def overlayCutout (request, webargs):
"""Get both data and annotation cubes as npz"""
token, cutout = webargs.split('/',1)
# Get the project and dataset
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj ( token )
dataurl = request.build_absolute_uri( '%s/emca/%s/%s' % ( proj.getDataURL(), proj.getDataset(), cutout ))
# RBTODO can't seen to get WSGIScriptAlias information from apache. So
# right now we have to hardwire. Yuck.
annourl = request.build_absolute_uri( '/emca/%s/%s' % ( token, cutout ))
# Get data
f = urllib2.urlopen ( dataurl )
fobj = cStringIO.StringIO ( f.read() )
dataimg = Image.open(fobj)
# Get annotations
f = urllib2.urlopen ( annourl )
fobj = cStringIO.StringIO ( f.read() )
annoimg = Image.open(fobj)
# convert data image to RGBA
dataimg = dataimg.convert("RGBA")
# Create blended image of the two
return Image.composite ( annoimg, dataimg, annoimg )
def main():
parser = argparse.ArgumentParser(
description='Create a new annotation project.')
parser.add_argument('token', action="store")
parser.add_argument('openid', action="store")
parser.add_argument('host', action="store")
parser.add_argument('project', action="store")
parser.add_argument('datatype',
action="store",
type=int,
help='1 8-bit data or 2 32-bit annotations')
parser.add_argument('dataset', action="store")
parser.add_argument('dataurl', action="store")
parser.add_argument(
'resolution',
action="store",
type=int,
)
parser.add_argument('--readonly',
action='store_true',
help='Project is readonly')
parser.add_argument('--noexceptions',
action='store_true',
help='Project has no exceptions. (FASTER).')
result = parser.parse_args()
# Get database info
pd = emcaproj.EMCAProjectsDB()
pd.newEMCAProj(result.token, result.openid, result.host, result.project,
result.datatype, result.dataset, result.dataurl,
result.resolution, result.readonly, not result.noexceptions)
def getCSV(webargs):
"""Fetch a RAMON object as CSV. Always includes bounding box. No data option."""
[token, csvliteral, annoid, reststr] = webargs.split('/', 3)
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
db = emcadb.EMCADB(dbcfg, proj)
# Make the HDF5 file
# Create an in-memory HDF5 file
tmpfile = tempfile.NamedTemporaryFile()
h5f = h5py.File(tmpfile.name)
dataoption = AR_BOUNDINGBOX
[resstr, sym, rest] = reststr.partition('/')
resolution = int(resstr) if resstr != '' else proj.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution)
# convert the HDF5 file to csv
csvstr = h5ann.h5toCSV(h5f)
return csvstr
def __init__(self, token):
"""Load the database and project"""
projdb = emcaproj.EMCAProjectsDB()
self.proj = projdb.getProj(token)
self.dbcfg = dbconfig.switchDataset(self.proj.getDataset())
# Bind the annotation database
self.imgDB = emcadb.EMCADB(self.dbcfg, self.proj)
def annopost(webargs, postdata):
"""Interface to the annotation write service
Load the annotation project and invoke the appropriate
dataset."""
[token, sym, rangeargs] = webargs.partition('/')
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
return selectPost(rangeargs, dbcfg, proj, postdata)
def listAnnoObjects(webargs, postdata=None):
""" Return a list of anno ids restricted by equality predicates.
Equalities are alternating in field/value in the url.
"""
[token, dontuse, restargs] = webargs.split('/', 2)
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
db = emcadb.EMCADB(dbcfg, proj)
# Split the URL and get the args
args = restargs.split('/')
predicates = dict(zip(args[::2], args[1::2]))
annoids = db.getAnnoObjects(predicates)
# We have a cutout as well
if postdata:
