def set_rendersettings(conn, scriptParams):
updateService = conn.getUpdateService()
message = ""
# Get the object IDs
objs, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
# Return if all input screens are not found or excluded
if not objs:
return message
# Filter object IDs by permissions (future)
# IDs = [ob.getId() for ob in objs if ob.canLink()]
# if len(IDs) != len(objs):
# permIDs = [str(ob.getId()) for ob in objs if not ob.canLink()]
# message += "You do not have permission to change rendering settings on images in"\
# " screen(s): %s." % ",".join(permIDs)
# if not IDs:
# return None, message
for ob in objs:
set_rendersettings_screen(conn, scriptParams, ob)
return message
def processImages(client, scriptParams):
message = ''
# for params with default values, we can get the value directly
dataType = scriptParams['Data_Type']
ids = scriptParams['IDs']
# Get the datasets
conn = BlitzGateway(client_obj = client)
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return message
datasets = conn.getObjects(dataType, ids)
good, chNames, msg = checkChannels(datasets)
message += msg
if not good:
raise omero.ServerError(
'Channel check failed, ' +
'all images must have the same channels: %s' % message)
return message
def processImages(client, scriptParams):
message = ''
dataType = scriptParams['Data_Type']
ids = scriptParams['IDs']
ftset = scriptParams['Feature_set']
try:
conn = omero.gateway.BlitzGateway(client_obj=client)
# Get the objects
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return message
if dataType not in supportedDataTypes:
m = 'Invalid datatype: %s\n' % datatype
sys.stderr.write(m)
return message + m
images = imageGenerator(objects)
for image in images:
message += 'Processing image id:%d\n' % image.getId()
m = deleteImageFeatures(conn, client, image, ftset, field=True)
message += m
except:
print message
raise
return message
def processImages(client, scriptParams):
message = ''
# for params with default values, we can get the value directly
dataType = scriptParams['Data_Type']
ids = scriptParams['IDs']
contextName = scriptParams['Context_Name']
tableName = '/Wndcharm/' + contextName + '/SmallFeatureSet.h5'
message += 'tableName:' + tableName + '\n'
ftb = WndcharmStorage.FeatureTable(client, tableName)
try:
# Get the datasets
objects, logMessage = script_utils.getObjects(ftb.conn, scriptParams)
message += logMessage
if not objects:
return message
datasets = WndcharmStorage.datasetGenerator(ftb.conn, dataType, ids)
for ds in datasets:
message += 'Processing dataset id:%d\n' % ds.getId()
msg = countCompleted(ftb, ds)
message += msg
except:
print message
raise
finally:
ftb.close()
return message
def processImages(client, conn, scriptParams):
"""
Process the script params to make a list of channel_offsets, then iterate
through the images creating a new image from each with the specified
channel offsets
"""
message = ""
# Get the images
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, None, message
# Concatenate images from datasets
if scriptParams["Data_Type"] == "Image":
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
pixelsService = conn.getPixelsService()
renderingService = conn.getRenderingSettingsService()
# Get the channel offsets
for image in images:
metadata = dict(image.loadOriginalMetadata()[1])
pi = image.getPrimaryPixels()
pixelsService.setChannelGlobalMinMax(pi.getId(), 0, metadata['Min'], metadata['Max'], conn.SERVICE_OPTS)
renderingService.setOriginalSettingsInImage(image.getId())
return message
def saveImages(conn, scriptParams):
dataType = scriptParams['Data_Type']
formatType = scriptParams['Format']
dirpath='tmp' #Use Root tmp dir so gets cleaned up
unique_folder = 'Exportfiles' + str(time.time()) #random
imagepath = path.join(dirpath, unique_folder)
imagepath = path.sep + imagepath + path.sep
print "Imagepath=", imagepath
# Get the images or datasets
message = ""
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
parent = objects[0] #??
if not objects:
return None, message
if dataType == 'Dataset':
images = []
for ds in objects:
images.extend(list(ds.listChildren()))
if not images:
message += "No image found in dataset(s)"
return None, message
else:
images = objects
imageIds = [i.getId() for i in images]
print "Selected %d images for processing" % len(imageIds)
#Create download folder
if len(imageIds) > 0:
mkdir(imagepath)
#chdir(imagepath)
imagefilenames =[]
for iId in imageIds:
img = conn.getObject("Image", iId)
if img is not None:
z = img.getSizeZ() / 2
t = 0
saveimage = img.renderImage(z,t) # returns PIL Image jpeg
imageFilename = getImageName(img, formatType.lower(), imagepath)
imagefilenames.append(imageFilename)
message += saveAs(saveimage,imageFilename,formatType)
#zip output files
zipfilename = path.join(dirpath, unique_folder)
zipfilename = path.sep + zipfilename + ".zip"
message += createZipFile(zipfilename, imagefilenames)
mimetype = 'application/zip'
outputDisplayName = "Image export zip"
namespace = NSCREATED + "/QBI/Utils/ExportImage"
fileAnnotation, annMessage = script_utils.createLinkFileAnnotation(
conn, zipfilename, parent, output=outputDisplayName, ns=namespace,
mimetype=mimetype)
message += annMessage
return fileAnnotation, message
def features(conn, scriptParams, uuid):
pass
cli = omero.cli.CLI()
cli.loadplugins()
feature_type = scriptParams["feature_type"]
CP_pipe_params = scriptParams["CP_params"]
images, logMessage = script_utils.getObjects(conn, scriptParams)
if not images:
return None, None, logMessage
imageIds = [i.getId() for i in images]
for iId in imageIds:
image = conn.getObject("Image", iId)
dataset = image.getParent().getId()
image_dir = os.path.join(OMERO_FS, image.getFileset().listFiles()[0].getPath()) # Given a single file per fileset
image_name = image.getFileset().listFiles()[0].getName()
image_path = os.path.join(image_dir, image_name)
# CellProfiler context manager
# CP_PATH='/project/projectdirs/ngbi/resources/CP2'
# my_image_directory='/project/projectdirs/ngbi/jobs/CP_pipes/test/test_in'
# my_output_directory='/project/projectdirs/ngbi/jobs/CP_pipes/test/test_out'
# # my_pipe='/project/projectdirs/ngbi/jobs/CP_pipes/pipeline.h5'
# my_pipe='/project/projectdirs/ngbi/jobs/CP_pipes/pipeline.cppipe'
CP_args = (CP_PATH, image_path, obj_mask_path, CP_pipe)
CP_process_str = "python %s/CellProfiler.py -c -r -i %s -o obj_mask_path -p %s" % CP_args # using sgnworker
new_dId, new_dObj = dataset_gen(conn, "datasetname_name")
# read obj_mask_path and split into objects
for image_object in object_list:
# crop image
cmd = "import -s sgn02 -d %s -n %s -k %s %s" % (new_dId, image_object.getName(), key, image)
u=cmd.split()
cli.invoke(u,strict=True)
new_iId, new_iObj = image_gen(conn, image_object.getName())
link2project(conn, new_dObj, new_iObj)
# save image and assotiate with iId
# save object as image using omeroFS
# create annotation link etc
# calculate feature of object
# picke feature and store
new_pId, new_pObj = project_gen(conn, image_object.getName())
link2project(conn, new_pObj, new_dObj)
addTag(conn, new_dId, tags, chans)
def processImages(client, scriptParams):
message = ''
# for params with default values, we can get the value directly
dataType = scriptParams['Data_Type']
ids = scriptParams['IDs']
contextName = scriptParams['Context_Name']
newOnly = scriptParams['New_Images_Only']
tableName = '/Wndcharm/' + contextName + '/SmallFeatureSet.h5'
message += 'tableName:' + tableName + '\n'
ftb = WndcharmStorage.FeatureTable(client, tableName)
try:
nimages = 0
# Get the datasets
objects, logMessage = script_utils.getObjects(ftb.conn, scriptParams)
message += logMessage
if not objects:
return message
datasets = list(WndcharmStorage.datasetGenerator(
ftb.conn, dataType, ids))
good, chNames, msg = checkChannels(datasets)
message += msg
if not good:
raise omero.ServerError(
'Channel check failed, ' +
'all images must have the same channels: %s' % message)
for d in datasets:
message += 'Processing dataset id:%d\n' % d.getId()
for image in d.listChildren():
message += 'Processing image id:%d\n' % image.getId()
msg = extractFeatures(ftb, d, newOnly, chNames, im=image)
message += msg + '\n'
except:
print message
raise
finally:
ftb.close()
return message
def processImages(client, conn, scriptParams):
"""
Process the script params to make a list of channel_offsets, then iterate
through the images creating a new image from each with the specified
channel offsets
"""
message = ""
# Get the images
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, None, message
# Concatenate images from datasets
if scriptParams["Data_Type"] == "Image":
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
pixelsService = conn.getPixelsService()
renderingService = conn.getRenderingSettingsService()
# Get the channel offsets
for image in images:
min, max = 0, 65535
for ann in image.listAnnotations():
if isinstance(ann, omero.gateway.MapAnnotationWrapper):
kvs = ann.getValue()
for k, v in kvs:
if k == "MinSampleValue":
min = v
elif k == "MaxSampleValue":
max = v
pi = image.getPrimaryPixels()
pixelsService.setChannelGlobalMinMax(pi.getId(), 0, int(min), int(max),
conn.SERVICE_OPTS)
renderingService.setOriginalSettingsInImage(image.getId())
return message
def processImages(client, scriptParams):
message = ''
dataType = scriptParams['Data_Type']
ids = scriptParams['IDs']
ftset = scriptParams['Feature_set']
try:
conn = omero.gateway.BlitzGateway(client_obj=client)
# Get the objects
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return message
if dataType == 'Image':
for image in objects:
message += 'Processing image id:%d\n' % image.getId()
m = deleteImageFeatures(conn, client, image, ftset, field=True)
message += m
else:
if dataType == 'Project':
datasets = [proj.listChildren() for proj in objects]
datasets = itertools.chain.from_iterable(datasets)
else:
datasets = objects
for d in datasets:
message += 'Processing dataset id:%d\n' % d.getId()
for image in d.listChildren():
message += 'Processing image id:%d\n' % image.getId()
m = deleteImageFeatures(
conn, client, image, ftset, field=True)
message += m
except:
print message
raise
return message
def set_rendersettings(conn, scriptParams):
updateService = conn.getUpdateService()
message = ""
# Get the object IDs
objs, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
# Return if all input containers are not found or excluded
if not objs:
return message
# Filter object IDs by permissions (future)
# IDs = [ob.getId() for ob in objs if ob.canLink()]
# if len(IDs) != len(objs):
# permIDs = [str(ob.getId()) for ob in objs if not ob.canLink()]
# message += "You do not have permission to change rendering settings on images in"\
# " screen(s): %s." % ",".join(permIDs)
# if not IDs:
# return None, message
for ob in objs:
dataType = scriptParams["Data_Type"]
if (dataType == "Screen"):
print "Setting rendering settings for Screen: %d %s" \
% (ob.getId(), ob.getName())
# sort plates by name (and possible filter by name in future)
plates = list(ob.listChildren())
for plate in plates:
set_rendersettings_plate(conn, scriptParams, plate)
elif (dataType == "Plate"):
set_rendersettings_plate(conn, scriptParams, ob)
else:
message += "Invalid Data_Type"
return message
def processImages(client, conn, scriptParams):
"""
Process the script params t, then iterate
through the images
"""
message = ""
# Get the images
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, None, message
# Concatenate images from datasets
if scriptParams["Data_Type"] == "Image":
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
updateService = conn.getUpdateService()
pixSize = omero.model.LengthI(3.81,
omero.model.enums.UnitsLength.NANOMETER)
# Get the channel offsets
for image in images:
metadata = dict(image.loadOriginalMetadata()[1])
pi = image.getPrimaryPixels()
pixels = pi._obj
pixels.setPhysicalSizeX(pixSize)
pixels.setPhysicalSizeY(pixSize)
updateService.saveObject(pixels)
return message
def processObjects(client, scriptParams):
message = ''
# for params with default values, we can get the value directly
dataType = scriptParams['Data_Type']
ids = scriptParams['IDs']
rmTables = scriptParams['Remove_tables']
rmComments = scriptParams['Remove_comments']
unlinkTags = scriptParams['Untag_images']
rmTagsets = scriptParams['Remove_tagsets']
# Get the images or datasets
conn = BlitzGateway(client_obj=client)
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, message
for o in objects:
message += removeAnnotations(
conn, o, rmTables, rmComments, unlinkTags, rmTagsets)
return 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))
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()
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_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)
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 processImages(conn, scriptParams):
fileAnns = []
message = ""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [
image for image in images
if image.getROICount(["Polyline", "Line"]) > 0
]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
for image in images:
print "\nAnalysing Image: %s ID: %s" \
% (image.getName(), image.getId())
if image.getSizeT() > 1:
message += "%s ID: %s appears to be a time-lapse Image," \
" not a kymograph." % (image.getName(), image.getId())
continue
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
secsPerPixelY = image.getPixelSizeY()
micronsPerPixelX = image.getPixelSizeX()
if secsPerPixelY and micronsPerPixelX:
micronsPerSec = micronsPerPixelX / secsPerPixelY
else:
micronsPerSec = None
# for each line or polyline, create a row in csv table: y(t), x,
# dy(dt), dx, x/t (line), x/t (average)
colNames = "\nt_start (pixels), x_start (pixels), t_end (pixels)," \
" x_end (pixels), dt (pixels), dx (pixels), x/t, average x/t," \
" speed(um/sec)"
tableData = ""
for roi in result.rois:
for s in roi.copyShapes():
if type(s) == omero.model.LineI:
tableData += "\nLine"
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
dx = abs(x1 - x2)
dy = abs(y1 - y2)
dxPerY = float(dx) / dy
tableData += "\n"
tableData += ",".join([
str(x)
for x in (y1, x1, y2, x2, dy, dx, dxPerY, dxPerY, "")
])
if micronsPerSec:
speed = dxPerY * micronsPerSec
tableData += "%s" % speed
elif type(s) == omero.model.PolylineI:
tableData += "\nPolyline"
points = pointsStringToXYlist(s.getPoints().getValue())
xStart, yStart = points[0]
for i in range(1, len(points)):
x1, y1 = points[i - 1]
x2, y2 = points[i]
dx = abs(x1 - x2)
dy = abs(y1 - y2)
dxPerY = float(dx) / dy
avXperY = abs(float(x2 - xStart) / (y2 - yStart))
tableData += "\n"
tableData += ",".join([
str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY,
avXperY, "")
])
if micronsPerSec:
speed = dxPerY * micronsPerSec
tableData += "%s" % speed
# write table data to csv...
if len(tableData) > 0:
tableString = "secsPerPixelY: %s" % secsPerPixelY
tableString += '\nmicronsPerPixelX: %s' % micronsPerPixelX
tableString += "\nmicronsPerSec: %s" % micronsPerSec
tableString += "\n"
tableString += colNames
tableString += tableData
print tableString
csvFileName = 'kymograph_velocities_%s.csv' % image.getId()
csvFile = open(csvFileName, 'w')
try:
csvFile.write(tableString)
finally:
csvFile.close()
fileAnn, faMessage = scriptUtil.createLinkFileAnnotation(
conn,
csvFileName,
image,
output="Line Plot csv (Excel) file",
mimetype="text/csv",
desc=None)
print fileAnn, faMessage
if fileAnn:
fileAnns.append(fileAnn)
else:
print "Found NO lines or polylines to analyse for Image"
if not fileAnns:
faMessage = "No Analysis files created. See 'Info' or 'Error'" \
" for more details"
elif len(fileAnns) > 1:
faMessage = "Created %s csv (Excel) files" % len(fileAnns)
message += faMessage
return fileAnns, message
def makeThumbnailFigure(conn, scriptParams):
"""
Makes the figure using the parameters in @scriptParams, attaches the
figure to the parent Project/Dataset, and returns the file-annotation ID
@ returns Returns the id of the originalFileLink child. (ID object,
not value)
"""
log("Thumbnail figure created by OMERO")
log("")
message = ""
# Get the objects (images or datasets)
objects, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, message
# Get parent
parent = None
if "Parent_ID" in scriptParams and len(scriptParams["IDs"]) > 1:
if scriptParams["Data_Type"] == "Image":
parent = conn.getObject("Dataset", scriptParams["Parent_ID"])
else:
parent = conn.getObject("Project", scriptParams["Parent_ID"])
if parent is None:
parent = objects[0] # Attach figure to the first object
parentClass = parent.OMERO_CLASS
log("Figure will be linked to %s%s: %s"
% (parentClass[0].lower(), parentClass[1:], parent.getName()))
tagIds = []
if "Tag_IDs" in scriptParams:
tagIds = scriptParams['Tag_IDs']
if len(tagIds) == 0:
tagIds = None
showUntagged = False
if (tagIds):
showUntagged = scriptParams["Show_Untagged_Images"]
thumbSize = scriptParams["Thumbnail_Size"]
maxColumns = scriptParams["Max_Columns"]
figHeight = 0
figWidth = 0
dsCanvases = []
if scriptParams["Data_Type"] == "Dataset":
for dataset in objects:
log("Dataset: %s ID: %d"
% (dataset.getName(), dataset.getId()))
images = list(dataset.listChildren())
dsCanvas = paintDatasetCanvas(
conn, images, dataset.getName(), tagIds, showUntagged,
length=thumbSize, colCount=maxColumns)
if dsCanvas is None:
continue
dsCanvases.append(dsCanvas)
figHeight += dsCanvas.size[1]
figWidth = max(figWidth, dsCanvas.size[0])
else:
imageCanvas = paintDatasetCanvas(
conn, objects, "", tagIds,
showUntagged, length=thumbSize, colCount=maxColumns)
dsCanvases.append(imageCanvas)
figHeight += imageCanvas.size[1]
figWidth = max(figWidth, imageCanvas.size[0])
if len(dsCanvases) == 0:
message += "No figure created"
return None, message
figure = Image.new("RGB", (figWidth, figHeight), WHITE)
y = 0
for ds in dsCanvases:
imgUtil.pasteImage(ds, figure, 0, y)
y += ds.size[1]
log("")
figLegend = "\n".join(logLines)
format = scriptParams["Format"]
figureName = scriptParams["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/Thumbnail_Figure"
fileAnnotation, faMessage = scriptUtil.createLinkFileAnnotation(
conn, output, parent, output="Thumbnail figure", mimetype=mimetype,
ns=namespace, desc=figLegend, origFilePathAndName=figureName)
message += faMessage
return fileAnnotation, message
def processImages(conn, scriptParams):
"""
Process the script params to make a list of channel_offsets, then iterate
through the images creating a new image from each with the specified
channel offsets
"""
message = ""
# Get the images
images, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, None, message
imageIds = [i.getId() for i in images]
# Get the channel offsets
channel_offsets = []
for i in range(1, 5):
pName = "Channel_%s" % i
if scriptParams[pName]:
index = i - 1 # UI channel index is 1-based - we want 0-based
x = "Channel%s_X_shift" % i in scriptParams and scriptParams["Channel%s_X_shift" % i] or 0
y = "Channel%s_Y_shift" % i in scriptParams and scriptParams["Channel%s_Y_shift" % i] or 0
z = "Channel%s_Z_shift" % i in scriptParams and scriptParams["Channel%s_Z_shift" % i] or 0
channel_offsets.append({"index": index, "x": x, "y": y, "z": z})
print channel_offsets
dataset = None
if "New_Dataset_Name" in scriptParams:
