 'value': 'controls', 'title': 'Controls'})
     columns.append({'type': 'record', 'value': 'size', 'title': 'Size'})
 
     if 'itemList' not in config:

girder/girder_large_image/web_client/templates/itemList.pug

@@ -78,15 +78,15 @@
                     <div class="flex items-center justify-left">
                       if downloadLinks
                         <div class="group relative">
-                          <a class="hover:bg-zinc-200 px-2 py-1 rounded-full tracking-wider uppercase text-lg" href="#{item.downloadUrl()}" title="Download File" >
+                          <a class="g-li-control hover:bg-zinc-200 px-2 py-1 rounded-full tracking-wider uppercase text-lg" href="#{item.downloadUrl()}" title="Download File" >
                             <i class="ri-file-download-line"></i>
                           </a>
                         </div>
                       if availableApps && availableApps.items[item.id]
                         - const apps = Object.entries(availableApps.items[item.id]).sort(([name1, app1], [name2, app2]) => { let diff = (app1.priority || 0) - (app2.priority || 0); return diff ? diff : (registeredApps[name1].name.toLowerCase() > registeredApps[name2].name.toLowerCase() ? 1 : -1); })
                         for app in apps
                           <div class="group relative">
-                            <a class="g-hui-open-link hover:bg-zinc-200 px-2 py-1 rounded-full tracking-wider uppercase text-lg" title="#{'Open in ' + registeredApps[app[0]].name}", href="#{app[1].url}" target="_blank">
+                            <a class="g-li-control g-hui-open-link hover:bg-zinc-200 px-2 py-1 rounded-full tracking-wider uppercase text-lg" title="#{'Open in ' + registeredApps[app[0]].name}", href="#{app[1].url}" target="_blank">
                               <i class="ri-external-link-line"></i>
                             </a>
                           </div>

girder/girder_large_image/web_client/views/configView.js

@@ -279,7 +279,7 @@ var ConfigView = View.extend({
             const li = {
                 columns: [
                     {type: 'record', value: 'name', title: 'Name'},
-                    {type: 'record', value: 'controls', title: 'Contols'},
+                    {type: 'record', value: 'controls', title: 'Controls'},
                     {type: 'record', value: 'size', title: 'Size'}]
             };
             const val = {itemList: li, itemListDialog: li};

large_image/tilesource/base.py

@@ -176,7 +176,7 @@ def __init__(self, encoding: str = 'JPEG', jpegQuality: int = 95,
         self.edge = edge
         self._setStyle(style)
 
-    def __getstate__(self):
+    def __getstate__(self) -> None:
         """
         Allow pickling.
 
@@ -203,7 +203,7 @@ def __reduce__(self) -> Tuple[functools.partial, Tuple[str]]:
     def __repr__(self) -> str:
         return self.getState()
 
-    def _repr_png_(self):
+    def _repr_png_(self) -> bytes:
         return self.getThumbnail(encoding='PNG')[0]
 
     @property
@@ -257,12 +257,12 @@ def getCenter(self, *args, **kwargs) -> Tuple[float, float]:
         return (bounds['sizeY'] / 2, bounds['sizeX'] / 2)
 
     @property
-    def style(self):
+    def style(self) -> Optional[JSONDict]:
         return self._style
 
     @style.setter
-    def style(self, value):
-        if not hasattr(self, '_unstyledStyle') and value == getattr(self, '_unstyledStyle', None):
+    def style(self, value: Any) -> None:
+        if value is None and not hasattr(self, '_unstyledStyle'):
             return
         if not getattr(self, '_noCache', False):
             msg = 'Cannot set the style of a cached source'
@@ -1139,8 +1139,9 @@ def _outputTileNumpyStyle(
         """
         tile, mode = _imageToNumpy(intile)
         if (applyStyle and (getattr(self, 'style', None) or hasattr(self, '_iccprofiles')) and
-                (not getattr(self, 'style', None) or len(self.style) != 1 or
-                 self.style.get('icc') is not False)):
+                (not getattr(self, 'style', None) or
+                 len(cast(JSONDict, self.style)) != 1 or
+                 cast(JSONDict, self.style).get('icc') is not False)):
             tile = self._applyStyle(tile, getattr(self, 'style', None), x, y, z, frame)
         if tile.shape[0] != self.tileHeight or tile.shape[1] != self.tileWidth:
             extend = np.zeros(
@@ -1242,7 +1243,7 @@ def _getAssociatedImage(self, imageKey: str) -> Optional[PIL.Image.Image]:
         return None
 
