def uploadImageToDataset(session, services, pixelsType, localImage, dataset=None, description="", imageName=None):
"""
Uploads a local Spider image to an OMERO dataset. Same function exists in spider2omero.py.
@param services Map of OMERO services
@param pixelsType The OMERO PixelsType object for new image.
@param imageName The local image path/name. Also used for new image name.
@param dataset Dataset to put images in, if specified. omero.model.Dataset
"""
renderingEngine = services["renderingEngine"]
queryService = services["queryService"]
pixelsService = services["pixelsService"]
rawPixelStore = services["rawPixelStore"]
updateService = services["updateService"]
rawFileStore = services["rawFileStore"]
namespace = omero.constants.namespaces.NSCOMPANIONFILE
fileName = omero.constants.annotation.file.ORIGINALMETADATA
if imageName == None: imageName = localImage
print "Importing image: %s" % imageName
plane2D = spider2array(localImage)
plane2Dlist = [plane2D] # single plane image
image = scriptUtil.createNewImage(session, plane2Dlist, imageName, description, dataset)
# header is a list of values corresponding to attributes
header = getSpiderHeader(localImage)
# if we know the pixel size, set it in the new image
if len(header) >= 38:
physicalSizeX = header[38]
physicalSizeY = header[38]
pixels = image.getPrimaryPixels()
pixels.setPhysicalSizeX(rdouble(physicalSizeX))
pixels.setPhysicalSizeY(rdouble(physicalSizeY))
updateService.saveObject(pixels)
# make a temp text file.
f = open(fileName, 'w')
f.write("[GlobalMetadata]\n")
# now add image attributes as "Original Metadata", sorted by key.
for i, h in enumerate(header):
if i in spiderHeaderMap:
f.write("%s=%s\n" % (spiderHeaderMap[i], h))
f.close()
scriptUtil.uploadAndAttachFile(queryService, updateService, rawFileStore, image, fileName, "text/plain", None, namespace)
# delete temp file
os.remove(fileName)
return image
def volume2imagelist(filename):
" converts a Spider volume into a list of PIL images"
imlist = []
V = spider2array(filename)
x = V.flat # flatten to 1D array to get extrema
amax = max(x)
amin = min(x)
m = 255.0 / (amax - amin)
b = -m * amin
N = ((m * V) + b).astype(Numeric.UnsignedInt8) # mV+b returns an array
zsize, ysize, xsize = N.shape
for z in range(zsize):
im = array2image(N[z])
im.info['filename'] = str(z)
imlist.append(im)
return imlist
def getPixelsType(queryService, imageName):
"""
Get the OMERO pixelsType object appropriate for the image named.
"""
plane2D = spider2array(imageName)
pType = plane2D.dtype.name
pixelsType = queryService.findByQuery("from PixelsType as p where p.value='%s'" % pType, None) # omero::model::PixelsType
if pixelsType == None and pType.startswith("float"):
# try 'float'
pixelsType = queryService.findByQuery("from PixelsType as p where p.value='%s'" % "float", None) # omero::model::PixelsType
if pixelsType == None:
print "Unknown pixels type for: " % pType
return
else:
print "Using pixels type ", pixelsType.getValue().getValue()
return pixelsType
def visit(arg, dirname, names):
rootpath = arg
datasetName = dirname.replace(rootpath, "")
pixelsType = None # set by first image result - assume all the same
dataset = None
for n in names:
fullname = os.path.join(dirname, n)
imageArray = None
try:
# attempt to read pixel data. Only way to tell if this is a Spider image?
imageArray = spider2array(fullname)
except:
print "."
if imageArray != None:
#print " " , fullname, " IS an image"
if pixelsType == None:
pixelsType = getPixelsType(queryService, imageArray)
if dataset == None:
print "Dataset" , datasetName
dataset = createDataset(updateService, project, datasetName)
uploadImageToDataset(services, pixelsType, imageArray, fullname, dataset)
def loadImageSeries(filelist=None, parent=None, byte=1, istart=None, iend=-1,
verbose=1, DISPLAY_ALL=None):
" create a list of PIL images from SPIDER files "
if filelist == None or len(filelist) < 1:
return []
# see if the first filelist argument is a flag or range (overrides istart?)
firstarg = filelist[0]
if firstarg == '-a' or firstarg == '-1':
if verbose: print "displaying all..."
DISPLAY_ALL = 1
filelist = filelist[1:]
istart=1; iend=len(filelist)
elif isNumberRange(firstarg):
istart,iend = isNumberRange(firstarg)
DISPLAY_ALL = 0
filelist = filelist[1:]
# check the first file, to see if exists, is stack, or is volume
Nfiles = len(filelist)
if Nfiles < 1: return []
file = filelist[0]
if not os.path.exists(file):
print "unable to find %s" % file
return []
info = spiderInfo(file)
if info:
type, size = info[0], info[1]
else:
type = 'non-spider'
try:
im = Image.open(file)
size = im.size
except:
size = (100,100) # placeholder
if type == "volume":
Nimages = size[2]
elif type == "stack":
hdr = getSpiderHeader(filelist[0])
Nimages = int(hdr[26])
else:
Nimages = Nfiles
if DISPLAY_ALL == 1:
istart = 1
iend = Nimages
# IF start,end not set by first argument in filelist, see if they will
# fit onscreen. Get number of images; if too many to fit, get start, end images.
if DISPLAY_ALL == None:
if istart == None:
if verbose: print "computing if images will fit on screen..."
res = getImageRange(Nimages, size, parent)
if not res:
return []
istart, iend = res
if istart==0: istart=1 # use Spider indexing
# Load the SPIDER files as PIL images
imglist = []
# ----------------------------------------------
if type == "image" or type == "non-spider":
newlist = filelist[istart-1:iend] # SHOULD USE FILE NUMBERS??!!!