# create new Dataset...
newDatasetName = scriptParams["New_Dataset_Name"]
dataset = omero.gateway.DatasetWrapper(conn, obj=omero.model.DatasetI())
dataset.setName(rstring(newDatasetName))
dataset.save()
# add to parent Project
parentDs = images[0].getParent()
project = parentDs is not None and parentDs.getParent() or None
if project is not None and project.canLink():
link = omero.model.ProjectDatasetLinkI()
link.parent = omero.model.ProjectI(project.getId(), False)
link.child = omero.model.DatasetI(dataset.getId(), False)
conn.getUpdateService().saveAndReturnObject(link)
# need to handle Datasets eventually - Just do images for now
newImages = []
links = []
for iId in imageIds:
newImg, link = newImageWithChannelOffsets(conn, iId, channel_offsets, dataset)
if newImg is not None:
newImages.append(newImg)
if link is not None:
links.append(link)
if not newImages:
message += "No image created."
else:
if len(newImages) == 1:
if not link:
linkMessage = " but could not be attached"
else:
linkMessage = ""
message += "New image created%s: %s." % (linkMessage, newImages[0].getName())
elif len(newImages) > 1:
message += "%s new images created" % len(newImages)
if not len(links) == len(newImages):
message += " but some of them could not be attached."
else:
message += "."
return newImages, dataset, message
def makeImagesFromRois(conn, parameterMap):
"""
Processes the list of Image_IDs, either making a new image-stack or a new dataset from each image,
with new image planes coming from the regions in Rectangular ROIs on the parent images.
"""
dataType = parameterMap["Data_Type"]
ids = parameterMap["IDs"]
imageStack = parameterMap['Make_Image_Stack']
message =""
# Get the images
objects, logMessage = script_utils.getObjects(conn, parameterMap)
message += logMessage
if not objects:
return None, message
# Concatenate images from datasets
if dataType == 'Image':
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
# 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
imageIds = [i.getId() for i in images]
newImages = []
newDatasets = []
links = []
for iId in imageIds:
newImage, newDataset, link = processImage(conn, iId, parameterMap)
if newImage is not None:
if isinstance(newImage,list):
newImages.extend(newImage)
else:
newImages.append(newImage)
if newDataset is not None:
newDatasets.append(newDataset)
if link is not None:
if isinstance(link,list):
links.extend(link)
else:
links.append(link)
if newImages:
if len(newImages)>1:
message += "Created %s new images" % len(newImages)
else:
message += "Created a new image"
else:
message += "No image created"
if newDatasets:
if len(newDatasets)>1:
message += " and %s new datasets" % len(newDatasets)
else:
message += " and a new dataset"
if not links or not len(links) == len(newImages):
message += " but some images could not be attached"
message += "."
robj = (len(newImages) > 0) and newImages[0]._obj or None
return robj, message
def batchImageExport(conn, scriptParams):
# for params with default values, we can get the value directly
splitCs = scriptParams["Export_Individual_Channels"]
mergedCs = scriptParams["Export_Merged_Image"]
greyscale = scriptParams["Individual_Channels_Grey"]
dataType = scriptParams["Data_Type"]
ids = scriptParams["IDs"]
folder_name = scriptParams["Folder_Name"]
format = scriptParams["Format"]
projectZ = "Choose_Z_Section" in scriptParams and scriptParams[
"Choose_Z_Section"] == 'Max projection'
if (not splitCs) and (not mergedCs):
log("Not chosen to save Individual Channels OR Merged Image")
return
# check if we have these params
channelNames = []
if "Channel_Names" in scriptParams:
channelNames = scriptParams["Channel_Names"]
imgWidth = None
if "Image_Width" in scriptParams:
imgWidth = scriptParams["Image_Width"]
# functions used below for each imaage.
def getZrange(sizeZ, scriptParams):
zRange = None
if "Choose_Z_Section" in scriptParams:
zChoice = scriptParams["Choose_Z_Section"]
# NB: all Z indices in this script are 1-based
if zChoice == 'ALL Z planes':
zRange = (1, sizeZ + 1)
elif "OR_specify_Z_index" in scriptParams:
zIndex = scriptParams["OR_specify_Z_index"]
zIndex = min(zIndex, sizeZ)
zRange = (zIndex, )
elif "OR_specify_Z_start_AND..." in scriptParams and "...specify_Z_end" in scriptParams:
start = scriptParams["OR_specify_Z_start_AND..."]
start = min(start, sizeZ)
end = scriptParams["...specify_Z_end"]
end = min(end, sizeZ)
zStart = min(start,
end) # in case user got zStart and zEnd mixed up
zEnd = max(start, end)
if zStart == zEnd:
zRange = (zStart, )
else:
zRange = (zStart, zEnd + 1)
return zRange
def getTrange(sizeT, scriptParams):
tRange = None
if "Choose_T_Section" in scriptParams:
tChoice = scriptParams["Choose_T_Section"]
# NB: all T indices in this script are 1-based
if tChoice == 'ALL T planes':
tRange = (1, sizeT + 1)
elif "OR_specify_T_index" in scriptParams:
tIndex = scriptParams["OR_specify_T_index"]
tIndex = min(tIndex, sizeT)
tRange = (tIndex, )
elif "OR_specify_T_start_AND..." in scriptParams and "...specify_T_end" in scriptParams:
start = scriptParams["OR_specify_T_start_AND..."]
start = min(start, sizeT)
end = scriptParams["...specify_T_end"]
end = min(end, sizeT)
tStart = min(start,
end) # in case user got zStart and zEnd mixed up
tEnd = max(start, end)
if tStart == tEnd:
tRange = (tStart, )
else:
tRange = (tStart, tEnd + 1)
return tRange
# Get the images or datasets
message = ""
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, message
# Attach figure to the first image
parent = objects[0]
if dataType == 'Dataset':
images = []
for ds in objects:
images.extend(list(ds.listChildren()))
if not images:
message += "No image found in dataset(s)"
return None, message
else:
images = objects
log("Processing %s images" % len(images))
# somewhere to put images
curr_dir = os.getcwd()
exp_dir = os.path.join(curr_dir, folder_name)
try:
os.mkdir(exp_dir)
except:
pass
# do the saving to disk
if format == 'OME-TIFF':
for img in images:
log("Exporting image as OME-TIFF: %s" % img.getName())
saveAsOmeTiff(conn, img, folder_name)
else:
for img in images:
log("\n----------- Saving planes from image: '%s' ------------" %
img.getName())
sizeC = img.getSizeC()
sizeZ = img.getSizeZ()
sizeT = img.getSizeT()
zRange = getZrange(sizeZ, scriptParams)
tRange = getTrange(sizeT, scriptParams)
log("Using:")
if zRange is None: log(" Z-index: Last-viewed")
elif len(zRange) == 1: log(" Z-index: %d" % zRange[0])
else: log(" Z-range: %s-%s" % (zRange[0], zRange[1] - 1))
if projectZ: log(" Z-projection: ON")
if tRange is None: log(" T-index: Last-viewed")
elif len(tRange) == 1: log(" T-index: %d" % tRange[0])
else: log(" T-range: %s-%s" % (tRange[0], tRange[1] - 1))
log(" Format: %s" % format)
if imgWidth is None: log(" Image Width: no resize")
else: log(" Image Width: %s" % imgWidth)
log(" Greyscale: %s" % greyscale)
log("Channel Rendering Settings:")
for ch in img.getChannels():
log(" %s: %d-%d" %
(ch.getLabel(), ch.getWindowStart(), ch.getWindowEnd()))
savePlanesForImage(conn,
img,
sizeC,
splitCs,
mergedCs,
channelNames,
zRange,
tRange,
greyscale,
imgWidth,
projectZ=projectZ,
format=format,
folder_name=folder_name)
# write log for exported images (not needed for ome-tiff)
logFile = open(os.path.join(exp_dir, 'Batch_Image_Export.txt'), 'w')
try:
for s in logStrings:
logFile.write(s)
logFile.write("\n")
finally:
logFile.close()
# zip everything up (unless we've only got a single ome-tiff)
if format == 'OME-TIFF' and len(os.listdir(exp_dir)) == 1:
export_file = os.path.join(folder_name, os.listdir(exp_dir)[0])
mimetype = 'image/tiff'
else:
export_file = "%s.zip" % folder_name
compress(export_file, folder_name)
mimetype = 'application/zip'
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)
message += annMessage
return fileAnnotation, message
def weka_segmentation(conn, scriptParams, uuid):
model = scriptParams["Segmentation_model"]
model_path=model
user = conn.getUser()
user = user.getName()
print("user: %s" % (user))
print(model_path)
images, logMessage = script_utils.getObjects(conn, scriptParams)
if not images:
return None, None, logMessage
imageIds = [i.getId() for i in images]
for iId in imageIds:
tmpdir_stack = tempfile.mkdtemp(dir=cache_dir)
tmpdir_out = tempfile.mkdtemp(dir=cache_dir)
image = conn.getObject("Image", iId)
dataset = image.getParent().getId()
sizeZ = image.getSizeZ()
print(sizeZ)
# job_liner=[]
# all_jobs = open("%s.job" % (os.path.join(cache_dir, tmpdir_out.split('/')[-1])), 'w+')
image_dir = os.path.join(OMERO_FS, image.getFileset().listFiles()[0].getPath())
image_name = image.getFileset().listFiles()[0].getName()
image_path = os.path.join(image_dir, image_name)
ijmacro_args = "%s:%s/:%s" % (image_path, tmpdir_out, model_path)
memory_ij=int(math.ceil((2.00*sizeZ)))
all_jobs = open("%s.job" % (os.path.join(cache_dir, tmpdir_out.split('/')[-1])), 'w+')
job_liner="%s -a %s -Xmx%sg -- -macro %s %s -batch" % (XVFBRUN_PATH, IMAGEJ_PATH, memory_ij, MACRO_PATH2, ijmacro_args)
all_jobs.writelines(job_liner)
print(job_liner)
system = scriptParams["System"]
wtime = scriptParams["Wall_time"]
pmem = scriptParams["Private_memory"]
bigmem = scriptParams["Big_memory_nodes"]
nodes = scriptParams["Nodes"]
ppn = scriptParams["PPN"]
if bigmem:
print("big memory nodes flag")
else:
# ijmacro_args = "%s/:%s/:%s" % (tmpdir_stack, tmpdir_out, model_path)
pbs_file = "%s.pbs" % (os.path.join(cache_dir, tmpdir_out.split('/')[-1]))
nodes = int(math.ceil(((2.00*sizeZ)+0.15*(2.00*sizeZ))/48))
stack_args = "%s/" % (tmpdir_out)
qsub_cmd = ". %s %s %s %s %s %s %s %s %s %s %s %s > %s" % (PBS_GEN, user, dataset, image_name, uuid, MACRO_PATH, stack_args, tmpdir_out, wtime, pmem, all_jobs.name, nodes, pbs_file)
# $ ./jobgen.sh <user> <dataset> <name> <uuid> <ijmacro> <ijmacro args> <outpath> <wtime> <pmem> <all_jobs> <no_nodes> > job.pbs
print(qsub_cmd)
os.system(qsub_cmd)
enableKeepAlive_time = (36*60*60)
conn.c.enableKeepAlive(enableKeepAlive_time)
os.system("ssh %s '/usr/syscom/opt/torque/4.2.6/bin/qsub %s'" % (system, pbs_file))
def runAsScript():
dataTypes = [rstring('Image')]
models_path="/project/projectdirs/ngbi/jobs/ij_macros/classifiers"
systems=['carver', 'sgnworker']
# modelPath = []
segmentationModel = []
for file in os.listdir(models_path):
if file.endswith(".model"):
segmentationModel.append(str(os.path.join(models_path,file)))
# segmentationModel.append(file)
# Include files metadata information; link to a web application
# segmentationModel = ['Desulfovibrio RCH1', 'Geobacter', 'Myxococcus Xanthus1', 'Myxococcus Xanthus2']
client = scripts.client('weka_serial.py', """Segment a dataset using Random Forest and a known classifier""",
scripts.String("Data_Type", optional=False, grouping="1",
description="Pick Images by 'Image' ID or by the ID of their 'Dataset'", values=dataTypes, default="Image"),
scripts.List("IDs", optional=False, grouping="1.1",
description="List of Dataset IDs or Image IDs to process.").ofType(rlong(0)),
scripts.String("Segmentation_model", optional=False, grouping="2",
description="Select model", values=segmentationModel, default=segmentationModel[0]),
scripts.String("System", optional=False, grouping="3",
description="Select the system", values=systems, default=systems[0]),
scripts.String("Wall_time", grouping="3.1",
description="Wall time", default='0:30:00'),
scripts.String("Private_memory", grouping="3.2",
description="Private memory", default='4GB'),
scripts.Bool("Big_memory_nodes", grouping="3.2.1",
description="Big memory nodes", default='False'),
scripts.String("Nodes", grouping="3.3",
description="Nodes", default='1'),
scripts.String("PPN", grouping="3.4",
description="PPN", default='5'),
version = "0",
authors = ["Joaquin Correa", "OSP Team"],
institutions = ["NERSC"],
contact = "*****@*****.**",
)
try:
session = client.getSession();
# print("session key: %s" % (session)
# process the list of args above.
scriptParams = {}
for key in client.getInputKeys():
if client.getInput(key):
scriptParams[key] = client.getInput(key, unwrap=True)
print scriptParams
print("key: %s" % (key))
# print("session key: %s" % (session))
# wrap client to use the Blitz Gateway
conn = BlitzGateway(client_obj=client)
admin = conn.getAdminService()
uuid = admin.getEventContext().sessionUuid
# uuid = uuid.split(":")[1]
print(uuid)
# print("key: %s" % (key))
# sizeZ, sizeC, sizeT, sizeX, sizeY, dataset = newFilteredImage(conn, scriptParams)
# newFilteredImage(conn, scriptParams)
# sloopy("/global/project/projectdirs/ngbi/omero-0.7/OMERO.server/lib/scripts/omero/tmp/WT_7B_duct2.mrc")
weka_segmentation(conn, scriptParams, uuid)
# print sizeZ, sizeC, sizeT, sizeX, sizeY, dataset
# Return message, new image and new dataset (if applicable) to the client
# client.setOutput("Message", rstring(message))
# if len(images) == 1:
# client.setOutput("Image", robject(images[0]._obj))
# if dataset is not None:
# client.setOutput("New Dataset", robject(dataset._obj))
finally:
client.closeSession()
if __name__ == "__main__":
runAsScript()
def datasets_to_plates(conn, scriptParams):
updateService = conn.getUpdateService()
message = ""
# Get the datasets ID
datasets, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not datasets:
return None, message
# Filter dataset IDs by permissions
IDs = [ds.getId() for ds in datasets if ds.canLink()]
if len(IDs) != len(datasets):
permIDs = [str(ds.getId()) for ds in datasets if not ds.canLink()]
message += "You do not have the permissions to add the images from"\
" the dataset(s): %s." % ",".join(permIDs)
if not IDs:
return None, message
# find or create Screen if specified
screen = None
newscreen = None
if "Screen" in scriptParams and len(scriptParams["Screen"]) > 0:
s = scriptParams["Screen"]
# see if this is ID of existing screen
try:
screenId = long(s)
screen = conn.getObject("Screen", screenId)
except ValueError:
pass
# if not, create one
if screen is None:
newscreen = omero.model.ScreenI()
newscreen.name = rstring(s)
newscreen = updateService.saveAndReturnObject(newscreen)
screen = conn.getObject("Screen", newscreen.id.val)
plates = []
links = []
deletes = []
for datasetId in IDs:
plate, link, deleteHandle = dataset_to_plate(conn, scriptParams,
datasetId, screen)
if plate is not None:
plates.append(plate)
if link is not None:
links.append(link)
if deleteHandle is not None:
deletes.append(deleteHandle)
# wait for any deletes to finish
for handle in deletes:
cb = omero.callbacks.DeleteCallbackI(conn.c, handle)
while True: # ms
if cb.block(100) is None:
print "Waiting for delete"
else:
break
err = handle.errors()
if err > 0:
print "Delete error", err
else:
print "Delete OK"
if newscreen:
message += "New screen created: %s." % newscreen.getName().val
robj = newscreen
elif plates:
robj = plates[0]
else:
robj = None
if plates:
if len(plates) == 1:
message += " New plate created: %s" % plates[0].name.val
else:
message += " %s plates created" % len(plates)
if len(plates) == len(links):
message += "."
else:
message += " but could not be attached."
else:
message += "No plate created."
return robj, message
def run_processing(conn, session, script_params):
"""
Processes the list of Image_IDs, either making a new image-stack or a new
dataset from each image, with new image planes coming from the regions in
Rectangular ROIs on the parent images.