# RB this is a brute force implementation. This probably needs to be
# optimized to use several different execution strategies based on the
# cutout size and the number of objects.
# Make a named temporary file for the HDF5
tmpfile = tempfile.NamedTemporaryFile()
tmpfile.write(postdata)
tmpfile.seek(0)
h5f = h5py.File(tmpfile.name, driver='core', backing_store=False)
corner = h5f['XYZOFFSET'][:]
dim = h5f['CUTOUTSIZE'][:]
resolution = h5f['RESOLUTION'][0]
if not dbcfg.checkCube(resolution, corner[0], corner[0] + dim[0],
corner[1], corner[1] + dim[1], corner[2],
corner[2] + dim[2]):
logger.warning("Illegal cutout corner=%s, dim=%s" % (corner, dim))
raise ANNError("Illegal cutout corner=%s, dim=%s" % (corner, dim))
# RBFIX this a hack
#
# the zstart in dbconfig is sometimes offset to make it aligned.
# Probably remove the offset is the best idea. and align data
# to zero regardless of where it starts. For now.
corner[2] -= dbcfg.slicerange[0]
cutout = db.cutout(corner, dim, resolution)
annoids = np.intersect1d(annoids, np.unique(cutout.data))
if postdata:
h5f.close()
tmpfile.close()
return h5ann.PackageIDs(annoids)
def emcaget(webargs):
"""Interface to the cutout service for annotations.
Load the annotation project and invoke the appropriate
dataset."""
[token, sym, rangeargs] = webargs.partition('/')
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
return selectService(rangeargs, dbcfg, proj)
def deleteAnnotation(webargs):
"""Delete a RAMON object"""
## TODO add retry loop for transaction
[token, sym, otherargs] = webargs.partition('/')
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
db = emcadb.EMCADB(dbcfg, proj)
# Split the URL and get the args
args = otherargs.split('/', 2)
# if the first argument is numeric. it is an annoid
if re.match('^[\d,]+$', args[0]):
annoids = map(int, args[0].split(','))
# if not..this is not a well-formed delete request
else:
logger.warning(
"Delete did not specify a legal object identifier = %s" % args[0])
raise ANNError(
"Delete did not specify a legal object identifier = %s" % args[0])
for annoid in annoids:
db.startTxn()
tries = 0
done = False
while not done and tries < 5:
try:
db.deleteAnnotation(annoid)
done = True
# rollback if you catch an error
except MySQLdb.OperationalError, e:
logger.warning("Transaction did not complete. %s" % (e))
tries += 1
db.rollback()
continue
except MySQLdb.Error, e:
logger.warning("Put transaction rollback. %s" % (e))
db.rollback()
raise
except Exception, e:
logger.exception(
"Put transaction rollback. Unknown error. %s" % (e))
db.rollback()
raise
def projInfo(webargs):
"""Return information about the project and database"""
[token, projinfoliteral, otherargs] = webargs.split('/', 2)
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
# Create an in-memory HDF5 file
tmpfile = tempfile.NamedTemporaryFile()
h5f = h5py.File(tmpfile.name)
# Populate the file with project information
proj.h5Info(h5f)
dbcfg.h5Info(h5f)
h5f.close()
tmpfile.seek(0)
return tmpfile.read()
def __init__(self, token, resolution, path):
self.path = path
self.resolution = resolution
self.projdb = emcaproj.EMCAProjectsDB()
self.proj = self.projdb.loadProject(token)
self._ximgsz = self.proj.datasetcfg.imagesz[resolution][0]
self._yimgsz = self.proj.datasetcfg.imagesz[resolution][1]
self.startslice = self.proj.datasetcfg.slicerange[0]
self.endslice = self.proj.datasetcfg.slicerange[1]
self.batchsz = self.proj.datasetcfg.cubedim[resolution][2]
self.alldirs = os.listdir(path)
# open the database
self.db = emcadb.EMCADB(self.proj)
# get a db cursor
self.cursor = self.db.conn.cursor()
def catmaid (request, webargs):
"""Convert a CATMAID request into an imgAnnoOverlay.
