Merge pull request #101 from will-moore/unicode_support

Unicode support

Author: sbesson

omero/export_scripts/Batch_Image_Export.py

@@ -59,6 +59,11 @@ def log(text):
     """
     Adds the text to a list of logs. Compiled into text file at the end.
     """
+    # Handle unicode
+    try:
+        text = text.encode('utf8')
+    except:
+        pass
     print text
     logStrings.append(str(text))
 

omero/figure_scripts/ROI_Split_Figure.py

@@ -45,7 +45,7 @@
 import omero.util.figureUtil as figUtil
 import omero.util.script_utils as scriptUtil
 from omero.gateway import BlitzGateway
-from omero.rtypes import rlong, robject, rstring, wrap
+from omero.rtypes import rlong, robject, rstring, wrap, unwrap
 import os
 from omero.constants.namespaces import NSCREATED
 from omero.constants.projection import ProjectionType
@@ -332,8 +332,8 @@ def getRectangle(roiService, imageId, roiLabel):
         # go through all the shapes of the ROI
         for shape in roi.copyShapes():
             if type(shape) == omero.model.RectI:
-                t = shape.getTheT().getValue()
-                z = shape.getTheZ().getValue()
+                t = unwrap(shape.getTheT())
+                z = unwrap(shape.getTheZ())
                 x = shape.getX().getValue()
                 y = shape.getY().getValue()
                 tv = shape.getTextValue()

omero/figure_scripts/Split_View_Figure.py

@@ -68,6 +68,11 @@ def log(text):
     """
     Adds the text to a list of logs. Compiled into figure legend at the end.
     """
+    # Handle unicode
+    try:
+        text = text.encode('utf8')
+    except:
+        pass
     print text
     logStrings.append(text)
 
@@ -474,7 +479,7 @@ def makeSplitViewFigure(conn, pixelIds, zStart, zEnd, splitIndexes,
             rgba = (0, 0, 0, 255)
             if index in mergedColours:
                 rgba = tuple(mergedColours[index])
-                print index, channelNames[index], rgba
+                log("%s %s %s" % (index, channelNames[index], rgba))
                 if rgba == (255, 255, 255, 255):    # if white (unreadable),
                                                     # needs to be black!
                     rgba = (0, 0, 0, 255)
@@ -515,16 +520,16 @@ def splitViewFigure(conn, scriptParams):
     # function for getting image labels.
     def getImageNames(fullName, tagsList, pdList):
         name = fullName.split("/")[-1]
-        return [name]
+        return [name.decode('utf8')]
 
     # default function for getting labels is getName (or use datasets / tags)
     if scriptParams["Image_Labels"] == "Datasets":
         def getDatasets(name, tagsList, pdList):
-            return [dataset for project, dataset in pdList]
+            return [dataset.decode('utf8') for project, dataset in pdList]
         getLabels = getDatasets
     elif scriptParams["Image_Labels"] == "Tags":
         def getTags(name, tagsList, pdList):
-            return tagsList
+            return [t.decode('utf8') for t in tagsList]
         getLabels = getTags
     else:
         getLabels = getImageNames
@@ -603,7 +608,7 @@ def getTags(name, tagsList, pdList):
         cNameMap = scriptParams["Channel_Names"]
         for c in cNameMap:
             index = int(c)
-            channelNames[index] = cNameMap[c]
+            channelNames[index] = cNameMap[c].decode('utf8')
 
     mergedIndexes = []  # the channels in the combined image,
     mergedColours = {}

omero/figure_scripts/Thumbnail_Figure.py

@@ -63,6 +63,10 @@ def log(text):
     Adds lines of text to the logLines list, so they can be collected into a
     figure legend.
     """
+    try:
+        text = text.encode('utf8')
+    except:
+        pass
     print text
     logLines.append(text)
 
@@ -179,7 +183,7 @@ def paintDatasetCanvas(conn, images, title, tagIds=None, showUntagged=False,
             for tag in tags:
                 tagId = tag.getId().getValue()
                 # make a dict of tag-names
-                tagNames[tagId] = tag.getTextValue().getValue()
+                tagNames[tagId] = tag.getTextValue().getValue().decode('utf8')
                 print "     Tag:", tagId, tagId in tagIds
                 imgTagIds.append(tagId)
             imgTags[imageId] = imgTagIds
@@ -403,8 +407,9 @@ def makeThumbnailFigure(conn, scriptParams):
             log("Dataset: %s     ID: %d"
                 % (dataset.getName(), dataset.getId()))
             images = list(dataset.listChildren())
+            title = dataset.getName().decode('utf8')
             dsCanvas = paintDatasetCanvas(
-                conn, images, dataset.getName(), tagIds, showUntagged,
+                conn, images, title, tagIds, showUntagged,
                 length=thumbSize, colCount=maxColumns)
             if dsCanvas is None:
                 continue

omero/util_scripts/Dataset_To_Plate.py

@@ -68,8 +68,8 @@ def addImageToPlate(conn, image, plateId, column, row, removeFrom=None):
     # remove from Datast
     if removeFrom is not None:
         links = list(image.getParentLinks(removeFrom.id))
-        print "     Removing image from %d Dataset: %s" \
-            % (len(links), removeFrom.name)
+        print "     Removing image from Dataset: %s" \
+            % removeFrom.id
         for l in links:
             conn.deleteObjectDirect(l._obj)
     return True
@@ -86,7 +86,7 @@ def dataset_to_plate(conn, scriptParams, datasetId, screen):
 
     # create Plate
     plate = omero.model.PlateI()
-    plate.name = rstring(str(dataset.name))
+    plate.name = omero.rtypes.RStringI(dataset.name)
     plate.columnNamingConvention = rstring(str(scriptParams["Column_Names"]))
     # 'letter' or 'number'
     plate.rowNamingConvention = rstring(str(scriptParams["Row_Names"]))
@@ -100,8 +100,8 @@ def dataset_to_plate(conn, scriptParams, datasetId, screen):
     else:
         link = None
 
-    print "Moving images from Dataset: %d %s to Plate: %d %s" \
-        % (dataset.id, dataset.name, plate.id.val, plate.name.val)
+    print "Moving images from Dataset: %d to Plate: %d" \
+        % (dataset.id, plate.id.val)
 
     row = 0
     col = 0
@@ -126,8 +126,8 @@ def dataset_to_plate(conn, scriptParams, datasetId, screen):
         removeFrom = dataset
 
     for image in images:
-        print "    moving image: %d %s to row: %d, column: %d" \
-            % (image.id, image.name, row, col)
+        print "    moving image: %d to row: %d, column: %d" \
+            % (image.id, row, col)
         addedCount = addImageToPlate(conn, image, plate.id.val, col, row,
                                      removeFrom)
         # update row and column index