def roiFigure(conn, commandArgs):
"""
This processes the script parameters, adding defaults if needed.
Then calls a method to make the figure, and finally uploads and attaches
this to the primary image.
@param: session The OMERO session
@param: commandArgs Map of String:Object parameters for the script.
Objects are not rtypes, since getValue() was
called when the map was processed below.
But, list and map objects may contain rtypes (need
to call getValue())
@return: the id of the originalFileLink child. (ID object,
not value)
"""
log("ROI figure created by OMERO on %s" % date.today())
log("")
message = "" # message to be returned to the client
pixelIds = []
imageIds = []
imageLabels = []
# function for getting image labels.
def getImageNames(fullName, tagsList, pdList):
name = fullName.split("/")[-1]
return [name]
# default function for getting labels is getName (or use datasets / tags)
if "Image_Labels" in commandArgs:
if commandArgs["Image_Labels"] == "Datasets":
def getDatasets(name, tagsList, pdList):
return [dataset for project, dataset in pdList]
getLabels = getDatasets
elif commandArgs["Image_Labels"] == "Tags":
def getTags(name, tagsList, pdList):
return tagsList
getLabels = getTags
else:
getLabels = getImageNames
else:
getLabels = getImageNames
# Get the images
images, logMessage = scriptUtil.getObjects(conn, commandArgs)
message += logMessage
if not images:
return None, message
# Check for rectangular ROIs and filter images list
images = [image for image in images if image.getROICount("Rectangle") > 0]
if not images:
message += "No rectangle ROI found."
return None, message
# Attach figure to the first image
omeroImage = images[0]
# process the list of images. If imageIds is not set, script can't run.
log("Image details:")
for image in images:
imageIds.append(image.getId())
pixelIds.append(image.getPrimaryPixels().getId())
# a map of imageId : list of (project, dataset) names.
pdMap = figUtil.getDatasetsProjectsFromImages(conn.getQueryService(),
imageIds)
tagMap = figUtil.getTagsFromImages(conn.getMetadataService(), imageIds)
# Build a legend entry for each image
for image in images:
name = image.getName()
imageDate = image.getAcquisitionDate()
iId = image.getId()
tagsList = tagMap[iId]
pdList = pdMap[iId]
tags = ", ".join(tagsList)
pdString = ", ".join(["%s/%s" % pd for pd in pdList])
log(" Image: %s ID: %d" % (name, iId))
if imageDate:
log(" Date: %s" % imageDate)
else:
log(" Date: not set")
log(" Tags: %s" % tags)
log(" Project/Datasets: %s" % pdString)
imageLabels.append(getLabels(name, tagsList, pdList))
# use the first image to define dimensions, channel colours etc.
sizeX = omeroImage.getSizeX()
sizeY = omeroImage.getSizeY()
sizeZ = omeroImage.getSizeZ()
sizeC = omeroImage.getSizeC()
width = sizeX
if "Width" in commandArgs:
w = commandArgs["Width"]
try:
width = int(w)
except:
log("Invalid width: %s Using default value: %d" % (str(w), sizeX))
height = sizeY
if "Height" in commandArgs:
h = commandArgs["Height"]
try:
height = int(h)
except:
log("Invalid height: %s Using default value" % (str(h), sizeY))
log("Image dimensions for all panels (pixels): width: %d height: %d"
% (width, height))
mergedIndexes = [] # the channels in the combined image,
mergedColours = {}
if "Merged_Colours" in commandArgs:
cColourMap = commandArgs["Merged_Colours"]
for c in cColourMap:
rgb = cColourMap[c]
try:
rgb = int(rgb)
cIndex = int(c)
except ValueError:
print "Merged_Colours map should be index:rgbInt. Not %s:%s" \
% (c, rgb)
continue
rgba = imgUtil.RGBIntToRGBA(rgb)
mergedColours[cIndex] = rgba
mergedIndexes.append(cIndex)
mergedIndexes.sort()
# make sure we have some merged channels
if len(mergedIndexes) == 0:
mergedIndexes = range(sizeC)
mergedIndexes.reverse()
mergedNames = False
if "Merged_Names" in commandArgs:
mergedNames = commandArgs["Merged_Names"]
# Make channel-names map. If argument wasn't specified, name by index
channelNames = {}
if "Channel_Names" in commandArgs:
cNameMap = commandArgs["Channel_Names"]
for c in range(sizeC):
if str(c) in cNameMap:
channelNames[c] = cNameMap[str(c)]
else:
