def findTargets(self, imdata, targetlist):
imdata_id = imdata.dbid
self.logger.info(imdata_id)
# convert to float
image2 = imdata['image']
image = numpy.asarray(image2,dtype=numpy.float)
self.setImage(image, 'Image')
if self.handle is None:
self.handle = pymat.open()
pymat.put(self.handle, 'image', image)
pymat.put(self.handle, 'image_id',imdata_id)
self.matlabFindTargets()
if self.settings['user check']:
# user now clicks on targets
self.notifyUserSubmit()
self.userpause.clear()
self.setStatus('user input')
self.userpause.wait()
self.setStatus('processing')
pymat.put(self.handle, 'image', [])
pymat.put(self.handle, 'focus', [])
pymat.put(self.handle, 'acquisition', [])
self.publishTargets(imdata, 'focus', targetlist)
self.publishTargets(imdata, 'acquisition', targetlist)
self.logger.info('Targets have been submitted')
def targetTestImage(self):
usercheck = self.settings['user check']
self.settings['user check'] = False
filename = self.settings['test image']
try:
image2 = mrc.read(filename)
image = numpy.asarray(image2,dtype=numpy.float)
except:
self.logger.error('Failed to load test image')
raise
return
self.setImage(image, 'Image')
if self.handle is None:
self.handle = pymat.open()
pymat.put(self.handle, 'image', image)
imdata_id = 0
pymat.put(self.handle, 'image_id',imdata_id)
self.matlabFindTargets()
self.settings['user check'] = usercheck
def matlabFindTargets(self):
pymat.put(self.handle, 'focus', [])
pymat.put(self.handle, 'acquisition', [])
d, f = os.path.split(self.settings['module path'])
if d:
pymat.eval(self.handle, 'path(path, \'%s\')' % d)
if not f[:-2]:
raise RuntimeError
pymat.eval(self.handle,
'[acquisition, focus] = %s(image,image_id)' % f[:-2])
focus = pymat.get(self.handle, 'focus')
acquisition = pymat.get(self.handle, 'acquisition')
self.setTargets(acquisition, 'acquisition')
self.setTargets(focus, 'focus')
import time
time.sleep(1)
if self.settings['user check']:
self.panel.foundTargets()
def __call__(self):
print 'loading model'
if self.chunk_size is not None:
dataset_family = self.dataset_family
which_set = self.which_set
dataset_descriptor = self.dataset_family[which_set][size]
d = serial.load(self.dict_file)
self.W = d['dictionary'].T
M.put(s, 'dictionary', d['dictionary'])
M.put(s, 'lambda', self.lamda)
self.size = 6
num_examples = dataset_descriptor.num_examples
assert num_examples % self.chunk_size == 0
self.chunk_id = 0
for i in xrange(0,num_examples, self.chunk_size):
self.restrict = (i, i + self.chunk_size)
self._execute()
self.chunk_id += 1
else:
self._execute()
def transform_points(self, points):
mlabraw.put(self.handle, "points", points)
mlabraw.eval(self.handle,"""
points_result = tps_eval(points, params);
""")
points_result = mlabraw.get(self.handle, "points_result")
return points_result
def _set(self, name, value):
r"""Directly set a variable `name` in matlab space to `value`.
This should normally not be used in user code."""
if isinstance(value, MlabObjectProxy):
mlabraw.eval(self._session, "%s = %s;" % (name, value._name))
else:
## mlabraw.put(self._session, name, self._as_mlabable_type(value))
mlabraw.put(self._session, name, value)
def _set(self, name, value):
r"""Directly set a variable `name` in matlab space to `value`.
This should normally not be used in user code."""
if isinstance(value, MlabObjectProxy):
mlabraw.eval(self._session, "%s = %s;" % (name, value._name))
else:
## mlabraw.put(self._session, name, self._as_mlabable_type(value))
mlabraw.put(self._session, name, value)
def branch_points(bw):
initialize()
mlabraw.put(MATLAB, "bw",bw)
mlabraw.eval(MATLAB, """
bp = bwmorph(bw,'branchpoints')
bp_d = double(bp);
""")
bp_d = mlabraw.get(MATLAB, "bp_d")
bp = bp_d.astype('uint8')
return bp
def fit_transformation(self, points0, points1):
assert len(points0) == len(points1)
mlabraw.put(self.handle, "points0", points0)
mlabraw.put(self.handle, "points1", points1)
mlabraw.eval(self.handle, """
opts = opts_fit;
opts.reg = .01;
params = tps_fit(points0, points1, opts);
save('/tmp/after_fitting.mat');
""")
def branch_points(bw):
initialize()
mlabraw.put(MATLAB, "bw", bw)
mlabraw.eval(
MATLAB, """
bp = bwmorph(bw,'branchpoints')
bp_d = double(bp);
""")
bp_d = mlabraw.get(MATLAB, "bp_d")
bp = bp_d.astype('uint8')
return bp
def _set(self, name, value):
r"""Directly set a variable `name` in matlab space to `value`.
