def getMission(self):
async_mission_list = self.async_client.get_missions().result()
missDict = self.regroupIntoDict(async_mission_list, "mission")
path = "mission.mat"
file = open(path, 'w')
scy.savemat(path, missDict)
file.close()
def write(self):
from postprocess import tfidf
K = len(self.nnz[MAP.PREDICATE])
N = len(self.nnz[MAP.ENTITY])
nnz_tensor = sum(self.nnz[0])
subs = np.zeros((nnz_tensor, 3), dtype=np.int)
vals = np.zeros((nnz_tensor, 1), dtype=np.double)
offset = 0
for s, p, o, val in self.relations():
# awesome matlab start-at-1 indexing...
subs[offset, :] = (s + 1, o + 1, p + 1)
vals[offset] = val
offset += 1
# remove zeros
nnzidx = vals.nonzero()[0]
vals = vals[nnzidx]
subs = subs[nnzidx, :]
eattr = self.__create_matlab_attr(self.entity_attributes, N, self.nnz[MAP.EATTR], postprocessor=tfidf)
rattr = self.__create_matlab_attr(self.predicate_attributes, K, self.nnz[MAP.RATTR], postprocessor=tfidf)
log.debug('Writing MATLAB tensor')
savemat(fjoin(TZArchive.SUBS_FOUT, 'mat', self.fname), {
'subs': subs,
'vals': vals,
'size': (N, N, K),
'eattr': eattr,
'rattr': rattr
}, oned_as='column')
return subs, vals
def cleanTip(file, outname):
dat = sio.loadmat(file)
tip_raw = dat['tip']
temp = tip_raw
temp[np.isnan(temp)] = np.nanmedian(tip_raw)
idx = abs(temp) > 2000
tip_raw[idx] = np.nan
plt.title('Click to the left of the first contact')
l = np.round(tip_raw.shape[0] / 5)
plt.plot(tip_raw[:l, :])
x, y = plt.ginput(1, timeout=0)[0]
plt.close('all')
x = int(np.round(x))
tip_raw[:x, :] = np.nanmedian(tip_raw, axis=0)
tip_interp = pd.DataFrame(tip_raw).interpolate(method=INTERP_METHOD,
limit=INTERP_WINDOW).values
# tip_interp = medfilt(tip_interp)
scaler = RobustScaler()
imp = Imputer(strategy='median')
tip_interp = imp.fit_transform(tip_interp)
tip = scaler.fit_transform(tip_interp)
plt.plot(tip)
plt.title('Cleaned')
plt.draw()
save_dict = {'tip_clean': tip}
sio.savemat(outname, save_dict)
def write_arr_to_matfile(arr, filepath, filename):
'''
stores the given numpy array into file in filepath
'''
output_dict = {}
output_dict[filename] = arr
ml.savemat(filepath, output_dict)
def subtract_background_from_stacks(scanfile, indir, outdir, scannumber=-1):
"""Subtract background from SAXS data in MAT-file stacks.
"""
scans = read_yaml(scanfile)
if scannumber > 0:
scannos = [ scannumber ]
else:
scannos = scans.keys()
scannos.sort()
for scanno in scannos:
print("Scan #%03d" % scanno)
try:
bufscan = scans[scanno][0]
except TypeError:
print("Scan #%03d is a buffer" % scanno)
continue
try:
conc = scans[scanno][1]
except TypeError:
print("No concentration for scan #02d." % scanno)
conc = 1.0
print("Using concentration %g g/l." % conc)
stackname = "s%03d" % scanno
stack = loadmat(indir+'/'+stackname+'.mat')[stackname]
subs = np.zeros_like(stack)
(npos, nrep, _, _) = stack.shape
for pos in range(npos):
print(pos)
buf = get_bg(indir, bufscan, pos)
for rep in range(nrep):
subs[pos,rep,...] = errsubtract(stack[pos,rep,...], buf)
subs[pos,rep,1:3,:] = subs[pos,rep,1:3,:] / conc
outname = "subs%03d" % scanno
savemat(outdir+'/'+outname + ".mat", {outname: subs}, do_compression=1,
oned_as='row')
def save(self,outfile):
# Populate matfile-friendly data structures for censoring regions
tmp = tempfile.NamedTemporaryFile()
save_attrs = []
for k in self.editable_traits():
if k.endswith("ts"):
continue
if k == "available_widgets":
continue
if k == "bpoint_classifier":
continue
if k == "bpoint_classifier_file":
continue
if k in ("censored_regions","event_names"):
continue
v = getattr(self,k)
if type(v) == np.ndarray:
if v.size == 0: continue
if type(v) is set: continue
save_attrs.append(k)
savedict = dict([(k,getattr(self,k)) \
for k in save_attrs if not (getattr(self,k) is None)])
savedict["censoring_sources"] = np.array(self.censoring_sources)
for evt in self.event_names:
savedict[evt] = getattr(self,evt)
savedict["event_names"] = np.array(self.event_names)
for k,v in savedict.iteritems():
try:
savemat( tmp, {k:v}, long_field_names=True)
except Exception, e:
logger.warn("unable to save %s because of %s", k,e)
def _post_run_hook(self, runtime):
atlas_config = self.inputs.atlas_config
atlas_name = self.inputs.atlas_name
# Aggregate the connectivity/network data from DSI Studio
official_labels = np.array(atlas_config['node_ids']).astype(np.int)
connectivity_data = {
atlas_name + "_region_ids": official_labels,
atlas_name + "_region_labels": np.array(atlas_config['node_names'])
}
# Gather the connectivity matrices
matfiles = glob(runtime.cwd + "/*.connectivity.mat")
for matfile in matfiles:
measure = "_".join(matfile.split(".")[-4:-2])
connectivity_data[atlas_name + "_" + measure + "_connectivity"] = \
_sanitized_connectivity_matrix(matfile, official_labels)
# Gather the network measure files
network_results = glob(runtime.cwd + "/*network*txt")
for network_result in network_results:
measure = "_".join(network_result.split(".")[-4:-2])
connectivity_data.update(
_sanitized_network_measures(network_result, official_labels,
atlas_name, measure))
merged_matfile = op.join(runtime.cwd, atlas_name + "_connectivity.mat")
savemat(merged_matfile, connectivity_data, long_field_names=True)
return runtime
def save(self,matfile):
if self.graph is None:
raise ValueError("No graph to save")
if self.graph.numberOfNodes() > self.nvoxels:
logger.warn("Non-voxel nodes are present in your graph.")
