def runSpf(session, parameterMap):
"""
This is where the action happens.
We get the parameters, download the images, run Spider file from command line.
Then we get the output from the folder where the results should be, and upload these
images into a new dataset.
"""
# create services we need
services = {}
services["renderingEngine"] = session.createRenderingEngine()
services["queryService"] = session.getQueryService()
services["pixelsService"] = session.getPixelsService()
services["rawPixelStore"] = session.createRawPixelsStore()
services["updateService"] = session.getUpdateService()
services["rawFileStore"] = session.createRawFileStore()
containerService = session.getContainerService()
queryService = services["queryService"]
rawFileStore = services["rawFileStore"]
rawPixelStore = services["rawPixelStore"]
updateService = services["updateService"]
imageIds = []
imageNames = {} # map of id:name
dataType = parameterMap["Data_Type"]
if dataType == "Image":
for imageId in parameterMap["IDs"]:
iId = long(imageId.getValue())
imageIds.append(iId)
else: # Dataset
for datasetId in parameterMap["IDs"]:
datasetIds = []
try:
dId = long(datasetId.getValue())
datasetIds.append(dId)
except: pass
# simply aggregate all images from the datasets
images = containerService.getImages("Dataset", datasetIds, None)
for i in images:
iId = i.getId().getValue()
imageIds.append(iId)
imageNames[iId] = i.name.val
if len(imageIds) == 0:
return
# get the project from the first image
project = None
dataset = None
imageId = imageIds[0]
query_string = "select i from Image i join fetch i.datasetLinks idl join fetch idl.parent d join fetch d.projectLinks pl join fetch pl.parent where i.id in (%s)" % imageId
image = queryService.findByQuery(query_string, None)
if image:
for link in image.iterateDatasetLinks():
dataset = link.parent
print "Dataset", dataset.name.val
for dpLink in dataset.iterateProjectLinks():
project = dpLink.parent
print "Project", project.name.val
break # only use 1st Project
break # only use 1st Dataset
if "New_Dataset_Name" in parameterMap:
# make a dataset for images
dataset = omero.model.DatasetI()
dataset.name = rstring(parameterMap["New_Dataset_Name"])
from datetime import datetime
dt = datetime.now()
dataset.description = rstring("Images generated by SPIDER procedure on %s" % dt.strftime("%A, %d. %B %Y %I:%M%p"))
dataset = updateService.saveAndReturnObject(dataset)
if project: # and put it in the same project
link = omero.model.ProjectDatasetLinkI()
link.parent = omero.model.ProjectI(project.id.val, False)
link.child = omero.model.DatasetI(dataset.id.val, False)
updateService.saveAndReturnObject(link)
fileExt = "dat"
inputName = "input"
if "Input_Name" in parameterMap:
inputName = parameterMap["Input_Name"]
outputName = "output"
if "Output_Name" in parameterMap:
outputName = parameterMap["Output_Name"]
# get the procdure file
spfName = "procedure.spf"
spf = parameterMap["Spf"]
spfText = None
try:
# either the user specified the SPF as a file annotation ID....
spfFileId = long(spf)
annotation = queryService.get('FileAnnotation', spfFileId)
origFileId = annotation.file.id.val
originalFile = queryService.findByQuery("from OriginalFile as o where o.id = %s" % origFileId, None)
scriptUtil.downloadFile(rawFileStore, originalFile, filePath=spfName)
except:
# or they specified Spider command and args separated by ; E.g. WI; 75,75 ; 1,75
spfCommands = [cmd.strip() for cmd in spf.split(";")]
spfCommands.insert(1, inputName)
spfCommands.insert(2, outputName)
spfText = "\n".join(spfCommands)
spfFile = open(spfName, "w")
spfFile.write(spfText)
spfFile.close()
# run command. E.g. spider spf/dat @bat01
spfCommand = "spider spf/%s @procedure" % fileExt
spfText = open(spfName, 'r').read()
print spfText
# for each image, download it, run the spider command and upload result to OMERO
inputImage = "%s.%s" % (inputName, fileExt)
outputImage = "%s.%s" % (outputName, fileExt)
pixelsType = None # set by first image result - assume all the same
newImages = []
for i, imageId in enumerate(imageIds):
downloadImage(queryService, rawPixelStore, imageId, inputImage)
#print "Image downloaded to ", inputImage, os.path.exists(inputImage)
