def downloadImage(queryService, rawPixelStore, imageId, imageName):
"""
This method downloads the first 3D data of the OMERO image and saves it as a local image.
@param session The OMERO session
@param imageId The ID of the image to download
@param imageName The name of the image to write. If no path, saved in the current directory.
"""
# set up pixel-store and get the pixels object
query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%d'" % imageId
pixels = queryService.findByQuery(query_string, None)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
sizeC = pixels.getSizeC().getValue()
sizeT = pixels.getSizeT().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixels.getId().getValue(), bypassOriginalFile)
em = EMData(sizeX,sizeY,sizeZ)
pixelsType = pixels.pixelsType
theC, theT = 0, 0
for theZ in range(sizeZ):
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
try: # method seems to depend which version of EMAN2 you have
EMNumPy.numpy2em(plane2D, e)
except:
e = EMNumPy.numpy2em(plane2D)
em.insert_clip(e,(0,0,theZ))
em.write_image(imageName)
def downloadImages(services, imageIds, local2dStack):
"""
This method downloads the first (only?) plane of the OMERO image and saves it as a local image.
@param session The OMERO session
@param imageId The ID of the image to download
@param imageName The name of the image to write. If no path, saved in the current directory.
"""
# get services
queryService = services["queryService"]
rawPixelsStore = services["rawPixelsStore"]
d = EMData()
for imageId in imageIds:
# 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)
# get the plane
theZ, theC, theT = (0,0,0)
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelsStore.setPixelsId(pixelsId, bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelsStore, pixels, theZ, theC, theT)
# convert to EMData and add to stack. See e2proc2d.py approx line 500.
try: # method seems to depend which version of EMAN2 you have
EMNumPy.numpy2em(plane2D, d)
except:
d = EMNumPy.numpy2em(plane2D)
d.write_image(local2dStack, -1, EMUtil.get_image_ext_type("hdf"), False, None, EMUtil.EMDataType.EM_FLOAT, True)
def downloadImage(session, imageId, imageName):
"""
This method downloads the first (only?) plane of the OMERO image and saves it as a local image.
@param session The OMERO session
@param imageId The ID of the image to download
@param imageName The name of the image to write. If no path, saved in the current directory.
"""
queryService = session.getQueryService()
rawPixelStore = session.createRawPixelsStore()
# 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)
theX = pixels.getSizeX().getValue()
theY = pixels.getSizeY().getValue()
# get the plane
theZ, theC, theT = (0,0,0)
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
p = Image.fromarray(plane2D)
#p.show()
p.save(imageName)
return (theX, theY)
def downloadImage(queryService, rawPixelsStore, imageId, imageName):
"""
This method downloads the first (only?) plane of the OMERO image and saves it as a local image.
@param session The OMERO session
@param imageId The ID of the image to download
@param imageName The name of the image to write. If no path, saved in the current directory.