This should normally not be used in user code."""
if isinstance(value, MlabObjectProxy):
mlabraw.eval(self._session, "%s = %s;" % (name, value._name))
else:
## mlabraw.put(self._session, name, self._as_mlabable_type(value))
if isinstance(value, numpy.ndarray):
value = value.copy() # XXX: mlabraw seems to badly handle strides.
mlabraw.put(self._session, name, value)
def transform_poses(self, points, rots):
mlabraw.put(self.handle, "points", points)
put3d(self.handle, "rots", rots)
mlabraw.eval(self.handle,"""
[points_result, rots_result] = tps_eval_frames(points, rots, params);
""")
points_result = mlabraw.get(self.handle,"points_result")
rots_result = get3d(self.handle, "rots_result")
return points_result, rots_result
def fit_transformation_icp(self, points0, points1):
mlabraw.put(self.handle, "points0", points0)
mlabraw.put(self.handle, "points1", points1)
mlabraw.eval(self.handle, """
opts = opts_icp;
opts.n_iter=6;
opts.lines_from_orig=1;
opts.corr_opts.method='bipartite';
opts.fit_opts.reg = .01;
%opts.plot_grid = 1;
opts.corr_opts.bipartite_opts.deficient_col_penalty=1;
opts.corr_opts.bipartite_opts.deficient_row_penalty=1;
params = tps_rpm(points0, points1, opts);
save('/tmp/after_fitting.mat');
""")
def remove_holes(labels,min_size):
initialize()
mlabraw.put(MATLAB, "L",labels)
mlabraw.put(MATLAB, "min_size",min_size)
mlabraw.eval(MATLAB, """
max_label = max(L(:));
good_pix = L==0;
for label = 1:max_label
good_pix = good_pix | bwareaopen(L==label,min_size,4);
end
bad_pix = ~logical(good_pix);
[~,I] = bwdist(good_pix,'Chessboard');
NewL = L;
NewL(bad_pix) = L(I(bad_pix));
NewL_d = double(NewL);
""")
NewL_d = mlabraw.get(MATLAB, "NewL_d")
return NewL_d.astype('uint8')
def remove_holes(labels, min_size):
initialize()
mlabraw.put(MATLAB, "L", labels)
mlabraw.put(MATLAB, "min_size", min_size)
mlabraw.eval(
MATLAB, """
max_label = max(L(:));
good_pix = L==0;
for label = 1:max_label
good_pix = good_pix | bwareaopen(L==label,min_size,4);
end
bad_pix = ~logical(good_pix);
[~,I] = bwdist(good_pix,'Chessboard');
NewL = L;
NewL(bad_pix) = L(I(bad_pix));
NewL_d = double(NewL);
""")
NewL_d = mlabraw.get(MATLAB, "NewL_d")
return NewL_d.astype('uint8')
def matlabFindTargets(self):
pymat.put(self.handle, 'focus', [])
pymat.put(self.handle, 'acquisition', [])
d, f = os.path.split(self.settings['module path'])
if d:
pymat.eval(self.handle, 'path(path, \'%s\')' % d)
if not f[:-2]:
raise RuntimeError
pymat.eval(self.handle, '[acquisition, focus] = %s(image,image_id)' % f[:-2])
focus = pymat.get(self.handle, 'focus')
acquisition = pymat.get(self.handle, 'acquisition')
self.setTargets(acquisition, 'acquisition')
self.setTargets(focus, 'focus')
import time
time.sleep(1)
if self.settings['user check']:
self.panel.foundTargets()
def _set(self, name, value):
if isinstance(value, MlabObjectProxy):
mlabraw.eval(self._session, "%s = %s;" % (name, value._name))
else:
## mlabraw.put(self._session, name, self._as_mlabable_type(value))
mlabraw.put(self._session, name, value)
def put(name, array):
mlabraw.put(MATLAB, name, array)
def put(name,array):
mlabraw.put(MATLAB, name, array)
def set(self, name, value):
if DEBUG: print "setting '%s' to %s"%(name, `value`)
mlabraw.put(self._engine, name, value)
def _do(self, cmd, *args, **kwargs):
"""Semi-raw execution of a matlab command.
Smartly handle calls to matlab, figure out what to do with `args`,
and when to use function call syntax and not.
If no `args` are specified, the ``cmd`` not ``result = cmd()`` form is
used in Matlab -- this also makes literal Matlab commands legal
(eg. cmd=``get(gca, 'Children')``).
If ``nout=0`` is specified, the Matlab command is executed as
procedure, otherwise it is executed as function (default), nout
specifying how many values should be returned (default 1).