@param conn: The BlitzGateway connection
@param session: A dictionart containing session ID and hostname
@param script_params: The script input parameters
"""
dataType = script_params["Data_Type"]
message = ""
# Get the images
objects, logMessage = script_utils.getObjects(conn, script_params)
message += logMessage
if not objects:
return None, message
# Concatenate images from datasets
if dataType == 'Image':
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
# Check for rectangular ROIs and filter images list
images = [
image for image in images if (image.getROICount("Rect") > 0) or (
image.getROICount("Polygon") > 0)
]
if not images:
message += "No Rectangle or Polygon ROI found."
return None, message
total_rects = sum([i.getROICount("Rect") for i in images])
total_polys = sum([i.getROICount("Polygon") for i in images])
if total_rects + total_polys > 10:
message += "Cannot start batch processing - too many rois (maximum is 10)."
return None, message
imageIds = [i.getId() for i in images]
newImages = []
newDatasets = []
links = []
for iId in imageIds:
newImage, newDataset, link, new_ids = process_image(
conn, iId, script_params, session)
if newImage is not None:
if isinstance(newImage, list):
newImages.extend(newImage)
else:
newImages.append(newImage)
if newDataset is not None:
newDatasets.append(newDataset)
if link is not None:
if isinstance(link, list):
links.extend(link)
else:
links.append(link)
if newImages:
if len(newImages) > 1:
message += "Created %s new images" % len(newImages)
else:
message += "Created a new image"
else:
message += "No image created"
if newDatasets:
if len(newDatasets) > 1:
message += " and %s new datasets" % len(newDatasets)
else:
message += " and a new dataset"
print script_params['Email_Results']
if script_params['Email_Results'] and (newImages or newDatasets):
email_results(conn, script_params, new_ids)
if not links or not len(links) == len(newImages):
message += " but some images could not be attached"
message += "."
robj = (len(newImages) > 0) and newImages[0]._obj or None
return robj, message
def run_processing(conn, session, script_params):
"""
Collects params and starts the processing
@param conn: the BlitzGateWay connection
@param script_params: the parameters collected from the script input
"""
global input_dir
global output_dir
input_dir = tempfile.mkdtemp(prefix='stitching_input')
output_dir = tempfile.mkdtemp(prefix='stitching_output')
def empty_dir(dir_path):
for old_file in os.listdir(dir_path):
file_path = os.path.join(dir_path, old_file)
os.unlink(file_path)
message = ""
dataType = script_params["Data_Type"]
# Get the images
objects, logMessage = script_utils.getObjects(conn, script_params)
message += logMessage
if not objects:
return None, message
# Concatenate images from datasets
if dataType == 'Image':
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
image_ids = [i.getId() for i in images]
if len(image_ids) > 10:
message = 'Max number of datasets for batch exceeded (10)'
return message
new_images = []
new_ids = []
for image in conn.getObjects("Image",image_ids):
# remove input and processed images
empty_dir(input_dir)
empty_dir(output_dir)
theC = None
if script_params['Single_Channel']:
theC = script_params['Channel']
theZ = None
sizeZ = image.getSizeZ()
if script_params['Single_Z']:
theZ = script_params['Z_slice']
sizeZ = 1
if script_params['Range_Z']:
zstart = script_params['Z_start']
zstop = script_params['Z_stop']
theZ = range(zstart,zstop+1)
sizeZ = len(theZ)
# download the image
image_names = download_tiles(conn,image,theC,theZ)
results_file = str(image.getId()) + "_stitching.txt"
stitching_args = (script_params['grid_x'], script_params['grid_y'], \
script_params['tile_overlap'], results_file,\
script_params['fusion_method'], script_params['regression_threshold'], \
script_params['ave_displacement_threshold'], script_params['abs_displacement_threshold'],\
sizeZ,"T{i}")
# new_image = run_stitching(conn,image,channels,zslices,stitching_args,results_file)
new_image = run_stitching(conn,session,stitching_args)
if new_image:
create_containers(conn,image, new_image)
new_images.append(new_image)
new_ids.append(new_image.getId())
if len(new_ids) == 0:
print "No new images created."
return
if new_images:
if len(new_images) > 1:
message += "Created %s new images" % len(new_images)
else:
message += "Created a new image"
else:
message += "No image created"
print script_params['Email_Results']
if script_params['Email_Results'] and new_images:
email_results(conn,script_params,new_ids)
shutil.rmtree(input_dir)
shutil.rmtree(output_dir)
#
robj = (len(new_images) > 0) and new_images[0]._obj or None
return robj, message
def makeImagesFromRois(conn, parameterMap):
"""
Processes the list of Image_IDs, either making a new image-stack or a new
dataset from each image, with new image planes coming from the regions in
Rectangular ROIs on the parent images.
"""
dataType = parameterMap["Data_Type"]
message = ""
# Get the images
objects, logMessage = script_utils.getObjects(conn, parameterMap)
message += logMessage
if not objects:
return None, message
# Concatenate images from datasets
if dataType == 'Image':
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
# 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
imageIds = [i.getId() for i in images]
newImages = []
newDatasets = []
links = []
for iId in imageIds:
newImage, newDataset, link = processImage(conn, iId, parameterMap)
if newImage is not None:
if isinstance(newImage, list):
newImages.extend(newImage)
else:
newImages.append(newImage)
if newDataset is not None:
newDatasets.append(newDataset)
if link is not None:
if isinstance(link, list):
links.extend(link)
else:
links.append(link)
if newImages:
if len(newImages) > 1:
message += "Created %s new images" % len(newImages)
else:
message += "Created a new image"
else:
message += "No image created"
if newDatasets:
if len(newDatasets) > 1:
message += " and %s new datasets" % len(newDatasets)
else:
message += " and a new dataset"
if not links or not len(links) == len(newImages):
message += " but some images could not be attached"
message += "."
robj = (len(newImages) > 0) and newImages[0]._obj or None
return robj, message
def combineImages(conn, parameterMap):
# get the services we need
services = {}
services["containerService"] = conn.getContainerService()
services["renderingEngine"] = conn.createRenderingEngine()
services["queryService"] = conn.getQueryService()
services["pixelsService"] = conn.getPixelsService()
services["rawPixelStore"] = conn.c.sf.createRawPixelsStore()
services["rawPixelStoreUpload"] = conn.c.sf.createRawPixelsStore()
services["updateService"] = conn.getUpdateService()
services["rawFileStore"] = conn.createRawFileStore()
queryService = services["queryService"]
containerService = services["containerService"]
colourMap = {}
if "Channel_Colours" in parameterMap:
for c, col in enumerate(parameterMap["Channel_Colours"]):
colour = col.getValue()
if colour in COLOURS:
colourMap[c] = COLOURS[colour]
# Get images or datasets
message = ""
objects, logMessage = scriptUtil.getObjects(conn, parameterMap)
message += logMessage
if not objects:
return None, message
# get the images IDs from list (in order) or dataset (sorted by name)
outputImages = []
links = []
dataType = parameterMap["Data_Type"]
if dataType == "Image":
dataset = None
imageIds = [image.id for image in objects]
# get dataset from first image
query_string = "select i from Image i join fetch i.datasetLinks idl join fetch idl.parent where i.id in (%s)" % imageIds[
0]
image = queryService.findByQuery(query_string, None)
if image:
for link in image.iterateDatasetLinks():
ds = link.parent
dataset = conn.getObject("Dataset", ds.id.val)
print "Dataset", dataset.getName()
break # only use 1st dataset
else:
print "No Dataset found for Image ID: %s Combined Image will not be put into dataset." % imageIds[
0]
newImg, link = makeSingleImage(services, parameterMap, imageIds,
dataset, colourMap)
if newImg:
outputImages.append(newImg)
if link:
links.append(link)
else:
for dataset in objects:
images = list(dataset.listChildren())
if not images:
print "No images found for Dataset ID: %s" % dataset.getId()
continue
images.sort(key=lambda x: (x.getName()))
imageIds = [i.getId() for i in images]
newImg, link = makeSingleImage(services, parameterMap, imageIds,
dataset, colourMap)
if newImg:
outputImages.append(newImg)
if link:
links.append(link)
# try and close any stateful services
for s in services:
try:
s.close()
except:
pass
if outputImages:
if len(outputImages) > 1:
message += "%s new images created" % len(outputImages)
else:
message += "New image created"
if not links or not len(links) == len(outputImages):
message += " but could not be attached"
else:
message += "No image created"
message += "."
return outputImages, message
def batchImageExport(conn, scriptParams):
# for params with default values, we can get the value directly
splitCs = scriptParams["Export_Individual_Channels"]
mergedCs = scriptParams["Export_Merged_Image"]
greyscale = scriptParams["Individual_Channels_Grey"]
dataType = scriptParams["Data_Type"]
ids = scriptParams["IDs"]
folder_name = scriptParams["Folder_Name"]
format = scriptParams["Format"]
projectZ = "Choose_Z_Section" in scriptParams and scriptParams["Choose_Z_Section"] == 'Max projection'
if (not splitCs) and (not mergedCs):
log("Not chosen to save Individual Channels OR Merged Image")
return
# check if we have these params
channelNames = []
if "Channel_Names" in scriptParams:
channelNames = scriptParams["Channel_Names"]
imgWidth = None
if "Image_Width" in scriptParams:
imgWidth = scriptParams["Image_Width"]
# functions used below for each imaage.
def getZrange(sizeZ, scriptParams):
zRange = None
if "Choose_Z_Section" in scriptParams:
zChoice = scriptParams["Choose_Z_Section"]
# NB: all Z indices in this script are 1-based
if zChoice == 'ALL Z planes':
zRange = (1, sizeZ+1)
elif "OR_specify_Z_index" in scriptParams:
zIndex = scriptParams["OR_specify_Z_index"]
zIndex = min(zIndex, sizeZ)
zRange = (zIndex,)
elif "OR_specify_Z_start_AND..." in scriptParams and "...specify_Z_end" in scriptParams:
start = scriptParams["OR_specify_Z_start_AND..."]
start = min(start, sizeZ)
end = scriptParams["...specify_Z_end"]
end = min(end, sizeZ)
zStart = min(start, end) # in case user got zStart and zEnd mixed up
zEnd = max(start, end)
if zStart == zEnd:
zRange = (zStart,)
else:
zRange = (zStart, zEnd+1)
return zRange
def getTrange(sizeT, scriptParams):
tRange = None
if "Choose_T_Section" in scriptParams:
tChoice = scriptParams["Choose_T_Section"]
# NB: all T indices in this script are 1-based
if tChoice == 'ALL T planes':
tRange = (1, sizeT+1)
elif "OR_specify_T_index" in scriptParams:
tIndex = scriptParams["OR_specify_T_index"]
tIndex = min(tIndex, sizeT)
tRange = (tIndex,)
elif "OR_specify_T_start_AND..." in scriptParams and "...specify_T_end" in scriptParams:
start = scriptParams["OR_specify_T_start_AND..."]
start = min(start, sizeT)
end = scriptParams["...specify_T_end"]
end = min(end, sizeT)
tStart = min(start, end) # in case user got zStart and zEnd mixed up
tEnd = max(start, end)
if tStart == tEnd:
tRange = (tStart,)
else:
tRange = (tStart, tEnd+1)
return tRange
# Get the images or datasets
message = ""
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, message
# Attach figure to the first image
parent = objects[0]
if dataType == 'Dataset':
images = []
for ds in objects:
images.extend( list(ds.listChildren()) )
if not images:
message += "No image found in dataset(s)"
return None, message
else:
images = objects
log("Processing %s images" % len(images))
# somewhere to put images
curr_dir = os.getcwd()
exp_dir = os.path.join(curr_dir, folder_name)
try:
os.mkdir(exp_dir)
except:
pass
# do the saving to disk
if format == 'OME-TIFF':
for img in images:
log("Exporting image as OME-TIFF: %s" % img.getName())
saveAsOmeTiff(conn, img, folder_name)
else:
for img in images:
log("\n----------- Saving planes from image: '%s' ------------" % img.getName())
sizeC = img.getSizeC()
sizeZ = img.getSizeZ()
sizeT = img.getSizeT()
zRange = getZrange(sizeZ, scriptParams)
tRange = getTrange(sizeT, scriptParams)
log("Using:")
if zRange is None: log(" Z-index: Last-viewed")
elif len(zRange) == 1: log(" Z-index: %d" % zRange[0])
else: log(" Z-range: %s-%s" % ( zRange[0],zRange[1]-1) )
if projectZ: log(" Z-projection: ON")
if tRange is None: log(" T-index: Last-viewed")
elif len(tRange) == 1: log(" T-index: %d" % tRange[0])
else: log(" T-range: %s-%s" % ( tRange[0],tRange[1]-1) )
log(" Format: %s" % format)
if imgWidth is None: log(" Image Width: no resize")
else: log(" Image Width: %s" % imgWidth)
log(" Greyscale: %s" % greyscale)
log("Channel Rendering Settings:")
for ch in img.getChannels():
log(" %s: %d-%d" % (ch.getLabel(), ch.getWindowStart(), ch.getWindowEnd()) )
savePlanesForImage(conn, img, sizeC, splitCs, mergedCs, channelNames,
zRange, tRange, greyscale, imgWidth, projectZ=projectZ, format=format, folder_name=folder_name)
# write log for exported images (not needed for ome-tiff)
logFile = open(os.path.join(exp_dir, 'Batch_Image_Export.txt'), 'w')
try:
for s in logStrings:
logFile.write(s)
logFile.write("\n")
finally:
logFile.close()
# zip everything up (unless we've only got a single ome-tiff)
if format == 'OME-TIFF' and len(os.listdir(exp_dir)) == 1:
export_file = os.path.join(folder_name, os.listdir(exp_dir)[0])
mimetype = 'image/tiff'
else:
export_file = "%s.zip" % folder_name
compress(export_file, folder_name)
mimetype='application/zip'
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)
message += annMessage
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(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 combineImages(conn, parameterMap):
# get the services we need
services = {}
services["containerService"] = conn.getContainerService()
services["renderingEngine"] = conn.createRenderingEngine()
services["queryService"] = conn.getQueryService()
services["pixelsService"] = conn.getPixelsService()
services["rawPixelStore"] = conn.c.sf.createRawPixelsStore()
services["rawPixelStoreUpload"] = conn.c.sf.createRawPixelsStore()
services["updateService"] = conn.getUpdateService()
services["rawFileStore"] = conn.createRawFileStore()
queryService = services["queryService"]
colourMap = {}
if "Channel_Colours" in parameterMap:
for c, colour in enumerate(parameterMap["Channel_Colours"]):
if colour in COLOURS:
colourMap[c] = COLOURS[colour]
print "colourMap", colourMap
# Get images or datasets
message = ""
objects, logMessage = scriptUtil.getObjects(conn, parameterMap)
message += logMessage
if not objects:
print message
return None, message
# get the images IDs from list (in order) or dataset (sorted by name)
outputImages = []
links = []
dataType = parameterMap["Data_Type"]
if dataType == "Image":
dataset = None
objects.sort(key=lambda x: (x.getName())) # Sort images by name
imageIds = [image.id for image in objects]
# get dataset from first image
query_string = "select i from Image i join fetch i.datasetLinks idl"\
" join fetch idl.parent where i.id in (%s)" % imageIds[0]
image = queryService.findByQuery(query_string, None)
if image:
for link in image.iterateDatasetLinks():
ds = link.parent
dataset = conn.getObject("Dataset", ds.id.val)
print "Dataset", dataset.getName()
break # only use 1st dataset
else:
print "No Dataset found for Image ID: %s Combined Image will "\
"not be put into dataset." % imageIds[0]
newImg, link = makeSingleImage(services, parameterMap, imageIds,
dataset, colourMap)
if newImg:
outputImages.append(newImg)
if link:
links.append(link)
else:
for dataset in objects:
images = list(dataset.listChildren())
if not images:
print "No images found for Dataset ID: %s" % dataset.getId()
continue
images.sort(key=lambda x: (x.getName()))
imageIds = [i.getId() for i in images]
newImg, link = makeSingleImage(services, parameterMap, imageIds,
dataset, colourMap)
if newImg:
outputImages.append(newImg)
if link:
links.append(link)
# try and close any stateful services
for s in services:
try:
s.close()
except:
pass
if outputImages:
if len(outputImages) > 1:
message += "%s new images created" % len(outputImages)
else:
message += "New image created"
if not links or not len(links) == len(outputImages):
message += " but could not be attached"
else:
message += "No image created"
message += "."