"""
print "Downloading image ID: %s to local file: %s using EMAN2" % (imageId, imageName)
# get pixels with pixelsType
query_string = "select p from Pixels p join fetch p.image i join fetch p.pixelsType pt where i.id='%s'" % imageId
pixels = queryService.findByQuery(query_string, None)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
em = EMData(sizeX,sizeY,sizeZ)
# get the planes
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelsStore.setPixelsId(pixelsId, bypassOriginalFile)
theC, theT = (0,0)
for theZ in range(sizeZ):
plane2D = scriptUtil.downloadPlane(rawPixelsStore, pixels, theZ, theC, theT)
e = EMNumPy.numpy2em(plane2D)
em.insert_clip(e,(0,0,theZ))
em.write_image(imageName)
def analyseEllipses(ellipses, pixels, rawPixelStore, theC, theT, theZ): """ Returns a list of average pixel intensities corresponding to the ellipses, which must all exist on a single plane, defined by pixels, and C, T, Z indexes. @param ellipses: A list of the ellipses to analyse, each defined as (cx, cy, rx, ry, z) @param pixels: The pixels object, with PixelsType object loaded, so that getPixelsType() can be called. @param rawPixelStore: The Omero rawPixelsStore @param theC: C index for plane to analyse @param theT: T index for plane to analyse @param theZ: Z index for plane to analyse """ plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT) results = [] for ellipse in ellipses: points = getEllipsePixels(ellipse) totalValue = 0 for p in points: x, y = p value = plane2D[y][x] totalValue += value average = totalValue/len(points) results.append(average) return results
def getImagePlane(imageId):
query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%s'" % imageId
pixels = queryService.findByQuery(query_string, None)
theZ, theC, theT = (0,0,0)
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixels.getId().getValue(), bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
return plane2D
def getImagePlane(imageId):
query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%s'" % imageId
pixels = queryService.findByQuery(query_string, None)
theZ, theC, theT = (0, 0, 0)
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixels.getId().getValue(),
bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC,
theT)
return plane2D
def eman(request, imageId, conn=None, **kwargs):
if not EMAN2_IMPORTED:
return HttpResponse("EMAN2 not found")
rawPixelStore = conn.createRawPixelsStore()
queryService = conn.getQueryService()
query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%s'" % imageId
pixels = queryService.findByQuery(query_string, None)
theZ, theC, theT = (0, 0, 0)
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixels.getId().getValue(), bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = 1
#em = EMData()
em = EMNumPy.numpy2em(plane2D)
f = kwargs['filter']
if f == "fft":
filterName = "basis.fft"
filterParamMap = {
"dir": 1,
}
em.process_inplace(filterName, filterParamMap)
elif f == "median":
if 'radius' in kwargs:
filterParamMap = {"radius": int(kwargs['radius'])}
em.process_inplace("eman1.filter.median", filterParamMap)
else:
em.process_inplace("eman1.filter.median")
elif f == "log":
em.process_inplace("math.log")
tempdir = settings.FILE_UPLOAD_TEMP_DIR
tempJpg = os.path.join(tempdir, ('%s.emanFilter.jpg' %
(conn._sessionUuid))).replace('\\', '/')
em.write_image(tempJpg)
originalFile_data = FileWrapper(file(tempJpg))
rsp = HttpResponse(originalFile_data)
rsp['Content-Type'] = "image/jpg"
return rsp
def eman(request, imageId, **kwargs):
if not EMAN2_IMPORTED:
return HttpResponse("EMAN2 not found")
conn = getConnection(request)
rawPixelStore = conn.createRawPixelsStore()
queryService = conn.getQueryService()
query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%s'" % imageId
pixels = queryService.findByQuery(query_string, None)
theZ, theC, theT = (0, 0, 0)
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixels.getId().getValue(), bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = 1
# em = EMData()
em = EMNumPy.numpy2em(plane2D)
f = kwargs["filter"]
if f == "fft":
filterName = "basis.fft"
filterParamMap = {"dir": 1}
em.process_inplace(filterName, filterParamMap)
elif f == "median":
if "radius" in kwargs:
filterParamMap = {"radius": int(kwargs["radius"])}
em.process_inplace("eman1.filter.median", filterParamMap)
else:
em.process_inplace("eman1.filter.median")
elif f == "log":
em.process_inplace("math.log")
tempdir = settings.FILE_UPLOAD_TEMP_DIR
tempJpg = os.path.join(tempdir, ("%s.emanFilter.jpg" % (conn._sessionUuid))).replace("\\", "/")
em.write_image(tempJpg)
originalFile_data = FileWrapper(file(tempJpg))
rsp = HttpResponse(originalFile_data)
rsp["Content-Type"] = "image/jpg"
return rsp
def getPlane( conn, iid, pixels=0, channel=0, zslice=0, timepoint=0 ):
'''
Returns a plane with the given image id (iid) as well as pixels, channels, zslice and timepoint index.