channelNames[c] = str(c)
else:
for c in range(sizeC):
channelNames[c] = str(c)
# 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)
colourChannels = True
if "Split_Panels_Grey" in commandArgs and commandArgs["Split_Panels_Grey"]:
colourChannels = False
algorithm = ProjectionType.MAXIMUMINTENSITY
if "Algorithm" in commandArgs:
a = commandArgs["Algorithm"]
if (a == "Mean Intensity"):
algorithm = ProjectionType.MEANINTENSITY
stepping = 1
if "Stepping" in commandArgs:
s = commandArgs["Stepping"]
if (0 < s < sizeZ):
stepping = s
scalebar = None
if "Scalebar" in commandArgs:
sb = commandArgs["Scalebar"]
try:
scalebar = int(sb)
if scalebar <= 0:
scalebar = None
else:
log("Scalebar is %d microns" % scalebar)
except:
log("Invalid value for scalebar: %s" % str(sb))
scalebar = None
overlayColour = (255, 255, 255)
if "Overlay_Colour" in commandArgs:
r, g, b, a = OVERLAY_COLOURS[commandArgs["Overlay_Colour"]]
overlayColour = (r, g, b)
roiZoom = None
if "ROI_Zoom" in commandArgs:
roiZoom = float(commandArgs["ROI_Zoom"])
if roiZoom == 0:
roiZoom = None
roiLabel = "FigureROI"
if "ROI_Label" in commandArgs:
roiLabel = commandArgs["ROI_Label"]
spacer = (width/50) + 2
fig = getSplitView(
conn, imageIds, pixelIds, splitIndexes, channelNames, mergedNames,
colourChannels, mergedIndexes, mergedColours, width, height,
imageLabels, spacer, algorithm, stepping, scalebar, overlayColour,
roiZoom, roiLabel)
if fig is None:
logMessage = "No figure produced"
log("\n"+logMessage)
message += logMessage
return None, message
# fig.show() # bug-fixing only
log("")
figLegend = "\n".join(logStrings)
# print figLegend # bug fixing only
format = commandArgs["Format"]
figureName = "roiFigure"
if "Figure_Name" in commandArgs:
figureName = commandArgs["Figure_Name"]
figureName = os.path.basename(figureName)
output = "localfile"
if format == 'PNG':
output = output + ".png"
figureName = figureName + ".png"
fig.save(output, "PNG")
mimetype = "image/png"
elif format == 'TIFF':
output = output + ".tiff"
figureName = figureName + ".tiff"
fig.save(output, "TIFF")
mimetype = "image/tiff"
else:
output = output + ".jpg"
figureName = figureName + ".jpg"
fig.save(output)
mimetype = "image/jpeg"
# Use util method to upload the figure 'output' to the server, attaching
# it to the omeroImage, adding the
# figLegend as the fileAnnotation description.
# Returns the id of the originalFileLink child. (ID object, not value)
namespace = NSCREATED + "/omero/figure_scripts/ROI_Split_Figure"
fileAnnotation, faMessage = scriptUtil.createLinkFileAnnotation(
conn, output, omeroImage, output="ROI Split figure",
mimetype=mimetype, ns=namespace, desc=figLegend,
origFilePathAndName=figureName)
message += faMessage
return fileAnnotation, message
def splitViewFigure(conn, scriptParams):
"""
Processes the arguments, populating defaults if necessary. Prints the details to log (fig-legend).
Even handles missing arguments that are not optional (from when this ran from commandline with everything optional)
then calls makeSplitViewFigure() to make the figure, attaches it to the Image as an 'originalFile' annotation,
with fig-legend as the description.
@return: the id of the originalFileLink child. (ID object, not value)
"""
log("Split-View figure created by OMERO on %s" % date.today())
log("")
message = "" # message to be returned to the client
imageIds = []
pixelIds = []
imageLabels = []
# function for getting image labels.
def getLabels(fullName, tagsList, pdList):
name = fullName.split("/")[-1]
return [name]
# 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]
getLabels = getDatasets
elif scriptParams["Image_Labels"] == "Tags":
def getTags(name, tagsList, pdList):
return tagsList
getLabels = getTags
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Attach figure to the first image
omeroImage = images[0]
# process the list of images
log("Image details:")
for image in images:
imageIds.append(image.getId())
pixelIds.append(image.getPrimaryPixels().getId())
pdMap = figUtil.getDatasetsProjectsFromImages(
conn.getQueryService(),
imageIds) # a map of imageId : list of (project, dataset) names.