return outputImages, message
def processImages(conn, scriptParams):
fileAnns = []
message = ""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [image for image in images if
image.getROICount(["Polyline", "Line"]) > 0]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
csvData = []
for image in images:
print "\nAnalysing Image: %s ID: %s" \
% (image.getName(), image.getId())
if image.getSizeT() > 1:
message += "%s ID: %s appears to be a time-lapse Image," \
" not a kymograph." % (image.getName(), image.getId())
continue
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
secsPerPixelY = image.getPixelSizeY()
micronsPerPixelX = image.getPixelSizeX()
if secsPerPixelY and micronsPerPixelX:
micronsPerSec = micronsPerPixelX / secsPerPixelY
else:
micronsPerSec = None
# for each line or polyline, create a row in csv table: y(t), x,
# dy(dt), dx, x/t (line), x/t (average)
colNames = "\nt_start (pixels), x_start (pixels), t_end (pixels)," \
" x_end (pixels), dt (pixels), dx (pixels), x/t, speed(um/sec)," \
"avg x/t, avg speed(um/sec)"
tableData = ""
for roi in result.rois:
for s in roi.copyShapes():
if s is None:
continue # seems possible in some situations
if type(s) == omero.model.LineI:
tableData += "\nLine ID: %s" % s.getId().getValue()
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
dx = abs(x1-x2)
dy = abs(y1-y2)
dxPerY = float(dx)/dy
speed = ""
if micronsPerSec:
speed = dxPerY * micronsPerSec
tableData += "\n"
tableData += ",".join(
[str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY,
speed)])
elif type(s) == omero.model.PolylineI:
tableData += "\nPolyline ID: %s" % s.getId().getValue()
points = pointsStringToXYlist(s.getPoints().getValue())
xStart, yStart = points[0]
for i in range(1, len(points)):
x1, y1 = points[i-1]
x2, y2 = points[i]
dx = abs(x1-x2)
dy = abs(y1-y2)
dxPerY = float(dx)/dy
avXperY = abs(float(x2-xStart)/(y2-yStart))
speed = ""
avgSpeed = ""
if micronsPerSec:
speed = dxPerY * micronsPerSec
avgSpeed = avXperY * micronsPerSec
tableData += "\n"
tableData += ",".join(
[str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY,
speed, avXperY, avgSpeed)])
# write table data to csv...
if len(tableData) > 0:
tableString = "Image ID:, %s," % image.getId()
tableString += "Name:, %s" % image.getName()
tableString += "\nsecsPerPixelY: %s" % secsPerPixelY
tableString += '\nmicronsPerPixelX: %s' % micronsPerPixelX
tableString += "\n"
tableString += colNames
tableString += tableData
print tableString
csvData.append(tableString)
else:
print "Found NO lines or polylines to analyze for Image"
iids = [str(i.getId()) for i in images]
toLinkCsv = [i.getId() for i in images if i.canAnnotate()]
csvFileName = 'kymograph_velocities_%s.csv' % "-".join(iids)
csvFile = open(csvFileName, 'w')
try:
csvFile.write("\n \n".join(csvData))
finally:
csvFile.close()
fileAnn = conn.createFileAnnfromLocalFile(csvFileName, mimetype="text/csv")
faMessage = "Created Line Plot csv (Excel) file"
links = []
if len(toLinkCsv) == 0:
faMessage += " but could not attach to images."
for iid in toLinkCsv:
print "linking csv to Image: ", iid
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = fileAnn._obj
links.append(link)
if len(links) > 0:
links = conn.getUpdateService().saveAndReturnArray(links)
if fileAnn:
fileAnns.append(fileAnn)
if not fileAnns:
faMessage = "No Analysis files created. See 'Info' or 'Error'" \
" for more details"
elif len(fileAnns) > 1:
faMessage = "Created %s csv (Excel) files" % len(fileAnns)
message += faMessage
return fileAnns, 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("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 processImages(conn, scriptParams):
fileAnns = []
message = ""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [
image for image in images
if image.getROICount(["Polyline", "Line"]) > 0
]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
csvData = []
for image in images:
print "\nAnalysing Image: %s ID: %s" \
% (image.getName(), image.getId())
if image.getSizeT() > 1:
message += "%s ID: %s appears to be a time-lapse Image," \
" not a kymograph." % (image.getName(), image.getId())
continue
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
secsPerPixelY = image.getPixelSizeY()
micronsPerPixelX = image.getPixelSizeX()
if secsPerPixelY and micronsPerPixelX:
micronsPerSec = micronsPerPixelX / secsPerPixelY
else:
micronsPerSec = None
# for each line or polyline, create a row in csv table: y(t), x,
# dy(dt), dx, x/t (line), x/t (average)
colNames = "\nt_start (pixels), x_start (pixels), t_end (pixels)," \
" x_end (pixels), dt (pixels), dx (pixels), x/t, speed(um/sec)," \
"avg x/t, avg speed(um/sec)"
tableData = ""
for roi in result.rois:
for s in roi.copyShapes():
if s is None:
continue # seems possible in some situations
if type(s) == omero.model.LineI:
tableData += "\nLine ID: %s" % s.getId().getValue()
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
dx = abs(x1 - x2)
dy = abs(y1 - y2)
dxPerY = float(dx) / dy
speed = ""
if micronsPerSec:
speed = dxPerY * micronsPerSec
tableData += "\n"
tableData += ",".join([
str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY, speed)
])
elif type(s) == omero.model.PolylineI:
tableData += "\nPolyline ID: %s" % s.getId().getValue()
points = pointsStringToXYlist(s.getPoints().getValue())
xStart, yStart = points[0]
for i in range(1, len(points)):
x1, y1 = points[i - 1]
x2, y2 = points[i]
dx = abs(x1 - x2)
dy = abs(y1 - y2)
dxPerY = float(dx) / dy
avXperY = abs(float(x2 - xStart) / (y2 - yStart))
speed = ""
avgSpeed = ""
if micronsPerSec:
speed = dxPerY * micronsPerSec
avgSpeed = avXperY * micronsPerSec
tableData += "\n"
tableData += ",".join([
str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY,
speed, avXperY, avgSpeed)
])
# write table data to csv...
if len(tableData) > 0:
tableString = "Image ID:, %s," % image.getId()
tableString += "Name:, %s" % image.getName()
tableString += "\nsecsPerPixelY: %s" % secsPerPixelY
tableString += '\nmicronsPerPixelX: %s' % micronsPerPixelX
tableString += "\n"
tableString += colNames
tableString += tableData
print tableString
csvData.append(tableString)
else:
print "Found NO lines or polylines to analyze for Image"
iids = [str(i.getId()) for i in images]
toLinkCsv = [i.getId() for i in images if i.canAnnotate()]
csvFileName = 'kymograph_velocities_%s.csv' % "-".join(iids)
csvFile = open(csvFileName, 'w')
try:
csvFile.write("\n \n".join(csvData))
finally:
csvFile.close()
fileAnn = conn.createFileAnnfromLocalFile(csvFileName, mimetype="text/csv")
faMessage = "Created Line Plot csv (Excel) file"
links = []
if len(toLinkCsv) == 0:
faMessage += " but could not attach to images."
for iid in toLinkCsv:
print "linking csv to Image: ", iid
link = ImageAnnotationLinkI()
link.parent = ImageI(iid, False)
link.child = fileAnn._obj
links.append(link)
if len(links) > 0:
links = conn.getUpdateService().saveAndReturnArray(links)
if fileAnn:
fileAnns.append(fileAnn)
if not fileAnns:
faMessage = "No Analysis files created. See 'Info' or 'Error'" \
" for more details"
elif len(fileAnns) > 1:
faMessage = "Created %s csv (Excel) files" % len(fileAnns)
message += faMessage
return fileAnns, message
def mwell_fields_to_plates(conn, scriptParams):
updateService = conn.getUpdateService()
message = ""
# Get the well IDs
wells, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
# Filter dataset IDs by permissions
IDs = [ws.getId() for ws in wells if ws.canLink()]
if len(IDs) != len(wells):
permIDs = [str(ws.getId()) for ws in wells if not ws.canLink()]
message += "You do not have the permissions to add the images from"\
" the well(s): %s." % ",".join(permIDs)
if not IDs:
return None, message
# find or create Screen if specified
screen = None
newscreen = None
if "Screen" in scriptParams and len(scriptParams["Screen"]) > 0:
s = scriptParams["Screen"]
# see if this is ID of existing screen
try:
screenId = long(s)
screen = conn.getObject("Screen", screenId)
except ValueError:
pass
# if not, create one
if screen is None:
newscreen = omero.model.ScreenI()
newscreen.name = rstring(s)
newscreen = updateService.saveAndReturnObject(newscreen)
screen = conn.getObject("Screen", newscreen.id.val)
plates = []
links = []
for wellId in IDs:
plate, link = well_fields_to_plate(conn, scriptParams,
wellId, screen)
if plate is not None:
plates.append(plate)
if link is not None:
links.append(link)
if newscreen:
message += "New screen created: %s." % newscreen.getName().val
robj = newscreen
elif plates:
robj = plates[0]
else:
robj = None
if plates:
if len(plates) == 1:
message += " New plate created: %s" % plates[0].name.val
else:
message += " %s plates created" % len(plates)
if len(plates) == len(links):
message += "."
else:
message += " but was not attached."
else:
message += "No plate created."
return robj, message
def writeMovie(commandArgs, conn):
"""
Makes the movie.
@ returns Returns the file annotation
"""
log("Movie created by OMERO")
log("")
message = ""
conn.SERVICE_OPTS.setOmeroGroup('-1')
session = conn.c.sf
gateway = conn
scriptService = session.getScriptService()
queryService = session.getQueryService()
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
# Get the images
images, logMessage = scriptUtil.getObjects(conn, commandArgs)
message += logMessage
if not images:
return None, message
omeroImage = images[
0] # Get the first valid image (should be expanded to process the list)
if commandArgs["RenderingDef_ID"] >= 0:
omeroImage._prepareRenderingEngine(rdid=commandArgs["RenderingDef_ID"])
pixels = omeroImage.getPrimaryPixels()
pixelsId = pixels.getId()
sizeX = pixels.getSizeX()
sizeY = pixels.getSizeY()
sizeZ = pixels.getSizeZ()
sizeC = pixels.getSizeC()
sizeT = pixels.getSizeT()
if (sizeX == None or sizeY == None or sizeZ == None or sizeT == None
or sizeC == None):
return
if (pixels.getPhysicalSizeX() == None):
commandArgs["Scalebar"] = 0
cRange = range(0, sizeC)
if "Channels" in commandArgs and validChannels(commandArgs["Channels"],
sizeC):
cRange = commandArgs["Channels"]
tzList = calculateRanges(sizeZ, sizeT, commandArgs)
timeMap = calculateAquisitionTime(conn, pixelsId, cRange, tzList)
if (timeMap == None):
commandArgs["Show_Time"] = False
if (timeMap != None):
if (len(timeMap) == 0):
commandArgs["Show_Time"] = False
pixelTypeString = pixels.getPixelsType().getValue()
frameNo = 1
omeroImage.setActiveChannels(map(lambda x: x + 1, cRange))
renderingEngine = omeroImage._re
overlayColour = (255, 255, 255)
if "Overlay_Colour" in commandArgs:
r, g, b, a = COLOURS[commandArgs["Overlay_Colour"]]
overlayColour = (r, g, b)
canvasColour = tuple(COLOURS[commandArgs["Canvas_Colour"]][:3])
mw = commandArgs["Min_Width"]
if mw < sizeX:
mw = sizeX
mh = commandArgs["Min_Height"]
if mh < sizeY:
mh = sizeY
ovlpos = None
canvas = None
if sizeX < mw or sizeY < mh:
ovlpos = ((mw - sizeX) / 2, (mh - sizeY) / 2)
canvas = Image.new("RGBA", (mw, mh), canvasColour)
format = commandArgs["Format"]
fileNames = []
# add intro...
if "Intro_Slide" in commandArgs and commandArgs["Intro_Slide"].id:
intro_duration = commandArgs["Intro_Duration"]
intro_fileId = commandArgs["Intro_Slide"].id.val
intro_filenames = write_intro_end_slides(conn, commandArgs,
intro_fileId, intro_duration,
mw, mh)
fileNames.extend(intro_filenames)
# prepare watermark
if "Watermark" in commandArgs and commandArgs["Watermark"].id:
watermark = prepareWatermark(conn, commandArgs, mw, mh)
# add movie frames...
for tz in tzList:
t = tz[0]
z = tz[1]
plane = getPlane(renderingEngine, z, t)
planeImage = numpy.array(plane, dtype='uint32')
planeImage = planeImage.byteswap()
planeImage = planeImage.reshape(sizeX, sizeY)
image = Image.frombuffer('RGBA', (sizeX, sizeY), planeImage.data,
'raw', 'ARGB', 0, 1)
if ovlpos is not None:
image2 = canvas.copy()
image2.paste(image, ovlpos, image)
image = image2
if "Scalebar" in commandArgs and commandArgs["Scalebar"]:
image = addScalebar(commandArgs["Scalebar"], image, pixels,
commandArgs)
planeInfo = "z:" + str(z) + "t:" + str(t)
if "Show_Time" in commandArgs and commandArgs["Show_Time"]:
time = timeMap[planeInfo]
image = addTimePoints(time, pixels, image, overlayColour)
if "Show_Plane_Info" in commandArgs and commandArgs["Show_Plane_Info"]:
image = addPlaneInfo(z, t, pixels, image, overlayColour)
if "Watermark" in commandArgs and commandArgs["Watermark"].id:
image = pasteWatermark(image, watermark)
if format == QT:
filename = str(frameNo) + '.png'
image.save(filename, "PNG")
else:
filename = str(frameNo) + '.jpg'
image.save(filename, "JPEG")
fileNames.append(filename)
frameNo += 1
# add exit frames... "outro"
# add intro...
if "Ending_Slide" in commandArgs and commandArgs["Ending_Slide"].id:
end_duration = commandArgs["Ending_Duration"]
end_fileId = commandArgs["Ending_Slide"].id.val
end_filenames = write_intro_end_slides(conn, commandArgs, end_fileId,
end_duration, mw, mh)
fileNames.extend(end_filenames)
filelist = ",".join(fileNames)
ext = formatMap[format]
movieName = "Movie"
if "Movie_Name" in commandArgs:
movieName = commandArgs["Movie_Name"]
if not movieName.endswith(".%s" % ext):
movieName = "%s.%s" % (movieName, ext)
movieName = re.sub("[$&\;|\(\)<>' ]", "",
movieName) # spaces etc in file name cause problems
framesPerSec = 2
if "FPS" in commandArgs:
framesPerSec = commandArgs["FPS"]
buildAVI(mw, mh, filelist, framesPerSec, movieName, format)
figLegend = "\n".join(logLines)
mimetype = formatMimetypes[format]
if not os.path.exists(movieName):
print "mencoder Failed to create movie file: %s" % movieName
return None, "Failed to create movie file: %s" % movieName
if not commandArgs["Do_Link"]:
originalFile = scriptUtil.createFile(updateService, movieName,
mimetype, movieName)
scriptUtil.uploadFile(rawFileStore, originalFile, movieName)
return originalFile, message
namespace = omero.constants.namespaces.NSCREATED + "/omero/export_scripts/Make_Movie"
fileAnnotation, annMessage = scriptUtil.createLinkFileAnnotation(
conn,
movieName,
omeroImage,
output="Movie",
ns=namespace,
mimetype=mimetype)
message += annMessage
return fileAnnotation._obj, message
def batchImageExport(conn, scriptParams):
# for params with default values, we can get the value directly
splitCs = scriptParams["Export_Individual_Channels"]
mergedCs = scriptParams["Export_Merged_Image"]
greyscale = scriptParams["Individual_Channels_Grey"]
dataType = scriptParams["Data_Type"]
folder_name = scriptParams["Folder_Name"]
folder_name = os.path.basename(folder_name)
format = scriptParams["Format"]
projectZ = "Choose_Z_Section" in scriptParams and scriptParams["Choose_Z_Section"] == "Max projection"
if (not splitCs) and (not mergedCs):
log("Not chosen to save Individual Channels OR Merged Image")
return
# check if we have these params
channelNames = []
if "Channel_Names" in scriptParams:
channelNames = scriptParams["Channel_Names"]
zoomPercent = None
if "Zoom" in scriptParams and scriptParams["Zoom"] != "100%":
zoomPercent = int(scriptParams["Zoom"][:-1])
# functions used below for each imaage.
def getZrange(sizeZ, scriptParams):
zRange = None
if "Choose_Z_Section" in scriptParams:
zChoice = scriptParams["Choose_Z_Section"]
# NB: all Z indices in this script are 1-based
if zChoice == "ALL Z planes":
zRange = (1, sizeZ + 1)
elif "OR_specify_Z_index" in scriptParams:
zIndex = scriptParams["OR_specify_Z_index"]
zIndex = min(zIndex, sizeZ)
zRange = (zIndex,)
elif "OR_specify_Z_start_AND..." in scriptParams and "...specify_Z_end" in scriptParams:
start = scriptParams["OR_specify_Z_start_AND..."]