**Beware that if you use don't specify ``nout=0`` for a `cmd` that
never returns a value will raise an error** (because assigning a
variable to a call that doesn't return a value is illegal in matlab).
``cast`` specifies which typecast should be applied to the result
(e.g. `int`), it defaults to none.
XXX: should we add ``parens`` parameter?
"""
handle_out = kwargs.get('handle_out', _flush_write_stdout)
#self._session = self._session or mlabraw.open()
# HACK
if self._autosync_dirs:
mlabraw.eval(self._session, "cd('%s');" % os.getcwd().replace("'", "''"))
nout = kwargs.get('nout', 1)
#XXX what to do with matlab screen output
argnames = []
tempargs = []
try:
for count, arg in enumerate(args):
if isinstance(arg, MlabObjectProxy):
argnames.append(arg._name)
else:
nextName = 'arg%d__' % count
argnames.append(nextName)
tempargs.append(nextName)
# have to convert these by hand
## try:
## arg = self._as_mlabable_type(arg)
## except TypeError:
## raise TypeError("Illegal argument type (%s.:) for %d. argument" %
## (type(arg), type(count)))
mlabraw.put(self._session, argnames[-1], arg)
if args:
cmd = "%s(%s)%s" % (cmd, ", ".join(argnames),
('',';')[kwargs.get('show',0)])
# got three cases for nout:
# 0 -> None, 1 -> val, >1 -> [val1, val2, ...]
if nout == 0:
handle_out(mlabraw.eval(self._session, cmd))
return
# deal with matlab-style multiple value return
resSL = ((["RES%d__" % i for i in range(nout)]))
handle_out(mlabraw.eval(self._session, '[%s]=%s;' % (", ".join(resSL), cmd)))
res = self._get_values(resSL)
if nout == 1: res = res[0]
else: res = tuple(res)
if kwargs.has_key('cast'):
if nout == 0: raise TypeError("Can't cast: 0 nout")
return kwargs['cast'](res)
else:
return res
finally:
if len(tempargs) and self._clear_call_args:
mlabraw.eval(self._session, "clear('%s');" %
"','".join(tempargs))
def _execute(self):
batch_size = self.batch_size
pooling_region_counts = self.pooling_region_counts
dataset_family = self.dataset_family
which_set = self.which_set
size = self.size
nan = 0
dataset_descriptor = dataset_family[which_set][size]
dataset = dataset_descriptor.dataset_maker()
expected_num_examples = dataset_descriptor.num_examples
full_X = dataset.get_design_matrix()
num_examples = full_X.shape[0]
assert num_examples == expected_num_examples
if self.restrict is not None:
assert self.restrict[1] <= full_X.shape[0]
print 'restricting to examples ',self.restrict[0],' through ',self.restrict[1],' exclusive'
full_X = full_X[self.restrict[0]:self.restrict[1],:]
assert self.restrict[1] > self.restrict[0]
#update for after restriction
num_examples = full_X.shape[0]
assert num_examples > 0
dataset.X = None
dataset.design_loc = None
dataset.compress = False
patchifier = ExtractGridPatches( patch_shape = (size,size), patch_stride = (1,1) )
pipeline = serial.load(dataset_descriptor.pipeline_path)
assert isinstance(pipeline.items[0], ExtractPatches)
pipeline.items[0] = patchifier
print 'defining features'
Z = T.matrix('Z')
if self.one_sided:
feat = abs(Z)
else:
pos = T.clip(Z,0.,1e30)
neg = T.clip(-Z,0.,1e30)
feat = T.concatenate((pos, neg), axis=1)
print 'compiling theano function'
f = function([Z],feat)
nfeat = self.W.shape[1] * (2 - self.one_sided)
if not (nfeat == 1600 or nfeat == 3200):
print nfeat
assert False
if config.device.startswith('gpu') and nfeat >= 4000:
f = halver(f, nfeat)
topo_feat_var = T.TensorType(broadcastable = (False,False,False,False), dtype='float32')()
region_features = function([topo_feat_var],
topo_feat_var.mean(axis=(1,2)) )
def average_pool( stride ):
def point( p ):
return p * ns / stride
rval = np.zeros( (topo_feat.shape[0], stride, stride, topo_feat.shape[3] ) , dtype = 'float32')
for i in xrange(stride):
for j in xrange(stride):
rval[:,i,j,:] = region_features( topo_feat[:,point(i):point(i+1), point(j):point(j+1),:] )
return rval
outputs = [ np.zeros((num_examples,count,count,nfeat),dtype='float32') for count in pooling_region_counts ]
assert len(outputs) > 0
fd = DenseDesignMatrix(X = np.zeros((1,1),dtype='float32'), view_converter = DefaultViewConverter([1, 1, nfeat] ) )
ns = 32 - size + 1