#print spfCommand
# Call SPIDER by command line...
os.system(spfCommand)
#print "Output image exists ", os.path.exists(outputImage)
if not os.path.exists(outputImage):
print "Image not created by SPIDER from Input Image ID: %s" % imageId
continue
if pixelsType == None: pixelsType = getPixelsType(queryService, outputImage)
name = None
if imageId in imageNames: name = imageNames[imageId]
description = "Created from Image ID: %s with the Spider Procedure\n%s" % (imageId, spfText)
image = uploadImageToDataset(session, services, pixelsType, outputImage, dataset, description, name)
newImages.append(image)
# attach Spf to new image (not so important, since we add the text to image description)
# This creates a new FileAnnotationI for each image. Really want a singe FA linked to all images.
#scriptUtil.attachFileToParent(services["updateService"], image, originalFile)
return (dataset, newImages)
def run(commandArgs):
# login details
host = commandArgs["host"]
user = commandArgs["username"]
password = commandArgs["password"]
client = omero.client(host)
session = client.createSession(user, password)
# create the services we need
scriptService = session.getScriptService()
rawFileStore = session.createRawFileStore()
queryService = session.getQueryService()
updateService = session.getUpdateService()
containerService = session.getContainerService()
ids = []
d = omero.api.ContainerClass.Dataset
if "image" in commandArgs:
iId = long(commandArgs["image"])
ids.append(iId)
elif "dataset" in commandArgs:
dIds = [long(commandArgs["dataset"])]
images = containerService.getImages("Dataset", dIds, None)
for i in images:
ids.append(i.getId().getValue())
else:
print "No image or dataset ID given"
return
if len(ids) == 0:
print "No images found"
return
# get the most recent (highest ID) original file with the correct script name
scriptName = "Save_Image_As_Em.py"
scriptId = -1
for s in scriptService.getScripts():
if s.getName().getValue() == scriptName:
scriptId = max(scriptId, s.getId().getValue())
print "Running script %s with ID: %s" % (scriptName, scriptId)
imageIds = omero.rtypes.rlist([omero.rtypes.rlong(iId) for iId in ids])
map = {
"Image_IDs": imageIds,
}
if "extension" in commandArgs:
map["Extension"] = omero.rtypes.rstring(commandArgs["extension"])
results = None
proc = scriptService.runScript(scriptId, map, None)
try:
cb = omero.scripts.ProcessCallbackI(client, proc)
while not cb.block(1000): # ms.
pass
cb.close()
results = proc.getResults(0) # ms
finally:
proc.close(False)
path = None
if "path" in commandArgs:
path = commandArgs["path"]
if "Original_Files" in results:
for r in results["Original_Files"].getValue():
# download the file from OMERO
f = r.getValue() # unloaded originalfile
fileId = f.getId().getValue()
originalFile = queryService.findByQuery(
"from OriginalFile as o where o.id = %s" % fileId, None)
name = originalFile.getName().getValue()
if path:
name = os.path.join(path, name)
filePath = scriptUtil.downloadFile(rawFileStore, originalFile,
name)
