def roiFigure(session, 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)
"""
# create the services we're going to need.
metadataService = session.getMetadataService()
queryService = session.getQueryService()
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
containerService = session.getContainerService()
log("ROI figure created by OMERO on %s" % date.today())
log("")
pixelIds = []
imageIds = []
imageLabels = []
imageNames = {}
omeroImage = None # this is set as the first image, to link figure to
# 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 "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
# process the list of images. If imageIds is not set, script can't run.
log("Image details:")
for idCount, imageId in enumerate(commandArgs["IDs"]):
iId = long(imageId.getValue())
image = containerService.getImages("Image", [iId], None)[0]
if image == None:
print "Image not found for ID:", iId
continue
imageIds.append(iId)
if idCount == 0:
omeroImage = image # remember the first image to attach figure to
pixelIds.append(image.getPrimaryPixels().getId().getValue())
imageNames[iId] = image.getName().getValue()
if len(imageIds) == 0:
print "No image IDs specified."
pdMap = figUtil.getDatasetsProjectsFromImages(queryService, imageIds) # a map of imageId : list of (project, dataset) names.
tagMap = figUtil.getTagsFromImages(metadataService, imageIds)
# Build a legend entry for each image
for iId in imageIds:
name = imageNames[iId]
imageDate = image.getAcquisitionDate().getValue()
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.
pixelsId = pixelIds[0]
pixels = queryService.get("Pixels", pixelsId)
sizeX = pixels.getSizeX().getValue();
sizeY = pixels.getSizeY().getValue();
sizeZ = pixels.getSizeZ().getValue();
sizeC = pixels.getSizeC().getValue();
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].getValue()
rgba = imgUtil.RGBIntToRGBA(rgb)
mergedColours[int(c)] = rgba
mergedIndexes.append(int(c))
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)].getValue()
else:
channelNames[c] = str(c)
else:
for c in range(sizeC):
channelNames[c] = str(c)
# Make split-indexes list. If argument wasn't specified, include them all.
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"]:
colourChannels = False
algorithm = omero.constants.projection.ProjectionType.MAXIMUMINTENSITY
if "Algorithm" in commandArgs:
a = commandArgs["Algorithm"]
if (a == "Mean Intensity"):
algorithm = omero.constants.projection.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(session, imageIds, pixelIds, splitIndexes, channelNames, mergedNames, colourChannels, mergedIndexes,
mergedColours, width, height, imageLabels, spacer, algorithm, stepping, scalebar, overlayColour, roiZoom, roiLabel)
if fig == None: # e.g. No ROIs found
return
#fig.show() # bug-fixing only
log("")
figLegend = "\n".join(logStrings)
#print figLegend # bug fixing only
format = JPEG
if "Format" in commandArgs:
if commandArgs["Format"] == "PNG":
format = PNG
output = "roiFigure"
if "Figure_Name" in commandArgs:
output = str(commandArgs["Figure_Name"])
if format == PNG:
output = output + ".png"
fig.save(output, "PNG")
else:
output = output + ".jpg"
fig.save(output)
# 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)
fileAnnotation = scriptUtil.uploadAndAttachFile(queryService, updateService, rawFileStore, omeroImage, output, format, figLegend)
return fileAnnotation
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 movieFigure(conn, commandArgs):
"""
Makes the figure using the parameters in @commandArgs, attaches the figure
to the parent Project/Dataset, and returns the file-annotation ID
@param session The OMERO session
@param commandArgs Map of parameters for the script
@ returns Returns the id of the originalFileLink child. (ID
object, not value)
"""
log("Movie figure created by OMERO on %s" % date.today())
log("")
timeLabels = {"SECS_MILLIS": "seconds",
"SECS": "seconds",
"MINS": "minutes",
"HOURS": "hours",
"MINS_SECS": "mins:secs",
"HOURS_MINS": "hours:mins"}
timeUnits = "SECS"
if "Time_Units" in commandArgs:
timeUnits = commandArgs["Time_Units"]
# convert from UI name to timeLabels key
timeUnits = timeUnits.replace(" ", "_")
if timeUnits not in timeLabels.keys():
timeUnits = "SECS"
log("Time units are in %s" % timeLabels[timeUnits])
pixelIds = []
imageIds = []
imageLabels = []
message = "" # message to be returned to the client
