Split view merged 10109

omero/export_scripts/Batch_Image_Export.py

@@ -115,6 +115,10 @@ def savePlane(image, format, cName, zRange, projectZ, t=0, channel=None, greysca
         imgName = makeImageName(originalName, cName, zRange, t, "png", folder_name)
         log("Saving image: %s" % imgName)
         plane.save(imgName, "PNG")
+    elif format == 'TIFF':
+        imgName = makeImageName(originalName, cName, zRange, t, "tiff", folder_name)
+        log("Saving image: %s" % imgName)
+        plane.save(imgName, 'TIFF')
     else:
         imgName = makeImageName(originalName, cName, zRange, t, "jpg", folder_name)
         log("Saving image: %s" % imgName)
@@ -383,16 +387,22 @@ def getTrange(sizeT, scriptParams):
 
     # zip everything up (unless we've only got a single ome-tiff)
     if format == 'OME-TIFF' and len(os.listdir(exp_dir)) == 1:
+        ometiffIds = [t.id for t in parent.listAnnotations(ns=omero.constants.namespaces.NSOMETIFF)]
+        print "Deleting OLD ome-tiffs: %s" % ometiffIds
+        conn.deleteObjects("Annotation", ometiffIds)
         export_file = os.path.join(folder_name, os.listdir(exp_dir)[0])
+        namespace = omero.constants.namespaces.NSOMETIFF
+        outputDisplayName = "OME-TIFF"
         mimetype = 'image/tiff'
     else:
         export_file = "%s.zip" % folder_name
         compress(export_file, folder_name)
         mimetype='application/zip'
+        outputDisplayName = "Batch export zip"
+        namespace = omero.constants.namespaces.NSCREATED+"/omero/export_scripts/Batch_Image_Export"
 
-    namespace = omero.constants.namespaces.NSCREATED+"/omero/export_scripts/Batch_Image_Export"
     fileAnnotation, annMessage = script_utils.createLinkFileAnnotation(conn, export_file, parent, 
-        output="Batch export zip", ns=namespace, mimetype=mimetype)
+        output=outputDisplayName, ns=namespace, mimetype=mimetype)
     message += annMessage
     return fileAnnotation, message
 
@@ -404,6 +414,7 @@ def runScript():
     dataTypes = [rstring('Dataset'),rstring('Image')]
     formats = [rstring('JPEG'),
         rstring('PNG'),
+        rstring('TIFF'),
         rstring('OME-TIFF')]
     defaultZoption = 'Default-Z (last-viewed)'
     zChoices = [rstring(defaultZoption),
@@ -465,7 +476,7 @@ def runScript():
         description="The max width of each image panel. Default is actual size", min=1),
 
     scripts.String("Format", grouping="8", 
-        description="Format to save image", values=formats, default='PNG'),
+        description="Format to save image", values=formats, default='JPEG'),
 
     scripts.String("Folder_Name", grouping="9",
         description="Name of folder (and zip file) to store images", default='Batch_Image_Export'),

omero/figure_scripts/Movie_Figure.py

@@ -48,6 +48,7 @@
 import StringIO
 from omero_sys_ParametersI import ParametersI
 from datetime import date
+import math
 
 try:
     from PIL import Image, ImageDraw # see ticket:2597
@@ -58,22 +59,19 @@
 COLOURS = scriptUtil.COLOURS    # name:(rgba) map
 OVERLAY_COLOURS = dict(COLOURS, **scriptUtil.EXTRA_COLOURS)
 
-JPEG = "image/jpeg"
-PNG = "image/png"
 
 logLines = []    # make a log / legend of the figure
 def log(text):
     print text
     logLines.append(text)
 
 
-def getImageFrames(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer,
-            algorithm, stepping, scalebar, overlayColour, timeUnits):
-
+def createMovieFigure(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer,
+            algorithm, stepping, scalebar, overlayColour, timeUnits, imageLabels, maxColCount):
     """
-    Makes a canvas showing an image per row with multiple columns showing 
+    Makes the complete Movie figure: A canvas showing an image per row with multiple columns showing 
     frames from each image/movie. Labels obove each frame to show the time-stamp of that frame in the 
-    specified units. 
+    specified units and labels on the left name each image. 
 