logger.info("Converting networkit Graph to csr matrix")
m = {
"flat_mask": self.flat_mask,
"nvoxels":self.nvoxels,
"voxel_size":self.voxel_size,
"volume_grid":self.volume_grid,
"weighting_scheme":self.weighting_scheme,
"step_size":self.step_size,
"odf_resolution":self.odf_resolution,
"angle_max":self.angle_max,
"angle_weights":self.angle_weights,
"normalize_doubleODF":self.normalize_doubleODF,
"angle_weighting_power":self.angle_weighting_power,
"graph":networkit.algebraic.adjacencyMatrix(self.graph, matrixType="sparse"),
"ras_affine":self.ras_affine,
"real_affine":self.real_affine
}
savemat(matfile,m,do_compression=True)
logger.info("Saved matfile to %s", matfile)
def _run_interface(self, runtime):
mat = loadmat(self.inputs.matfile, squeeze_me=True)
outfile = fname_presuffix(self.inputs.matfile, suffix="_controllability",
newpath=runtime.cwd)
connectivity_info = _calculate_controllability(mat)
LOGGER.info("writing %s", outfile)
savemat(outfile, connectivity_info, do_compression=True)
self._results['controllability'] = outfile
return runtime
def _merge_conmats(matfile_lists, recon_args, outfile):
"""Merge the many matfiles output by dsi studio and ensure they conform"""
connectivity_values = {}
for matfile_list, (atlas_name, atlas_config, ifargs) in zip(matfile_lists, recon_args):
matfiles = [f for f in matfile_list if f.endswith('.mat')]
txtfiles = [f for f in matfile_list if f.endswith('.txt')]
labels = np.array(atlas_config['node_ids']).astype(np.int)
connectivity_values[atlas_name + "_region_ids"] = labels
connectivity_values[atlas_name + "_region_labels"] = np.array(atlas_config['node_names'])
n_atlas_labels = len(labels)
for conmat in matfiles:
m = loadmat(conmat)
measure = "_".join(conmat.split(".")[-4:-2])
# Column names are binary strings. Very confusing.
column_names = "".join(
[s.decode('UTF-8') for s in m["name"].squeeze().view("S1")]).split("\n")[:-1]
region_ids = np.array([int(name[6:]) for name in column_names])
# Where does each column go? Make an index array
connectivity = m['connectivity']
in_this_mask = np.in1d(labels, region_ids)
truncated_labels = labels[in_this_mask]
assert np.all(truncated_labels == region_ids)
output = np.zeros((n_atlas_labels, n_atlas_labels))
new_row = np.searchsorted(labels, region_ids)
for row_index, conn in zip(new_row, connectivity):
tmp = np.zeros(n_atlas_labels)
tmp[in_this_mask] = conn
output[row_index] = tmp
connectivity_values[atlas_name + "_" + measure + "_connectivity"] = output
for network_txt in txtfiles:
measure = "_".join(network_txt.split(".")[-4:-2])
network_data = _parse_network_file(network_txt)
# Make sure to get the full atlas
region_ids = np.array(network_data.pop('region_ids')).astype(np.int)
in_this_mask = np.in1d(labels, region_ids)
truncated_labels = labels[in_this_mask]
assert np.all(truncated_labels == region_ids)
new_row = np.searchsorted(labels, region_ids)
for net_measure_name, net_measure_data in network_data.items():
variable_name = atlas_name + "_" + measure + "_" + net_measure_name
if type(net_measure_data) is np.ndarray:
tmp = np.zeros_like(net_measure_data)
tmp[in_this_mask] = net_measure_data
connectivity_values[variable_name] = tmp
else:
connectivity_values[variable_name] = net_measure_data
savemat(outfile, connectivity_values)
def main(args):
dset = biggie.Stash(args.input_file)
labseg = json.load(open(args.labseg))
out_dir = futils.create_directory(args.output_directory)
total_count = len(dset)
for idx, key in enumerate(dset.keys()):
out_file = path.join(out_dir, "%s.%s" % (key, FILE_EXT))
mdict = entity_to_mdict(dset.get(key), labseg[key])
MLAB.savemat(out_file, mdict=mdict)
print "[%s] %12d / %12d: %s" % (time.asctime(), idx, total_count, key)
def main(args):
dset = biggie.Stash(args.input_file)
labseg = json.load(open(args.labseg))
out_dir = futils.create_directory(args.output_directory)
total_count = len(dset)
for idx, key in enumerate(dset.keys()):
out_file = path.join(out_dir, "%s.%s" % (key, FILE_EXT))
mdict = entity_to_mdict(dset.get(key), labseg[key])
MLAB.savemat(out_file, mdict=mdict)
print "[%s] %12d / %12d: %s" % (time.asctime(), idx, total_count, key)
def _merge_conmats(matfile_list, outfile):
"""Merge the many matfiles output by dsi studio and ensure they conform"""
connectivity_values = {}