@param connection (conn)
@param image id (iid)
@param pixels index
@param channel index
@param zslice index
@param timepoint index
@return plane
'''
if not conn.isConnected():
return None
if not hasImage( conn, iid ):
return None
#create pixel service (needed to extract pixels from image object)
rawPixelsStore = conn.createRawPixelsStore()
#get image
image = conn.getObject( "Image", long(iid) )
#get plane id from image (we use zero because our images have only
#one pixel object per image object
pid = image.getPixelsId();
#retrieve pixel object
pixels = conn.getPixelsService().retrievePixDescription(pid);
#update pixel service to match the current pixel object
rawPixelsStore.setPixelsId( pid, True )
try:
#extract pixel object
plane = utils.downloadPlane( rawPixelsStore, pixels, zslice, channel, timepoint );
except:
plane = None
#close services
rawPixelsStore.close()
#return plane
return plane
def getPlane(rawPixelStore, pixels, theZ, theC, theT):
"""
This method downloads the specified plane of the OMERO image and returns
it as a numpy array.
@param session The OMERO session
@param imageId The ID of the image to download
@param pixels The pixels object, with pixelsType
@param imageName The name of the image to write. If no path, saved in
the current directory.
"""
# get the plane
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
return plane2D
def getPlane(rawPixelStore, pixels, theZ, theC, theT):
"""
This method downloads the specified plane of the OMERO image and returns it as a numpy array.
@param session The OMERO session
@param imageId The ID of the image to download
@param pixels The pixels object, with pixelsType
@param imageName The name of the image to write. If no path, saved in the current directory.
"""
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
# get the plane
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
return plane2D
def omeroToEm(commandArgs):
# log-in
client = omero.client(commandArgs["host"])
session = client.createSession(commandArgs["username"], commandArgs["password"])
# get the services we need
queryService = session.getQueryService()
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
rawPixelStore = session.createRawPixelsStore()
containerService = session.getContainerService()
images = []
if "image" in commandArgs:
iId = long(commandArgs["image"])
i = containerService.getImages("Image", [iId], None)[0]
images.append(i)
elif "dataset" in commandArgs:
dIds = [long(commandArgs["dataset"])]
images = containerService.getImages("Dataset", dIds, None)
else:
print "No image or dataset ID given"
return
path = None
if "path" in commandArgs:
path = commandArgs["path"]
if not os.path.exists(path):
print "Given path: %s not found. Saving images in current directory." % path
path = None
extension = "dat" # default
format = None
if "extension" in commandArgs:
ext = commandArgs["extension"]
if ext in filetypes:
extension = ext
print "Saving all images as .%s files." % extension
else:
print "Invalid extension: %s (not supported by Spider). Using %s" % (ext, extension)
for image in images:
iName = image.getName().getValue()
imageName = os.path.basename(iName) # make sure no dir separators in name.
imageId = image.getId().getValue()
if not imageName.endswith(".%s" % extension):
imageName = "%s.%s" % (imageName, extension)
if path:
imageName = os.path.join(path,imageName)
i = 1 # don't overwrite. Add number before extension
dirName, ext = imageName.rsplit(".", 1)
while os.path.exists(imageName):
imageName = "%s_%s.%s" % (dirName,i,ext)
i +=1
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)
ptype = pixels.pixelsType.getValue().getValue()
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
# prepare rawPixelStore
theC, theT = (0, 0)
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
if sizeZ == 1:
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, 0, theC, theT)
array2spider(plane2D, imageName)
else:
numpyType = pixelstypetopython.toNumpy(ptype)
array3D = zeros( (sizeZ, sizeY, sizeX), dtype=numpyType )
for z in range(sizeZ):
# get each plane and add to 3D array
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, z, theC, theT)
array3D[z] = plane2D
array2spider(array3D, imageName)
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
def omeroToEm(commandArgs):
# log-in
client = omero.client(commandArgs["host"])
session = client.createSession(commandArgs["username"], commandArgs["password"])
# get the services we need
queryService = session.getQueryService()
updateService = session.getUpdateService()
rawFileStore = session.createRawFileStore()
rawPixelStore = session.createRawPixelsStore()
containerService = session.getContainerService()
images = []
if "image" in commandArgs:
iId = long(commandArgs["image"])
i = containerService.getImages("Image", [iId], None)[0]
images.append(i)
elif "dataset" in commandArgs:
dIds = [long(commandArgs["dataset"])]
images = containerService.getImages("Dataset", dIds, None)
else:
print "No image or dataset ID given"
return
path = None
if "path" in commandArgs:
path = commandArgs["path"]
if not os.path.exists(path):
print "Given path: %s not found. Saving images in current directory." % path
path = None
extension = None
format = None
if "extension" in commandArgs:
extension = commandArgs["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."