Webargs are going to be in the form of project/res/xtile/ytile/ztile/"""
try:
token, imageargs = webargs.split('/',1)
# Get the project and dataset
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj ( token )
annimg = emcarest.emcacatmaid(webargs)
# fetch data from url
dataurl = request.build_absolute_uri( '%s/emca/catmaid/%s/%s' % ( proj.getDataURL(), proj.getDataset(), imageargs ))
# Get data
f = urllib2.urlopen ( dataurl )
fobj = cStringIO.StringIO ( f.read() )
dataimg = Image.open(fobj)
# upsample the dataimage to 32 bit RGBA
dataimg = dataimg.convert("RGBA")
# make a composite of the two images
compimg = Image.composite ( annimg, dataimg, annimg )
# write the merged image to a buffer
fobj2 = cStringIO.StringIO ( )
compimg.save ( fobj2, "PNG" )
fobj2.seek(0)
return django.http.HttpResponse(fobj2.read(), mimetype="image/png" )
except Exception, e:
return django.http.HttpResponseNotFound(e)
def putAnnotation(webargs, postdata):
"""Put a RAMON object as HDF5 by object identifier"""
[token, sym, optionsargs] = webargs.partition('/')
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
db = emcadb.EMCADB(dbcfg, proj)
# Don't write to readonly projects
if proj.getReadOnly() == 1:
logger.warning("Attempt to write to read only project. %s: %s" %
(proj.getDBName(), webargs))
raise ANNError("Attempt to write to read only project. %s: %s" %
(proj.getDBName(), webargs))
options = optionsargs.split('/')
# return string of id values
retvals = []
# Make a named temporary file for the HDF5
tmpfile = tempfile.NamedTemporaryFile()
tmpfile.write(postdata)
tmpfile.seek(0)
h5f = h5py.File(tmpfile.name, driver='core', backing_store=False)
try:
for k in h5f.keys():
idgrp = h5f.get(k)
# Convert HDF5 to annotation
anno = h5ann.H5toAnnotation(k, idgrp)
# set the identifier (separate transaction)
if not ('update' in options or 'dataonly' in options
or 'reduce' in options):
anno.setID(db)
tries = 0
done = False
while not done and tries < 5:
# start a transaction: get mysql out of line at a time mode
db.startTxn()
try:
if anno.__class__ in [
annotation.AnnNeuron, annotation.AnnSeed
] and (idgrp.get('VOXELS') or idgrp.get('CUTOUT')):
logger.warning("Cannot write to annotation type %s" %
(anno.__class__))
raise ANNError("Cannot write to annotation type %s" %
(anno.__class__))
if 'update' in options and 'dataonly' in options:
logger.warning(
"Illegal combination of options. Cannot use udpate and dataonly together"
)
raise ANNError(
"Illegal combination of options. Cannot use udpate and dataonly together"
)
elif not 'dataonly' in options and not 'reduce' in options:
# Put into the database
db.putAnnotation(anno, options)
retvals.append(anno.annid)
# Is a resolution specified? or use default
h5resolution = idgrp.get('RESOLUTION')
if h5resolution == None:
resolution = proj.getResolution()
else:
resolution = h5resolution[0]
# Load the data associated with this annotation
# Is it voxel data?
voxels = idgrp.get('VOXELS')
if voxels and 'reduce' not in options:
if 'preserve' in options:
conflictopt = 'P'
elif 'exception' in options:
conflictopt = 'E'
else:
conflictopt = 'O'
# Check that the voxels have a conforming size:
if voxels.shape[1] != 3:
logger.warning(
"Voxels data not the right shape. Must be (:,3). Shape is %s"
% str(voxels.shape))
raise ANNError(
"Voxels data not the right shape. Must be (:,3). Shape is %s"
% str(voxels.shape))
exceptions = db.annotate(anno.annid, resolution,
voxels, conflictopt)
# Otherwise this is a shave operation
elif voxels and 'reduce' in options:
# Check that the voxels have a conforming size:
if voxels.shape[1] != 3:
logger.warning(
"Voxels data not the right shape. Must be (:,3). Shape is %s"
% str(voxels.shape))
raise ANNError(
"Voxels data not the right shape. Must be (:,3). Shape is %s"
% str(voxels.shape))
db.shave(anno.annid, resolution, voxels)
# Is it dense data?
cutout = idgrp.get('CUTOUT')
h5xyzoffset = idgrp.get('XYZOFFSET')
if cutout != None and h5xyzoffset != None and 'reduce' not in options:
if 'preserve' in options:
conflictopt = 'P'
elif 'exception' in options:
conflictopt = 'E'
else:
conflictopt = 'O'