start = min(start, sizeZ)
end = scriptParams["...specify_Z_end"]
end = min(end, sizeZ)
# in case user got zStart and zEnd mixed up
zStart = min(start, end)
zEnd = max(start, end)
if zStart == zEnd:
zRange = (zStart,)
else:
zRange = (zStart, zEnd + 1)
return zRange
def getTrange(sizeT, scriptParams):
tRange = None
if "Choose_T_Section" in scriptParams:
tChoice = scriptParams["Choose_T_Section"]
# NB: all T indices in this script are 1-based
if tChoice == "ALL T planes":
tRange = (1, sizeT + 1)
elif "OR_specify_T_index" in scriptParams:
tIndex = scriptParams["OR_specify_T_index"]
tIndex = min(tIndex, sizeT)
tRange = (tIndex,)
elif "OR_specify_T_start_AND..." in scriptParams and "...specify_T_end" in scriptParams:
start = scriptParams["OR_specify_T_start_AND..."]
start = min(start, sizeT)
end = scriptParams["...specify_T_end"]
end = min(end, sizeT)
# in case user got zStart and zEnd mixed up
tStart = min(start, end)
tEnd = max(start, end)
if tStart == tEnd:
tRange = (tStart,)
else:
tRange = (tStart, tEnd + 1)
return tRange
# Get the images or datasets
message = ""
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, message
# Attach figure to the first image
parent = objects[0]
if dataType == "Dataset":
images = []
for ds in objects:
images.extend(list(ds.listChildren()))
if not images:
message += "No image found in dataset(s)"
return None, message
else:
images = objects
log("Processing %s images" % len(images))
# somewhere to put images
curr_dir = os.getcwd()
exp_dir = os.path.join(curr_dir, folder_name)
try:
os.mkdir(exp_dir)
except:
pass
# max size (default 12kx12k)
size = conn.getDownloadAsMaxSizeSetting()
size = int(size)
ids = []
# do the saving to disk
for img in images:
pixels = img.getPrimaryPixels()
if pixels.getId() in ids:
continue
ids.append(pixels.getId())
sizeX = pixels.getSizeX()
sizeY = pixels.getSizeY()
if sizeX * sizeY > size:
log(" ** Can't export a 'Big' image to %s. **" % format)
if len(images) == 1:
return None, "Can't export a 'Big' image to %s." % format
continue
else:
log("Exporting image as %s: %s" % (format, img.getName()))
if format == "OME-TIFF":
saveAsOmeTiff(conn, img, folder_name)
else:
if img._prepareRE().requiresPixelsPyramid():
log(" ** Can't export a 'Big' image to OME-TIFF. **")
log("\n----------- Saving planes from image: '%s' ------------" % img.getName())
sizeC = img.getSizeC()
sizeZ = img.getSizeZ()
sizeT = img.getSizeT()
zRange = getZrange(sizeZ, scriptParams)
tRange = getTrange(sizeT, scriptParams)
log("Using:")
if zRange is None:
log(" Z-index: Last-viewed")
elif len(zRange) == 1:
log(" Z-index: %d" % zRange[0])
else:
log(" Z-range: %s-%s" % (zRange[0], zRange[1] - 1))
if projectZ:
log(" Z-projection: ON")
if tRange is None:
log(" T-index: Last-viewed")
elif len(tRange) == 1:
log(" T-index: %d" % tRange[0])
else:
log(" T-range: %s-%s" % (tRange[0], tRange[1] - 1))
log(" Format: %s" % format)
if zoomPercent is None:
log(" Image Zoom: 100%")
else:
log(" Image Zoom: %s" % zoomPercent)
log(" Greyscale: %s" % greyscale)
log("Channel Rendering Settings:")
for ch in img.getChannels():
log(" %s: %d-%d" % (ch.getLabel(), ch.getWindowStart(), ch.getWindowEnd()))
try:
savePlanesForImage(
conn,
img,
sizeC,
splitCs,
mergedCs,
channelNames,
zRange,
tRange,
greyscale,
zoomPercent,
projectZ=projectZ,
format=format,
folder_name=folder_name,
)
finally:
# Make sure we close Rendering Engine
img._re.close()
# write log for exported images (not needed for ome-tiff)
logFile = open(os.path.join(exp_dir, "Batch_Image_Export.txt"), "w")
try:
for s in logStrings:
logFile.write(s)
logFile.write("\n")
finally:
logFile.close()
if len(os.listdir(exp_dir)) == 0:
return None, "No files exported. See 'info' for more details"
# 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=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 = 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 = NSCREATED + "/omero/export_scripts/Batch_Image_Export"
fileAnnotation, annMessage = script_utils.createLinkFileAnnotation(
conn, export_file, parent, output=outputDisplayName, ns=namespace, mimetype=mimetype
)
message += annMessage
return fileAnnotation, message
def batchImageExport(conn, scriptParams):
# for params with default values, we can get the value directly
splitCs = scriptParams["Export_Individual_Channels"]
mergedCs = scriptParams["Export_Merged_Image"]
greyscale = scriptParams["Individual_Channels_Grey"]
dataType = scriptParams["Data_Type"]
folder_name = scriptParams["Folder_Name"]
folder_name = os.path.basename(folder_name)
format = scriptParams["Format"]
projectZ = "Choose_Z_Section" in scriptParams and \
scriptParams["Choose_Z_Section"] == 'Max projection'
if (not splitCs) and (not mergedCs):
log("Not chosen to save Individual Channels OR Merged Image")
return
# check if we have these params
channelNames = []
if "Channel_Names" in scriptParams:
channelNames = scriptParams["Channel_Names"]
zoomPercent = None
if "Zoom" in scriptParams and scriptParams["Zoom"] != "100%":
zoomPercent = int(scriptParams["Zoom"][:-1])
# functions used below for each imaage.
def getZrange(sizeZ, scriptParams):
zRange = None
if "Choose_Z_Section" in scriptParams:
zChoice = scriptParams["Choose_Z_Section"]
# NB: all Z indices in this script are 1-based
if zChoice == 'ALL Z planes':
zRange = (1, sizeZ+1)
elif "OR_specify_Z_index" in scriptParams:
zIndex = scriptParams["OR_specify_Z_index"]
zIndex = min(zIndex, sizeZ)
zRange = (zIndex,)
elif "OR_specify_Z_start_AND..." in scriptParams and \
"...specify_Z_end" in scriptParams:
start = scriptParams["OR_specify_Z_start_AND..."]
start = min(start, sizeZ)
end = scriptParams["...specify_Z_end"]
end = min(end, sizeZ)
# in case user got zStart and zEnd mixed up
zStart = min(start, end)
zEnd = max(start, end)
if zStart == zEnd:
zRange = (zStart,)
else:
zRange = (zStart, zEnd+1)
return zRange
def getTrange(sizeT, scriptParams):
tRange = None
if "Choose_T_Section" in scriptParams:
tChoice = scriptParams["Choose_T_Section"]
# NB: all T indices in this script are 1-based
if tChoice == 'ALL T planes':
tRange = (1, sizeT+1)
elif "OR_specify_T_index" in scriptParams:
tIndex = scriptParams["OR_specify_T_index"]
tIndex = min(tIndex, sizeT)
tRange = (tIndex,)
elif "OR_specify_T_start_AND..." in scriptParams and \
"...specify_T_end" in scriptParams:
start = scriptParams["OR_specify_T_start_AND..."]
start = min(start, sizeT)
end = scriptParams["...specify_T_end"]
end = min(end, sizeT)
# in case user got zStart and zEnd mixed up
tStart = min(start, end)
tEnd = max(start, end)
if tStart == tEnd:
tRange = (tStart,)
else:
tRange = (tStart, tEnd+1)
return tRange
# Get the images or datasets
message = ""
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, message
# Attach figure to the first image
parent = objects[0]
if dataType == 'Dataset':
images = []
for ds in objects:
images.extend(list(ds.listChildren()))
if not images:
message += "No image found in dataset(s)"
return None, message
else:
images = objects
log("Processing %s images" % len(images))
# somewhere to put images
curr_dir = os.getcwd()
exp_dir = os.path.join(curr_dir, folder_name)
try:
os.mkdir(exp_dir)
except:
pass
# max size (default 12kx12k)
size = conn.getDownloadAsMaxSizeSetting()
size = int(size)
ids = []
# do the saving to disk
for img in images:
pixels = img.getPrimaryPixels()
if (pixels.getId() in ids):
continue
ids.append(pixels.getId())
sizeX = pixels.getSizeX()
sizeY = pixels.getSizeY()
if sizeX*sizeY > size:
log(" ** Can't export a 'Big' image to %s. **" % format)
if len(images) == 1:
return None, "Can't export a 'Big' image to %s." % format
continue
else:
log("Exporting image as %s: %s" % (format, img.getName()))
if format == 'OME-TIFF':
saveAsOmeTiff(conn, img, folder_name)
else:
if img._prepareRE().requiresPixelsPyramid():
log(" ** Can't export a 'Big' image to OME-TIFF. **")
log("\n----------- Saving planes from image: '%s' ------------"
% img.getName())
sizeC = img.getSizeC()
sizeZ = img.getSizeZ()
sizeT = img.getSizeT()
zRange = getZrange(sizeZ, scriptParams)
tRange = getTrange(sizeT, scriptParams)
log("Using:")
if zRange is None:
log(" Z-index: Last-viewed")
elif len(zRange) == 1:
log(" Z-index: %d" % zRange[0])
else:
log(" Z-range: %s-%s" % (zRange[0], zRange[1]-1))
if projectZ:
log(" Z-projection: ON")
if tRange is None:
log(" T-index: Last-viewed")
elif len(tRange) == 1:
log(" T-index: %d" % tRange[0])
else:
log(" T-range: %s-%s" % (tRange[0], tRange[1]-1))
log(" Format: %s" % format)
if zoomPercent is None:
log(" Image Zoom: 100%")
else:
log(" Image Zoom: %s" % zoomPercent)
log(" Greyscale: %s" % greyscale)
log("Channel Rendering Settings:")
for ch in img.getChannels():
log(" %s: %d-%d"
% (ch.getLabel(), ch.getWindowStart(), ch.getWindowEnd()))
try:
savePlanesForImage(
conn, img, sizeC, splitCs, mergedCs, channelNames, zRange,
tRange, greyscale, zoomPercent, projectZ=projectZ,
format=format, folder_name=folder_name)
finally:
# Make sure we close Rendering Engine
img._re.close()
# write log for exported images (not needed for ome-tiff)
logFile = open(os.path.join(exp_dir, 'Batch_Image_Export.txt'), 'w')
try:
for s in logStrings:
logFile.write(s)
logFile.write("\n")
finally:
logFile.close()
if len(os.listdir(exp_dir)) == 0:
return None, "No files exported. See 'info' for more details"
# 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=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 = 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 = NSCREATED + "/omero/export_scripts/Batch_Image_Export"
fileAnnotation, annMessage = script_utils.createLinkFileAnnotation(
conn, export_file, parent, output=outputDisplayName, ns=namespace,
mimetype=mimetype)
message += annMessage
return fileAnnotation, message
def weka_segmentation(conn, scriptParams, uuid):
model = scriptParams["Segmentation_model"]
big_mem = scriptParams["Big_memory_nodes"] #TODO: implement big memory nodes
model_path=model
user = conn.getUser()
user = user.getName()
# print("user: %s" % (user))
# print(model_path)
images, logMessage = script_utils.getObjects(conn, scriptParams)
if not images:
return None, None, logMessage
imageIds = [i.getId() for i in images]
for iId in imageIds:
tmpdir_stack = tempfile.mkdtemp(dir=cache_dir)
tmpdir_out = tempfile.mkdtemp(dir=cache_dir)
image = conn.getObject("Image", iId)
dataset = image.getParent().getId()
sizeZ = image.getSizeZ()
print(sizeZ)
# job_liner=[]
all_jobs = open("%s.job" % (os.path.join(cache_dir, tmpdir_out.split('/')[-1])), 'w+')
for z in range(sizeZ):
plane = image.renderImage(z, 0)
img_path = os.path.join(tmpdir_stack, "plane_%02d.tiff" % z)
plane.save(img_path)
ijmacro_args = "%s*%s/*%s" % (img_path, tmpdir_out, model_path)
img_path2 = os.path.join(tmpdir_out, "plane_%02d.tiff" % z)
job_liner=("%s -a %s -Xmx2g -- -macro %s %s -batch:%s:0 \n" % (XVFBRUN_PATH, IMAGEJ_PATH, MACRO_PATH2, ijmacro_args, img_path2))
all_jobs.writelines(job_liner)
all_jobs.close()
system = scriptParams["System"]
wtime = scriptParams["Wall_time"]
pmem = scriptParams["Private_memory"]
pbs_file = "%s.pbs" % (os.path.join(cache_dir, tmpdir_out.split('/')[-1]))
nodes = int(math.ceil(((2.00*sizeZ)+0.15*(2.00*sizeZ))/48))
stack_args = "%s/" % (tmpdir_out)
image_name = image.getName()
qsub_cmd = ". %s %s %s %s %s %s %s %s %s %s %s %s > %s" % (PBS_GEN, user, dataset, image_name, uuid, MACRO_PATH, stack_args, tmpdir_out, wtime, pmem, all_jobs.name, nodes, pbs_file)
print(qsub_cmd)
os.system(qsub_cmd)
enableKeepAlive_time = (72*60*60)
conn.c.enableKeepAlive(enableKeepAlive_time)
os.system("ssh %s '%s %s'" % (system, qsub_path, pbs_file))
def processImages(conn, scriptParams):
lineWidth = scriptParams['Line_Width']
newKymographs = []
message = ""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [image for image in images if
image.getROICount(["Polyline", "Line"]) > 0]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
for image in images:
if image.getSizeT() == 1:
print "Image: %s is not a movie (sizeT = 1)"\
" - Can't create Kymograph" % image.getId()
continue
newImages = [] # kymographs derived from the current image.
cNames = []
colors = []
for ch in image.getChannels():
cNames.append(ch.getLabel())
colors.append(ch.getColor().getRGB())
sizeT = image.getSizeT()
pixels = image.getPrimaryPixels()
dataset = image.getDataset()
if dataset is not None and not dataset.canLink():
dataset = None
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
# kymograph strategy - Using Line and Polyline ROIs:
# NB: Use ALL time points unless >1 shape AND 'use_all_timepoints' =
# False
# If > 1 shape per time-point (per ROI), pick one!
# 1 - Single line. Use this shape for all time points
# 2 - Many lines. Use the first one to fix length. Subsequent lines to
# update start and direction
# 3 - Single polyline. Use this shape for all time points
# 4 - Many polylines. Use the first one to fix length.
for roi in result.rois:
lines = {} # map of theT: line
polylines = {} # map of theT: polyline
for s in roi.copyShapes():
theZ = s.getTheZ() and s.getTheZ().getValue() or 0
theT = s.getTheT() and s.getTheT().getValue() or 0
# TODO: Add some filter of shapes. E.g. text? / 'lines' only
# etc.
if type(s) == omero.model.LineI:
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
lines[theT] = {'theZ': theZ, 'x1': x1, 'y1': y1, 'x2': x2,
'y2': y2}
elif type(s) == omero.model.PolylineI:
points = pointsStringToXYlist(s.getPoints().getValue())
polylines[theT] = {'theZ': theZ, 'points': points}
if len(lines) > 0:
newImg = linesKymograph(
conn, scriptParams, image, lines, lineWidth, dataset)
newImages.append(newImg)
lines = []
elif len(polylines) > 0:
newImg = polyLineKymograph(
conn, scriptParams, image, polylines, lineWidth, dataset)
newImages.append(newImg)
else:
print "ROI: %s had no lines or polylines" \
% roi.getId().getValue()
# look-up the interval for each time-point
tInterval = None
infos = list(pixels.copyPlaneInfo(theC=0, theT=sizeT-1, theZ=0))
if len(infos) > 0:
duration = infos[0].deltaT
print "duration", duration
if sizeT == 1:
tInterval = duration
else:
tInterval = duration/(sizeT-1)
elif pixels.timeIncrement is not None:
print "pixels.timeIncrement", pixels.timeIncrement
tInterval = pixels.timeIncrement
elif "Time_Increment" in scriptParams:
tInterval = scriptParams["Time_Increment"]
pixel_size = None
if pixels.physicalSizeX is not None:
pixel_size = pixels.physicalSizeX
elif "Pixel_Size" in scriptParams:
pixel_size = scriptParams['Pixel_Size']
# Save channel names and colors for each new image
for img in newImages:
print "Applying channel Names:", cNames, " Colors:", colors
for i, c in enumerate(img.getChannels()):
lc = c.getLogicalChannel()
lc.setName(cNames[i])
lc.save()
r, g, b = colors[i]
# need to reload channels to avoid optimistic lock on update
cObj = conn.getQueryService().get("Channel", c.id)
cObj.red = omero.rtypes.rint(r)
cObj.green = omero.rtypes.rint(g)
cObj.blue = omero.rtypes.rint(b)
cObj.alpha = omero.rtypes.rint(255)
conn.getUpdateService().saveObject(cObj)
img.resetRDefs() # reset based on colors above
# If we know pixel sizes, set them on the new image
if pixel_size is not None or tInterval is not None:
px = conn.getQueryService().get("Pixels", img.getPixelsId())
if pixel_size is not None:
px.setPhysicalSizeX(rdouble(pixel_size))
if tInterval is not None:
t_per_pixel = tInterval / lineWidth
px.setPhysicalSizeY(rdouble(t_per_pixel))
conn.getUpdateService().saveObject(px)
newKymographs.extend(newImages)
if not newKymographs:
message += "No kymograph created. See 'Error' or 'Info' for details."