for matfile in matfile_list:
connectivity_values.update(loadmat(matfile))
savemat(outfile,
connectivity_values,
long_field_names=True,
do_compression=True)
def getObstacles(self):
async_future = self.async_client.get_obstacles()
stationary, moving = async_future.result()
obstacles = stationary + moving
dictObs = self.regroupIntoDict(obstacles, "obst")
self.addMovingObsField(dictObs)
path = "obstacles.mat"
file = open(path, 'w')
scy.savemat(path, dictObs)
file.close()
def save_fake_fib(fname):
"""returns a dict to get saved"""
inds = np.arange(QSDR_SHAPE[0] * QSDR_SHAPE[1] * QSDR_SHAPE[2])
mx, my, mz = np.unravel_index(inds,QSDR_SHAPE,order="F")
fop = gzopen(fname,"wb")
savemat(fop,
{"dimension":np.array(QSDR_SHAPE),
"mx":mx,"my":my,"mz":mz},
format='4'
)
fop.close()
def segments_pixeldist(self):
segmdist_fn = os.path.join(self.ds.path, "cpmc", "MySegmentsMat", self.name, "top_masks_dists.mat")
if os.path.exists(segmdist_fn):
data = ml.loadmat(segmdist_fn)
dist = data["top_masks_dist"]
segm_ids = data["segment_ids"]
else:
prop = self.top_masks
gt = self.ground_truth
dist, segm_ids = segments.get_class_distributions(gt, prop, num_classes=self.ds.classnum)
ml.savemat(segmdist_fn, {"top_masks_dist": dist, "segment_ids": segm_ids})
segm_ids = list(np.array(segm_ids).ravel())
return dist, segm_ids
def regions(self):
""" regions created for the top proposals"""
region_fn = os.path.join(self.ds.path, "cpmc", "MySegmentsMat", self.name, "top_regions.mat")
if os.path.exists(region_fn):
regions = ml.loadmat(region_fn)["top_regions"]
else:
proposals = self.top_masks
regions = reg.produce_regions(proposals)
ml.savemat(region_fn, {"top_regions": regions})
logging.debug("Storing regions in %s" % region_fn)
if not np.any(np.isnan(regions)):
logging.debug("All pixels are covered in one region")
return regions
def save_fake_fib(fname):
"""returns a dict to get saved"""
inds = np.arange(QSDR_SHAPE[0] * QSDR_SHAPE[1] * QSDR_SHAPE[2])
mx, my, mz = np.unravel_index(inds, QSDR_SHAPE, order="F")
fop = gzopen(fname, "wb")
savemat(fop, {
"dimension": np.array(QSDR_SHAPE),
"mx": mx,
"my": my,
"mz": mz
},
format='4')
fop.close()
def main(argv):
for patch_size in ['8x8', '16x16']:
data = load('data/vanhateren.{0}.0.npz'.format(patch_size))['data']
data = preprocess(data)
savemat('data/vanhateren.{0}.test.mat'.format(patch_size), {'data': data})
data = load('data/vanhateren.{0}.1.npz'.format(patch_size))['data']
data = preprocess(data)
savemat('data/vanhateren.{0}.train.mat'.format(patch_size), {'data': data})
return 0
def segments_pixeldist(self):
segmdist_fn = os.path.join(self.ds.path, 'cpmc', 'MySegmentsMat', self.name, 'top_masks_dists.mat')
if os.path.exists(segmdist_fn):
data = ml.loadmat(segmdist_fn)
dist = data['top_masks_dist']
segm_ids = data["segment_ids"]
else:
prop = self.top_masks
gt = self.ground_truth
dist, segm_ids = segments.get_class_distributions(gt, prop, num_classes=self.ds.classnum)
ml.savemat(segmdist_fn, {'top_masks_dist':dist, 'segment_ids': segm_ids})
segm_ids = list(np.array(segm_ids).ravel())
return dist, segm_ids
def regions(self):
""" regions created for the top proposals"""
region_fn = os.path.join(self.ds.path, 'cpmc', 'MySegmentsMat', self.name, 'top_regions.mat')
if os.path.exists(region_fn):
regions = ml.loadmat(region_fn)['top_regions']
else:
proposals = self.top_masks
regions = reg.produce_regions(proposals)
ml.savemat(region_fn, {'top_regions':regions})
logging.debug("Storing regions in %s" % region_fn)
if not np.any(np.isnan(regions)):
logging.debug("All pixels are covered in one region")
return regions
def write_dict_to_mat(mat_file_path,
dict_to_write,
version='7.3'): # field must be a dict
assert HAVE_HDF5STORAGE, "To use the MATSortingExtractor write_dict_to_mat function install hdf5storage: " \
"\n\n pip install hdf5storage\n\n"
if version == '7.3':
hdf5storage.write(dict_to_write,
'/',
mat_file_path,
matlab_compatible=True,
options='w')
elif version < '7.3' and version > '4':
savemat(mat_file_path, dict_to_write)
def applyModel(mdl, data_fname):
data = sio.loadmat(data_fname)
root = re.search('rat\d{4}_\d\d_[A-Z]{3}\d\d_VG_[A-Z]\d_t\d\d',
data_fname).group()
p = os.path.split(data_fname)[0]
data_out_name = os.path.join(p, root + '_contact2D.mat')