# the zstart in dbconfig is sometimes offset to make it aligned.
# Probably remove the offset is the best idea. and align data
# to zero regardless of where it starts. For now.
corner = h5xyzoffset[:]
corner[2] -= dbcfg.slicerange[0]
db.annotateEntityDense(anno.annid, corner, resolution,
np.array(cutout), conflictopt)
elif cutout != None and h5xyzoffset != None and 'reduce' in options:
corner = h5xyzoffset[:]
corner[2] -= dbcfg.slicerange[0]
db.shaveEntityDense(anno.annid, corner, resolution,
np.array(cutout))
elif cutout != None or h5xyzoffset != None:
#TODO this is a loggable error
pass
# Commit if there is no error
db.commit()
# Here with no error is successful
done = True
# rollback if you catch an error
except MySQLdb.OperationalError, e:
logger.warning("Transaction did not complete. %s" % (e))
tries += 1
db.rollback()
continue
except MySQLdb.Error, e:
logger.warning("Put transaction rollback. %s" % (e))
db.rollback()
raise
# Web transfer limitations. # include the paths EM_BASE_PATH = os.path.abspath(os.path.join(os.path.dirname(__file__), ".." )) EM_UTIL_PATH = os.path.join(EM_BASE_PATH, "util" ) EM_EMCA_PATH = os.path.join(EM_BASE_PATH, "emca" ) EM_DBCONFIG_PATH = os.path.join(EM_BASE_PATH, "dbconfig" ) sys.path += [ EM_UTIL_PATH, EM_DBCONFIG_PATH, EM_EMCA_PATH ] import emcaproj import emcadb import dbconfig # load the project projdb = emcaproj.EMCAProjectsDB() proj = projdb.getProj ( 'kasthuri11' ) dbcfg = dbconfig.switchDataset ( proj.getDataset() ) #Load the database db = emcadb.EMCADB ( dbcfg, proj ) _ximagesz = 4096 _yimagesz = 4096 fid = open ( "/data/formisha/rasdamancutout", "w" ) for zstart in range(1,1024,16): zend = min(zstart+16,1025)
def setup_class(self):
"""Create the unittest database"""
self.pd = emcaproj.EMCAProjectsDB()
self.pd.newEMCAProj('unittest', 'test', 'localhost', 'unittest', 2,
'kasthuri11', None, 0, False, True)
def mcFalseColor(webargs):
"""False color image of multiple channels"""
[token, mcfcstr, chanstr, service, imageargs] = webargs.split('/', 4)
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
if proj.getDBType() != emcaproj.CHANNELS:
logger.warning("Not a multiple channel project.")
raise ANNError("Not a multiple channel project.")