# 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
# 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())
# 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()
iId = image.getId()
imageDate = image.getAcquisitionDate()
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()
sizeT = omeroImage.getSizeT()
tIndexes = []
if "T_Indexes" in commandArgs:
for t in commandArgs["T_Indexes"]:
tIndexes.append(t)
print "T_Indexes", tIndexes
if len(tIndexes) == 0: # if no t-indexes given, use all t-indices
tIndexes = range(sizeT)
zStart = -1
zEnd = -1
if "Z_Start" in commandArgs:
zStart = commandArgs["Z_Start"]
if "Z_End" in commandArgs:
zEnd = commandArgs["Z_End"]
width = sizeX
if "Width" in commandArgs:
width = commandArgs["Width"]
height = sizeY
if "Height" in commandArgs:
height = commandArgs["Height"]
spacer = (width/25) + 2
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 "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,
maxColCount)
log("")
figLegend = "\n".join(logLines)
# print figLegend # bug fixing only
format = commandArgs["Format"]
figureName = "movieFigure"
if "Figure_Name" in commandArgs:
figureName = str(commandArgs["Figure_Name"])
figureName = os.path.basename(figureName)
output = "localfile"
if format == 'PNG':
output = output + ".png"
figureName = figureName + ".png"
figure.save(output, "PNG")
mimetype = "image/png"
elif format == 'TIFF':
output = output + ".tiff"
figureName = figureName + ".tiff"
figure.save(output, "TIFF")
mimetype = "image/tiff"
else:
output = output + ".jpg"
figureName = figureName + ".jpg"
figure.save(output)
mimetype = "image/jpeg"
namespace = NSCREATED + "/omero/figure_scripts/Movie_Figure"
fileAnnotation, faMessage = scriptUtil.createLinkFileAnnotation(
conn, output, omeroImage, output="Movie figure", mimetype=mimetype,
ns=namespace, desc=figLegend, origFilePathAndName=figureName)
message += faMessage
return fileAnnotation, message
def split_view_figure(conn, script_params):
"""
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 make_split_view_figure() 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
image_ids = []
pixel_ids = []
image_labels = []
# function for getting image labels.
def get_image_names(full_name, tags_list, pd_list):
name = full_name.split("/")[-1]
return [name.decode('utf8')]
# default function for getting labels is getName (or use datasets / tags)
if script_params["Image_Labels"] == "Datasets":
def get_datasets(name, tags_list, pd_list):
return [dataset.decode('utf8') for project, dataset in pd_list]
get_labels = get_datasets
elif script_params["Image_Labels"] == "Tags":
def get_tags(name, tags_list, pd_list):
return [t.decode('utf8') for t in tags_list]
get_labels = get_tags
else:
get_labels = get_image_names
# Get the images
images, log_message = script_utils.get_objects(conn, script_params)
message += log_message
if not images:
return None, message
# Attach figure to the first image
omero_image = images[0]
# process the list of images
log("Image details:")
for image in images:
image_ids.append(image.getId())
pixel_ids.append(image.getPrimaryPixels().getId())
# a map of imageId : list of (project, dataset) names.
pd_map = figUtil.getDatasetsProjectsFromImages(conn.getQueryService(),
image_ids)
tag_map = figUtil.getTagsFromImages(conn.getMetadataService(), image_ids)
# Build a legend entry for each image
for image in images:
name = image.getName()
image_date = image.getAcquisitionDate()
iid = image.getId()
tags_list = tag_map[iid]
pd_list = pd_map[iid]
tags = ", ".join(tags_list)
pd_string = ", ".join(["%s/%s" % pd for pd in pd_list])
log(" Image: %s ID: %d" % (name, iid))
if image_date:
log(" Date: %s" % image_date)
else:
log(" Date: not set")
log(" Tags: %s" % tags)
log(" Project/Datasets: %s" % pd_string)
image_labels.append(get_labels(name, tags_list, pd_list))
# use the first image to define dimensions, channel colours etc.
size_x = omero_image.getSizeX()
size_y = omero_image.getSizeY()
size_z = omero_image.getSizeZ()
size_c = omero_image.getSizeC()
# set image dimensions
z_start = -1
z_end = -1
if "Z_Start" in script_params:
z_start = script_params["Z_Start"]
if "Z_End" in script_params:
z_end = script_params["Z_End"]
width = "Width" in script_params and script_params["Width"] or size_x
height = "Height" in script_params and script_params["Height"] or size_y
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.