for file in newlist:
if not os.path.exists(file):
print "Unable to find %s" % file
continue
try:
im = Image.open(file)
if byte and im.format == 'SPIDER':
im = im.convert2byte()
else:
im = Image.open(file)
im.info['filename'] = os.path.basename(file)
imglist.append(im)
except:
print "Unable to load %s" % file
# ----------------------------------------------
elif type == "stack":
basename = os.path.basename(file)
try:
im = Image.open(file)
ni = im.nimages
s1 = istart - 1 # go from SPIDER 1 to Python 0
if iend > s1 and iend < ni:
s2 = iend # don't subtract 1, cos used by range()
else:
s2 = ni
for i in range(s1,s2): #ni):
im.seek(i)
im.info['filename'] = "%s@%d" % (basename[:-4], i+1)
#im.info['filename'] = str(i+1)
if byte:
imglist.append(im.convert2byte())
else:
imglist.append(im)
except:
print "Error trying to load SPIDER stack " + file
return []
# ----------------------------------------------
elif type == "volume":
V = spider2array(file) # V is a 3D numpy array
N = V[istart-1:iend]
if byte:
V = N
amax = max(V.flat) # flatten to 1D array to get extrema
amin = min(V.flat)
if amax == amin:
print "*** Error: volume slices contain constant data"
return []
m = 255.0 / (amax-amin)
b = -m * amin
if _HAS_NUMPY_:
N = ((m*V)+b).astype(numpy.uint8) # mV+b returns an array
else:
N = ((m*V)+b).astype(Numeric.UnsignedInt8)
zsize, ysize, xsize = N.shape
for z in range(zsize):
im = array2image(N[z])
im.info['filename'] = str(z+1 + istart-1)
imglist.append(im)
return imglist
def loadImageSeries(filelist=None, parent=None, byte=1, istart=None, iend=-1,
verbose=1, DISPLAY_ALL=None):
" create a list of PIL images from SPIDER files "
print "Hunting "
if filelist == None or len(filelist) < 1:
return []
# see if the first filelist argument is a flag or range (overrides istart?)
firstarg = filelist[0]
if firstarg == '-a' or firstarg == '-1':
if verbose: print "displaying all..."
DISPLAY_ALL = 1
filelist = filelist[1:]
istart=1; iend=len(filelist)
elif isNumberRange(firstarg):
istart,iend = isNumberRange(firstarg)
DISPLAY_ALL = 0
filelist = filelist[1:]
# check the first file, to see if exists, is stack, or is volume
Nfiles = len(filelist)
if Nfiles < 1: return []
file = filelist[0]
if not os.path.exists(file):
print "unable to find %s" % file
return []
print "Found %s" % file
info = spiderInfo(file)
if info:
type, size = info[0], info[1]
else:
type = 'non-spider'
try:
im = Image.open(file)
size = im.size
except:
size = (100,100) # placeholder
if type == "volume":
Nimages = size[2]
elif type == "stack":
hdr = getSpiderHeader(filelist[0])
Nimages = int(hdr[26])
else:
Nimages = Nfiles
if DISPLAY_ALL == 1:
istart = 1
iend = Nimages
# IF start,end not set by first argument in filelist, see if they will
# fit onscreen. Get number of images; if too many to fit, get start, end images.
if DISPLAY_ALL == None:
if istart == None:
if verbose: print "computing if images will fit on screen..."
res = getImageRange(Nimages, size, parent)
if not res:
return []
istart, iend = res
if istart==0: istart=1 # use Spider indexing
# Load the SPIDER files as PIL images
imglist = []
# ----------------------------------------------
if type == "image" or type == "non-spider":
newlist = filelist[istart-1:iend] # SHOULD USE FILE NUMBERS??!!!
for file in newlist:
if not os.path.exists(file):
print "Unable to find %s" % file
continue
try:
im = Image.open(file)
if byte and im.format == 'SPIDER':
im = im.convert2byte()
else:
im = Image.open(file)
im.info['filename'] = os.path.basename(file)
imglist.append(im)
except:
print "Unable to sleep:: %s" % file
print "Unable to load:: %s" % file
# ----------------------------------------------
elif type == "stack":
basename = os.path.basename(file)
try:
im = Image.open(file)
ni = im.nimages
s1 = istart - 1 # go from SPIDER 1 to Python 0
if iend > s1 and iend < ni:
s2 = iend # don't subtract 1, cos used by range()
else:
s2 = ni
for i in range(s1,s2): #ni):
im.seek(i)
im.info['filename'] = "%s@%d" % (basename[:-4], i+1)
#im.info['filename'] = str(i+1)
if byte:
imglist.append(im.convert2byte())
else:
imglist.append(im)
except:
print "Error trying to load SPIDER stack " + file
return []
# ----------------------------------------------
elif type == "volume":
V = spider2array(file) # V is a 3D numpy array
N = V[istart-1:iend]
if byte:
V = N
amax = max(V.flat) # flatten to 1D array to get extrema
amin = min(V.flat)
if amax == amin:
print "*** Error: volume slices contain constant data"
return []
m = 255.0 / (amax-amin)
b = -m * amin
if _HAS_NUMPY_:
N = ((m*V)+b).astype(numpy.uint8) # mV+b returns an array
else:
N = ((m*V)+b).astype(Numeric.UnsignedInt8)
zsize, ysize, xsize = N.shape
for z in range(zsize):
im = array2image(N[z])
im.info['filename'] = str(z+1 + istart-1)
imglist.append(im)
return imglist