channels = chanstr.split(",")
combined_img = None
for i in range(len(channels)):
if service == 'xy':
cb = xySlice(str(channels[i]) + "/" + imageargs, dbcfg, proj)
elif service == 'xz':
cb = xzSlice(str(channels[i]) + "/" + imageargs, dbcfg, proj)
elif service == 'yz':
cb = yzSlice(str(channels[i]) + "/" + imageargs, dbcfg, proj)
else:
logger.warning("No such service %s. Args: %s" % (service, webargs))
raise ANNError("No such service %s" % (service))
# First channel is cyan
if i == 0:
data32 = np.array(cb.data * (1. / 256), dtype=np.uint32)
combined_img = 0xFF000000 + np.left_shift(
data32, 8) + np.left_shift(data32, 16)
# Second is yellow
elif i == 1:
data32 = np.array(cb.data * (1. / 256), dtype=np.uint32)
combined_img += np.left_shift(data32, 8) + data32
# Third is Magenta
elif i == 2:
data32 = np.array(cb.data * (1. / 256), dtype=np.uint32)
combined_img += np.left_shift(data32, 16) + data32
# Fourth is Red
elif i == 3:
data32 = np.array(cb.data * (1. / 256), dtype=np.uint32)
combined_img += data32
# Fifth is Green
elif i == 4:
data32 = np.array(cb.data * (1. / 256), dtype=np.uint32)
combined_img += np.left_shift(data32, 8)
# Sixth is Blue
elif i == 5:
data32 = np.array(cb.data * (1. / 256), dtype=np.uint32)
combined_img += np.left_shift(data32, 16)
else:
logger.warning(
"Only support six channels at a time. You requested %s " %
(chanstr))
raise ANNError(
"Only support six channels at a time. You requested %s " %
(chanstr))
if service == 'xy':
ydim, xdim = combined_img.shape[1:3]
outimage = Image.frombuffer('RGBA', (xdim, ydim),
combined_img[0, :, :].flatten(), 'raw',
'RGBA', 0, 1)
elif service == 'xz':
ydim = combined_img.shape[0]
xdim = combined_img.shape[2]
outimage = Image.frombuffer('RGBA', (xdim, ydim),
combined_img[:, 0, :].flatten(), 'raw',
'RGBA', 0, 1)
elif service == 'yz':
ydim = combined_img.shape[0]
xdim = combined_img.shape[1]
outimage = Image.frombuffer('RGBA', (xdim, ydim),
combined_img[:, :, 0].flatten(), 'raw',
'RGBA', 0, 1)
# Enhance the image
import ImageEnhance
enhancer = ImageEnhance.Brightness(outimage)
outimage = enhancer.enhance(4.0)
fileobj = cStringIO.StringIO()
outimage.save(fileobj, "PNG")
fileobj.seek(0)
return fileobj.read()
def emcacatmaid(webargs):
"""Interface to the cutout service for catmaid request. It does address translation."""
CM_TILESIZE = 256
token, plane, resstr, xtilestr, ytilestr, zslicestr, rest = webargs.split(
'/', 7)
xtile = int(xtilestr)
ytile = int(ytilestr)
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
# datatype from the project
if proj.getDBType() == emcaproj.IMAGES:
datatype = np.uint8
else:
datatype = np.uint32
resolution = int(resstr)
# build the cutout request
if plane == 'xy':
# figure out the cutout (limit to max image size)
xstart = xtile * CM_TILESIZE
ystart = ytile * CM_TILESIZE
xend = min((xtile + 1) * CM_TILESIZE, dbcfg.imagesz[resolution][0])
yend = min((ytile + 1) * CM_TILESIZE, dbcfg.imagesz[resolution][1])
# Return empty data if request is outside bounds. don't like it.
if xstart >= xend or ystart >= yend:
cutoutdata = np.zeros([CM_TILESIZE, CM_TILESIZE], dtype=datatype)
else:
imageargs = '%s/%s,%s/%s,%s/%s/' % (resstr, xstart, xend, ystart,
yend, zslicestr)
cb = xySlice(imageargs, dbcfg, proj)
# reshape (if it's not a full cutout)
if cb.data.shape != [1, CM_TILESIZE, CM_TILESIZE]:
cutoutdata = np.zeros([CM_TILESIZE, CM_TILESIZE],
dtype=cb.data.dtype)
cutoutdata[0:cb.data.shape[1],
0:cb.data.shape[2]] = cb.data.reshape(
[cb.data.shape[1], cb.data.shape[2]])
else:
cutoutdata = cb.data.reshape([CM_TILESIZE, CM_TILESIZE])
elif plane == 'xz' or plane == 'yz':