split_indexes = []
if "Split_Indexes" in script_params:
split_indexes = script_params["Split_Indexes"]
else:
split_indexes = range(size_c)
# Make channel-names map. If argument wasn't specified, name by index
channel_names = {}
for c in range(size_c):
channel_names[c] = str(c)
if "Channel_Names" in script_params:
c_name_map = script_params["Channel_Names"]
for c in c_name_map:
index = int(c)
channel_names[index] = c_name_map[c].decode('utf8')
merged_indexes = [] # the channels in the combined image,
merged_colours = {}
if "Merged_Colours" in script_params:
c_colour_map = script_params["Merged_Colours"]
for c in c_colour_map:
rgb = c_colour_map[c]
try:
rgb = int(rgb)
c_index = int(c)
except ValueError:
continue
rgba = image_utils.int_to_rgba(rgb)
merged_colours[c_index] = rgba
merged_indexes.append(c_index)
merged_indexes.sort()
else:
merged_indexes = range(size_c)
colour_channels = not script_params["Split_Panels_Grey"]
algorithm = ProjectionType.MAXIMUMINTENSITY
if "Mean Intensity" == script_params["Algorithm"]:
algorithm = ProjectionType.MEANINTENSITY
stepping = min(script_params["Stepping"], size_z)
scalebar = None
if "Scalebar" in script_params:
scalebar = script_params["Scalebar"]
log("Scalebar is %d microns" % scalebar)
r, g, b, a = OVERLAY_COLOURS[script_params["Overlay_Colour"]]
overlay_colour = (r, g, b)
merged_names = script_params["Merged_Names"]
fig = make_split_view_figure(conn, pixel_ids, z_start, z_end,
split_indexes, channel_names, colour_channels,
merged_indexes, merged_colours, merged_names,
width, height, image_labels, algorithm,
stepping, scalebar, overlay_colour)
fig_legend = "\n".join(log_strings)
figure_name = script_params["Figure_Name"]
figure_name = os.path.basename(figure_name)
output = "localfile"
format = script_params["Format"]
if format == 'PNG':
output = output + ".png"
figure_name = figure_name + ".png"
fig.save(output, "PNG")
mimetype = "image/png"
elif format == 'TIFF':
output = output + ".tiff"
figure_name = figure_name + ".tiff"
fig.save(output, "TIFF")
mimetype = "image/tiff"
else:
output = output + ".jpg"
figure_name = figure_name + ".jpg"
fig.save(output)
mimetype = "image/jpeg"
# Upload the figure 'output' to the server, creating a file annotation and
# attaching it to the omero_image, adding the
# fig_legend as the fileAnnotation description.
namespace = NSCREATED + "/omero/figure_scripts/Split_View_Figure"
file_annotation, fa_message = script_utils.create_link_file_annotation(
conn,
output,
omero_image,
output="Split view figure",
mimetype=mimetype,
namespace=namespace,
description=fig_legend,
orig_file_path_and_name=figure_name)
message += fa_message
return file_annotation, message
def movie_figure(conn, command_args):
"""
Makes the figure using the parameters in @command_args, attaches the figure
to the parent Project/Dataset, and returns the file-annotation ID
@param session The OMERO session
@param command_args Map of parameters for the script
@ returns Returns the id of the originalFileLink child. (ID
object, not value)
"""
log("Movie figure created by OMERO on %s" % date.today())
log("")
time_labels = {
"SECS_MILLIS": "seconds",
"SECS": "seconds",
"MINS": "minutes",
"HOURS": "hours",
"MINS_SECS": "mins:secs",
"HOURS_MINS": "hours:mins"
}
time_units = "SECS"
if "Time_Units" in command_args:
time_units = command_args["Time_Units"]
# convert from UI name to time_labels key
time_units = time_units.replace(" ", "_")
if time_units not in time_labels.keys():
time_units = "SECS"
log("Time units are in %s" % time_labels[time_units])
pixel_ids = []
image_ids = []
image_labels = []