     @param session        The OMERO session
     @param pixelIds        A list of the Pixel IDs for the images in the figure
@@ -88,6 +86,7 @@ def getImageFrames(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer
     @param scalebar        A number of microns for scale-bar
     @param overlayColour     Colour of the scale-bar as tuple (255,255,255)
     @param timeUnits    A string such as "SECS"
+    @param imageLabels    A list of lists, corresponding to pixelIds, for labelling each image with one or more strings.
     """
 
     mode = "RGB"
@@ -179,17 +178,20 @@ def getImageFrames(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer
 
 
         # make a canvas for the row of splitview images...(will add time labels above each row)
+        colCount = min(maxColCount, len(renderedImages))
+        rowCount = math.ceil(float(len(renderedImages)) / colCount)
         font = imgUtil.getFont(width/12)
         fontHeight = font.getsize("Textq")[1]
-        canvasWidth = ((width + spacer) * len(renderedImages)) + spacer
-        canvasHeight = spacer/2 + fontHeight + spacer + height
+        canvasWidth = ((width + spacer) * colCount) + spacer
+        canvasHeight = rowCount * (spacer/2 + fontHeight + spacer + height)
         size = (canvasWidth, canvasHeight)
         canvas = Image.new(mode, size, white)        # create a canvas of appropriate width, height
 
         # add text labels
         queryService = conn.getQueryService()
         textX = spacer
         textY = spacer/4
+        colIndex = 0
         timeLabels = figUtil.getTimeLabels(queryService, pixelsId, tIndexes, sizeT, timeUnits)
         for t, tIndex in enumerate(tIndexes):
             if tIndex >= sizeT:
@@ -200,6 +202,11 @@ def getImageFrames(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer
             textdraw = ImageDraw.Draw(canvas)
             textdraw.text((textX+inset, textY), time, font=font, fill=(0,0,0))
             textX += width + spacer
+            colIndex += 1
+            if colIndex >= maxColCount:
+                colIndex = 0
+                textX = spacer
+                textY += (spacer/2 + fontHeight + spacer + height)
 
         # add scale bar to last frame...
         if scalebar:
@@ -214,13 +221,23 @@ def getImageFrames(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer
 
         px = spacer
         py = spacer + fontHeight
+        colIndex = 0
         # paste the images in
-        for img in renderedImages:
+        for i, img in enumerate(renderedImages):
             imgUtil.pasteImage(img, canvas, px, py)
             px = px + width + spacer
-
-        totalWidth = max(totalWidth, canvasWidth)    # most should be same width anyway
-        totalHeight = totalHeight + canvasHeight    # add together the heights of each row
+            colIndex += 1
+            if colIndex >= maxColCount:
+                colIndex = 0
+                px = spacer
+                py += (spacer/2 + fontHeight + spacer + height)
+
+        # Add labels to the left of the panel
+        canvas = addLeftLabels(canvas, imageLabels, row, width, spacer)
+
+        totalWidth = max(totalWidth, canvas.size[0])    # most should be same width anyway
+        totalHeight = totalHeight + canvas.size[1]    # add together the heights of each row
+
         rowPanels.append(canvas)
 
     # make a figure to combine all split-view rows
@@ -236,70 +253,58 @@ def getImageFrames(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer
     return figureCanvas
 
 
-def createMovieFigure(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer,
-                            algorithm, stepping, scalebar, overlayColour, timeUnits, imageLabels):
+def addLeftLabels(panelCanvas, imageLabels, rowIndex, width, spacer):
     """
-    Makes the complete Movie figure: A canvas showing an image per row with multiple columns showing 
-    frames from each image/movie. Labels obove each frame to show the time-stamp of that frame in the 
-    specified units and labels on the left name each image. 
-
-    @param session        The OMERO session
-    @param pixelIds        A list of the Pixel IDs for the images in the figure
-    @param tIndexes        A list of tIndexes to display frames from
-    @param zStart        Projection Z-start
-    @param zEnd            Projection Z-end
-    @param width        Maximum width of panels
-    @param height        Max height of panels
-    @param spacer        Space between panels
-    @param algorithm    Projection algorithm e.g. "MAXIMUMINTENSITY"
-    @param stepping        Projecttion z-step
-    @param scalebar        A number of microns for scale-bar
-    @param overlayColour     Colour of the scale-bar as tuple (255,255,255)
-    @param timeUnits    A string such as "SECS"
-    @param imageLabels    A list of lists, corresponding to pixelIds, for labelling each image with one or more strings.
+    Takes a canvas of panels and adds one or more labels to the left,
+    with the text aligned vertically.
+    NB: We are passed the set of labels for ALL image panels (as well as the
+    index of the current image panel) so that we know what is the max label count
+    and can give all panels the same margin on the left.
+
+    @param panelCanvas:     PIL image - add labels to the left of this
+    @param imageLabels:     A series of label lists, one per image. We only add labels from one list
+    @param rowIndex:        The index of the label list we're going to use from imageLabels
+    @param width:           Simply used for finding a suitable font size
+    @param spacer:          Space between panels
     """
-
-    panelCanvas = getImageFrames(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer,
-                            algorithm, stepping, scalebar, overlayColour, timeUnits)
-
+
     # add lables to row...
     mode = "RGB"
     white = (255,255,255)
     font = imgUtil.getFont(width/12)
     textHeight = font.getsize("Sampleq")[1]
     textGap = spacer /2
-    rowSpacing = panelCanvas.size[1]/len(pixelIds)
+    #rowSpacing = panelCanvas.size[1]/len(pixelIds)
 