# The x or y plane is normal. The z plane needs some translation.
# the ytilestr actually represents data in the z-plane
pixelsperslice = dbcfg.zscale[int(resstr)]
if plane == 'xz':
# figure out the cutout (limit to max image size)
xstart = xtile * CM_TILESIZE
xend = min((xtile + 1) * CM_TILESIZE, dbcfg.imagesz[resolution][0])
# Now we need the ytile'th set of CM_TILESZ
ystart = ytile * int(
float(CM_TILESIZE) / pixelsperslice) + dbcfg.slicerange[0]
# get more data so that we always have 512 pixels
yend = min(
(ytile + 1) * int(float(CM_TILESIZE) / pixelsperslice + 1),
dbcfg.slicerange[1] - dbcfg.slicerange[0] +
1) + dbcfg.slicerange[0]
# Return empty data if request is outside bounds. don't like it.
if xstart == xend or ystart == yend:
cutoutdata = np.zeros([CM_TILESIZE, CM_TILESIZE],
dtype=datatype)
else:
imageargs = '%s/%s,%s/%s/%s,%s/' % (resstr, xstart, xend,
zslicestr, ystart, yend)
cb = xzSlice(imageargs, dbcfg, proj)
if cb.data.shape != [CM_TILESIZE, 1, CM_TILESIZE]:
cutoutdata = np.zeros([CM_TILESIZE, CM_TILESIZE],
dtype=cb.data.dtype)
cutoutdata[0:cb.data.shape[0],
0:cb.data.shape[2]] = cb.data.reshape(
[cb.data.shape[0], cb.data.shape[2]])
else:
# reshape
cutoutdata = cb.data.reshape([CM_TILESIZE, CM_TILESIZE])
elif plane == 'yz':
# figure out the cutout (limit to max image size)
xtart = xtile * CM_TILESIZE
xend = min((xtile + 1) * CM_TILESIZE, dbcfg.imagesz[resolution][1])
ystart = ytile * int(
float(CM_TILESIZE) / pixelsperslice) + dbcfg.slicerange[0]
yend = min(
(ytile + 1) * int(float(CM_TILESIZE) / pixelsperslice + 1),
dbcfg.slicerange[1] - dbcfg.slicerange[0] +
1) + dbcfg.slicerange[0]
# Return empty data if request is outside bounds. don't like it.
if xstart == xend or ystart == yend:
cutoutdata = np.zeros([CM_TILESIZE, CM_TILESIZE],
dtype=datatype)
else:
imageargs = '%s/%s/%s,%s/%s,%s/' % (
resstr, zslicestr, xtile * CM_TILESIZE,
(xtile + 1) * CM_TILESIZE, ystart, yend)
cb = yzSlice(imageargs, dbcfg, proj)
if cb.data.shape != [CM_TILESIZE, CM_TILESIZE, 1]:
cutoutdata = np.zeros([CM_TILESIZE, CM_TILESIZE],
dtype=cb.data.dtype)
cutoutdata[0:cb.data.shape[0],
0:cb.data.shape[1]] = cb.data.reshape(
[cb.data.shape[0], cb.data.shape[1]])
else:
cutoutdata = cb.data.reshape([CM_TILESIZE, CM_TILESIZE])
else:
logger.warning(
"No such cutout plane: %s. Must be (xy|xz|yz).. Args %s" %
(service, webargs))
raise ANNError("No such cutout plane: %s. Must be (xy|xz|yz)." %
plane)
# Write the image to a readable stream
if cutoutdata.dtype == np.uint8:
outimage = Image.frombuffer('L', [CM_TILESIZE, CM_TILESIZE],
cutoutdata, 'raw', 'L', 0, 1)
elif cutoutdata.dtype == np.uint32:
recolor_cy(cutoutdata, cutoutdata)
outimage = Image.frombuffer('RGBA', [CM_TILESIZE, CM_TILESIZE],
cutoutdata, 'raw', 'RGBA', 0, 1)
return outimage
def main():
parser = argparse.ArgumentParser(description='Ingest a tiff stack.')