message = "" # message to be returned to the client
# function for getting image labels.
def get_image_names(full_name, tags_list, pd_list):
name = full_name.split("/")[-1]
return [name]
# default function for getting labels is getName (or use datasets / tags)
if "Image_Labels" in command_args:
if command_args["Image_Labels"] == "Datasets":
def get_datasets(name, tags_list, pd_list):
return [dataset for project, dataset in pd_list]
get_labels = get_datasets
elif command_args["Image_Labels"] == "Tags":
def get_tags(name, tags_list, pd_list):
return tags_list
get_labels = get_tags
else:
get_labels = get_image_names
else:
get_labels = get_image_names
# Get the images
images, log_message = script_utils.get_objects(conn, command_args)
message += log_message
if not images:
return None, message
# Attach figure to the first image
omero_image = images[0]
# process the list of images
log("Image details:")
for image in images:
image_ids.append(image.getId())
pixel_ids.append(image.getPrimaryPixels().getId())
# a map of imageId : list of (project, dataset) names.
pd_map = figUtil.getDatasetsProjectsFromImages(conn.getQueryService(),
image_ids)
tag_map = figUtil.getTagsFromImages(conn.getMetadataService(), image_ids)
# Build a legend entry for each image
for image in images:
name = image.getName()
iid = image.getId()
image_date = image.getAcquisitionDate()
tags_list = tag_map[iid]
pd_list = pd_map[iid]
tags = ", ".join(tags_list)
pd_string = ", ".join(["%s/%s" % pd for pd in pd_list])
log(" Image: %s ID: %d" % (name, iid))
if image_date:
log(" Date: %s" % image_date)
else:
log(" Date: not set")
log(" Tags: %s" % tags)
log(" Project/Datasets: %s" % pd_string)
image_labels.append(get_labels(name, tags_list, pd_list))
# use the first image to define dimensions, channel colours etc.
size_x = omero_image.getSizeX()
size_y = omero_image.getSizeY()
size_z = omero_image.getSizeZ()
size_t = omero_image.getSizeT()
t_indexes = []
if "T_Indexes" in command_args:
for t in command_args["T_Indexes"]:
t_indexes.append(t)
if len(t_indexes) == 0: # if no t-indexes given, use all t-indices
t_indexes = range(size_t)
z_start = -1
z_end = -1
if "Z_Start" in command_args:
z_start = command_args["Z_Start"]
if "Z_End" in command_args:
z_end = command_args["Z_End"]
width = size_x
if "Width" in command_args:
width = command_args["Width"]
height = size_y
if "Height" in command_args:
height = command_args["Height"]
spacer = (width / 25) + 2
algorithm = ProjectionType.MAXIMUMINTENSITY
if "Algorithm" in command_args:
a = command_args["Algorithm"]
if (a == "Mean Intensity"):
algorithm = ProjectionType.MEANINTENSITY
stepping = 1
if "Stepping" in command_args:
s = command_args["Stepping"]
if (0 < s < size_z):
stepping = s
scalebar = None
if "Scalebar" in command_args:
sb = command_args["Scalebar"]
try:
scalebar = int(sb)
if scalebar <= 0:
scalebar = None
else:
log("Scalebar is %d microns" % scalebar)
except ValueError:
log("Invalid value for scalebar: %s" % str(sb))
scalebar = None
overlay_colour = (255, 255, 255)
if "Scalebar_Colour" in command_args:
r, g, b, a = OVERLAY_COLOURS[command_args["Scalebar_Colour"]]
overlay_colour = (r, g, b)
max_col_count = 10
if "Max_Columns" in command_args:
max_col_count = command_args["Max_Columns"]
figure = createmovie_figure(conn, pixel_ids, t_indexes, z_start, z_end,
width, height, spacer, algorithm, stepping,
scalebar, overlay_colour, time_units,
image_labels, max_col_count)
log("")
fig_legend = "\n".join(log_lines)
# print figLegend # bug fixing only
format = command_args["Format"]
figure_name = "movie_figure"
if "Figure_Name" in command_args:
figure_name = str(command_args["Figure_Name"])
figure_name = os.path.basename(figure_name)
output = "localfile"
if format == 'PNG':
output = output + ".png"
figure_name = figure_name + ".png"
figure.save(output, "PNG")
mimetype = "image/png"
elif format == 'TIFF':
output = output + ".tiff"
figure_name = figure_name + ".tiff"
figure.save(output, "TIFF")
mimetype = "image/tiff"
else:
output = output + ".jpg"
figure_name = figure_name + ".jpg"
figure.save(output)
mimetype = "image/jpeg"
namespace = NSCREATED + "/omero/figure_scripts/Movie_Figure"
file_annotation, fa_message = script_utils.create_link_file_annotation(
conn,
output,
omero_image,
output="Movie figure",
mimetype=mimetype,
namespace=namespace,
description=fig_legend,
orig_file_path_and_name=figure_name)
message += fa_message
return file_annotation, 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
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("Rect") > 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
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()
iId = image.getId()
imageDate = image.getAcquisitionDate()
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()
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))
# the channels in the combined image,
if "Merged_Channels" in commandArgs:
# convert to 0-based
mergedIndexes = [c-1 for c in commandArgs["Merged_Channels"]]
else:
mergedIndexes = range(sizeC) # show all
mergedIndexes.reverse()