else:
if not dataset:
linkMessage = " but could not be attached"
else:
linkMessage = ""
if len(newImages) == 1:
message += "New kymograph created%s: %s." \
% (linkMessage, newImages[0].getName())
elif len(newImages) > 1:
message += "%s new kymographs created%s." \
% (len(newImages), linkMessage)
return newKymographs, message
def processImages(conn, scriptParams):
"""
Process the script params to make a list of channel_offsets, then iterate through
the images creating a new image from each with the specified channel offsets
"""
message =""
# Get the images
images, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, None, message
imageIds = [i.getId() for i in images]
# Get the channel offsets
channel_offsets = []
for i in range(1, 5):
pName = "Channel_%s" % i
if scriptParams[pName]:
index = i-1 # UI channel index is 1-based - we want 0-based
x = "Channel%s_X_shift"%i in scriptParams and scriptParams["Channel%s_X_shift"%i] or 0
y = "Channel%s_Y_shift"%i in scriptParams and scriptParams["Channel%s_Y_shift"%i] or 0
z = "Channel%s_Z_shift"%i in scriptParams and scriptParams["Channel%s_Z_shift"%i] or 0
channel_offsets.append({'index':index, 'x':x, 'y':y, 'z':z})
print channel_offsets
dataset = None
if "New_Dataset_Name" in scriptParams:
# create new Dataset...
newDatasetName = scriptParams["New_Dataset_Name"]
dataset = omero.gateway.DatasetWrapper(conn, obj=omero.model.DatasetI())
dataset.setName(rstring(newDatasetName))
dataset.save()
# add to parent Project
parentDs = images[0].getParent()
project = parentDs is not None and parentDs.getParent() or None
if project is not None and project.canLink():
link = omero.model.ProjectDatasetLinkI()
link.parent = omero.model.ProjectI(project.getId(), False)
link.child = omero.model.DatasetI(dataset.getId(), False)
conn.getUpdateService().saveAndReturnObject(link)
# need to handle Datasets eventually - Just do images for now
newImages = []
links = []
for iId in imageIds:
newImg, link = newImageWithChannelOffsets(conn, iId, channel_offsets, dataset)
if newImg is not None:
newImages.append(newImg)
if link is not None:
links.append(link)
if not newImages:
message += "No image created."
else:
if len(newImages) == 1:
if not link:
linkMessage = " but could not be attached"
else:
linkMessage = ""
message += "New image created%s: %s." % (linkMessage, newImages[0].getName())
elif len(newImages) > 1:
message += "%s new images created" % len(newImages)
if not len(links) == len(newImages):
message +=" but some of them could not be attached."
else:
message += "."
return newImages, dataset, message
def run_processing(conn, script_params):
"""
Collects params and starts the processing
@param conn: the BlitzGateWay connection
@param script_params: the parameters collected from the script input
"""
dataType = script_params["Data_Type"]
updateService = conn.getUpdateService()
file_anns = []
message = ""
if script_params['Convert_coordinates_to_nm']:
cam_pix_size = script_params['Parent_Image_Pixel_Size']
else:
cam_pix_size = 1
file_type = script_params['File_Type']
rmax = script_params['Max_radius']
file_ids = script_params['AnnotationIDs']
# Get the images
objects, logMessage = script_utils.getObjects(conn, script_params)
message += logMessage
if not objects:
return None, message
# Concatenate images from datasets
if dataType == 'Image':
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
# 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
total_rois = sum([i.getROICount("Rect") for i in images])
if total_rois > 10:
message += "Cannot start batch processing - too many rois (maximum is 10)."
return None, message
image_ids = [i.getId() for i in images]
ripley = []
figures = []
figure_ids = []
for i, id in enumerate(image_ids):
image = conn.getObject("Image", id)
if not image:
message = 'Could not find specified image'
return message
ann = conn.getObject("Annotation", file_ids[i])
if not ann:
message = 'Could not find specified annotation'
return message
path_to_ann = ann.getFile().getPath() + '/' + ann.getFile().getName()
name, ext = os.path.splitext(path_to_ann)
if ('txt' in ext) or ('csv' in ext):
#download the localisations data file
path_to_data = download_data(ann)
#get all xy coords from the file
coords = parse_sr_data(path_to_data, file_type, cam_pix_size)
#determine the number of channels
sizeC = len(coords)
#get the regions of interest
rectangles = get_rectangles(conn, id)
#calculate the ripley function in each roi
ripley_data, ripley_figure = process_data(conn, image, file_type,
sizeC, rectangles,
coords, rmax)
ripley.append(ripley_data)
figures.append(ripley_figure)
figure_ids.append(ripley_figure.getId())
create_containers(conn, image, ripley_figure)
new_file_ann = attach_results(conn, ann, ripley_figure,
ripley_data, sizeC, rectangles)
if new_file_ann:
file_anns.append(new_file_ann)
if not file_anns:
faMessage = "No Analysis files created. See 'Info' or 'Error' for"\
" more details"
elif len(file_anns) > 1:
faMessage = "Created %s csv (Excel) files" % len(file_anns)
elif len(file_anns) == 1:
faMessage = "Created a new csv (Excel) file and attached to image ID %s" \
% ripley_figure.getId()
# clean up
delete_downloaded_data(ann)
message += faMessage
else:
message = 'file annotation must be txt or csv'
return message
robj = (len(figures) > 0) and figures[0]._obj or None
return robj, message
def makeThumbnailFigure(conn, scriptParams):
"""
Makes the figure using the parameters in @scriptParams, attaches the
figure to the parent Project/Dataset, and returns the file-annotation ID
@ returns Returns the id of the originalFileLink child. (ID object,
not value)
"""
log("Thumbnail figure created by OMERO")
log("")
message = ""
# Get the objects (images or datasets)
objects, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, message
# Get parent
parent = None
if "Parent_ID" in scriptParams and len(scriptParams["IDs"]) > 1:
if scriptParams["Data_Type"] == "Image":
parent = conn.getObject("Dataset", scriptParams["Parent_ID"])
else:
parent = conn.getObject("Project", scriptParams["Parent_ID"])
if parent is None:
parent = objects[0] # Attach figure to the first object
parentClass = parent.OMERO_CLASS
log("Figure will be linked to %s%s: %s" %
(parentClass[0].lower(), parentClass[1:], parent.getName()))
tagIds = []
if "Tag_IDs" in scriptParams:
tagIds = scriptParams['Tag_IDs']
if len(tagIds) == 0:
tagIds = None
showUntagged = False
if (tagIds):
showUntagged = scriptParams["Show_Untagged_Images"]
thumbSize = scriptParams["Thumbnail_Size"]
maxColumns = scriptParams["Max_Columns"]
figHeight = 0
figWidth = 0
dsCanvases = []
if scriptParams["Data_Type"] == "Dataset":
for dataset in objects:
log("Dataset: %s ID: %d" %
(dataset.getName(), dataset.getId()))
images = list(dataset.listChildren())
title = dataset.getName().decode('utf8')
dsCanvas = paintDatasetCanvas(conn,
images,
title,
tagIds,
showUntagged,
length=thumbSize,
colCount=maxColumns)
if dsCanvas is None:
continue
dsCanvases.append(dsCanvas)
figHeight += dsCanvas.size[1]
figWidth = max(figWidth, dsCanvas.size[0])
else:
imageCanvas = paintDatasetCanvas(conn,
objects,
"",
tagIds,
showUntagged,
length=thumbSize,
colCount=maxColumns)
dsCanvases.append(imageCanvas)
figHeight += imageCanvas.size[1]
figWidth = max(figWidth, imageCanvas.size[0])
if len(dsCanvases) == 0:
message += "No figure created"
return None, message
figure = Image.new("RGB", (figWidth, figHeight), WHITE)
y = 0
for ds in dsCanvases:
imgUtil.pasteImage(ds, figure, 0, y)
y += ds.size[1]
log("")
figLegend = "\n".join(logLines)
format = scriptParams["Format"]
figureName = scriptParams["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/Thumbnail_Figure"
fileAnnotation, faMessage = scriptUtil.createLinkFileAnnotation(
conn,
output,
parent,
output="Thumbnail figure",
mimetype=mimetype,
ns=namespace,
desc=figLegend,
origFilePathAndName=figureName)
message += faMessage
return fileAnnotation, message
def dataset_to_platewell(conn, scriptParams):
updateService = conn.getUpdateService()
message = ""
# Get the datasets ID
datasets, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
def has_images_linked_to_well(dataset):
params = omero.sys.ParametersI()
query = "select count(well) from Well as well "\
"left outer join well.wellSamples as ws " \
"left outer join ws.image as img "\
"where img.id in (:ids)"
params.addIds([i.getId() for i in dataset.listChildren()])
n_wells = unwrap(conn.getQueryService().projection(
query, params, conn.SERVICE_OPTS)[0])[0]
if n_wells > 0:
print "Dataset %s contains images linked to wells." \
% dataset.getId()
return True
else:
return False
# Exclude datasets containing images already linked to a well
nDatasets = len(datasets)
datasets = [x for x in datasets if not has_images_linked_to_well(x)]
if len(datasets) < nDatasets:
message += "Excluded %s out of %s dataset(s). " \
% (nDatasets - len(datasets), nDatasets)
# Return if all input dataset are not found or excluded
if not datasets:
return message
# Filter dataset IDs by permissions
IDs = [ds.getId() for ds in datasets if ds.canLink()]
if len(IDs) != len(datasets):
permIDs = [str(ds.getId()) for ds in datasets if not ds.canLink()]
message += "You do not have the permissions to add the images from"\
" the dataset(s): %s." % ",".join(permIDs)
if not IDs:
return message
plate = None
newplate = None
if "Plate" in scriptParams and len(scriptParams["Plate"]) > 0:
sp = scriptParams["Plate"]
# see if this is an ID of existing plate
try:
plateId = long(sp)
plate = conn.getObject("Plate", plateId)
except ValueError:
pass
# if not, create one
if plate is None:
newplate = omero.model.PlateI()
newplate.name = rstring(sp)
newplate.columnNamingConvention = rstring(
str(scriptParams["Column_Names"]))
# 'letter' or 'number'
newplate.rowNamingConvention = rstring(
str(scriptParams["Row_Names"]))
newplate = updateService.saveAndReturnObject(newplate)
plate = conn.getObject("Plate", newplate.id.val)
deletes = []
for datasetId in IDs:
deleteHandle = dataset_to_well(conn, scriptParams, datasetId, plate.id)
if deleteHandle is not None:
deletes.append(deleteHandle)
# wait for any deletes to finish
for handle in deletes:
cb = omero.callbacks.DeleteCallbackI(conn.c, handle)
while True: # ms
if cb.block(100) is None:
print "Waiting for delete"
else:
break
err = handle.errors()
if err > 0:
print "Delete error", err
else:
print "Delete OK"
if newplate:
message += "New plate created: %s." % newplate.getName().val
robj = newplate
else:
robj = None
return robj, message
def datasets_to_plates(conn, scriptParams):
updateService = conn.getUpdateService()
message = ""
# Get the datasets ID
datasets, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
def has_images_linked_to_well(dataset):
params = omero.sys.ParametersI()
query = "select count(well) from Well as well "\
"left outer join well.wellSamples as ws " \
"left outer join ws.image as img "\
"where img.id in (:ids)"
params.addIds([i.getId() for i in dataset.listChildren()])
n_wells = unwrap(conn.getQueryService().projection(
query, params, conn.SERVICE_OPTS)[0])[0]
if n_wells > 0:
print "Dataset %s contains images linked to wells." \
% dataset.getId()
return True
else:
return False
# Exclude datasets containing images already linked to a well
nDatasets = len(datasets)
datasets = [x for x in datasets if not has_images_linked_to_well(x)]
if len(datasets) < nDatasets:
message += "Excluded %s out of %s dataset(s). " \
% (nDatasets - len(datasets), nDatasets)
# Return if all input dataset are not found or excluded
if not datasets:
return None, message
# Filter dataset IDs by permissions
IDs = [ds.getId() for ds in datasets if ds.canLink()]
if len(IDs) != len(datasets):
permIDs = [str(ds.getId()) for ds in datasets if not ds.canLink()]
message += "You do not have the permissions to add the images from"\
" the dataset(s): %s." % ",".join(permIDs)
if not IDs:
return None, message
# find or create Screen if specified
screen = None
newscreen = None
if "Screen" in scriptParams and len(scriptParams["Screen"]) > 0:
s = scriptParams["Screen"]
# see if this is ID of existing screen
try:
screenId = long(s)
screen = conn.getObject("Screen", screenId)
except ValueError:
pass
# if not, create one
if screen is None:
newscreen = omero.model.ScreenI()
newscreen.name = rstring(s)
newscreen = updateService.saveAndReturnObject(newscreen)
screen = conn.getObject("Screen", newscreen.id.val)
plates = []
links = []
deletes = []
for datasetId in IDs:
plate, link, deleteHandle = dataset_to_plate(conn, scriptParams,
datasetId, screen)
if plate is not None:
plates.append(plate)
if link is not None:
links.append(link)
if deleteHandle is not None:
deletes.append(deleteHandle)
# wait for any deletes to finish
for handle in deletes:
cb = omero.callbacks.DeleteCallbackI(conn.c, handle)
while True: # ms
if cb.block(100) is None:
print "Waiting for delete"
else:
break
err = handle.errors()
if err > 0:
print "Delete error", err
else:
print "Delete OK"
if newscreen:
message += "New screen created: %s." % newscreen.getName().val
robj = newscreen
elif plates:
robj = plates[0]
else:
robj = None
if plates:
if len(plates) == 1:
message += " New plate created: %s" % plates[0].name.val
else:
message += " %s plates created" % len(plates)
if len(plates) == len(links):
message += "."
else:
message += " but could not be attached."
else:
message += "No plate created."
return robj, message
def processImages(client, conn, scriptParams):
"""
Process the script params to make a list of channel_offsets, then iterate
through the images creating a new image from each with the specified
channel offsets
"""
message = ""
# Get the images
objects, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not objects:
return None, None, message
# Concatenate images from datasets
if scriptParams["Data_Type"] == "Image":
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
queryService = conn.getQueryService()
roiService = conn.getRoiService()
print "Showing X ; Y coordinates in micrometer"
for image in images:
print "---------- {0} ---------- ".format(image.getName())
metadata = dict(image.loadOriginalMetadata()[1])
params = ParametersI()
params.addId(image.getId())
roiResult = roiService.findByImage(image.getId(), None)
for roi in roiResult.rois:
for shape in roi.copyShapes():
if type(shape) != omero.model.PointI:
continue
# From tem-hole-finder:XYpic2XYstage.m
# RotM=1e-9*[tt(1),tt(2);tt(3),tt(4)];
# Offset=1e-6*[tt(5),tt(6)];
# XYstageHoles=RotM*XYpixHolesOverview'+repmat(Offset',[1,l1]);
# TODO: Eval is of course not really safe...
tt = eval(metadata['Conversion matrix'])
RotM = [x * 1e-9 for x in [tt[0], tt[1], tt[2], tt[3]]]
Offset = [x * 1e-6 for x in [tt[4], tt[5]]]
xRoi = int(shape.getCx().getValue())
yRoi = int(shape.getCy().getValue())
stageX = RotM[0] * xRoi + RotM[1] * yRoi + Offset[0]
stageY = RotM[2] * xRoi + RotM[3] * yRoi + Offset[1]
name = roi.getName().getValue() if roi.getName() is not None else "Unnamed"
print "{0} [ {1} ; {2} ] ".format(name, stageX * 1e6, stageY * 1e6)
print "--------------------------------------"
return "Finished calculating"
def processImages(conn, scriptParams):
lineWidth = scriptParams['Line_Width']
newKymographs = []
message = ""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [
image for image in images
if image.getROICount(["Polyline", "Line"]) > 0
]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
for image in images:
if image.getSizeT() == 1:
print "Image: %s is not a movie (sizeT = 1)"\
" - Can't create Kymograph" % image.getId()
continue
newImages = [] # kymographs derived from the current image.