for image in images:
iName = image.getName().getValue()
imageName = os.path.basename(iName) # make sure no dir separators in name.
imageId = image.getId().getValue()
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)
if path:
imageName = os.path.join(path,imageName)
i = 1 # don't overwrite. Add number before extension
dirName, ext = imageName.rsplit(".", 1)
while os.path.exists(imageName):
imageName = "%s_%s.%s" % (dirName,i,ext)
i +=1
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()
# prepare rawPixelStore
theC, theT = (0, 0)
pixelsId = pixels.getId().getValue()
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixelsId, bypassOriginalFile)
e = EMData()
em = EMData(xSize,ySize,zSize)
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)
EMNumPy.numpy2em(plane2D, e)
em.insert_clip(e,(0,0,z))
em.write_image(imageName)
def split_image(client, imageId, dir, unformattedImageName = "tubulin_P037_T%05d_C%s_Z%d_S1.tif", dims = ('T', 'C', 'Z')):
"""
** NB: This method is implemented in script_utils. I have simply copied it here temporarily since I have made
some edits that are not yet committed and updated on nightshade. **
Splits the image into component planes, which are saved as local tiffs according to unformattedImageName.
E.g. myLocalDir/tubulin_P037_T%05d_C%s_Z%d_S1.tif which will be formatted according to dims, E.g. ('T', 'C', 'Z')
Channel will be formatted according to channel name, not index.
@param rawPixelsStore The rawPixelStore
@param queryService
@param c The C-Section to retrieve.
@param t The T-Section to retrieve.
@param imageName the local location to save the image.
"""
unformattedImageName = os.path.join(dir, unformattedImageName)
session = client.getSession()
queryService = session.getQueryService()
rawPixelsStore = session.createRawPixelsStore()
pixelsService = session.getPixelsService()
from numpy import zeros, int8, fromfunction
try:
from PIL import Image
except:
import Image
query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%s'" % imageId
pixels = queryService.findByQuery(query_string, None)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
sizeC = pixels.getSizeC().getValue()
sizeT = pixels.getSizeT().getValue()
rawPixelsStore.setPixelsId(pixels.getId().getValue(), True)
channelMap = {}
cIndex = 0
pixels = pixelsService.retrievePixDescription(pixels.id.val) # load channels
for c in pixels.iterateChannels():
lc = c.getLogicalChannel()
channelMap[cIndex] = lc.getName() and lc.getName().getValue() or str(cIndex)
cIndex += 1
def formatName(unformatted, z, c, t):
# need to turn dims E.g. ('T', 'C', 'Z') into tuple, E.g. (t, c, z)
dimMap = {'T': t, 'C':channelMap[c], 'Z': z}
dd = tuple([dimMap[d] for d in dims])