# if no colours added, use existing rendering settings.
mergedColours = {}
# Actually, nicer to always use existing rendering settings.
# if "Merged_Colours" in commandArgs:
# for i, c in enumerate(commandArgs["Merged_Colours"]):
# if c in COLOURS:
# mergedColours[i] = COLOURS[c]
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 "Scalebar_Colour" in commandArgs:
if commandArgs["Scalebar_Colour"] in OVERLAY_COLOURS:
r, g, b, a = OVERLAY_COLOURS[commandArgs["Scalebar_Colour"]]
overlayColour = (r, g, b)
roiZoom = None
if "Roi_Zoom" in commandArgs:
roiZoom = float(commandArgs["Roi_Zoom"])
if roiZoom == 0:
roiZoom = None
maxColumns = None
if "Max_Columns" in commandArgs:
maxColumns = commandArgs["Max_Columns"]
showRoiDuration = False
if "Show_ROI_Duration" in commandArgs:
showRoiDuration = commandArgs["Show_ROI_Duration"]
roiLabel = "FigureROI"
if "Roi_Selection_Label" in commandArgs:
roiLabel = commandArgs["Roi_Selection_Label"]
spacer = (width/50) + 2
print "showRoiDuration", showRoiDuration
fig = getSplitView(
conn, imageIds, pixelIds, mergedIndexes, mergedColours, width, height,
imageLabels, spacer, algorithm, stepping, scalebar, overlayColour,
roiZoom, maxColumns, showRoiDuration, roiLabel)
# fig.show() # bug-fixing only
if fig is None:
logMessage = "No figure produced"
log("\n"+logMessage)
message += logMessage
return None, message
figLegend = "\n".join(logStrings)
# print figLegend # bug fixing only
format = commandArgs["Format"]
figureName = "movieROIFigure"
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/Movie_ROI_Figure"
fileAnnotation, faMessage = scriptUtil.createLinkFileAnnotation(
conn, output, omeroImage, output="Movie ROI 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
def roiFigure(session, 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)
"""
# create the services we're going to need.
metadataService = session.getMetadataService()
queryService = session.getQueryService()
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
containerService = session.getContainerService()
log("ROI figure created by OMERO on %s" % date.today())
log("")
pixelIds = []
imageIds = []
imageLabels = []
imageNames = {}
omeroImage = None # this is set as the first image, to link figure to
# 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 "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
# process the list of images. If imageIds is not set, script can't run.
log("Image details:")
dataType = commandArgs["Data_Type"]
ids = commandArgs["IDs"]
images = containerService.getImages(dataType, ids, None)
for idCount, image in enumerate(images):
iId = image.getId().getValue()
imageIds.append(iId)
if idCount == 0:
omeroImage = image # remember the first image to attach figure to
pixelIds.append(image.getPrimaryPixels().getId().getValue())
imageNames[iId] = image.getName().getValue()
if len(imageIds) == 0:
print "No image IDs specified."
return
pdMap = figUtil.getDatasetsProjectsFromImages(queryService, imageIds) # a map of imageId : list of (project, dataset) names.
tagMap = figUtil.getTagsFromImages(metadataService, imageIds)
# Build a legend entry for each image
for iId in imageIds:
name = imageNames[iId]
imageDate = image.getAcquisitionDate().getValue()
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.
pixelsId = pixelIds[0]
pixels = queryService.get("Pixels", pixelsId)
sizeX = pixels.getSizeX().getValue();
sizeY = pixels.getSizeY().getValue();
sizeZ = pixels.getSizeZ().getValue();
sizeC = pixels.getSizeC().getValue();
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))
# the channels in the combined image,
if "Merged_Channels" in commandArgs:
mergedIndexes = [c-1 for c in commandArgs["Merged_Channels"]] # convert to 0-based
else:
mergedIndexes = range(sizeC) # show all
mergedIndexes.reverse()
mergedColours = {} # if no colours added, use existing rendering settings.