cNames = []
colors = []
for ch in image.getChannels():
cNames.append(ch.getLabel())
colors.append(ch.getColor().getRGB())
sizeT = image.getSizeT()
pixels = image.getPrimaryPixels()
dataset = image.getDataset()
if dataset is not None and not dataset.canLink():
dataset = None
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
# kymograph strategy - Using Line and Polyline ROIs:
# NB: Use ALL time points unless >1 shape AND 'use_all_timepoints' =
# False
# If > 1 shape per time-point (per ROI), pick one!
# 1 - Single line. Use this shape for all time points
# 2 - Many lines. Use the first one to fix length. Subsequent lines to
# update start and direction
# 3 - Single polyline. Use this shape for all time points
# 4 - Many polylines. Use the first one to fix length.
for roi in result.rois:
lines = {} # map of theT: line
polylines = {} # map of theT: polyline
for s in roi.copyShapes():
theZ = s.getTheZ() and s.getTheZ().getValue() or 0
theT = s.getTheT() and s.getTheT().getValue() or 0
# TODO: Add some filter of shapes. E.g. text? / 'lines' only
# etc.
if type(s) == omero.model.LineI:
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
lines[theT] = {
'theZ': theZ,
'x1': x1,
'y1': y1,
'x2': x2,
'y2': y2
}
elif type(s) == omero.model.PolylineI:
points = pointsStringToXYlist(s.getPoints().getValue())
polylines[theT] = {'theZ': theZ, 'points': points}
if len(lines) > 0:
newImg = linesKymograph(conn, scriptParams, image, lines,
lineWidth, dataset)
newImages.append(newImg)
lines = []
elif len(polylines) > 0:
newImg = polyLineKymograph(conn, scriptParams, image,
polylines, lineWidth, dataset)
newImages.append(newImg)
else:
print "ROI: %s had no lines or polylines" \
% roi.getId().getValue()
# look-up the interval for each time-point
tInterval = None
infos = list(pixels.copyPlaneInfo(theC=0, theT=sizeT - 1, theZ=0))
if len(infos) > 0:
duration = infos[0].deltaT
print "duration", duration
if sizeT == 1:
tInterval = duration
else:
tInterval = duration / (sizeT - 1)
elif pixels.timeIncrement is not None:
print "pixels.timeIncrement", pixels.timeIncrement
tInterval = pixels.timeIncrement
elif "Time_Increment" in scriptParams:
tInterval = scriptParams["Time_Increment"]
pixel_size = None
if pixels.physicalSizeX is not None:
pixel_size = pixels.physicalSizeX
elif "Pixel_Size" in scriptParams:
pixel_size = scriptParams['Pixel_Size']
# Save channel names and colors for each new image
for img in newImages:
print "Applying channel Names:", cNames, " Colors:", colors
for i, c in enumerate(img.getChannels()):
lc = c.getLogicalChannel()
lc.setName(cNames[i])
lc.save()
r, g, b = colors[i]
# need to reload channels to avoid optimistic lock on update
cObj = conn.getQueryService().get("Channel", c.id)
cObj.red = omero.rtypes.rint(r)
cObj.green = omero.rtypes.rint(g)
cObj.blue = omero.rtypes.rint(b)
cObj.alpha = omero.rtypes.rint(255)
conn.getUpdateService().saveObject(cObj)
img.resetRDefs() # reset based on colors above
# If we know pixel sizes, set them on the new image
if pixel_size is not None or tInterval is not None:
px = conn.getQueryService().get("Pixels", img.getPixelsId())
if pixel_size is not None:
px.setPhysicalSizeX(rdouble(pixel_size))
if tInterval is not None:
t_per_pixel = tInterval / lineWidth
px.setPhysicalSizeY(rdouble(t_per_pixel))
conn.getUpdateService().saveObject(px)
newKymographs.extend(newImages)
if not newKymographs:
message += "No kymograph created. See 'Error' or 'Info' for details."
else:
if not dataset:
linkMessage = " but could not be attached"
else:
linkMessage = ""
if len(newImages) == 1:
message += "New kymograph created%s: %s." \
% (linkMessage, newImages[0].getName())
elif len(newImages) > 1:
message += "%s new kymographs created%s." \
% (len(newImages), linkMessage)
return newKymographs, message
def run_processing(conn, session, script_params):
"""
Collects params and starts the processing
@param conn: the BlitzGateWay connection
@param script_params: the parameters collected from the script input
"""
global input_dir
global output_dir
input_dir = tempfile.mkdtemp(prefix='stitching_input')
output_dir = tempfile.mkdtemp(prefix='stitching_output')
def empty_dir(dir_path):
for old_file in os.listdir(dir_path):
file_path = os.path.join(dir_path, old_file)
os.unlink(file_path)
message = ""
dataType = script_params["Data_Type"]
# Get the images
objects, logMessage = script_utils.getObjects(conn, script_params)
message += logMessage
if not objects:
return None, message
# Concatenate images from datasets
if dataType == 'Image':
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
image_ids = [i.getId() for i in images]
if len(image_ids) > 10:
message = 'Max number of datasets for batch exceeded (10)'
return message
new_images = []
new_ids = []
for image in conn.getObjects("Image", image_ids):
# remove input and processed images
empty_dir(input_dir)
empty_dir(output_dir)
theC = None
if script_params['Single_Channel']:
theC = script_params['Channel']
theZ = None
sizeZ = image.getSizeZ()
if script_params['Single_Z']:
theZ = script_params['Z_slice']
sizeZ = 1
if script_params['Range_Z']:
zstart = script_params['Z_start']
zstop = script_params['Z_stop']
theZ = range(zstart, zstop + 1)
sizeZ = len(theZ)
# download the image
image_names = download_tiles(conn, image, theC, theZ)
results_file = str(image.getId()) + "_stitching.txt"
stitching_args = (results_file, script_params['grid_x'],
script_params['grid_y'],
script_params['tile_overlap'],
script_params['fusion_method'],
script_params['regression_threshold'],
script_params['ave_displacement_threshold'],
script_params['abs_displacement_threshold'], sizeZ)
# do the stitching using dockerized fiji
new_image = run_stitching(conn, session, stitching_args)
# if the new image is created
# link it to the original omero image
if new_image:
create_containers(conn, image, new_image)
new_images.append(new_image)
new_ids.append(new_image.getId())
if len(new_ids) == 0:
print("No new images created.")
return
if new_images:
if len(new_images) > 1:
message += "Created %s new images" % len(new_images)
else:
message += "Created a new image"
else:
message += "No image created"
print(script_params['Email_Results'])
# if new images were created email the omero user
if script_params['Email_Results'] and new_images:
email_results(conn, script_params, new_ids)
# remove downloaded image and outputs
shutil.rmtree(input_dir)
shutil.rmtree(output_dir)
robj = (len(new_images) > 0) and new_images[0]._obj or None
return robj, 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 run_processing(conn, session, script_params):
"""
Collects params and starts the processing
@param conn: the BlitzGateWay connection
@param script_params: the parameters collected from the script input
"""
global input_dir
global output_dir
input_dir = tempfile.mkdtemp(prefix='clearing_input')
output_dir = tempfile.mkdtemp(prefix='clearing_output')
def empty_dir(dir_path):
for old_file in os.listdir(dir_path):
file_path = os.path.join(dir_path, old_file)
os.unlink(file_path)
message = ""
dataType = script_params["Data_Type"]
# Get the images
objects, logMessage = script_utils.getObjects(conn, script_params)
message += logMessage
if not objects:
return None, message
# Concatenate images from datasets
if dataType == 'Image':
images = objects
else:
images = []
for ds in objects:
images += ds.listChildren()
image_ids = [i.getId() for i in images]
if len(image_ids) > 10:
message = 'Max number of datasets for batch exceeded (10)'
return message
new_images = []
new_ids = []
for source in conn.getObjects("Image", image_ids):
# remove input and processed images
empty_dir(input_dir)
empty_dir(output_dir)
# get the polygon rois
rects, polys = get_polygons_from_rois(conn, source)
# download the image and write polys to metadata
target, target_path = download_image(conn, source, polys)
# run the clearing
new_image = run_clearing(conn, session, source, target)
# put images in datasets, datasets in projects
create_containers(conn, source, new_image)
if new_image:
# set_attributes(conn,image, new_image)
new_images.append(new_image)
new_ids.append(new_image.getId())
if len(new_ids) == 0:
print "No new images created."
return
if new_images:
if len(new_images) > 1:
message += "Created %s new images" % len(new_images)
else:
message += "Created a new image"
else:
message += "No image created"
print script_params['Email_Results']
if script_params['Email_Results'] and new_images:
email_results(conn, script_params, new_ids)
shutil.rmtree(input_dir)
shutil.rmtree(output_dir)
#
robj = (len(new_images) > 0) and new_images[0]._obj or None
return robj, message
def processImages(conn, scriptParams):
fileAnns = []
message =""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [image for image in images if image.getROICount(["Polyline","Line"])>0]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
for image in images:
print "\nAnalysing Image: %s ID: %s" % (image.getName(), image.getId())
if image.getSizeT() > 1:
message += "%s ID: %s appears to be a time-lapse Image, not a kymograph." % (image.getName(), image.getId())
continue
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
secsPerPixelY = image.getPixelSizeY()
micronsPerPixelX = image.getPixelSizeX()
if secsPerPixelY and micronsPerPixelX:
micronsPerSec = micronsPerPixelX / secsPerPixelY
else: micronsPerSec = None
# for each line or polyline, create a row in csv table: y(t), x, dy(dt), dx, x/t (line), x/t (average)
colNames = "\nt_start (pixels), x_start (pixels), t_end (pixels), x_end (pixels), dt (pixels), dx (pixels), x/t, average x/t, speed(um/sec)"
tableData = ""
for roi in result.rois:
for s in roi.copyShapes():
if type(s) == omero.model.LineI:
tableData += "\nLine"
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
dx = abs(x1-x2)
dy = abs(y1-y2)
dxPerY = float(dx)/dy
tableData += "\n"
tableData += ",".join([str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY, dxPerY, "")])
if micronsPerSec:
speed = dxPerY * micronsPerSec
tableData += "%s" % speed
elif type(s) == omero.model.PolylineI:
tableData += "\nPolyline"
points = pointsStringToXYlist(s.getPoints().getValue())
xStart, yStart = points[0]
for i in range(1, len(points)):
x1, y1 = points[i-1]
x2, y2 = points[i]
dx = abs(x1-x2)
dy = abs(y1-y2)
dxPerY = float(dx)/dy
avXperY = abs(float(x2-xStart)/(y2-yStart))
tableData += "\n"
tableData += ",".join([str(x) for x in (y1, x1, y2, x2, dy, dx, dxPerY, avXperY, "")])
if micronsPerSec:
speed = dxPerY * micronsPerSec
tableData += "%s" % speed
# write table data to csv...
if len(tableData) > 0:
tableString = "secsPerPixelY: %s" % secsPerPixelY
tableString += '\nmicronsPerPixelX: %s' % micronsPerPixelX
tableString += "\nmicronsPerSec: %s" % micronsPerSec
tableString += "\n"
tableString += colNames
tableString += tableData
print tableString
csvFileName = 'kymograph_velocities_%s.csv' % image.getId()
csvFile = open(csvFileName, 'w')
try:
csvFile.write(tableString)
finally:
csvFile.close()
fileAnn, faMessage = scriptUtil.createLinkFileAnnotation(conn, csvFileName, image,
output="Line Plot csv (Excel) file", mimetype="text/csv", desc=None)
print fileAnn, faMessage
if fileAnn:
fileAnns.append(fileAnn)
else:
print "Found NO lines or polylines to analyse for Image"
if not fileAnns:
faMessage = "No Analysis files created. See 'Info' or 'Error' for more details"
elif len(fileAnns) > 1:
faMessage = "Created %s csv (Excel) files" % len(fileAnns)
message += faMessage
return fileAnns, message
def processImages(conn, scriptParams):
lineWidth = scriptParams['Line_Width']
fileAnns = []
message = ""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [
image for image in images
if image.getROICount(["Polyline", "Line"]) > 0
]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
for image in images:
cNames = []
colors = []
for ch in image.getChannels():
cNames.append(ch.getLabel())
colors.append(ch.getColor().getRGB())
sizeC = image.getSizeC()
if 'Channels' in scriptParams:
scriptParams['Channels'] = [
i - 1 for i in scriptParams['Channels']
]
# Convert user input from 1-based to 0-based
for i in scriptParams['Channels']:
print i, type(i)
else:
scriptParams['Channels'] = range(sizeC)
# channelMinMax = []
# for c in image.getChannels():
# minC = c.getWindowMin()
# maxC = c.getWindowMax()
# channelMinMax.append((minC, maxC))
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
lines = []
polylines = []
for roi in result.rois:
roiId = roi.getId().getValue()
for s in roi.copyShapes():
theZ = s.getTheZ() and s.getTheZ().getValue() or 0
theT = s.getTheT() and s.getTheT().getValue() or 0
# TODO: Add some filter of shapes. E.g. text? / 'lines' only
# etc.
if type(s) == omero.model.LineI:
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
lines.append({
'id': roiId,
'theT': theT,
'theZ': theZ,
'x1': x1,
'y1': y1,
'x2': x2,
'y2': y2
})
elif type(s) == omero.model.PolylineI:
points = pointsStringToXYlist(s.getPoints().getValue())
polylines.append({
'id': roiId,
'theT': theT,
'theZ': theZ,
'points': points
})
if len(lines) == 0 and len(polylines) == 0:
print "Image: %s had no lines or polylines" % image.getId()
continue
# prepare column headers, including line-id if we are going to output
# raw data.
lineId = scriptParams['Sum_or_Average'] == 'Average, with raw data' \
and 'Line, ' or ""
colHeader = 'Image_ID, ROI_ID, Z, T, C, %sLine data %s of Line" \
" Width %s\n' % (lineId, scriptParams['Sum_or_Average'],
scriptParams['Line_Width'])
print 'colHeader', colHeader
# prepare a csv file to write our data to...
fileName = "Plot_Profile_%s.csv" % image.getId()
try:
f = open(fileName, 'w')
f.write(colHeader)
if len(lines) > 0:
processLines(conn, scriptParams, image, lines, lineWidth, f)
if len(polylines) > 0:
processPolyLines(conn, scriptParams, image, polylines,
lineWidth, f)
finally:
f.close()
fileAnn, faMessage = scriptUtil.createLinkFileAnnotation(
conn,
fileName,
image,
output="Line Plot csv (Excel) file",
mimetype="text/csv",
desc=None)
if fileAnn:
fileAnns.append(fileAnn)
if not fileAnns:
faMessage = "No Analysis files created. See 'Info' or 'Error' for"\
" more details"
elif len(fileAnns) > 1:
faMessage = "Created %s csv (Excel) files" % len(fileAnns)
message += faMessage
return fileAnns, 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 datasets_to_plates(conn, scriptParams):
updateService = conn.getUpdateService()
message = ""
# Get the datasets ID
datasets, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
def has_images_linked_to_well(dataset):
params = omero.sys.ParametersI()
query = "select count(well) from Well as well "\
"left outer join well.wellSamples as ws " \
"left outer join ws.image as img "\
"where img.id in (:ids)"
params.addIds([i.getId() for i in dataset.listChildren()])
n_wells = unwrap(conn.getQueryService().projection(
query, params, conn.SERVICE_OPTS)[0])[0]
if n_wells > 0:
print "Dataset %s contains images linked to wells." \
% dataset.getId()
return True
else:
return False
# Exclude datasets containing images already linked to a well
nDatasets = len(datasets)
datasets = [x for x in datasets if not has_images_linked_to_well(x)]
if len(datasets) < nDatasets:
message += "Excluded %s out of %s dataset(s). " \
% (nDatasets - len(datasets), nDatasets)
# Return if all input dataset are not found or excluded
if not datasets:
return None, message
# Filter dataset IDs by permissions
IDs = [ds.getId() for ds in datasets if ds.canLink()]
if len(IDs) != len(datasets):
permIDs = [str(ds.getId()) for ds in datasets if not ds.canLink()]
message += "You do not have the permissions to add the images from"\
" the dataset(s): %s." % ",".join(permIDs)
if not IDs:
return None, message
# find or create Screen if specified
screen = None
newscreen = None
if "Screen" in scriptParams and len(scriptParams["Screen"]) > 0:
s = scriptParams["Screen"]
# see if this is ID of existing screen
try:
screenId = long(s)
screen = conn.getObject("Screen", screenId)
except ValueError:
pass
# if not, create one
if screen is None:
newscreen = omero.model.ScreenI()
newscreen.name = rstring(s)
newscreen = updateService.saveAndReturnObject(newscreen)
screen = conn.getObject("Screen", newscreen.id.val)
plates = []
links = []
deletes = []
for datasetId in IDs:
plate, link, deleteHandle = dataset_to_plate(conn, scriptParams,
datasetId, screen)
if plate is not None:
plates.append(plate)
if link is not None:
links.append(link)
if deleteHandle is not None:
deletes.append(deleteHandle)
# wait for any deletes to finish
for handle in deletes:
cb = omero.callbacks.DeleteCallbackI(conn.c, handle)
while True: # ms
if cb.block(100) is None:
print "Waiting for delete"
else:
break
err = handle.errors()
if err > 0:
print "Delete error", err
else:
print "Delete OK"
if newscreen:
message += "New screen created: %s." % newscreen.getName().val
robj = newscreen
elif plates:
robj = plates[0]
else:
robj = None
if plates:
if len(plates) == 1:
message += " New plate created: %s" % plates[0].name.val
else:
message += " %s plates created" % len(plates)
if len(plates) == len(links):
message += "."