     # find max number of labels
     maxCount = 0 
     rowHeights = []
     for row in imageLabels:
         maxCount = max(maxCount, len(row))
-    leftTextWidth = (textHeight + textGap) * maxCount
-    size = (panelCanvas.size[1], leftTextWidth)    # make the canvas as wide as the panels height
+    leftTextHeight = (textHeight + textGap) * maxCount
+    leftTextWidth = panelCanvas.size[1]    # make the canvas as wide as the panels height
+    size = (leftTextWidth, leftTextHeight)
     textCanvas = Image.new(mode, size, white)
     textdraw = ImageDraw.Draw(textCanvas)
     px = spacer
-    imageLabels.reverse()
-    for row in imageLabels:
-        py = leftTextWidth - textGap # start at bottom
-        for l, label in enumerate(row):
-            py = py - textHeight    # find the top of this row
-            w = textdraw.textsize(label, font=font) [0]
-            inset = int((height - w) / 2)
-            textdraw.text((px+inset, py), label, font=font, fill=(0,0,0))
-            py = py - textGap    # add space between rows
-        px = px + rowSpacing         # 2 spacers between each row
-
+
+    labels = imageLabels[rowIndex]
+    py = leftTextHeight - textGap # start at bottom
+    for l, label in enumerate(labels):
+        py = py - textHeight    # find the top of this row
+        w = textdraw.textsize(label, font=font) [0]
+        inset = int((leftTextWidth - w) / 2)
+        textdraw.text((inset, py), label, font=font, fill=(0,0,0))
+        py = py - textGap    # add space between rows
 
     # make a canvas big-enough to add text to the images. 
-    canvasWidth = leftTextWidth + panelCanvas.size[0]
+    canvasWidth = leftTextHeight + panelCanvas.size[0]      # TextHeight will be width once rotated
     canvasHeight = panelCanvas.size[1]
     size = (canvasWidth, canvasHeight)
     canvas = Image.new(mode, size, white)        # create a canvas of appropriate width, height
 
     # add the panels to the canvas 
-    pasteX = leftTextWidth
+    pasteX = leftTextHeight
     pasteY = 0
     imgUtil.pasteImage(panelCanvas, canvas, pasteX, pasteY)
 
@@ -310,8 +315,8 @@ def createMovieFigure(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spa
         imgUtil.pasteImage(textV, canvas, spacer/2, 0)
 
     return canvas
-    
-    
+
+
 def movieFigure(conn, commandArgs):
     """
     Makes the figure using the parameters in @commandArgs, attaches the figure to the 
@@ -332,8 +337,9 @@ def movieFigure(conn, commandArgs):
                 "MINS_SECS": "mins:secs",
                 "HOURS_MINS": "hours:mins"}
     timeUnits = "SECS"
-    if "timeUnits" in commandArgs:
-        timeUnits = commandArgs["timeUnits"]
+    if "Time_Units" in commandArgs:
+        timeUnits = commandArgs["Time_Units"]
+        timeUnits = timeUnits.replace(" ", "_")     # convert from UI name to timeLabels key
     if timeUnits not in timeLabels.keys():
         timeUnits = "SECS"
     log("Time units are in %s" % timeLabels[timeUnits])
@@ -455,30 +461,33 @@ def getTags(name, tagsList, pdList):
     if "Scalebar_Colour" in commandArgs:
         r,g,b,a = OVERLAY_COLOURS[commandArgs["Scalebar_Colour"]]
         overlayColour = (r,g,b)
+
+    maxColCount = 10
+    if "Max_Columns" in commandArgs:
+        maxColCount = commandArgs["Max_Columns"]
 
     figure = createMovieFigure(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer,
-                            algorithm, stepping, scalebar, overlayColour, timeUnits, imageLabels)
-
-    #figure.show()
+                            algorithm, stepping, scalebar, overlayColour, timeUnits, imageLabels, maxColCount)
 
     log("")
     figLegend = "\n".join(logLines)
 