X = data['X'][:, :4]
C = np.zeros(X.shape[0], dtype='bool')
window_size = mdl.layers[0].input_shape[1] / 2
XX = make_tensor(X, window_size)
C = mdl.predict_classes(XX)
C = C.astype('bool')
data_struct = {'C': C, 'X': X, 'tip': data['tip']}
sio.savemat(data_out_name, data_struct)
def save_spm_mat_for_1st_level_glm(self, mat_file, session=0):
ordered_names = sorted(self.stimOnsets.keys())
to_save = {
'onsets' : np.array([self.stimOnsets[n][session] \
for n in ordered_names],
dtype=object),
'names' : np.array(ordered_names, dtype=object),
'durations' : np.array([self.stimDurations[n][session] \
for n in ordered_names], dtype=object),
}
# print 'to_save:'
# print to_save
# print 'stimOnsets:', self.stimOnsets
savemat(mat_file, to_save, oned_as='row')
def matlab_get_smooth_circ():
for f in glob.glob(os.path.join(p_in, 'rat*.pkl')):
print(os.path.basename(f))
fid = PIO(f)
blk = fid.read_block()
M = get_var(blk)
MB, MD = get_MB_MD(M)
for unit in blk.channel_indexes[-1].units:
unit_num = int(unit.name[-1])
r, b = get_rate_b(blk, unit_num)
root = get_root(blk, unit_num)
output_fname = 'circ_stats_{}.mat'.format(root)
w, edges = PD_fitting(MD, r)
save_dict = {'w': w, 'alpha': edges[:-1], 'root': root}
savemat(os.path.join(p_out, output_fname), save_dict)
def _merge_conmats(matfile_list, recon_args, outfile):
"""Merge the many matfiles output by dsi studio and ensure they conform"""
connectivity_values = {}
for matfile, (atlas_name, atlas_config, tck_file, ifargs) in zip(matfile_list, recon_args):
labels = np.array(atlas_config['node_ids']).astype(np.int)
connectivity_values[atlas_name + "_region_ids"] = labels
connectivity_values[atlas_name + "_region_labels"] = np.array(atlas_config['node_names'])
measure_name = atlas_name + '_' + ifargs['stat_edge']
if isdefined(ifargs['length_scale']):
measure_name += "_" + ifargs['length_scale']
if isdefined(ifargs['scale_invnodevol']):
measure_name += "_invroiscale"
connectivity_values[measure_name + "_connectivity"] = np.loadtxt(matfile)
connectivity_values[measure_name + "_tck"] = tck_file
connectivity_values[measure_name + "_image"] = atlas_config['dwi_resolution_mif']
savemat(outfile, connectivity_values, do_compression=True)
def smoothed_best():
df = pd.read_csv(min_entropy, index_col='id')
smooth_vals = np.arange(5, 100, 10).tolist()
best_smooth = df.mode(axis=1)[0]
best_idx = [smooth_vals.index(x) for x in best_smooth]
best_idx = pd.DataFrame({'idx': best_idx}, index=best_smooth.index)
for f in glob.glob(os.path.join(p_load, '*NEO.h5')):
try:
blk = neoUtils.get_blk(f)
blk_smooth = GLM.get_blk_smooth(f, p_smooth)
num_units = len(blk.channel_indexes[-1].units)
for unit_num in range(num_units):
varlist = ['M', 'F', 'TH', 'PHIE']
root = neoUtils.get_root(blk, unit_num)
print('Working on {}'.format(root))
if root not in best_idx.index:
print('{} not found in best smoothing derivative data'.
format(root))
continue
outname = os.path.join(
p_save,
'best_smoothing_deriv\\{}_best_smooth_pillowX.mat'.format(
root))
X = GLM.create_design_matrix(blk, varlist)
smoothing_to_use = best_idx.loc[root][0]
Xdot = GLM.get_deriv(blk,
blk_smooth,
varlist,
smoothing=[smoothing_to_use])[0]
X = np.concatenate([X, Xdot], axis=1)
y = neoUtils.get_rate_b(blk, unit_num)[1]
cbool = neoUtils.get_Cbool(blk)
arclengths = get_arclength_bool(blk, unit_num)
sio.savemat(
outname, {
'X': X,
'y': y,
'cbool': cbool,
'smooth': best_smooth.loc[root],
'arclengths': arclengths
})
except Exception as ex:
print('Problem with {}:{}'.format(os.path.basename(f), ex))
def save_spm_mat_for_1st_level_glm(self, mat_file, session=0):
ordered_names = sorted(self.stimOnsets.keys())
to_save = {
'onsets':
np.array([self.stimOnsets[n][session] for n in ordered_names],
dtype=object),
'names':
np.array(ordered_names, dtype=object),
'durations':
np.array([self.stimDurations[n][session] for n in ordered_names],
dtype=object),
}
# print 'to_save:'
# print to_save
# print 'stimOnsets:', self.stimOnsets
savemat(mat_file, to_save, oned_as='row')
def main(argv):
# Set defaults:
n_components_embedding = 25
comp_min = 2
comp_max = 20 + 1
varname = 'data'
filename = './test'
# Import files
f = h5py.File(('%s.mat' % filename), 'r')
dataCorr = np.array(f.get('%s' % varname))
# Prep matrix
K = (dataCorr + 1) / 2.