     @classmethod
-    def canRead(cls, *args, **kwargs):
+    def canRead(cls, *args, **kwargs) -> bool:
         """
         Check if we can read the input.  This takes the same parameters as
         __init__.
@@ -1315,7 +1316,7 @@ def getMetadata(self) -> JSONDict:
     def metadata(self) -> JSONDict:
         return self.getMetadata()
 
-    def _getFrameValueInformation(self, frames: List[Dict]):
+    def _getFrameValueInformation(self, frames: List[Dict]) -> Dict[str, Any]:
         """
         Given a `frames` list from a metadata response, return a dictionary describing
         the value info for any frame axes. Keys in this dictionary follow the pattern "Value[AXIS]"
@@ -1412,7 +1413,7 @@ def _addMetadataFrameInformation(
             for frame in metadata['frames']:
                 frame['Channel'] = channels[frame.get('IndexC', 0)]
 
-    def getInternalMetadata(self, **kwargs):
+    def getInternalMetadata(self, **kwargs) -> Optional[Dict[Any, Any]]:
         """
         Return additional known metadata about the tile source.  Data returned
         from this method is not guaranteed to be in any particular format or
@@ -1485,10 +1486,12 @@ def _getFrame(self, frame: Optional[int] = None, **kwargs) -> int:
         :returns: an integer frame number.
         """
         frame = int(frame or 0)
-        if (hasattr(self, '_style') and 'bands' in self.style and
-                len(self.style['bands']) and
-                all(entry.get('frame') is not None for entry in self.style['bands'])):
-            frame = int(self.style['bands'][0]['frame'])
+        if (hasattr(self, '_style') and
+                'bands' in cast(JSONDict, self.style) and
+                len(cast(JSONDict, self.style)['bands']) and
+                all(entry.get('frame') is not None
+                    for entry in cast(JSONDict, self.style)['bands'])):
+            frame = int(cast(JSONDict, self.style)['bands'][0]['frame'])
         return frame
 
     def _xyzInRange(
@@ -1627,8 +1630,10 @@ def _getTileFromEmptyLevel(self, x: int, y: int, z: int, **kwargs) -> Tuple[
             getattr(PIL.Image, 'Resampling', PIL.Image).LANCZOS).convert(mode), TILE_FORMAT_PIL
 
     @methodcache()
-    def getTile(self, x, y, z, pilImageAllowed=False, numpyAllowed=False,
-                sparseFallback=False, frame=None):
+    def getTile(self, x: int, y: int, z: int, pilImageAllowed: bool = False,
+                numpyAllowed: Union[bool, str] = False,
+                sparseFallback: bool = False, frame: Optional[int] = None) -> Union[
+                    ImageBytes, PIL.Image.Image, bytes, np.ndarray]:
         """
         Get a tile from a tile source, returning it as an binary image, a PIL
         image, or a numpy array.