     #print figLegend    # bug fixing only
 
-    format = JPEG
-    if "Format" in commandArgs:
-        if commandArgs["Format"] == "PNG":
-            format = PNG
+    format = commandArgs["Format"]
 
     output = "movieFigure"
     if "Figure_Name" in commandArgs:
         output = str(commandArgs["Figure_Name"])
 
-    if format == PNG:
+    if format == 'PNG':
         output = output + ".png"
         figure.save(output, "PNG")
         mimetype = "image/png"
+    elif format == 'TIFF':
+        output = output + ".tiff"
+        figure.save(output, "TIFF")
+        mimetype = "image/tiff"
     else:
         output = output + ".jpg"
         figure.save(output)
@@ -501,7 +510,7 @@ def runAsScript():
     labels = [rstring('Image Name'), rstring('Datasets'), rstring('Tags')]
     algorithums = [rstring('Maximum Intensity'),rstring('Mean Intensity')]
     tunits =  [rstring("SECS"), rstring("MINS"), rstring("HOURS"), rstring("MINS SECS"), rstring("HOURS MINS")]
-    formats = [rstring('JPEG'),rstring('PNG')]
+    formats = [rstring('JPEG'),rstring('PNG'),rstring('TIFF')]
     ckeys = COLOURS.keys()
     ckeys.sort()
     cOptions = wrap(ckeys)
@@ -541,11 +550,13 @@ def runAsScript():
     scripts.String("Scalebar_Colour", grouping="10.2",
         description="The colour of the scalebar.",default='White',values=oColours),
     scripts.String("Format", grouping="11",
-        description="Format to save image.", values=formats),
+        description="Format to save image.", values=formats, default='JPEG'),
     scripts.String("Figure_Name", grouping="12",
         description="File name of the figure to save."),
     scripts.String("Time_Units", grouping="13",
         description="The units to use for time display", values=tunits),
+    scripts.Int("Max_Columns", grouping="04.1", default=10,
+        description="The maximum number of columns in the figure, for movie frames.", min=1),
 
     version = "4.3.0",
     authors = ["William Moore", "OME Team"],

omero/figure_scripts/Movie_ROI_Figure.py

@@ -54,8 +54,6 @@
 except ImportError:
     import Image, ImageDraw # see ticket:2597
 
-JPEG = "image/jpeg"
-PNG = "image/png"
 
 COLOURS = scriptUtil.COLOURS
 OVERLAY_COLOURS = dict(COLOURS, **scriptUtil.EXTRA_COLOURS)
@@ -628,19 +626,20 @@ def getTags(name, tagsList, pdList):
 
     #print figLegend    # bug fixing only
 
-    format = JPEG
-    if "Format" in commandArgs:
-        if commandArgs["Format"] == "PNG":
-            format = PNG
+    format = commandArgs["Format"]
 
     output = "movieROIFigure"
     if "Figure_Name" in commandArgs:
         output = str(commandArgs["Figure_Name"])
 
-    if format == PNG:
+    if format == 'PNG':
         output = output + ".png"
         fig.save(output, "PNG")
         mimetype = "image/png"
+    elif format == 'TIFF':
+        output = output + ".tiff"
+        fig.save(output, "TIFF")
+        mimetype = "image/tiff"
     else:
         output = output + ".jpg"
         fig.save(output)
@@ -666,7 +665,7 @@ def runAsScript():
     algorithums = [rstring('Maximum Intensity'),rstring('Mean Intensity')]
     roiLabel = """Specify an ROI to pick by specifying it's shape label. 'FigureROI' by default,
 (not case sensitive). If matching ROI not found, use any ROI."""
-    formats = [rstring('JPEG'),rstring('PNG')]
+    formats = [rstring('JPEG'),rstring('PNG'),rstring('TIFF')]
     ckeys = COLOURS.keys()
     ckeys.sort()
     cOptions = wrap(ckeys)