parser.add_argument('token', action="store" )
parser.add_argument('channel', type=int, action="store" )
parser.add_argument('path', action="store" )
parser.add_argument('numslices', type=int, action="store" )
result = parser.parse_args()
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj ( result.token )
dbcfg = dbconfig.switchDataset ( proj.getDataset() )
_ximgsz = None
_yimgsz = None
for sl in range(result.numslices):
filenm = result.path + '/' + '{:0>4}'.format(sl) + '.png'
print filenm
img = Image.open ( filenm, "r" )
if _ximgsz==None and _yimgsz==None:
_ximgsz,_yimgsz = img.size
imarray = np.zeros ( [result.numslices, _yimgsz, _ximgsz], dtype=np.uint16 )
else:
assert _ximgsz == img.size[0] and _yimgsz == img.size[1]
imarray[sl,:,:] = np.asarray ( img )
# get the size of the cube
xcubedim,ycubedim,zcubedim = dbcfg.cubedim[0]
# and the limits of iteration
xlimit = (_ximgsz-1) / xcubedim + 1
ylimit = (_yimgsz-1) / ycubedim + 1
zlimit = (result.numslices-1) / zcubedim + 1
# open the database
db = emcadb.EMCADB ( dbcfg, proj )
# get a db cursor
cursor = db.conn.cursor()
for z in range(zlimit):
db.commit()
for y in range(ylimit):
for x in range(xlimit):
zmin = z*zcubedim
zmax = min((z+1)*zcubedim,result.numslices)
zmaxrel = ((zmax-1)%zcubedim)+1
ymin = y*ycubedim
ymax = min((y+1)*ycubedim,_yimgsz)
ymaxrel = ((ymax-1)%ycubedim)+1
xmin = x*xcubedim
xmax = min((x+1)*xcubedim,_ximgsz)
xmaxrel = ((xmax-1)%xcubedim)+1
# morton key
key = zindex.XYZMorton ( [x,y,z] )
# Create a channel cube
cube = chancube.ChanCube ( [xcubedim,ycubedim,zcubedim] )
# data for this key
cube.data[0:zmaxrel,0:ymaxrel,0:xmaxrel] = imarray[zmin:zmax,ymin:ymax,xmin:xmax]
# compress the cube
npz = cube.toNPZ ()
# add the cube to the database
sql = "INSERT INTO " + proj.getTable(RESOLUTION) + "(zindex, channel, cube) VALUES (%s, %s, %s)"
print sql
try:
cursor.execute ( sql, (key, result.channel, npz))
except MySQLdb.Error, e:
raise ANNError ( "Error updating data cube: %d: %s. sql=%s" % (e.args[0], e.args[1], sql))
def getAnnotation(webargs):
"""Fetch a RAMON object as HDF5 by object identifier"""
[token, sym, otherargs] = webargs.partition('/')
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
db = emcadb.EMCADB(dbcfg, proj)
# Split the URL and get the args
args = otherargs.split('/', 2)
# Make the HDF5 file
# Create an in-memory HDF5 file
tmpfile = tempfile.NamedTemporaryFile()
h5f = h5py.File(tmpfile.name)
# if the first argument is numeric. it is an annoid
if re.match('^[\d,]+$', args[0]):
annoids = map(int, args[0].split(','))
for annoid in annoids:
# default is no data
if args[1] == '' or args[1] == 'nodata':
dataoption = AR_NODATA
getAnnoById(annoid, h5f, db, dbcfg, dataoption)
# if you want voxels you either requested the resolution id/voxels/resolution
# or you get data from the default resolution
elif args[1] == 'voxels':
dataoption = AR_VOXELS
[resstr, sym, rest] = args[2].partition('/')
resolution = int(
resstr) if resstr != '' else proj.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution)
elif args[1] == 'cutout':
# if there are no args or only resolution, it's a tight cutout request
if args[2] == '' or re.match('^\d+[\/]*$', args[2]):
dataoption = AR_TIGHTCUTOUT
[resstr, sym, rest] = args[2].partition('/')
resolution = int(
resstr) if resstr != '' else proj.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution)
else:
dataoption = AR_CUTOUT
# Perform argument processing
brargs = restargs.BrainRestArgs()
brargs.cutoutArgs(args[2], dbcfg)
# Extract the relevant values
corner = brargs.getCorner()
dim = brargs.getDim()
resolution = brargs.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution,
corner, dim)
elif args[1] == 'boundingbox':
dataoption = AR_BOUNDINGBOX
[resstr, sym, rest] = args[2].partition('/')
resolution = int(
resstr) if resstr != '' else proj.getResolution()
getAnnoById(annoid, h5f, db, dbcfg, dataoption, resolution)
else:
logger.warning(
"Fetch identifier %s. Error: no such data option %s " %
(annoid, args[1]))
raise ANNError(
"Fetch identifier %s. Error: no such data option %s " %
(annoid, args[1]))
# the first argument is not numeric. it is a service other than getAnnotation
else:
logger.warning(
"Get interface %s requested. Illegal or not implemented. Args: %s"
% (args[0], webargs))
raise ANNError(
"Get interface %s requested. Illegal or not implemented" %
(args[0]))
h5f.flush()
tmpfile.seek(0)
return tmpfile.read()
def getAnnotations(webargs, postdata):
"""Get multiple annotations. Takes an HDF5 that lists ids in the post."""
