Merge pull request #40 from will-moore/4-3-4-hotfixes

4 3 4 hotfixes

components/tools/OmeroPy/scripts/omero/export_scripts/Batch_Image_Export.py

@@ -410,7 +410,7 @@ def runScript():
 
     client = scripts.client('Batch_Image_Export.py', """Save multiple images as jpegs or pngs in a zip
 file available for download as a batch export. 
-See http://www.openmicroscopy.org/site/support/omero4/getting-started/tutorial/running-util-scripts""", 
+See http://www.openmicroscopy.org/site/support/omero4/getting-started/tutorial/running-scripts/running-util-scripts/""", 
 
     scripts.String("Data_Type", optional=False, grouping="1",
         description="The data you want to work with.", values=dataTypes, default="Image"),

components/tools/OmeroPy/scripts/omero/export_scripts/Make_Movie.py

@@ -276,15 +276,15 @@ def calculateRanges(sizeZ, sizeT, commandArgs):
     if "Plane_Map" not in commandArgs:
         zStart = 0
         zEnd = sizeZ
-        if "Z_Start" in commandArgs and commandArgs["Z_Start"] > 0 and commandArgs["Z_Start"] < sizeZ:
+        if "Z_Start" in commandArgs and commandArgs["Z_Start"] >= 0 and commandArgs["Z_Start"] < sizeZ:
             zStart = commandArgs["Z_Start"]
-        if "Z_End" in commandArgs and commandArgs["Z_End"] > 0 and commandArgs["Z_End"] < sizeZ:
+        if "Z_End" in commandArgs and commandArgs["Z_End"] >= 0 and commandArgs["Z_End"] < sizeZ and commandArgs["Z_End"] >= zStart:
             zEnd = commandArgs["Z_End"]+1
         tStart = 0
         tEnd = sizeT-1
-        if "T_Start" in commandArgs and commandArgs["T_Start"] > 0 and commandArgs["T_Start"] < sizeT:
+        if "T_Start" in commandArgs and commandArgs["T_Start"] >= 0 and commandArgs["T_Start"] < sizeT:
             tStart = commandArgs["T_Start"]
-        if "T_End" in commandArgs and commandArgs["T_End"] > 0 and commandArgs["T_End"] < sizeT:
+        if "T_End" in commandArgs and commandArgs["T_End"] >= 0 and commandArgs["T_End"] < sizeT and commandArgs["T_End"] >= tStart:
             tEnd = commandArgs["T_End"]+1
         if(zEnd==zStart):
             zEnd=zEnd+1;

components/tools/OmeroPy/scripts/omero/figure_scripts/ROI_Split_Figure.py

@@ -165,6 +165,7 @@ def getROIsplitView    (re, pixels, zStart, zEnd, splitIndexes, channelNames, me
         re.setActive(i, False)
 
     # for each channel in the splitview...
+    box = (roiX, roiY, roiX+roiWidth, roiY+roiHeight)
     for index in splitIndexes:
         if index >= sizeC:
             channelMismatch = True        # can't turn channel on - simply render black square! 
@@ -180,7 +181,6 @@ def getROIsplitView    (re, pixels, zStart, zEnd, splitIndexes, channelNames, me
                 re.setRGBA(index,255,255,255,255)    # if not colourChannels - channels are white
             info = (channelNames[index], re.getChannelWindowStart(index), re.getChannelWindowEnd(index))
             log("  Render channel: %s  start: %d  end: %d" % info)
-            box = (roiX, roiY, roiX+roiWidth, roiY+roiHeight)
             if proStart == proEnd:
                 # if it's a single plane, we can render a region (region not supported with projection)
                 planeDef = omero.romio.PlaneDef()
@@ -236,7 +236,10 @@ def getROIsplitView    (re, pixels, zStart, zEnd, splitIndexes, channelNames, me
 
     if channelMismatch:
         log(" WARNING channel mismatch: The current image has fewer channels than the primary image.")
-
+
+    if panelWidth == 0: # E.g. No split-view panels
+        panelWidth = roiMergedImage.size[0]
+
     # now assemble the roi split-view canvas
     font = imgUtil.getFont(fontsize)
     textHeight = font.getsize("Textq")[1]
@@ -248,7 +251,8 @@ def getROIsplitView    (re, pixels, zStart, zEnd, splitIndexes, channelNames, me
             topSpacer = textHeight + spacer
     imageCount = len(renderedImages) + 1     # extra image for merged image
     canvasWidth = ((panelWidth + spacer) * imageCount) - spacer    # no spaces around panels
-    canvasHeight = renderedImages[0].size[1] + topSpacer
+    canvasHeight = roiMergedImage.size[1] + topSpacer
+    print "imageCount", imageCount, "canvasWidth", canvasWidth, "canvasHeight", canvasHeight
     size = (canvasWidth, canvasHeight)
     canvas = Image.new(mode, size, white)        # create a canvas of appropriate width, height
 
@@ -678,14 +682,11 @@ def getTags(name, tagsList, pdList):
         for c in range(sizeC):
             channelNames[c] = str(c)
 
-    # Make split-indexes list. If argument wasn't specified, include them all. 
+    # Make split-indexes list. If no "Split_Indexes", show none: http://www.openmicroscopy.org/community/viewtopic.php?f=4&t=940
     splitIndexes = []
     if "Split_Indexes" in commandArgs:
         for index in commandArgs["Split_Indexes"]:
             splitIndexes.append(index.getValue())
-    else:
-        for c in range(sizeC):
-            splitIndexes = range(sizeC)
 
     colourChannels = True
     if "Split_Panels_Grey" in commandArgs and commandArgs["Split_Panels_Grey"]:

components/tools/OmeroPy/src/omero/gateway/__init__.py

@@ -3408,7 +3408,7 @@ def isOriginalMetadata(self):
         """
 
         try:
-            if self._obj.ns is not None and self._obj.ns.val == omero.constants.namespaces.NSCOMPANIONFILE and self._obj.file.name.val.startswith("original_metadata"):
+            if self._obj.ns is not None and self._obj.ns.val == omero.constants.namespaces.NSCOMPANIONFILE and self.getFile().getName() == omero.constants.annotation.file.ORIGINALMETADATA:
                 return True
         except:
             logger.info(traceback.format_exc())

components/tools/OmeroWeb/omeroweb/webgateway/static/webgateway/js/3rdparty/panojs/control_thumbnail.js

@@ -84,6 +84,7 @@ ThumbnailControl.prototype.init = function() {
   this.thumbscale = this.tw / this.viewer.imageSize().width;
 
   this.viewer.notifyViewerZoomed();
+  this.viewer.notifyViewerMoved();
 }
 
 ThumbnailControl.prototype.createDOMElements = function() {
@@ -170,6 +171,7 @@ ThumbnailControl.prototype.toggleMinimize = function(e) {
 }
 
 ThumbnailControl.prototype.viewerMoved = function(e) {
+    if (this.dom_image.onload) return
     if (!this.dom_roi || typeof this.dom_roi == 'undefined') return;
     var img_x = -1.0 * (e.x / this.scale);
     var img_y = -1.0 * (e.y / this.scale);