v = np.sqrt(np.sum(K, axis=1))
A = K / (v[:, None] * v[None, :])
del K
A = np.squeeze(A * [A > 0])
# Run embedding
lambdas, vectors = eigsh(A, k=n_components_embedding)
lambdas = lambdas[::-1]
vectors = vectors[:, ::-1]
psi = vectors / vectors[:, 0][:, None]
lambdas = lambdas[1:] / (1 - lambdas[1:])
embedding = psi[:, 1:(n_components_embedding +
1)] * lambdas[:n_components_embedding][None, :]
# Run kmeans clustering
def kmeans(embedding, n_components):
est = KMeans(n_clusters=n_components,
n_jobs=-1,
init='k-means++',
n_init=300)
est.fit_transform(embedding)
labels = est.labels_
data = labels.astype(np.float)
return data
results = list()
for n_components in xrange(comp_min, comp_max):
results.append(kmeans(embedding, n_components))
savemat(('%s_results.mat' % filename), {'results': results})
def _post_run_hook(self, runtime):
atlas_config = self.inputs.atlas_config
atlas_name = self.inputs.atlas_name
# Aggregate the connectivity/network data from DSI Studio
official_labels = np.array(atlas_config['node_ids']).astype(np.int)
connectivity_data = {
atlas_name + "_region_ids": official_labels,
atlas_name + "_region_labels": np.array(atlas_config['node_names'])
}
# get the connectivity matrix
prefix = atlas_name + "_" + self.inputs.measure
connectivity_data[prefix + "_connectivity"] = np.loadtxt(
self.inputs.out_file)
merged_matfile = op.join(runtime.cwd, prefix + "_connectivity.mat")
savemat(merged_matfile, connectivity_data, long_field_names=True)
return runtime
def object_masks(self):
ob_fn = os.path.join(self.ds.path, "cpmc", "MySegmentsMat", self.name, "obj_gt_masks.mat")
if os.path.exists(ob_fn):
data = ml.loadmat(ob_fn)
masks = data["masks"]
classes = data["classes"]
else:
masks = segments.seperate_gt_segments(self.object_ground_truth)
gt = self.ground_truth
dists, ids = segments.get_class_distributions(gt, masks)
classes = np.argmax(dists, axis=0)
assert masks.shape[2] == len(ids)
ml.savemat(ob_fn, {"masks": masks, "classes": classes})
assert masks.shape[2] == classes.size
return masks, classes
def regions_pixeldist(self):
""" returns the regions distributions for the given image."""
regiondist_fn = os.path.join(self.ds.path, 'cpmc', 'MySegmentsMat', self.name, 'region_dists.mat')
if os.path.exists(regiondist_fn):
data = ml.loadmat(regiondist_fn)
dist = data['dists']
segm_ids = data["region_ids"]
else:
regions = self.regions
n_reg = np.max(regions) + 1
gt = self.ground_truth
prop = np.zeros((regions.shape[0], regions.shape[1], n_reg), dtype='bool')
for i in range(n_reg):
prop[:, :, i] = (regions == i)
dist, segm_ids = segments.get_class_distributions(gt, prop, num_classes=self.ds.classnum)
ml.savemat(regiondist_fn, {'dists':dist, 'region_ids': segm_ids})
segm_ids = list(np.array(segm_ids).ravel())
return dist, segm_ids
def object_masks(self):
ob_fn = os.path.join(self.ds.path, 'cpmc', 'MySegmentsMat', self.name, 'obj_gt_masks.mat')
if os.path.exists(ob_fn):
data = ml.loadmat(ob_fn)
masks = data['masks']
classes = data["classes"]
else:
masks = segments.seperate_gt_segments(self.object_ground_truth)
gt = self.ground_truth
dists, ids = segments.get_class_distributions(gt, masks)
classes = np.argmax(dists, axis=0)
assert masks.shape[2] == len(ids)
ml.savemat(ob_fn, {'masks':masks, 'classes': classes})
assert masks.shape[2] == classes.size
return masks, classes
def regions_pixeldist(self):
""" returns the regions distributions for the given image."""
regiondist_fn = os.path.join(self.ds.path, "cpmc", "MySegmentsMat", self.name, "region_dists.mat")
if os.path.exists(regiondist_fn):
data = ml.loadmat(regiondist_fn)
dist = data["dists"]
segm_ids = data["region_ids"]
else:
regions = self.regions
n_reg = np.max(regions) + 1
gt = self.ground_truth
prop = np.zeros((regions.shape[0], regions.shape[1], n_reg), dtype="bool")
for i in range(n_reg):
prop[:, :, i] = regions == i
dist, segm_ids = segments.get_class_distributions(gt, prop, num_classes=self.ds.classnum)
ml.savemat(regiondist_fn, {"dists": dist, "region_ids": segm_ids})
segm_ids = list(np.array(segm_ids).ravel())
return dist, segm_ids
def save_to_matlab_file(self, filename, format = '5'):
"""
Saves shape measurements to Matlab's .mat format.
This uses the `scipy.io.matlab.savemat` function. See that functions documentation for
details on input options.