large_image/tilesource/geo.py

@@ -143,7 +143,8 @@ def _styleBands(self) -> List[Dict[str, Any]]:
         }
         style = []
         if hasattr(self, '_style'):
-            styleBands = self.style['bands'] if 'bands' in self.style else [self.style]
+            styleBands = (cast(JSONDict, self.style)['bands']
+                          if 'bands' in cast(JSONDict, self.style) else [self.style])
             for styleBand in styleBands:
 
                 styleBand = styleBand.copy()
@@ -189,7 +190,8 @@ def _setDefaultStyle(self) -> None:
                 not self._style or 'icc' in self._style and len(self._style) == 1):
             return
         if hasattr(self, '_style'):
-            styleBands = self.style['bands'] if 'bands' in self.style else [self.style]
+            styleBands = (cast(JSONDict, self.style)['bands']
+                          if 'bands' in cast(JSONDict, self.style) else [self.style])
             if not len(styleBands) or (len(styleBands) == 1 and isinstance(
                     styleBands[0].get('band', 1), int) and styleBands[0].get('band', 1) <= 0):
                 del self._style

large_image/tilesource/tiledict.py

@@ -1,4 +1,4 @@
-from typing import Any, Dict, Optional, Tuple, cast
+from typing import Any, Dict, Optional, Tuple, Union, cast
 
 import numpy as np
 import PIL
@@ -8,7 +8,7 @@
 
 from .. import exceptions
 from ..constants import TILE_FORMAT_IMAGE, TILE_FORMAT_NUMPY, TILE_FORMAT_PIL
-from .utilities import _encodeImage, _imageToNumpy, _imageToPIL
+from .utilities import ImageBytes, _encodeImage, _imageToNumpy, _imageToPIL
 
 
 class LazyTileDict(dict):
@@ -159,6 +159,48 @@ def _retileTile(self) -> np.ndarray:
                     :th, :tw, :retile.shape[2]]  # type: ignore[misc]
         return cast(np.ndarray, retile)
 
+    def _resample(self, tileData: Union[ImageBytes, PIL.Image.Image, bytes, np.ndarray]) -> Tuple[
+        Union[ImageBytes, PIL.Image.Image, bytes, np.ndarray], Optional[PIL.Image.Image],
+    ]:
+        """
+        If we need to resample a tile, use PIL if it is uint8 or we are using
+        a specific resampling mode that is PIL-specific.  Otherwise, use
+        skimage if available.
+
+        :param tileData: the image to scale.
+        :returns: tileData, pilData.  pilData will be None if the results are a
+            numpy array.
+        """
+        pilData = None
+        if self.resample in (False, None) or not self.requestedScale:
+            return tileData, pilData
+        pilResize = True
+        if (isinstance(tileData, np.ndarray) and tileData.dtype.kind != np.uint8 and
+                TILE_FORMAT_NUMPY in self.format and self.resample in {True, 2, 3}):
+            try:
+                import skimage.transform
+                pilResize = False
+            except ImportError:
+                pass
+        if pilResize:
+            pilData = _imageToPIL(tileData)
+
+            self['width'] = max(1, int(
+                pilData.size[0] / self.requestedScale))
+            self['height'] = max(1, int(
+                pilData.size[1] / self.requestedScale))
+            pilData = tileData = pilData.resize(
+                (self['width'], self['height']),
+                resample=getattr(PIL.Image, 'Resampling', PIL.Image).LANCZOS
+                if self.resample is True else self.resample)
+        else:
+            tileData = skimage.transform.resize(
+                cast(np.ndarray, tileData),
+                (self['width'], self['height'],
+                 cast(np.ndarray, tileData).shape[2]),  # type: ignore[misc]
+                order=3 if self.resample is True else self.resample)
+        return tileData, pilData
+
     def __getitem__(self, key: str, *args, **kwargs) -> Any:
         """
         If this is the first time either the tile or format key is requested,
@@ -187,16 +229,7 @@ def __getitem__(self, key: str, *args, **kwargs) -> Any:
             pilData = None
             # resample if needed
             if self.resample not in (False, None) and self.requestedScale:
-                pilData = _imageToPIL(tileData)
-
-                self['width'] = max(1, int(
-                    pilData.size[0] / self.requestedScale))
-                self['height'] = max(1, int(
-                    pilData.size[1] / self.requestedScale))
-                pilData = tileData = pilData.resize(
-                    (self['width'], self['height']),
-                    resample=getattr(PIL.Image, 'Resampling', PIL.Image).LANCZOS
-                    if self.resample is True else self.resample)
+                tileData, pilData = self._resample(tileData)
 
             tileFormat = (TILE_FORMAT_PIL if isinstance(tileData, PIL.Image.Image)
                           else (TILE_FORMAT_NUMPY if isinstance(tileData, np.ndarray)

test/lisource_compare.py

@@ -391,7 +391,9 @@ def source_compare(sourcePath, opts):  # noqa
             sys.stdout.flush()
 
