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 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 saveImageAs(session, parameterMap):
# get the services we need
queryService = session.getQueryService()
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
rawPixelStore = session.createRawPixelsStore()
imageIds = []
if "Image_IDs" in parameterMap:
for idCount, imageId in enumerate(parameterMap["Image_IDs"]):
iId = long(imageId.getValue())
imageIds.append(iId)
else:
print "No images"
return
cIndexes = None
theT = 0
if "Channel_Index" in parameterMap:
cIndexes = [parameterMap["Channel_Index"]]
extension = None
format = None
if "Extension" in parameterMap:
extension = parameterMap["Extension"]
if extension in filetypes:
format = filetypes[extension]
print "Saving all images as .%s files. Format: %s" % (extension, filetypes[extension])
else:
print "Invalid extension: %s (not supported by EMAN2). Will attempt to get extensions from image names." % extension
extension = None
else:
print "No extension specified. Will attempt get extensions from image names."
originalFiles = []
for imageId in imageIds:
image = queryService.get("Image", imageId)
n = image.getName().getValue()
imageName = os.path.basename(n) # make sure we don't have path as name.
if imageName == "":
imageName = os.path.basename(n[:-1])
if (extension == None) or (extension not in filetypes):
# try to get extension from image name
lastDotIndex = imageName.rfind(".") # .rpartition(sep)
if lastDotIndex >= 0:
extension = imageName[lastDotIndex+1:]
if extension in filetypes:
format = filetypes[extension]
if (extension == None) or (extension not in filetypes):
print "File extension from image invalid. Could not export image ID: %d Name: %s Extension: %s" % (imageId, imageName, extension)
continue
if not imageName.endswith(".%s" % extension):
imageName = "%s.%s" % (imageName, extension)
print "Preparing to save image: %s" % imageName
figLegend = ""
# get pixels, with pixelsType
query_string = "select p from Pixels p join fetch p.image i join fetch p.pixelsType pt where i.id='%d'" % imageId
pixels = queryService.findByQuery(query_string, None)
xSize = pixels.getSizeX().getValue()
ySize = pixels.getSizeY().getValue()
zSize = pixels.getSizeZ().getValue()
cSize = pixels.getSizeC().getValue()
if pixels.getPhysicalSizeX() == None: physicalSizeX = 1.0
else: physicalSizeX = pixels.getPhysicalSizeX().getValue()
if pixels.getPhysicalSizeY() == None: physicalSizeY = 1.0
else: physicalSizeY = pixels.getPhysicalSizeY().getValue()
if pixels.getPhysicalSizeZ() == None: physicalSizeZ = 1.0
else: physicalSizeZ = pixels.getPhysicalSizeZ().getValue()
if cIndexes == None:
cIndexes = range(cSize)
# prepare rawPixelStore
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
# export an EM image for every channel
for theC in cIndexes:
e = EMData()
em = EMData(xSize,ySize,zSize)
# if the physical size was in microns (in OMERO) now it's in Angstroms!
em.set_attr('apix_x', physicalSizeX)
em.set_attr('apix_y', physicalSizeY)
em.set_attr('apix_z', physicalSizeZ)
if theC > 0:
saveName = imageName.replace(extension, "%s.%s" % (theC, extension))
else: saveName = imageName
for z in range(zSize):
# get each plane and add to EMData
#print "Downloading plane: %d" % z
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, z, theC, theT)
e = EMNumPy.numpy2em(plane2D)
em.insert_clip(e,(0,0,z))
em.write_image(saveName)
if format == None:
format = "" # upload method will pick generic format.
print "Uploading image: %s to server with file type: %s" % (saveName, format)
# attach to image
#fileId = scriptUtil.uploadAndAttachFile(queryService, updateService, rawFileStore, image, imageName, format, figLegend)
# want to return the image to client, without attaching it to anything the server
# still need to upload it...
fileformat = scriptUtil.getFormat(queryService, format)
if fileformat == None: # if we didn't find a matching format in the DB, use a generic format.
fileformat = scriptUtil.getFormat(queryService, "text/plain")
originalFile = scriptUtil.createFile(updateService, saveName, fileformat, saveName)
scriptUtil.uploadFile(rawFileStore, originalFile, saveName)
print "File uploaded with ID:", originalFile.getId().getValue()
originalFiles.append(originalFile)
return originalFiles