tagMap = figUtil.getTagsFromImages(conn.getMetadataService(), imageIds)
# Build a legend entry for each image
for image in images:
name = image.getName()
imageDate = image.getAcquisitionDate()
iId = image.getId()
tagsList = tagMap[iId]
pdList = pdMap[iId]
tags = ", ".join(tagsList)
pdString = ", ".join(["%s/%s" % pd for pd in pdList])
log(" Image: %s ID: %d" % (name, iId))
log(" Date: %s" % date.fromtimestamp(imageDate / 1000))
log(" Tags: %s" % tags)
log(" Project/Datasets: %s" % pdString)
imageLabels.append(getLabels(name, tagsList, pdList))
# use the first image to define dimensions, channel colours etc.
sizeX = omeroImage.getSizeX()
sizeY = omeroImage.getSizeY()
sizeZ = omeroImage.getSizeZ()
sizeC = omeroImage.getSizeC()
# set image dimensions
zStart = -1
zEnd = -1
if "Z_Start" in scriptParams:
zStart = scriptParams["Z_Start"]
if "Z_End" in scriptParams:
zEnd = scriptParams["Z_End"]
width = "Width" in scriptParams and scriptParams["Width"] or sizeX
height = "Height" in scriptParams and scriptParams["Height"] or sizeY
log("Image dimensions for all panels (pixels): width: %d height: %d" %
(width, height))
# Make split-indexes list. If argument wasn't specified, include them all.
splitIndexes = []
if "Split_Indexes" in scriptParams:
splitIndexes = scriptParams["Split_Indexes"]
else:
splitIndexes = range(sizeC)
# Make channel-names map. If argument wasn't specified, name by index
channelNames = {}
for c in range(sizeC):
channelNames[c] = str(c)
if "Channel_Names" in scriptParams:
cNameMap = scriptParams["Channel_Names"]
for c in cNameMap:
index = int(c)
channelNames[index] = cNameMap[c]
mergedIndexes = [] # the channels in the combined image,
mergedColours = {}
if "Merged_Colours" in scriptParams:
cColourMap = scriptParams["Merged_Colours"]
for c in cColourMap:
rgb = cColourMap[c]
rgba = imgUtil.RGBIntToRGBA(rgb)
mergedColours[int(c)] = rgba
mergedIndexes.append(int(c))
mergedIndexes.sort()
else:
mergedIndexes = range(sizeC)
colourChannels = not scriptParams["Split_Panels_Grey"]
algorithm = omero.constants.projection.ProjectionType.MAXIMUMINTENSITY
if "Mean Intensity" == scriptParams["Algorithm"]:
algorithm = omero.constants.projection.ProjectionType.MEANINTENSITY
stepping = min(scriptParams["Stepping"], sizeZ)
scalebar = None
if "Scalebar" in scriptParams:
scalebar = scriptParams["Scalebar"]
log("Scalebar is %d microns" % scalebar)
r, g, b, a = OVERLAY_COLOURS[scriptParams["Overlay_Colour"]]
overlayColour = (r, g, b)
mergedNames = scriptParams["Merged_Names"]
print "splitIndexes", splitIndexes
print "channelNames", channelNames
print "colourChannels", colourChannels
print "mergedIndexes", mergedIndexes
print "mergedColours", mergedColours
print "mergedNames", mergedNames
fig = makeSplitViewFigure(conn, pixelIds, zStart, zEnd, splitIndexes,
channelNames, colourChannels, mergedIndexes,
mergedColours, mergedNames, width, height,
imageLabels, algorithm, stepping, scalebar,
overlayColour)
figLegend = "\n".join(logStrings)
format = JPEG
if scriptParams["Format"] == "PNG":
format = PNG
output = scriptParams["Figure_Name"]
if format == PNG:
output = output + ".png"
fig.save(output, "PNG")
mimetype = "image/png"
else:
output = output + ".jpg"
fig.save(output)
mimetype = "image/jpeg"
# Upload the figure 'output' to the server, creating a file annotation and attaching it to the omeroImage, adding the
# figLegend as the fileAnnotation description.
namespace = omero.constants.namespaces.NSCREATED + "/omero/figure_scripts/Split_View_Figure"
fileAnnotation, faMessage = scriptUtil.createLinkFileAnnotation(
conn,
output,
omeroImage,
output="Split view figure",
mimetype=mimetype,
ns=namespace,
desc=figLegend)
message += faMessage
return fileAnnotation, message