             # get maxval for other histograms
-            h = ts.histogram(onlyMinMax=True, output=dict(maxWidth=2048, maxHeight=2048), **kwargs)
+            h = ts.histogram(
+                onlyMinMax=True, output=dict(maxWidth=2048, maxHeight=2048),
+                resample=0, **kwargs)
             if 'max' not in h:
                 sys.stdout.write(' fail\n')
                 sys.stdout.flush()
@@ -400,7 +402,7 @@ def source_compare(sourcePath, opts):  # noqa
             maxval = 2 ** (int(math.log(maxval or 1) / math.log(2)) + 1) if maxval > 1 else 1
             # thumbnail histogram
             h = ts.histogram(bins=9, output=dict(maxWidth=256, maxHeight=256),
-                             range=[0, maxval], **kwargs)
+                             range=[0, maxval], resample=0, **kwargs)
             maxchan = len(h['histogram'])
             if maxchan == 4:
                 maxchan = 3
@@ -409,13 +411,13 @@ def source_compare(sourcePath, opts):  # noqa
             sys.stdout.flush()
             # full image histogram
             h = ts.histogram(bins=9, output=dict(maxWidth=2048, maxHeight=2048),
-                             range=[0, maxval], **kwargs)
+                             range=[0, maxval], resample=0, **kwargs)
             result['full_2048_histogram'] = histotext(h, maxchan)
             sys.stdout.write(' %s' % histotext(h, maxchan))
             sys.stdout.flush()
             if opts.full:
                 # at full res
-                h = ts.histogram(bins=9, range=[0, maxval], **kwargs)
+                h = ts.histogram(bins=9, range=[0, maxval], resample=0, **kwargs)
                 result['full_max_histogram'] = histotext(h, maxchan)
                 sys.stdout.write(' %s' % histotext(h, maxchan))
                 sys.stdout.flush()
@@ -426,12 +428,14 @@ def source_compare(sourcePath, opts):  # noqa
                 if not opts.full:
                     h = ts.histogram(
                         bins=9, output=dict(maxWidth=2048, maxHeight=2048),
-                        range=[0, maxval], frame=frames - 1, **kwargs)
+                        range=[0, maxval], frame=frames - 1, resample=0,
+                        **kwargs)
                     result['full_f_2048_histogram'] = histotext(h, maxchan)
                     sys.stdout.write(' %s' % histotext(h, maxchan))
                 else:
                     # at full res
-                    h = ts.histogram(bins=9, range=[0, maxval], frame=frames - 1, **kwargs)
+                    h = ts.histogram(bins=9, range=[0, maxval],
+                                     frame=frames - 1, resample=0, **kwargs)
                     result['full_f_max_histogram'] = histotext(h, maxchan)
                     sys.stdout.write(' %s' % histotext(h, maxchan))
                 sys.stdout.flush()
@@ -444,7 +448,7 @@ def source_compare(sourcePath, opts):  # noqa
                         h = ts.histogram(bins=32, output=dict(
                             maxWidth=int(math.ceil(ts.sizeX / 2 ** (levels - 1 - ll))),
                             maxHeight=int(math.ceil(ts.sizeY / 2 ** (levels - 1 - ll))),
-                        ), range=[0, maxval], frame=f, **kwargs)
+                        ), range=[0, maxval], frame=f, resample=0, **kwargs)
                         t += time.time()
                         result[f'level_{ll}_f_{f}_histogram'] = histotext(h, maxchan)
                         sys.stdout.write('%3d%5d %s' % (ll, f, histotext(h, maxchan)))