# Actually, nicer to always use existing rendering settings.
#if "Merged_Colours" in commandArgs:
# for i, c in enumerate(commandArgs["Merged_Colours"]):
# if c in COLOURS:
# mergedColours[i] = COLOURS[c]
algorithm = omero.constants.projection.ProjectionType.MAXIMUMINTENSITY
if "Algorithm" in commandArgs:
a = commandArgs["Algorithm"]
if (a == "Mean Intensity"):
algorithm = omero.constants.projection.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 "Scalebar_Colour" in commandArgs:
if commandArgs["Scalebar_Colour"] in OVERLAY_COLOURS:
r,g,b,a = OVERLAY_COLOURS[commandArgs["Scalebar_Colour"]]
overlayColour = (r,g,b)
roiZoom = None
if "Roi_Zoom" in commandArgs:
roiZoom = float(commandArgs["Roi_Zoom"])
if roiZoom == 0:
roiZoom = None
maxColumns = None
if "Max_Columns" in commandArgs:
maxColumns = commandArgs["Max_Columns"]
showRoiDuration = False
if "Show_Roi_Duration" in commandArgs:
showRoiDuration = commandArgs["Show_Roi_Duration"]
roiLabel = "FigureROI"
if "Roi_Selection_Label" in commandArgs:
roiLabel = commandArgs["Roi_Selection_Label"]
spacer = (width/50) + 2
fig = getSplitView(session, imageIds, pixelIds, mergedIndexes,
mergedColours, width, height, imageLabels, spacer, algorithm, stepping, scalebar, overlayColour, roiZoom,
maxColumns, showRoiDuration, roiLabel)
#fig.show() # bug-fixing only
log("")
figLegend = "\n".join(logStrings)
#print figLegend # bug fixing only
format = JPEG
if "Format" in commandArgs:
if commandArgs["Format"] == "PNG":
format = PNG
output = "movieROIFigure"
if "Figure_Name" in commandArgs:
output = str(commandArgs["Figure_Name"])
if format == PNG:
output = output + ".png"
fig.save(output, "PNG")
else:
output = output + ".jpg"
fig.save(output)
# 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)
fileAnnotation = scriptUtil.uploadAndAttachFile(queryService, updateService, rawFileStore, omeroImage, output, format, figLegend)
return (fileAnnotation, omeroImage)
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
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()
iId = image.getId()
imageDate = image.getAcquisitionDate()
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))
# the channels in the combined image,
if "Merged_Channels" in commandArgs:
# convert to 0-based
mergedIndexes = [c - 1 for c in commandArgs["Merged_Channels"]]
else:
mergedIndexes = range(sizeC) # show all
mergedIndexes.reverse()
# if no colours added, use existing rendering settings.
mergedColours = {}
# Actually, nicer to always use existing rendering settings.
# if "Merged_Colours" in commandArgs:
# for i, c in enumerate(commandArgs["Merged_Colours"]):
# if c in COLOURS:
# mergedColours[i] = COLOURS[c]
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 "Scalebar_Colour" in commandArgs:
if commandArgs["Scalebar_Colour"] in OVERLAY_COLOURS:
r, g, b, a = OVERLAY_COLOURS[commandArgs["Scalebar_Colour"]]
overlayColour = (r, g, b)
roiZoom = None
if "Roi_Zoom" in commandArgs:
roiZoom = float(commandArgs["Roi_Zoom"])
if roiZoom == 0:
roiZoom = None
maxColumns = None
if "Max_Columns" in commandArgs:
maxColumns = commandArgs["Max_Columns"]
showRoiDuration = False
if "Show_ROI_Duration" in commandArgs:
showRoiDuration = commandArgs["Show_ROI_Duration"]
roiLabel = "FigureROI"
if "Roi_Selection_Label" in commandArgs:
roiLabel = commandArgs["Roi_Selection_Label"]
spacer = (width / 50) + 2
print "showRoiDuration", showRoiDuration
fig = getSplitView(conn, imageIds, pixelIds, mergedIndexes, mergedColours,
width, height, imageLabels, spacer, algorithm, stepping,
scalebar, overlayColour, roiZoom, maxColumns,
showRoiDuration, roiLabel)
# fig.show() # bug-fixing only
if fig is None:
logMessage = "No figure produced"
log("\n" + logMessage)
message += logMessage
return None, message
figLegend = "\n".join(logStrings)
# print figLegend # bug fixing only
format = commandArgs["Format"]
figureName = "movieROIFigure"