>>> table = MeasurementsTable( "data/testing/seq140[autotraj].measurements" )
>>> table.save_to_matlab_file( "data/testing/trash.mat" ) # doctest:+ELLIPSIS
<...MeasurementsTable object at ...>
"""
from scipy.io.matlab import savemat
kwargs = locals().copy()
for k in [ 'self', 'savemat', 'filename' ]:
del kwargs[k]
savemat( filename,
{ 'measurements': self.asarray() },
**kwargs)
return self
def smoothed_mechanics():
"""
use this function to grab the data from the smoothed mechanics and the
derivative of the same
"""
f_arclength = '/projects/p30144/_VG3D/deflections/direction_arclength_FR_group_data.csv'
f_list = glob.glob(os.path.join(p_load, '*NEO.h5'))
f_list.sort()
for f in f_list:
try:
blk = neoUtils.get_blk(f)
blk_smooth = GLM.get_blk_smooth(f, p_smooth)
num_units = len(blk.channel_indexes[-1].units)
for unit_num in range(num_units):
varlist = ['M', 'F', 'TH', 'PHIE']
root = neoUtils.get_root(blk, unit_num)
print('Working on {}'.format(root))
outname = os.path.join(p_save,
'{}_smooth_mechanicsX.mat'.format(root))
Xdot, X = GLM.get_deriv(blk,
blk_smooth,
varlist,
smoothing=[5])
X = np.concatenate([X, Xdot], axis=1)
y = neoUtils.get_rate_b(blk, unit_num)[1]
cbool = neoUtils.get_Cbool(blk)
arclengths = get_arclength_bool(blk,
unit_num,
fname=f_arclength)
sio.savemat(
outname, {
'X': X,
'y': y,
'cbool': cbool,
'smooth': 55,
'arclengths': arclengths
})
except Exception as ex:
print('Problem with {}:{}'.format(os.path.basename(f), ex))
def main(argv):
# Set defaults:
n_components_embedding = 25
comp_min = 2
comp_max = 20 + 1
varname = 'data'
filename = './test'
# Import files
f = h5py.File(('%s.mat' % filename),'r')
dataCorr = np.array(f.get('%s' % varname))
# Prep matrix
K = (dataCorr + 1) / 2.
v = np.sqrt(np.sum(K, axis=1))
A = K/(v[:, None] * v[None, :])
del K
A = np.squeeze(A * [A > 0])
# Run embedding
lambdas, vectors = eigsh(A, k=n_components_embedding)
lambdas = lambdas[::-1]
vectors = vectors[:, ::-1]
psi = vectors/vectors[:, 0][:, None]
lambdas = lambdas[1:] / (1 - lambdas[1:])
embedding = psi[:, 1:(n_components_embedding + 1)] * lambdas[:n_components_embedding][None, :]
# Run kmeans clustering
def kmeans(embedding, n_components):
est = KMeans(n_clusters=n_components, n_jobs=-1, init='k-means++', n_init=300)
est.fit_transform(embedding)
labels = est.labels_
data = labels.astype(np.float)
return data
results = list()
for n_components in xrange(comp_min,comp_max):
results.append(kmeans(embedding, n_components))
savemat(('%s_results.mat' % filename), {'results':results})
def main():
fname = sys.argv[1]
model_name = sys.argv[2]
data = sio.loadmat(fname)
tip = data['tip']
tip = cleanVar(tip)
model = loadModel(model_name)
window_size = model.layers[0].input_shape[1] / 2
X = make_tensor(tip, window_size)
print('\nPredicting Contact Variable...')
C = model.predict_classes(X)
data['C'] = C[:, model.output_shape[1] / 2]
C = C.astype('bool')
data['tip_scale'] = tip
print('\nSaving Data to .mat file\n')
sio.savemat(fname, data, oned_as='column')
print('C Vector Saved\n')
def cleanTip(filename, outname):
dat = sio.loadmat(filename)
t3d = dat['tracked_3D']
tip = np.empty((t3d.shape[-1], 3))
tip[:] = np.nan
for ii in xrange(t3d['x'].shape[-1]):
if len(t3d['x'][0, ii]) > 0:
if len(t3d['x'][0, ii][0]) > 1:
x = t3d['x'][0, ii][0, -1]
y = t3d['y'][0, ii][0, -1]
z = t3d['z'][0, ii][0, -1]
tip[ii, :] = np.hstack((x, y, z))
########### This section is for de novo cleaning ############
plt.title('Click to the left of the first contact')
l = np.round(tip.shape[0] / 5)
plt.plot(tip[:l, :])
x, y = plt.ginput(1, timeout=0)[0]
plt.close('all')
x = int(np.round(x))
######### ==================== ################
# ########## This section is for if we have already manually found the start #############
# dat_smooth = sio.loadmat(outname)
# tip_smooth = dat_smooth['tip']
# x = np.where(np.diff(tip_smooth[:,0])!=0)[0][0]
# ########## -------------------- ################
tip[:x, :] = np.nanmedian(tip, axis=0)
tip[-1, :] = np.nanmedian(tip, axis=0)
tip_interp = pd.DataFrame(tip).interpolate(method=INTERP_METHOD,
limit=INTERP_WINDOW).values
tip_interp_med = np.empty_like(tip_interp)
scaler = RobustScaler()
imp = Imputer(strategy='median')
tip_interp_imp = imp.fit_transform(tip_interp)
tip_out = scaler.fit_transform(tip_interp_imp)
save_dict = {'tip': tip_out}
sio.savemat(outname, save_dict)
def main(fname,use_var='M',outlier_thresh=0.05,plot_tgl=True):
fname_out = os.path.splitext(fname)[0] + '_outliers'
if os.path.isfile(fname_out+'.mat'):
print('File already completed. Delete outlier file if you want to recompute')
return 0
print('Using variable: {}\t Using outlier_thresh={}'.format(use_var,outlier_thresh))
print('Loading {} ...'.format(os.path.basename(fname)))
fid = sio.loadmat(fname)
print('Loaded!')
var = fid[use_var]
cbool = fid['C']
use_flags,outliers = cleanup(var,cbool,outlier_thresh=outlier_thresh,plot_tgl=plot_tgl)
if type(use_flags)==int and use_flags == 1:
return 1
print('Saving to {}...'.format(fname_out))
sio.savemat(fname_out,{'use_flags':use_flags,'outliers':outliers})
print('Saved')
return 0
def stack_files(scanfile, conffile, outdir, modulus=10, eiger=0, matfile=1, scannumber=-1):
"""Create stacks from scans read from YAML-file `scanfile`.