print "Saved file at:", filePath
# This only deletes the DB row, not the data on disk! utils.cleanse.py removes files that are not in db.
updateService.deleteObject(originalFile)
else:
print "No files generated by %s script on the server" % scriptName
def run(commandArgs):
# login details
host = commandArgs["host"]
user = commandArgs["username"]
password = commandArgs["password"]
client = omero.client(host)
session = client.createSession(user, password)
# create the services we need
scriptService = session.getScriptService()
rawFileStore = session.createRawFileStore()
queryService = session.getQueryService()
re = session.createRenderingEngine()
updateService = session.getUpdateService()
imageId = None
if "image" in commandArgs:
imageId = long(commandArgs["image"])
else:
print "No image ID given"
return
# get the most recent (highest ID) script with the correct name
scriptName = "/EMAN2/Save_Image_As_Em.py"
scriptId = scriptService.getScriptID(scriptName)
print "Running %s with script ID: %s" % (scriptName, scriptId)
imageIds = omero.rtypes.rlist([omero.rtypes.rlong(imageId)])
map = {
"Image_IDs": imageIds,
"Extension": omero.rtypes.rstring("mrc") # export as mrc file
}
results = None
proc = scriptService.runScript(scriptId, map, None)
try:
cb = omero.scripts.ProcessCallbackI(client, proc)
while not cb.block(1000): # ms.
pass
cb.close()
results = proc.getResults(0) # ms
finally:
proc.close(False)
path = None
if "path" in commandArgs:
path = commandArgs["path"]
fileNames = [] # need names for passing to chimera
if "Original_Files" in results:
for r in results["Original_Files"].getValue():
# download the file from OMERO
f = r.getValue()
fileId = f.getId().getValue()
print "Downloading Original File ID:", fileId
originalFile = queryService.findByQuery("from OriginalFile as o where o.id = %s" % fileId, None)
name = originalFile.getName().getValue()
if path:
name = os.path.join(path, name)
filePath = scriptUtil.downloadFile(rawFileStore, originalFile, name)
print " file saved to:", filePath
fileNames.append(filePath) # if 'name' file already exists, filePath will be different
# This only deletes the DB row, not the data on disk! utils.cleanse.py removes files that are not in db.
updateService.deleteObject(originalFile)
else:
print "No OriginalFileIds returned by script"
if 'stdout' in results:
origFile = results['stdout'].getValue()
fileId = origFile.getId().getValue()
print "\n******** Script: %s generated StdOut in file:%s *******" % (scriptName, fileId)
print scriptUtil.readFromOriginalFile(rawFileStore, queryService, fileId)
if 'stderr' in results:
origFile = results['stderr'].getValue()
fileId = origFile.getId().getValue()
print "\n******** Script: %s generated StdErr in file:%s *******" % (scriptName, fileId)
print scriptUtil.readFromOriginalFile(rawFileStore, queryService, fileId)
return
# need to get colours for each channel, to pass to chimera. Chimera uses [(0.0, 0.0, 1.0, 1.0),(0.0, 1.0, 0.0, 1.0)]
# This returns e.g. [[0, 0, 255, 255], [0, 255, 0, 255], [255, 0, 0, 255], [255, 0, 0, 255]] but seems to work OK.
pixels = containerService.getImages('Image', [imageId], None)[0].getPrimaryPixels()
pixelsId = pixels.getId().getValue()
sizeC = pixels.getSizeC().getValue()
colours = getColours(re, sizeC, pixelsId)
# now we need to make a Chimera script to open the images (channels) and colour them!
scriptLines = []
scriptLines.append("from chimera import openModels")
scriptLines.append("from VolumeViewer import Volume")
for fn in fileNames:
scriptLines.append("openModels.open('%s')" % fn)
scriptLines.append("colors = %s" % colours) # the colours list is rendered suitably as a string
scriptLines.append("for c, v in enumerate(openModels.list(modelTypes=[Volume])):")
scriptLines.append(" v.set_parameters(surface_colors = [colors[c]])")
scriptLines.append(" v.show()")
print "\n".join(scriptLines)
scriptName = "colourMaps.py"
f = open(scriptName, 'w') # will overwrite each time.
for line in scriptLines:
f.write(line)
f.write("\n")
f.close()
command = "chimera --script %s" % scriptName
print command
os.system(command)