return unformatted % dd
# cecog does this, but other formats may want to start at 0
zStart = 1
tStart = 1
# loop through dimensions, saving planes as tiffs.
for z in range(sizeZ):
for c in range(sizeC):
for t in range(sizeT):
imageName = formatName(unformattedImageName, z+zStart, c, t+tStart)
print "downloading plane z: %s c: %s t: %s to %s" % (z, c, t, imageName)
plane = script_utils.downloadPlane(rawPixelsStore, pixels, z, c, t)
print "plane dtype: %s min: %s max: %s" % (plane.dtype.name, plane.min(), plane.max())
# need plane dtype to be int8 for conversion to tiff by PIL
if plane.dtype.name == 'int16' or plane.dtype.name == 'uint16':
minVal = plane.min()
maxVal = plane.max()
valRange = maxVal - minVal
scaled = (plane - minVal) * (float(255) / valRange)
convArray = zeros(plane.shape, dtype=int8)
convArray += scaled
print "using converted int8 plane: dtype: %s min: %s max: %s" % (convArray.dtype.name, convArray.min(), convArray.max())
i = Image.fromarray(convArray)
else:
i = Image.fromarray(plane)
i.save(imageName)
def projection_axis(request,
imageId,
axis,
get_slice=False,
conn=None,
**kwargs):
import time
startTime = time.time()
x_proj_key = "x_proj_%s" % imageId
y_proj_key = "y_proj_%s" % imageId
z_proj_key = "z_proj_%s" % imageId
x_slice_key = "x_slice_%s" % imageId
y_slice_key = "y_slice_%s" % imageId
z_slice_key = "z_slice_%s" % imageId
# see if we have cached the projection we need
key = "%s_proj_%s" % (axis, imageId)
if get_slice:
key = "%s_slice_%s" % (axis, imageId)
#print "\n\nchecking cache for array: %s" % key
#print " %s secs" % (time.time() - startTime)
proj = cache.get(key)
if proj == None:
#print "creating cube of data..."
#print " %s secs" % (time.time() - startTime)
rawPixelStore = conn.createRawPixelsStore()
queryService = conn.getQueryService()
query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%s'" % imageId
pixels = queryService.findByQuery(query_string, None)
theZ, theC, theT = (0, 0, 0)
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixels.getId().getValue(),
bypassOriginalFile)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
# create a 3D numpy array, and populate it with data
cube = zeros((sizeZ, sizeY, sizeX))
theC, theT = (0, 0)
for theZ in range(sizeZ):
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ,
theC, theT)
cube[sizeZ - theZ - 1] = plane2D
# do the 3 projections and 3 central slices while we have the cube - save projections, not cube
#print "doing projection"
#print " %s secs" % (time.time() - startTime)
proj_z = zeros((sizeY, sizeX))
for z in range(sizeZ):
zPlane = cube[z, :, :]
proj_z += zPlane
slice_z = cube[sizeZ / 2, :, :]
proj_x = zeros((sizeZ, sizeY))
for x in range(sizeX):
xPlane = cube[:, :, x]
proj_x += xPlane
slice_x = cube[:, :, sizeX / 2]
proj_y = zeros((sizeZ, sizeX))
for y in range(sizeY):
yPlane = cube[:, y, :]
proj_y += yPlane
slice_y = cube[:, sizeY / 2, :]
#print "setting cache"
#print " %s secs" % (time.time() - startTime)
# save arrays to cache
cache.set(x_proj_key, proj_x)
cache.set(x_slice_key, slice_x)
cache.set(y_proj_key, proj_y)
cache.set(y_slice_key, slice_y)
cache.set(z_proj_key, proj_z)
cache.set(z_slice_key, slice_z)
if axis == "z":
if get_slice:
proj = slice_z
else:
proj = proj_z
elif axis == "x":
if get_slice:
proj = slice_x
else:
proj = proj_x
elif axis == "y":
if get_slice:
proj = slice_y
else:
proj = proj_y
#print "got 2D plane...", proj.shape
#print " %s secs" % (time.time() - startTime)
tempdir = settings.FILE_UPLOAD_TEMP_DIR
tempJpg = os.path.join(tempdir, ('%s.projection.jpg' %
(conn._sessionUuid))).replace('\\', '/')
#import matplotlib.pyplot as plt
#plt.savefig(tempJpg)
#import scipy
#scipy.misc.imsave(tempJpg, proj)
em = EMNumPy.numpy2em(proj)
em.write_image(tempJpg)
originalFile_data = FileWrapper(file(tempJpg))
rsp = HttpResponse(originalFile_data)
rsp['Content-Type'] = "image/jpg"
return rsp
def emanFilter(session, parameterMap):
"""
This is where the action happens.
For each image, we get the data from OMERO as an EMData object, do the filtering and write back to OMERO.