If `matfile` is true (default), write output stacks to a MAT-file.
Otherwise writes (slowly) to a YAML-file.
"""
if not os.path.isdir(outdir):
# FIXME: Create the directory
raise IOError("Output directory does not exist.")
conf = read_experiment_conf(conffile)
specscans = read_spec(conf['Specfile'])
radind = read_matclean(conf['Indfile'])['radind']
q = radind['q']
if scannumber > 0:
scannos = [ scannumber ]
else:
scans = read_yaml(scanfile)
scannos = scans.keys()
scannos.sort()
for scanno in scannos:
outname = "s%03d" % scanno
if eiger:
stack, fnames, dvals = \
stack_eiger(conf, scanno, specscans, radind, modulus)
else:
stack, fnames, dvals = \
stack_scan(conf, scanno, specscans, radind, modulus)
stack = stack.squeeze()
if matfile:
outfn = outdir+'/'+outname + ".mat"
savemat(outfn, {outname: stack}, do_compression=1, oned_as='row')
print("Wrote output to '%s'." % outfn)
else:
for pos in range(stack.shape[0]):
outfn = outname+'.p%02d.all.ydat' % pos
write_stack_ydat(outdir+'/'+outfn, stack[pos], fnames[pos], dvals[pos], conf)
print("Wrote output to '%s'." % outfn)
chip_name,trg,inp=line.strip().split()
print chip_name,trg,inp
profile_matrix_trg,mapped_reads_trg=calculate_profile_matrix_bed_bam(bed_filename,trg,window_size=WINDOW_SIZE,use_strand=True)
profile_matrix_inp,mapped_reads_inp=calculate_profile_matrix_bed_bam(bed_filename,inp,window_size=WINDOW_SIZE,use_strand=True)
chip_profiles[chip_name]= (profile_matrix_trg/float(mapped_reads_trg)).mean(0) *1000000
chip_regions[chip_name]= profile_matrix_trg/float(mapped_reads_trg) *1000000
chip_profiles_bg[chip_name]= (profile_matrix_inp/float(mapped_reads_inp)).mean(0) *1000000
chip_regions_bg[chip_name]= profile_matrix_inp/float(mapped_reads_inp) *1000000
else:
chip_name,trg=line.strip().split()
print chip_name,trg
profile_matrix_trg,mapped_reads_trg=calculate_profile_matrix_bed_bam(bed_filename,trg,window_size=WINDOW_SIZE, use_strand=True)
chip_profiles[chip_name]=(profile_matrix_trg/float(mapped_reads_trg)).mean(0)*1000000
chip_regions[chip_name]=(profile_matrix_trg/float(mapped_reads_trg))*1000000
print chip_profiles[chip_name]
if USE_INPUT:
savemat(output_filename,{'chip_profiles':chip_profiles,'chip_regions':chip_regions,'chip_profiles_bg':chip_profiles_bg,'chip_regions_bg':chip_regions_bg,'window_size':WINDOW_SIZE})
else:
savemat(output_filename,{'chip_profiles':chip_profiles,'chip_regions':chip_regions,'window_size':WINDOW_SIZE})
random_scores=np.zeros((len(input_coordinates),random_factor))
for idx,c in enumerate(input_coordinates):
print idx, c
try:
input_scores[idx]=read_from_wig(c,wig_path,wig_mask=wig_mask,only_average=True)[1]
if labels[idx] ==0:
random_scores[idx,:]=extract_random_scores(c,exons_coordinates,random_factor)
elif labels[idx]==1:
random_scores[idx,:]=extract_random_scores(c,introns_coordinates,random_factor)
else:
random_scores[idx,:]=extract_random_scores(c,intergenic_coordinates,random_factor)
except:
print 'problema in:',idx,c,input_scores[idx],labels[idx]
np.save(prefix_to_add+'_scores',input_scores)
np.save(prefix_to_add+'random_scores',random_scores)
np.save(prefix_to_add+'labels',labels)
savemat(prefix_to_add+'risultati_conservation',{prefix_to_add+'labels':labels,prefix_to_add+'random_scores':random_scores,prefix_to_add+'_scores':input_scores})
def save_annotation_track_matlab(self,filename):
savemat(filename,{'annotation_track':self.annotation_track,'mapping':self.annotation_names_to_prime})
print 'Annotation track saved to:',filename
for ilind, lind in enumerate(linds):
shape = (7, len(t), len(lind))
Fo = np.zeros(shape, dtype=float)
Uo = Fo.copy()
Vo = Fo.copy()
flags = [[0, 0, 0, 0],
[0, 1, 0, 0],
[0, 0, 0, 1],
[0, 1, 0, 1],
[1, 0, 0, 0],
[0, 0, 1, 0],
[1, 0, 1, 0]]
for i, flag in enumerate(flags):
print(flag)
try:
F, U, V = octave.ut_FUV(t, t0, lind, lat, flag)
Fo[i] = F
Uo[i] = U
Vo[i] = V
except Oct2PyError:
print('failed')
save_args = dict(t=t, t0=t0, lat=lat, lind=lind, flags=flags,
Fo=Fo, Uo=Uo, Vo=Vo)
np.savez('FUV%d.npz' % ilind, **save_args)
savemat('FUV%d.mat' % ilind, save_args)
def save_connectivity_matrices(scan):
out_data = {}
opath = scan.pkl_trk_path + ".mat"
for lnum, label_source in enumerate(scan.track_label_items):