[token, objectsliteral, otherargs] = webargs.split('/', 2)
# Get the annotation database
projdb = emcaproj.EMCAProjectsDB()
proj = projdb.getProj(token)
dbcfg = dbconfig.switchDataset(proj.getDataset())
db = emcadb.EMCADB(dbcfg, proj)
# Read the post data HDF5 and get a list of identifiers
tmpinfile = tempfile.NamedTemporaryFile()
tmpinfile.write(postdata)
tmpinfile.seek(0)
h5in = h5py.File(tmpinfile.name)
# IDENTIFIERS
if not h5in.get('ANNOIDS'):
logger.warning(
"Requesting multiple annotations. But no HDF5 \'ANNOIDS\' field specified."
)
raise ANNError(
"Requesting multiple annotations. But no HDF5 \'ANNOIDS\' field specified."
)
# GET the data out of the HDF5 file. Never operate on the data in place.
annoids = h5in['ANNOIDS'][:]
# set variables to None: need them in call to getAnnoByID, but not all paths set all
corner = None
dim = None
resolution = None
dataarg = ''
# process options
# Split the URL and get the args
if otherargs != '':
(dataarg, cutout) = otherargs.split('/', 1)
if dataarg == '' or dataarg == 'nodata':
dataoption = AR_NODATA
elif dataarg == 'voxels':
dataoption = AR_VOXELS
# only arg to voxels is resolution
[resstr, sym, rest] = cutout.partition('/')
resolution = int(resstr) if resstr != '' else proj.getResolution()
elif dataarg == 'cutout':
# if blank of just resolution then a tightcutout
if cutout == '' or re.match('^\d+[\/]*$', cutout):
dataoption = AR_TIGHTCUTOUT
[resstr, sym, rest] = cutout.partition('/')
resolution = int(resstr) if resstr != '' else proj.getResolution()
else:
dataoption = AR_CUTOUT
# Perform argument processing
brargs = restargs.BrainRestArgs()
brargs.cutoutArgs(cutout, dbcfg)
# Extract the relevant values
corner = brargs.getCorner()
dim = brargs.getDim()
resolution = brargs.getResolution()
# RBTODO test this interface
elif dataarg == 'boundingbox':
# if blank of just resolution then a tightcutout
if cutout == '' or re.match('^\d+[\/]*$', cutout):
dataoption = AR_BOUNDINGBOX
[resstr, sym, rest] = cutout.partition('/')
resolution = int(resstr) if resstr != '' else proj.getResolution()
else:
logger.warning("In getAnnotations: Error: no such data option %s " %
(dataarg))
raise ANNError("In getAnnotations: Error: no such data option %s " %
(dataarg))
# Make the HDF5 output file
# Create an in-memory HDF5 file
tmpoutfile = tempfile.NamedTemporaryFile()
h5fout = h5py.File(tmpoutfile.name)
# get annotations for each identifier
for annoid in annoids:
# the int here is to prevent using a numpy value in an inner loop. This is a 10x performance gain.
getAnnoById(int(annoid), h5fout, db, dbcfg, dataoption, resolution,
corner, dim)
# close temporary file
h5in.close()
tmpinfile.close()
# Transmit back the populated HDF5 file
h5fout.flush()
tmpoutfile.seek(0)
return tmpoutfile.read()