else:
message += " but could not be attached."
else:
message += "No plate created."
return robj, message
def processImages(conn, scriptParams):
"""
Process the script params to make a list of channel_offsets, then iterate
through the images creating a new image from each with the specified
channel offsets
"""
message = ""
images, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not images:
raise Exception("No images found")
imageIds = sorted(set([i.getId() for i in images]))
choice = scriptParams["Choice"]
debug = bool(scriptParams.get("Debug", False))
globalmin = defaultdict(list)
globalmax = defaultdict(list)
tb = TableBuilder("Context", "Channel", "Min", "Max")
statsInfos = dict()
for iId in imageIds:
statsInfo = calcStatsInfo(conn, iId, choice, debug)
statsInfos[iId] = statsInfo
for c, si in sorted(statsInfo.items()):
c_min, c_max = si
globalmin[c].append(c_min)
globalmax[c].append(c_max)
tb.row("Image:%s" % iId, c, c_min, c_max)
tb.row("", "", "", "")
for c in globalmin:
c_min = globalmin[c]
c_max = globalmax[c]
tb.row("Total: outer ", c, min(c_min), max(c_max))
tb.row("Total: inner ", c, max(c_min), min(c_max))
tb.row("Total: average", c, int(avg(c_min)), int(avg(c_max)))
if scriptParams["DryRun"]:
print str(tb.build())
else:
combine = scriptParams["Combine"]
for iId in imageIds:
img = conn.getObject("Image", iId)
for c, ch in enumerate(img.getChannels(noRE=True)):
si = ch.getStatsInfo()
if si is None:
si = StatsInfoI()
action = "creating"
else:
si = si._obj
action = "updating"
if combine == "no":
si.globalMin = rdouble(statsInfos[iId][c][0])
si.globalMax = rdouble(statsInfos[iId][c][1])
elif combine == "outer":
si.globalMin = rdouble(min(globalmin[c]))
si.globalMax = rdouble(max(globalmax[c]))
elif combine == "inner":
si.globalMin = rdouble(max(globalmin[c]))
si.globalMax = rdouble(min(globalmax[c]))
elif combine == "average":
si.globalMin = rdouble(avg(globalmin[c]))
si.globalMax = rdouble(avg(globalmax[c]))
else:
raise Exception("unknown combine: %s" % combine)
if debug:
print "Image:%s(c=%s) - %s StatsInfo(%s, %s)" % (
iId, c, action, si.globalMin.val, si.globalMax.val)
ch._obj.statsInfo = si
ch.save()
count = sum(map(len, statsInfos.values()))
message += "%s stats info object(s) processed" % count
return message
def runScript():
"""
The main entry point of the script, as called by the client via the scripting service, passing the required parameters.
"""
orders = [rstring('T-Z-C'), rstring('T-C-Z'), rstring('Z-T-C'), rstring('Z-C-T'), rstring('C-Z-T'),
rstring('C-T-Z')]
dataTypes = [rstring('Dataset'), rstring('Image')]
client = scripts.client('ExplodeImages.py',
'Explode multiplane/multitemporal images into multiple images, '
+ 'split based on channels, number of planes, and timestamps.',
scripts.String("Data_Type", optional=False, grouping="1",
description="The data you want to work with.", values=dataTypes,
default="Image"),
scripts.List("IDs", optional=False, grouping="1.1",
description="List of Dataset IDs or Image IDs").ofType(rlong(0)),
scripts.String("Storing_Dataset", optional=False, grouping="2",
description="Name of data set to store images", default='Explode'),
scripts.String("Base_Image_Path", grouping="2.1", description="Base name of image."),
scripts.String("Image_Order", grouping="2.2",
description="The order in which explosion information is displayed in"
+ " the image name. (T=time, Z=depth, C=color)",
values=orders, default="T-Z-C"),
version="1.0",
authors=["WebvalleyTeam 2013"],
institutions=["FBK"],
contact="*****@*****.**", )
try:
# process the list of args above.
scriptParams = {}
for key in client.getInputKeys():
if client.getInput(key):
scriptParams[key] = client.getInput(key, unwrap=True)
# establish connection to omero
conn = BlitzGateway(client_obj=client)
#get objects
objects, logMessage = script_utils.getObjects(conn, scriptParams)
# gather all images
images = []
if (scriptParams["Data_Type"] == "Dataset"):
for dataSet in objects:
images.extend(list(dataSet.listChildren()))
if not images:
print "No images found in selected dataset."
else:
images = objects
datasetObj = omero.model.DatasetI()
datasetObj.setName(rstring(scriptParams["Storing_Dataset"]))
datasetObj = conn.getUpdateService().saveAndReturnObject(datasetObj)
savePlanes(images, conn, datasetObj, scriptParams)
finally:
client.closeSession()
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 processImages(conn, scriptParams):
lineWidth = scriptParams['Line_Width']
fileAnns = []
message = ""
# Get the images
images, logMessage = scriptUtil.getObjects(conn, scriptParams)
message += logMessage
if not images:
return None, message
# Check for line and polyline ROIs and filter images list
images = [image for image in images if
image.getROICount(["Polyline", "Line"]) > 0]
if not images:
message += "No ROI containing line or polyline was found."
return None, message
for image in images:
cNames = []
colors = []
for ch in image.getChannels():
cNames.append(ch.getLabel())
colors.append(ch.getColor().getRGB())
sizeC = image.getSizeC()
if 'Channels' in scriptParams:
scriptParams['Channels'] = [i-1 for i in scriptParams['Channels']]
# Convert user input from 1-based to 0-based
for i in scriptParams['Channels']:
print i, type(i)
else:
scriptParams['Channels'] = range(sizeC)
# channelMinMax = []
# for c in image.getChannels():
# minC = c.getWindowMin()
# maxC = c.getWindowMax()
# channelMinMax.append((minC, maxC))
roiService = conn.getRoiService()
result = roiService.findByImage(image.getId(), None)
lines = []
polylines = []
for roi in result.rois:
roiId = roi.getId().getValue()
for s in roi.copyShapes():
theZ = s.getTheZ() and s.getTheZ().getValue() or 0
theT = s.getTheT() and s.getTheT().getValue() or 0
# TODO: Add some filter of shapes. E.g. text? / 'lines' only
# etc.
if type(s) == omero.model.LineI:
x1 = s.getX1().getValue()
x2 = s.getX2().getValue()
y1 = s.getY1().getValue()
y2 = s.getY2().getValue()
lines.append({'id': roiId, 'theT': theT, 'theZ': theZ,
'x1': x1, 'y1': y1, 'x2': x2, 'y2': y2})
elif type(s) == omero.model.PolylineI:
points = pointsStringToXYlist(s.getPoints().getValue())
polylines.append({'id': roiId, 'theT': theT, 'theZ': theZ,
'points': points})
if len(lines) == 0 and len(polylines) == 0:
print "Image: %s had no lines or polylines" % image.getId()
continue
# prepare column headers, including line-id if we are going to output
# raw data.
lineId = scriptParams['Sum_or_Average'] == 'Average, with raw data' \
and 'Line, ' or ""
colHeader = 'Image_ID, ROI_ID, Z, T, C, %sLine data %s of Line" \
" Width %s\n' % (lineId, scriptParams['Sum_or_Average'],
scriptParams['Line_Width'])
print 'colHeader', colHeader
# prepare a csv file to write our data to...
fileName = "Plot_Profile_%s.csv" % image.getId()
try:
f = open(fileName, 'w')
f.write(colHeader)
if len(lines) > 0:
processLines(conn, scriptParams, image, lines, lineWidth, f)
if len(polylines) > 0:
processPolyLines(
conn, scriptParams, image, polylines, lineWidth, f)
finally:
f.close()
fileAnn, faMessage = scriptUtil.createLinkFileAnnotation(
conn, fileName, image, output="Line Plot csv (Excel) file",
mimetype="text/csv", desc=None)
if fileAnn:
fileAnns.append(fileAnn)
if not fileAnns:
faMessage = "No Analysis files created. See 'Info' or 'Error' for"\
" more details"
elif len(fileAnns) > 1:
faMessage = "Created %s csv (Excel) files" % len(fileAnns)
message += faMessage
return fileAnns, message
def writeMovie(commandArgs, conn):
"""
Makes the movie.
@ returns Returns the file annotation
"""
log("Movie created by OMERO")
log("")
message = ""
session = conn.c.sf
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
# Get the images
images, logMessage = scriptUtil.getObjects(conn, commandArgs)
message += logMessage
if not images:
return None, message
# Get the first valid image (should be expanded to process the list)
omeroImage = images[0]
if commandArgs["RenderingDef_ID"] >= 0:
omeroImage._prepareRenderingEngine(rdid=commandArgs["RenderingDef_ID"])
pixels = omeroImage.getPrimaryPixels()
pixelsId = pixels.getId()
sizeX = pixels.getSizeX()
sizeY = pixels.getSizeY()
sizeZ = pixels.getSizeZ()
sizeC = pixels.getSizeC()
sizeT = pixels.getSizeT()
if (sizeX is None or sizeY is None or sizeZ is None or sizeT is None or
sizeC is None):
return
if (pixels.getPhysicalSizeX() is None):
commandArgs["Scalebar"] = 0
cRange = range(0, sizeC)
cWindows = None
cColours = None
if "ChannelsExtended" in commandArgs and \
validChannels(commandArgs["ChannelsExtended"], sizeC):
cRange = []
cWindows = []
cColours = []
for c in commandArgs["ChannelsExtended"]:
m = re.match('^(?P<i>\d+)(\|(?P<ws>\d+)' +
'\:(?P<we>\d+))?(\$(?P<c>.+))?$', c)
if m is not None:
cRange.append(int(m.group('i'))-1)
cWindows.append([float(m.group('ws')), float(m.group('we'))])
cColours.append(m.group('c'))
elif "Channels" in commandArgs and \
validChannels(commandArgs["Channels"], sizeC):
cRange = commandArgs["Channels"]
tzList = calculateRanges(sizeZ, sizeT, commandArgs)
timeMap = calculateAquisitionTime(conn, pixelsId, cRange, tzList)
if (timeMap is None):
commandArgs["Show_Time"] = False
if (timeMap is not None):
if (len(timeMap) == 0):
commandArgs["Show_Time"] = False
frameNo = 1
omeroImage.setActiveChannels(map(lambda x: x+1, cRange),
cWindows,
cColours)
renderingEngine = omeroImage._re
overlayColour = (255, 255, 255)
if "Overlay_Colour" in commandArgs:
r, g, b, a = COLOURS[commandArgs["Overlay_Colour"]]
overlayColour = (r, g, b)
canvasColour = tuple(COLOURS[commandArgs["Canvas_Colour"]][:3])
mw = commandArgs["Min_Width"]
if mw < sizeX:
mw = sizeX
mh = commandArgs["Min_Height"]
if mh < sizeY:
mh = sizeY
ovlpos = None
canvas = None
if sizeX < mw or sizeY < mh:
ovlpos = ((mw-sizeX) / 2, (mh-sizeY) / 2)
canvas = Image.new("RGBA", (mw, mh), canvasColour)
format = commandArgs["Format"]
fileNames = []
# add intro...
if "Intro_Slide" in commandArgs and commandArgs["Intro_Slide"].id:
intro_duration = commandArgs["Intro_Duration"]
intro_fileId = commandArgs["Intro_Slide"].id.val
intro_filenames = write_intro_end_slides(
conn, commandArgs, intro_fileId, intro_duration, mw, mh)
fileNames.extend(intro_filenames)
# prepare watermark
if "Watermark" in commandArgs and commandArgs["Watermark"].id:
watermark = prepareWatermark(conn, commandArgs, mw, mh)
# add movie frames...
for tz in tzList:
t = tz[0]
z = tz[1]
plane = getPlane(renderingEngine, z, t)
planeImage = numpy.array(plane, dtype='uint32')
planeImage = planeImage.byteswap()
planeImage = planeImage.reshape(sizeX, sizeY)
image = Image.frombuffer('RGBA', (sizeX, sizeY), planeImage.data,
'raw', 'ARGB', 0, 1)
if ovlpos is not None:
image2 = canvas.copy()
image2.paste(image, ovlpos, image)
image = image2
if "Scalebar" in commandArgs and commandArgs["Scalebar"]:
image = addScalebar(
commandArgs["Scalebar"], image, pixels, commandArgs)
planeInfo = "z:"+str(z)+"t:"+str(t)
if "Show_Time" in commandArgs and commandArgs["Show_Time"]:
time = timeMap[planeInfo]
image = addTimePoints(time, pixels, image, overlayColour)
if "Show_Plane_Info" in commandArgs and \
commandArgs["Show_Plane_Info"]:
image = addPlaneInfo(z, t, pixels, image, overlayColour)
if "Watermark" in commandArgs and commandArgs["Watermark"].id:
image = pasteWatermark(image, watermark)
if format == QT:
filename = str(frameNo) + '.png'
image.save(filename, "PNG")
else:
filename = str(frameNo) + '.jpg'
image.save(filename, "JPEG")
fileNames.append(filename)
frameNo += 1
# add exit frames... "outro"
# add intro...
if "Ending_Slide" in commandArgs and commandArgs["Ending_Slide"].id:
end_duration = commandArgs["Ending_Duration"]
end_fileId = commandArgs["Ending_Slide"].id.val
end_filenames = write_intro_end_slides(
conn, commandArgs, end_fileId, end_duration, mw, mh)
fileNames.extend(end_filenames)
filelist = ",".join(fileNames)
ext = formatMap[format]
movieName = "Movie"
if "Movie_Name" in commandArgs:
movieName = commandArgs["Movie_Name"]
movieName = os.path.basename(movieName)
if not movieName.endswith(".%s" % ext):
movieName = "%s.%s" % (movieName, ext)
# spaces etc in file name cause problems
movieName = re.sub("[$&\;|\(\)<>' ]", "", movieName)
framesPerSec = 2
if "FPS" in commandArgs:
framesPerSec = commandArgs["FPS"]
output = "localfile.%s" % ext
buildAVI(mw, mh, filelist, framesPerSec, output, format)
mimetype = formatMimetypes[format]
if not os.path.exists(output):
print "mencoder Failed to create movie file: %s" % output
return None, "Failed to create movie file: %s" % output
if not commandArgs["Do_Link"]:
originalFile = scriptUtil.createFile(
updateService, output, mimetype, movieName)
scriptUtil.uploadFile(rawFileStore, originalFile, movieName)
return originalFile, message
namespace = NSCREATED + "/omero/export_scripts/Make_Movie"
fileAnnotation, annMessage = scriptUtil.createLinkFileAnnotation(
conn, output, omeroImage, ns=namespace,
mimetype=mimetype, origFilePathAndName=movieName)
message += annMessage
return fileAnnotation._obj, message
def datasets_to_plates(conn, scriptParams):
updateService = conn.getUpdateService()
message = ""
# Get the datasets ID
datasets, logMessage = script_utils.getObjects(conn, scriptParams)
message += logMessage
if not datasets:
return None, message
IDs = [ds.getId() for ds in datasets]
# find or create Screen if specified
screen = None
newscreen = None
if "Screen" in scriptParams and len(scriptParams["Screen"]) > 0:
s = scriptParams["Screen"]
# see if this is ID of existing screen
try:
screenId = long(s)
screen = conn.getObject("Screen", screenId)
except ValueError:
pass
# if not, create one
if screen is None:
newscreen = omero.model.ScreenI()
newscreen.name = rstring(s)
newscreen = updateService.saveAndReturnObject(newscreen)
screen = conn.getObject("Screen", newscreen.id.val)
plates = []
links = []
deletes = []
for datasetId in IDs:
plate, link, deleteHandle = dataset_to_plate(conn, scriptParams,
datasetId, screen)
if plate is not None:
plates.append(plate)
if link is not None:
links.append(link)
if deleteHandle is not None:
deletes.append(deleteHandle)
# wait for any deletes to finish
for handle in deletes:
cb = omero.callbacks.DeleteCallbackI(conn.c, handle)
while True: # ms
if cb.block(100) is None:
print "Waiting for delete"
else:
break
err = handle.errors()
if err > 0:
print "Delete error", err
else:
print "Delete OK"
if newscreen:
message += "New screen created: %s." % newscreen.getName().val
robj = newscreen
elif plates:
robj = plates[0]
else:
robj = None
if plates:
if len(plates) == 1:
message += " New plate created: %s" % plates[0].name.val
else:
message += " %s plates created" % len(plates)
if len(plates) == len(links):
message += "."
else:
message += " but could not be attached."
else:
message += "No plate created."
return robj, message