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/Movie_ROI_Figure"
fileAnnotation, faMessage = scriptUtil.createLinkFileAnnotation(
conn,
output,
omeroImage,
output="Movie ROI figure",
mimetype=mimetype,
ns=namespace,
desc=figLegend,
origFilePathAndName=figureName)
message += faMessage
return fileAnnotation, message
def movieFigure(conn, commandArgs):
"""
Makes the figure using the parameters in @commandArgs, attaches the figure to the
parent Project/Dataset, and returns the file-annotation ID
@param session The OMERO session
@param commandArgs Map of parameters for the script
@ returns Returns the id of the originalFileLink child. (ID object, not value)
"""
log("Movie figure created by OMERO on %s" % date.today())
log("")
timeLabels = {"SECS_MILLIS": "seconds",
"SECS": "seconds",
"MINS": "minutes",
"HOURS": "hours",
"MINS_SECS": "mins:secs",
"HOURS_MINS": "hours:mins"}
timeUnits = "SECS"
if "timeUnits" in commandArgs:
timeUnits = commandArgs["timeUnits"]
if timeUnits not in timeLabels.keys():
timeUnits = "SECS"
log("Time units are in %s" % timeLabels[timeUnits])
pixelIds = []
imageIds = []
imageLabels = []
message = "" # message to be returned to the client
# 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 "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
# Get the images
images, logMessage = scriptUtil.getObjects(conn, commandArgs)
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()
iId = image.getId()
imageDate = image.getAcquisitionDate()
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()
sizeT = omeroImage.getSizeT()
tIndexes = []
if "T_Indexes" in commandArgs:
for t in commandArgs["T_Indexes"]:
tIndexes.append(t)
print "T_Indexes", tIndexes
if len(tIndexes) == 0: # if no t-indexes given, use all t-indices
tIndexes = range(sizeT)
zStart = -1
zEnd = -1
if "Z_Start" in commandArgs:
zStart = commandArgs["Z_Start"]
if "Z_End" in commandArgs:
zEnd = commandArgs["Z_End"]
width = sizeX
if "Width" in commandArgs:
width = commandArgs["Width"]
height = sizeY
if "Height" in commandArgs:
height = commandArgs["Height"]
spacer = (width/25) + 2
algorithm = omero.constants.projection.ProjectionType.MAXIMUMINTENSITY
if "Algorithm" in commandArgs:
a = commandArgs["Algorithm"]
if (a == "Mean Intensity"):
algorithm = omero.constants.projection.ProjectionType.MEANINTENSITY
stepping = 1
if "Stepping" in commandArgs:
s = commandArgs["Stepping"]
if (0 < s < sizeZ):
stepping = s
scalebar = None
if "Scalebar_Size" in commandArgs:
sb = commandArgs["Scalebar_Size"]
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 "Scalebar_Colour" in commandArgs:
r,g,b,a = OVERLAY_COLOURS[commandArgs["Scalebar_Colour"]]
overlayColour = (r,g,b)
figure = createMovieFigure(conn, pixelIds, tIndexes, zStart, zEnd, width, height, spacer,
algorithm, stepping, scalebar, overlayColour, timeUnits, imageLabels)
#figure.show()
log("")
figLegend = "\n".join(logLines)
#print figLegend # bug fixing only
format = JPEG
if "Format" in commandArgs:
if commandArgs["Format"] == "PNG":
format = PNG
output = "movieFigure"
if "Figure_Name" in commandArgs:
output = str(commandArgs["Figure_Name"])
if format == PNG:
output = output + ".png"
figure.save(output, "PNG")
mimetype = "image/png"
else:
output = output + ".jpg"
figure.save(output)
mimetype = "image/jpeg"
namespace = omero.constants.namespaces.NSCREATED+"/omero/figure_scripts/Movie_Figure"
fileAnnotation, faMessage = scriptUtil.createLinkFileAnnotation(conn, output, omeroImage,
output="Movie figure", mimetype=mimetype, ns=namespace, desc=figLegend)
message += faMessage
return fileAnnotation, message
def movieFigure(session, commandArgs):
"""
Makes the figure using the parameters in @commandArgs, attaches the figure to the
parent Project/Dataset, and returns the file-annotation ID
@param session The OMERO session
@param commandArgs Map of parameters for the script
@ returns Returns the id of the originalFileLink child. (ID object, not value)
"""