"""
# create services we need
queryService = session.getQueryService()
rawFileStore = session.createRawFileStore()
rawPixelStore = session.createRawPixelsStore()
rawPixelStoreUpload = session.createRawPixelsStore()
renderingEngine = session.createRenderingEngine()
pixelsService = session.getPixelsService()
containerService = session.getContainerService()
updateService = session.getUpdateService()
imageIds = []
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:
imageIds.append(i.getId().getValue())
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 EMAN2 Filtering 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)
filterName = parameterMap["Filter_Name"]
paramStrings = []
filterParamMap = None
if "Filter_Params" in parameterMap:
filterParamMap = {}
fpMap = parameterMap["Filter_Params"]
for p, v in fpMap.items():
paramStrings.append("%s: %s" % (p, v.getValue())) # get value from rtype
try:
filterParamMap[p] = float(v.getValue()) # if the value is a float
except:
filterParamMap[p] = v.getValue()
paramString = ", ".join(paramStrings) # just for adding to new image description
e = EMData()
bypassOriginalFile = True
newImages = []
for imageId in imageIds:
# set up pixel-store and get the pixels object
query_string = "select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%d'" % imageId
pixels = queryService.findByQuery(query_string, None)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
sizeC = pixels.getSizeC().getValue()
sizeT = pixels.getSizeT().getValue()
rawPixelStore.setPixelsId(pixels.getId().getValue(), bypassOriginalFile)
em = EMData(sizeX,sizeY,sizeZ)
pixelsType = pixels.pixelsType
# create the new image, ready to take planes
description = "Created from image ID: %s by applying EMAN2 filter: '%s' with parameters: %s" % (imageId, filterName, paramString)
imageName = pixels.image.name.val # new image has same name
print imageName, description
iId = None
image = None
# need to loop through extra dimensions, since EMAN2 only handles 3D.
for theC in range(sizeC):
minValue = None
maxValue = 0
for theT in range(sizeT):
for z in range(sizeZ):
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, z, theC, theT)
try: # method seems to depend which version of EMAN2 you have
EMNumPy.numpy2em(plane2D, e)
except:
e = EMNumPy.numpy2em(plane2D)
em.insert_clip(e,(0,0,z))
# do the filtering
if filterParamMap: em.process_inplace(filterName, filterParamMap)
else: em.process_inplace(filterName)
# convert back to numpy (datatype may be different) and upload to OMERO as new image
filteredPlanes = EMNumPy.em2numpy(em)
print "em.get_zsize()", em.get_zsize()
print "filteredPlanes", filteredPlanes.shape
if iId == None:
iId = createImage(pixelsService, queryService, filteredPlanes, sizeT, sizeC, imageName, description)
image = containerService.getImages("Image", [iId], None)[0]
pixelsId = image.getPrimaryPixels().getId().getValue()
rawPixelStoreUpload.setPixelsId(pixelsId, bypassOriginalFile)
if em.get_zsize() > 1: # 3D array
for z, plane in enumerate(filteredPlanes):
if minValue == None: minValue = plane.min()
minValue = min(minValue, plane.min())
maxValue = max(maxValue, plane.max())
scriptUtil.uploadPlane(rawPixelStoreUpload, plane, z, theC, theT)
else: # 2D array
if minValue == None: minValue = filteredPlanes.min()
minValue = min(minValue, filteredPlanes.min())
maxValue = max(maxValue, filteredPlanes.max())
scriptUtil.uploadPlane(rawPixelStoreUpload, filteredPlanes, z, theC, theT)
print "Setting the min, max ", minValue, maxValue
pixelsService.setChannelGlobalMinMax(pixelsId, theC, float(minValue), float(maxValue))
scriptUtil.resetRenderingSettings(renderingEngine, pixelsId, theC, minValue, maxValue)
image.name = rstring(imageName)
image.description = rstring(description)
newImages.append(updateService.saveAndReturnObject(image))
# put image in dataset
if dataset:
dlink = omero.model.DatasetImageLinkI()
dlink.parent = omero.model.DatasetI(dataset.id.val, False)
dlink.child = omero.model.ImageI(iId, False)
updateService.saveAndReturnObject(dlink)
return (dataset, newImages)
def projection_axis(request, imageId, axis, get_slice=False):
conn = getConnection(request)
import time
startTime = time.time()
x_proj_key = "x_proj_%s" % imageId
y_proj_key = "y_proj_%s" % imageId
z_proj_key = "z_proj_%s" % imageId
x_slice_key = "x_slice_%s" % imageId
y_slice_key = "y_slice_%s" % imageId
z_slice_key = "z_slice_%s" % imageId
# see if we have cached the projection we need
key = "%s_proj_%s" % (axis, imageId)
if get_slice:
key = "%s_slice_%s" % (axis, imageId)
# print "\n\nchecking cache for array: %s" % key
# print " %s secs" % (time.time() - startTime)
proj = cache.get(key)
if proj == None:
# print "creating cube of data..."
# print " %s secs" % (time.time() - startTime)
rawPixelStore = conn.createRawPixelsStore()
queryService = conn.getQueryService()
query_string = (
"select p from Pixels p join fetch p.image as i join fetch p.pixelsType where i.id='%s'" % imageId
)
pixels = queryService.findByQuery(query_string, None)
theZ, theC, theT = (0, 0, 0)
bypassOriginalFile = True
rawPixelStore.setPixelsId(pixels.getId().getValue(), bypassOriginalFile)
sizeX = pixels.getSizeX().getValue()
sizeY = pixels.getSizeY().getValue()
sizeZ = pixels.getSizeZ().getValue()
# create a 3D numpy array, and populate it with data
cube = zeros((sizeZ, sizeY, sizeX))
theC, theT = (0, 0)
for theZ in range(sizeZ):
plane2D = scriptUtil.downloadPlane(rawPixelStore, pixels, theZ, theC, theT)
cube[sizeZ - theZ - 1] = plane2D
# do the 3 projections and 3 central slices while we have the cube - save projections, not cube
# print "doing projection"
# print " %s secs" % (time.time() - startTime)
proj_z = zeros((sizeY, sizeX))
for z in range(sizeZ):
zPlane = cube[z, :, :]
proj_z += zPlane
slice_z = cube[sizeZ / 2, :, :]
proj_x = zeros((sizeZ, sizeY))
for x in range(sizeX):
xPlane = cube[:, :, x]
proj_x += xPlane
slice_x = cube[:, :, sizeX / 2]
proj_y = zeros((sizeZ, sizeX))
for y in range(sizeY):
yPlane = cube[:, y, :]
proj_y += yPlane
slice_y = cube[:, sizeY / 2, :]
# print "setting cache"
# print " %s secs" % (time.time() - startTime)
# save arrays to cache
cache.set(x_proj_key, proj_x)
cache.set(x_slice_key, slice_x)
cache.set(y_proj_key, proj_y)
cache.set(y_slice_key, slice_y)
cache.set(z_proj_key, proj_z)
cache.set(z_slice_key, slice_z)
if axis == "z":
if get_slice:
proj = slice_z
else:
proj = proj_z
elif axis == "x":
if get_slice:
proj = slice_x
else:
proj = proj_x
elif axis == "y":
if get_slice:
proj = slice_y
else:
proj = proj_y
# print "got 2D plane...", proj.shape
# print " %s secs" % (time.time() - startTime)
tempdir = settings.FILE_UPLOAD_TEMP_DIR
tempJpg = os.path.join(tempdir, ("%s.projection.jpg" % (conn._sessionUuid))).replace("\\", "/")
# import matplotlib.pyplot as plt
# plt.savefig(tempJpg)
# import scipy
# scipy.misc.imsave(tempJpg, proj)
em = EMNumPy.numpy2em(proj)
em.write_image(tempJpg)
originalFile_data = FileWrapper(file(tempJpg))
rsp = HttpResponse(originalFile_data)
rsp["Content-Type"] = "image/jpg"
return rsp