# Load the mask
# File containing the corresponding label vector
npy_path = label_source.numpy_path
if not os.path.exists(npy_path):
raise ValueError(
"\t\t++ [%s]"%sid, npy_path, "does not exist")
conn_ids = np.load(npy_path)
# Make a prefix
prefix = "_".join(
["%s_%s" % (k,v) for k,v in label_source.parameters.iteritems()]) + "_"
# Get the region labels from the parcellation
graphml = graphml_from_label_source(label_source)
if graphml is None:
raise ValueError("\t\t++ No graphml exists")
graphml_data = lookup_cache[label_source.parameters['scale']]
regions = graphml_data['regions']
# Empty connectivity matrix
out_data[prefix+'streamline_count'] = np.zeros((len(regions),len(regions)))
connectivity = out_data[prefix+'streamline_count']
scalars = {}
for scalar in scan.track_scalar_items:
# Load the actual array
scalars[prefix + scalar.name] = np.load(scalar.numpy_path)
# Empty matrix for
out_data[prefix + scalar.name] = np.zeros((len(regions),len(regions)))
out_data[prefix + scalar.name + "_sd"] = np.zeros((len(regions),len(regions)))
# extract the streamline lengths and put them into an array
out_data[prefix+'length'] = np.zeros((len(regions),len(regions)))
out_data[prefix+'length_sd'] = np.zeros((len(regions),len(regions)))
streams, hdr = nib.trackvis.read(scan.trk_file)
lengths = np.array([len(arr) for arr in streams])
# extract the streamline scalar index
for conn, (_i,_j) in graphml_data["index_to_region_pairs"].iteritems():
i,j = _i-1, _j-1
indexes = conn_ids == conn
sl_count = np.sum(indexes)
connectivity[i,j] = connectivity[j,i] = sl_count
out_data[prefix+'length'][i,j] = out_data[prefix+'length'][j,i] = lengths[indexes].mean()
out_data[prefix+'length_sd'][i,j] = out_data[prefix+'length_sd'][j,i] = lengths[indexes].std()
# Fill in the average scalar value
for scalar_name, scalar_data in scalars.iteritems():
scalar_vals = scalars[scalar_name][indexes]
scalar_mean = scalars_vals.mean()
out_data[scalar_name][i,j] = out_data[scalar_name][j,i] = scalar_mean
scalar_std = scalars_vals.std()
out_data[scalar_name+"_sd"][i,j] = out_data[scalar_name + "_sd"][j,i] = scalar_std
print "saving", opath
savemat(opath, out_data)
new_data["2"] = data["2"]
new_data["2"] = np.append(new_data["2"], data["4"])
new_data["2"] = np.append(new_data["2"], data["5"])
#new_data["2"] = np.append(new_data["2"], data["14"])
#new_data["2"] = np.append(new_data["2"], data["15"])
#new_data["3"] = data["5"]
#new_data["3"] = np.append(new_data["3"], data["9"])
#new_data["4"] = data["9"]
#new_data["3"] = np.append(new_data["3"], data["15"])
#new_data["3"] = np.append(new_data["3"], data["16"])
#new_data["3"] = np.append(new_data["3"], data["24"])
#new_data["3"] = np.append(new_data["3"], data["26"])
#
#
#
#new_data["4"] = data["17"]
#new_data["4"] = np.append(new_data["4"], data["18"])
#new_data["4"] = np.append(new_data["4"], data["19"])
#new_data["4"] = np.append(new_data["4"], data["20"])
#new_data["4"] = np.append(new_data["4"], data["21"])
#new_data["4"] = np.append(new_data["4"], data["22"])
for key in new_data.keys():
new_data[key] = np.sort(new_data[key])
matl.savemat(target_path + source_file, new_data)
#splt.plot( new_data["2"] )
previous_interval = st_int
#print (stims.size, stims_in_series, stims_in_series / stims.size)
print ("Всего стимуляций в файле %i" % (counter-1))
plt.title(title + " n stims = " + str(counter-1))
plt.show(block=True)
return stimulations
#######################################################################
main_path = '/home/ivan/Data/Ach_full/'
reading_path = main_path + 'source_data_simulations/'
saving_path = main_path + 'discrimination_simulation/'
for wavfile in sorted(os.listdir(reading_path)):
if (wavfile[0] == "." or os.path.splitext(wavfile)[1] != ".wav"):
continue
saving_file = saving_path + os.path.splitext(wavfile)[0] + '_stims_descr.mat'
if (os.path.isfile(saving_file)):
continue
wavcontent = read(reading_path + wavfile)
fd = wavcontent[0]
wavdata = wavcontent[1]
wavdata = wavdata.astype(float)
wavdata = 2 * ( wavdata - wavdata.min() ) / (wavdata.max() - wavdata.min()) - 1
print ('###############################################')
print (wavfile)
stimulations = descriminate_stimulations(wavdata, fd, os.path.splitext(wavfile)[0])
savemat(saving_file, stimulations)