depatchifier = ReassembleGridPatches( orig_shape = (ns, ns), patch_shape=(1,1) )
if len(range(0,num_examples-batch_size+1,batch_size)) <= 0:
print num_examples
print batch_size
for i in xrange(0,num_examples-batch_size+1,batch_size):
print i
t1 = time.time()
d = copy.copy(dataset)
d.set_design_matrix(full_X[i:i+batch_size,:])
t2 = time.time()
#print '\tapplying preprocessor'
d.apply_preprocessor(pipeline, can_fit = False)
X2 = d.get_design_matrix()
t3 = time.time()
M.put(s,'batch',X2)
M.eval(s, 'Z = sparse_codes(batch, dictionary, lambda)')
Z = M.get(s, 'Z')
feat = f(np.cast['float32'](Z))
t4 = time.time()
assert feat.dtype == 'float32'
feat_dataset = copy.copy(fd)
if np.any(np.isnan(feat)):
nan += np.isnan(feat).sum()
feat[np.isnan(feat)] = 0
feat_dataset.set_design_matrix(feat)
#print '\treassembling features'
feat_dataset.apply_preprocessor(depatchifier)
#print '\tmaking topological view'
topo_feat = feat_dataset.get_topological_view()
assert topo_feat.shape[0] == batch_size
t5 = time.time()
#average pooling
for output, count in zip(outputs, pooling_region_counts):
output[i:i+batch_size,...] = average_pool(count)
t6 = time.time()
print (t6-t1, t2-t1, t3-t2, t4-t3, t5-t4, t6-t5)
for output, save_path in zip(outputs, self.save_paths):
if self.chunk_size is not None:
assert save_path.endswith('.npy')
save_path_pieces = save_path.split('.npy')
assert len(save_path_pieces) == 2
assert save_path_pieces[1] == ''
save_path = save_path_pieces[0] + '_' + chr(ord('A')+self.chunk_id)+'.npy'
np.save(save_path,output)
if nan > 0:
warnings.warn(str(nan)+' features were nan')
def _do(self, cmd, *args, **kwargs):
"""Semi-raw execution of a matlab command.
Smartly handle calls to matlab, figure out what to do with `args`,
and when to use function call syntax and not.
If no `args` are specified, the ``cmd`` not ``result = cmd()`` form is
used in Matlab -- this also makes literal Matlab commands legal
(eg. cmd=``get(gca, 'Children')``).
If ``nout=0`` is specified, the Matlab command is executed as
procedure, otherwise it is executed as function (default), nout
specifying how many values should be returned (default 1).
**Beware that if you use don't specify ``nout=0`` for a `cmd` that
never returns a value will raise an error** (because assigning a
variable to a call that doesn't return a value is illegal in matlab).
``cast`` specifies which typecast should be applied to the result
(e.g. `int`), it defaults to none.
XXX: should we add ``parens`` parameter?
"""
handle_out = kwargs.get('handle_out', _flush_write_stdout)
#self._session = self._session or mlabraw.open()
# HACK
if self._autosync_dirs:
mlabraw.eval(self._session,
"cd('%s');" % os.getcwd().replace("'", "''"))
nout = kwargs.get('nout', 1)
#XXX what to do with matlab screen output
argnames = []
tempargs = []
try:
for count, arg in enumerate(args):
if isinstance(arg, MlabObjectProxy):
argnames.append(arg._name)
else:
nextName = 'arg%d__' % count
argnames.append(nextName)
tempargs.append(nextName)
# have to convert these by hand
## try:
## arg = self._as_mlabable_type(arg)
## except TypeError:
## raise TypeError("Illegal argument type (%s.:) for %d. argument" %
## (type(arg), type(count)))
mlabraw.put(self._session, argnames[-1], arg)
if args:
cmd = "%s(%s)%s" % (cmd, ", ".join(argnames),
('', ';')[kwargs.get('show', 0)])
# got three cases for nout:
# 0 -> None, 1 -> val, >1 -> [val1, val2, ...]
if nout == 0:
handle_out(mlabraw.eval(self._session, cmd))
return
# deal with matlab-style multiple value return
resSL = ((["RES%d__" % i for i in range(nout)]))
handle_out(
mlabraw.eval(self._session,
'[%s]=%s;' % (", ".join(resSL), cmd)))
res = self._get_values(resSL)
if nout == 1: res = res[0]
else: res = tuple(res)
if kwargs.has_key('cast'):
if nout == 0: raise TypeError("Can't cast: 0 nout")
return kwargs['cast'](res)
else:
return res
finally:
if len(tempargs) and self._clear_call_args:
mlabraw.eval(self._session,
"clear('%s');" % "','".join(tempargs))
def put3d(handle, name, array):
mlabraw.put(handle, "flat_array", array.flatten("F"))
mlabraw.eval(handle, "%s = reshape(flat_array, %i, %i, %i);"%(name, array.shape[0], array.shape[1], array.shape[2]))