# create the services we're going to need.
metadataService = session.getMetadataService()
queryService = session.getQueryService()
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
containerService = session.getContainerService()
log("Movie figure created by OMERO on %s" % date.today())
log("")
timeLabels = {"SECS_MILLIS": "seconds",
"SECS": "seconds",
"MINS": "minutes",
"HOURS": "hours",
"MINS_SECS": "mins:secs",
"HOURS_MINS": "hours:mins"}
timeUnits = "SECS"
if "timeUnits" in commandArgs:
timeUnits = commandArgs["timeUnits"]
if timeUnits not in timeLabels.keys():
timeUnits = "SECS"
log("Time units are in %s" % timeLabels[timeUnits])
pixelIds = []
imageIds = []
imageLabels = []
imageNames = {}
omeroImage = None # this is set as the first image, to link figure to
# 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 "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
# process the list of images. If imageIds is not set, script can't run.
log("Image details:")
for idCount, imageId in enumerate(commandArgs["IDs"]):
iId = long(imageId.getValue())
image = containerService.getImages("Image", [iId], None)[0]
if image == None:
print "Image not found for ID:", iId
continue
imageIds.append(iId)
if idCount == 0:
omeroImage = image # remember the first image to attach figure to
pixelIds.append(image.getPrimaryPixels().getId().getValue())
imageNames[iId] = image.getName().getValue()
if len(imageIds) == 0:
print "No image IDs specified."
pdMap = figUtil.getDatasetsProjectsFromImages(queryService, imageIds) # a map of imageId : list of (project, dataset) names.
tagMap = figUtil.getTagsFromImages(metadataService, imageIds)
# Build a legend entry for each image
for iId in imageIds:
name = imageNames[iId]
imageDate = image.getAcquisitionDate().getValue()
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.
pixelsId = pixelIds[0]
pixels = queryService.get("Pixels", pixelsId)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
sizeC = pixels.getSizeC().getValue()
sizeT = pixels.getSizeT().getValue()
tIndexes = []
if "T_Indexes" in commandArgs:
for t in commandArgs["T_Indexes"]:
tIndexes.append(t.getValue())
print "T_Indexes", tIndexes
if len(tIndexes) == 0: # if no t-indexes given, use all t-indices
tIndexes = range(sizeT)
zStart = -1
zEnd = -1
if "Z_Start" in commandArgs:
zStart = commandArgs["Z_Start"]
if "Z_End" in commandArgs:
zEnd = commandArgs["Z_End"]
width = sizeX
if "Width" in commandArgs:
width = commandArgs["Width"]
height = sizeY
if "Height" in commandArgs:
height = commandArgs["Height"]
spacer = (width/25) + 2
algorithm = omero.constants.projection.ProjectionType.MAXIMUMINTENSITY
if "Algorithm" in commandArgs:
a = commandArgs["Algorithm"]
if (a == "Mean Intensity"):
algorithm = omero.constants.projection.ProjectionType.MEANINTENSITY
stepping = 1
if "Stepping" in commandArgs:
s = commandArgs["Stepping"]
if (0 < s < sizeZ):
stepping = s
scalebar = None
if "Scalebar_Size" in commandArgs:
sb = commandArgs["Scalebar_Size"]
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 "Scalebar_Colour" in commandArgs:
r,g,b,a = OVERLAY_COLOURS[commandArgs["Scalebar_Colour"]]
overlayColour = (r,g,b)
figure = createMovieFigure(session, pixelIds, tIndexes, zStart, zEnd, width, height, spacer,
algorithm, stepping, scalebar, overlayColour, timeUnits, imageLabels)
#figure.show()
log("")
figLegend = "\n".join(logLines)
#print figLegend # bug fixing only
format = JPEG
if "Format" in commandArgs:
if commandArgs["Format"] == "PNG":
format = PNG
output = "movieFigure"
if "Figure_Name" in commandArgs:
output = str(commandArgs["Figure_Name"])
if format == PNG:
output = output + ".png"
figure.save(output, "PNG")
else:
output = output + ".jpg"
figure.save(output)
fileAnnotation = scriptUtil.uploadAndAttachFile(queryService, updateService, rawFileStore, omeroImage, output, format, figLegend)
return (fileAnnotation, omeroImage)
